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2024
Han Min-Jin, Luo Chaorui, Hu Hai, Lin Meixing, Lu Kunpeng, Shen Jianghong, Ren Jianyu, Ye Yanzhuo, Westhof Eric, Tong Xiaoling, Dai Fangyin
Multiple independent origins of the female W chromosome in moths and butterflies Journal Article
In: Sci Adv, vol. 10, no. 25, pp. eadm9851, 2024, ISSN: 2375-2548.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid38896616,
title = {Multiple independent origins of the female W chromosome in moths and butterflies},
author = {Min-Jin Han and Chaorui Luo and Hai Hu and Meixing Lin and Kunpeng Lu and Jianghong Shen and Jianyu Ren and Yanzhuo Ye and Eric Westhof and Xiaoling Tong and Fangyin Dai},
doi = {10.1126/sciadv.adm9851},
issn = {2375-2548},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Sci Adv},
volume = {10},
number = {25},
pages = {eadm9851},
abstract = {Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect () and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of . Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect () and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of . Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.
Pellequer Jean-Luc, Westhof Eric
Marc van Regenmortel, personal recollections on a forward-thinking editor Journal Article
In: J Mol Recognit, pp. e3080, 2024, ISSN: 1099-1352.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid38439188,
title = {Marc van Regenmortel, personal recollections on a forward-thinking editor},
author = {Jean-Luc Pellequer and Eric Westhof},
doi = {10.1002/jmr.3080},
issn = {1099-1352},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {J Mol Recognit},
pages = {e3080},
abstract = {Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.
2023
Kompatscher Maria, Bartosik Karolina, Erharter Kevin, Plangger Raphael, Juen Fabian Sebastian, Kreutz Christoph, Micura Ronald, Westhof Eric, Erlacher Matthias D
Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons Journal Article
In: Nucleic Acids Res, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid38050960,
title = {Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons},
author = {Maria Kompatscher and Karolina Bartosik and Kevin Erharter and Raphael Plangger and Fabian Sebastian Juen and Christoph Kreutz and Ronald Micura and Eric Westhof and Matthias D Erlacher},
doi = {10.1093/nar/gkad1136},
issn = {1362-4962},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Nucleic Acids Res},
abstract = {tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
Lu Kunpeng, Pan Yifei, Shen Jianghong, Yang Lin, Zhan Chengyu, Liang Shubo, Tai Shuaishuai, Wan Linrong, Li Tian, Cheng Tingcai, Ma Bi, Pan Guoqing, He Ningjia, Lu Cheng, Westhof Eric, Xiang Zhonghuai, Han Min-Jin, Tong Xiaoling, Dai Fangyin
SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data Journal Article
In: Nucleic Acids Res, vol. 52, iss. D1, pp. D1024-D1032, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid37941143,
title = {SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data},
author = {Kunpeng Lu and Yifei Pan and Jianghong Shen and Lin Yang and Chengyu Zhan and Shubo Liang and Shuaishuai Tai and Linrong Wan and Tian Li and Tingcai Cheng and Bi Ma and Guoqing Pan and Ningjia He and Cheng Lu and Eric Westhof and Zhonghuai Xiang and Min-Jin Han and Xiaoling Tong and Fangyin Dai},
doi = {10.1093/nar/gkad956},
issn = {1362-4962},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Nucleic Acids Res},
volume = {52},
issue = {D1},
pages = {D1024-D1032},
abstract = {The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.
Das Rhiju, Kretsch Rachael C, Simpkin Adam J, Mulvaney Thomas, Pham Phillip, Rangan Ramya, Bu Fan, Keegan Ronan M, Topf Maya, Rigden Daniel J, Miao Zhichao, Westhof Eric
Assessment of three-dimensional RNA structure prediction in CASP15 Journal Article
In: Proteins, vol. 91, iss. 12, pp. 1747-1770, 2023, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid37876231,
title = {Assessment of three-dimensional RNA structure prediction in CASP15},
author = {Rhiju Das and Rachael C Kretsch and Adam J Simpkin and Thomas Mulvaney and Phillip Pham and Ramya Rangan and Fan Bu and Ronan M Keegan and Maya Topf and Daniel J Rigden and Zhichao Miao and Eric Westhof},
doi = {10.1002/prot.26602},
issn = {1097-0134},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Proteins},
volume = {91},
issue = {12},
pages = {1747-1770},
abstract = {The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.
2022
Westhof E
Data, data, burning deep, in the forests of the net Journal Article
In: Biochem Biophys Res Commun, vol. 633, pp. 42-44, 2022, ISSN: 1090-2104.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid36344159,
title = {Data, data, burning deep, in the forests of the net},
author = {E Westhof},
doi = {10.1016/j.bbrc.2022.09.030},
issn = {1090-2104},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Biochem Biophys Res Commun},
volume = {633},
pages = {42-44},
abstract = {Continuous and imaginative technological developments are leading to a massive accumulation of various types of data in all areas of biological research. As a result, the central importance of databases is increasing. Databases related to biology must not only be structured using controlled vocabularies, but also be fully integrated into the whole biological domain. To achieve this goal, they must be systematically grounded in biological evolution and exploit the available tools of evolutionary systematics to contribute to our understanding of life processes.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Continuous and imaginative technological developments are leading to a massive accumulation of various types of data in all areas of biological research. As a result, the central importance of databases is increasing. Databases related to biology must not only be structured using controlled vocabularies, but also be fully integrated into the whole biological domain. To achieve this goal, they must be systematically grounded in biological evolution and exploit the available tools of evolutionary systematics to contribute to our understanding of life processes.
Tong Xiaoling, Han Min-Jin, Lu Kunpeng, Tai Shuaishuai, Liang Shubo, Liu Yucheng, Hu Hai, Shen Jianghong, Long Anxing, Zhan Chengyu, Ding Xin, Liu Shuo, Gao Qiang, Zhang Bili, Zhou Linli, Tan Duan, Yuan Yajie, Guo Nangkuo, Li Yan-Hong, Wu Zhangyan, Liu Lulu, Li Chunlin, Lu Yaru, Gai Tingting, Zhang Yahui, Yang Renkui, Qian Heying, Liu Yanqun, Luo Jiangwen, Zheng Lu, Lou Jinghou, Peng Yunwu, Zuo Weidong, Song Jiangbo, He Songzhen, Wu Songyuan, Zou Yunlong, Zhou Lei, Cheng Lan, Tang Yuxia, Cheng Guotao, Yuan Lianwei, He Weiming, Xu Jiabao, Fu Tao, Xiao Yang, Lei Ting, Xu Anying, Yin Ye, Wang Jian, Monteiro Antónia, Westhof E, Lu Cheng, Tian Zhixi, Wang Wen, Xiang Zhonghuai, Dai Fangyin
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation Journal Article
In: Nat Commun, vol. 13, no. 1, pp. 5619, 2022, ISSN: 2041-1723.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid36153338,
title = {High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation},
author = {Xiaoling Tong and Min-Jin Han and Kunpeng Lu and Shuaishuai Tai and Shubo Liang and Yucheng Liu and Hai Hu and Jianghong Shen and Anxing Long and Chengyu Zhan and Xin Ding and Shuo Liu and Qiang Gao and Bili Zhang and Linli Zhou and Duan Tan and Yajie Yuan and Nangkuo Guo and Yan-Hong Li and Zhangyan Wu and Lulu Liu and Chunlin Li and Yaru Lu and Tingting Gai and Yahui Zhang and Renkui Yang and Heying Qian and Yanqun Liu and Jiangwen Luo and Lu Zheng and Jinghou Lou and Yunwu Peng and Weidong Zuo and Jiangbo Song and Songzhen He and Songyuan Wu and Yunlong Zou and Lei Zhou and Lan Cheng and Yuxia Tang and Guotao Cheng and Lianwei Yuan and Weiming He and Jiabao Xu and Tao Fu and Yang Xiao and Ting Lei and Anying Xu and Ye Yin and Jian Wang and Antónia Monteiro and E Westhof and Cheng Lu and Zhixi Tian and Wen Wang and Zhonghuai Xiang and Fangyin Dai},
doi = {10.1038/s41467-022-33366-x},
issn = {2041-1723},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {Nat Commun},
volume = {13},
number = {1},
pages = {5619},
abstract = {The silkworm Bombyx mori is an important economic insect for producing silk, the "queen of fabrics". The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The silkworm Bombyx mori is an important economic insect for producing silk, the "queen of fabrics". The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.
Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F
Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses Journal Article
In: Rna, vol. 28, iss. 5, pp. 729-741, 2022, ISBN: 35236777, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, Unité ARN, WESTHOF
@article{nokey,
title = {Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses},
author = {P Sosnowski and A Tidu and G Eriani and E Westhof and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35236777},
doi = {10.1261/rna.078972.121},
isbn = {35236777},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Rna},
volume = {28},
issue = {5},
pages = {729-741},
abstract = {The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {ERIANI, MARTIN, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.
Westhof E, Thornlow B, Chan P P, Lowe T M
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Journal Article
In: Nucleic Acids Res, vol. 50, iss. 7, pp. 4100-4112, 2022, ISBN: 35380696, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{nokey,
title = {Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures},
author = {E Westhof and B Thornlow and P P Chan and T M Lowe},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35380696},
doi = {10.1093/nar/gkac222},
isbn = {35380696},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Nucleic Acids Res},
volume = {50},
issue = {7},
pages = {4100-4112},
abstract = {Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson-Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson-Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.
Vincens Q, Westhof E
Brief considerations on targeting RNA with small molecules Journal Article
In: Faculty Reviews, vol. 11, no. 39, 2022.
Abstract | Links | BibTeX | Tags: Drug discovery RNA structure & dynamics RNA targeting SARS-CoV2, Unité ARN, WESTHOF
@article{nokey,
title = {Brief considerations on targeting RNA with small molecules},
author = {Q Vincens and E Westhof},
url = {https://facultyopinions.com/prime/reports/b/11/39/},
doi = {10.12703/r/11-39},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Faculty Reviews},
volume = {11},
number = {39},
abstract = {For more than three decades, RNA has been known to be a relevant and attractive macromolecule to target but figuring out which RNA should be targeted and how remains challenging. Recent years have seen the confluence of approaches for screening, drug optimization, and target validation that have led to the approval of a few RNA-targeting therapeutics for clinical applications. This focused perspective aims to highlight but not exhaustively review key factors accounting for these successes while pointing at crucial aspects worth considering for further breakthroughs.},
keywords = {Drug discovery RNA structure & dynamics RNA targeting SARS-CoV2, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
For more than three decades, RNA has been known to be a relevant and attractive macromolecule to target but figuring out which RNA should be targeted and how remains challenging. Recent years have seen the confluence of approaches for screening, drug optimization, and target validation that have led to the approval of a few RNA-targeting therapeutics for clinical applications. This focused perspective aims to highlight but not exhaustively review key factors accounting for these successes while pointing at crucial aspects worth considering for further breakthroughs.
2021
Moore P B, Petrov A, Westhof E, Zirbel C L
Neocles B. Leontis (1955 - 2020) Journal Article
In: Rna, 2021, ISBN: 33452229, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: WESTHOF
@article{,
title = {Neocles B. Leontis (1955 - 2020)},
author = {P B Moore and A Petrov and E Westhof and C L Zirbel},
url = {https://ibmc.cnrs.fr/wp-content/uploads/2021/01/Neocles-B_RNA.pdf},
doi = {10.1261/rna.078673.121},
isbn = {33452229},
year = {2021},
date = {2021-01-01},
journal = {Rna},
abstract = {None.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {WESTHOF},
pubstate = {published},
tppubtype = {article}
}
None.
Westhof E, Leontis N B
An RNA-centric historical narrative around the Protein Data Bank Journal Article
In: J Biol Chem, vol. 296, pp. 100555, 2021, ISBN: 33744291, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article Review).
Abstract | Links | BibTeX | Tags: Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF
@article{Westhof2021,
title = {An RNA-centric historical narrative around the Protein Data Bank},
author = {E Westhof and N B Leontis},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33744291},
doi = {10.1016/j.jbc.2021.100555},
isbn = {33744291},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Biol Chem},
volume = {296},
pages = {100555},
abstract = {Some of the amazing contributions brought to the scientific community by the PDB are described. The focus is on nucleic acid structures with a bias towards RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article
Review},
keywords = {Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Some of the amazing contributions brought to the scientific community by the PDB are described. The focus is on nucleic acid structures with a bias towards RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
Marszalkowski M, Werner A, Feltens R, Helmecke D, Gossringer M, Westhof E, Hartmann R K
In: Rna, 2021, ISBN: 34266994, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant and a thermophilic bacterium},
author = {M Marszalkowski and A Werner and R Feltens and D Helmecke and M Gossringer and E Westhof and R K Hartmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34266994},
doi = {10.1261/rna.078735.121},
isbn = {34266994},
year = {2021},
date = {2021-01-01},
journal = {Rna},
abstract = {In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8-P4 and L18-P8) help to orient the two independently folding S- and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyze the effects of mutations in these tertiary contacts in P RNAs from three different species: (i) the psychrophilic bacterium Pseudoalteromonas translucida (Ptr), (ii) the mesophilic radiation-resistant bacterium Deinococcus radiodurans (Dra), and (iii) the thermophilic bacterium Thermus thermophilus (Tth). We show by UV melting experiments that simultaneous disruption of these two interdomain contacts has a stabilizing effect on all three P RNAs. This can be inferred from reduced RNA unfolding at lower temperatures and a more concerted unfolding at higher temperatures. Thus, when the two domains tightly interact via the tertiary contacts, one domain facilitates structural transitions in the other. P RNA mutants with disrupted interdomain contacts showed severe kinetic defects that were most pronounced upon simultaneous disruption of the L8-P4 and L18-P8 contacts. At 37 degrees C, the mildest effects were observed for the thermostable Tth RNA. A third interdomain contact, L9-P1, makes only a minor contribution to P RNA tertiary folding. Furthermore, D. radiodurans RNase P RNA forms an additional pseudoknot structure between the P9 and P12 of its S-domain. This interaction was found to be particularly crucial for RNase P holoenzyme activity at near-physiological Mg2+ concentrations (2 mM). We further analyzed an exceptionally stable folding trap of the G,C-rich Tth P RNA.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8-P4 and L18-P8) help to orient the two independently folding S- and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyze the effects of mutations in these tertiary contacts in P RNAs from three different species: (i) the psychrophilic bacterium Pseudoalteromonas translucida (Ptr), (ii) the mesophilic radiation-resistant bacterium Deinococcus radiodurans (Dra), and (iii) the thermophilic bacterium Thermus thermophilus (Tth). We show by UV melting experiments that simultaneous disruption of these two interdomain contacts has a stabilizing effect on all three P RNAs. This can be inferred from reduced RNA unfolding at lower temperatures and a more concerted unfolding at higher temperatures. Thus, when the two domains tightly interact via the tertiary contacts, one domain facilitates structural transitions in the other. P RNA mutants with disrupted interdomain contacts showed severe kinetic defects that were most pronounced upon simultaneous disruption of the L8-P4 and L18-P8 contacts. At 37 degrees C, the mildest effects were observed for the thermostable Tth RNA. A third interdomain contact, L9-P1, makes only a minor contribution to P RNA tertiary folding. Furthermore, D. radiodurans RNase P RNA forms an additional pseudoknot structure between the P9 and P12 of its S-domain. This interaction was found to be particularly crucial for RNase P holoenzyme activity at near-physiological Mg2+ concentrations (2 mM). We further analyzed an exceptionally stable folding trap of the G,C-rich Tth P RNA.
2020
Li B, Cao Y, Westhof E, Miao Z
Advances in RNA 3D Structure Modeling Using Experimental Data Journal Article
In: Front Genet ., vol. 11, no. 574485, 2020.
Abstract | Links | BibTeX | Tags: 3D shape, chemical probing, RNA structure, RNA-puzzles, structure prediction, Unité ARN, WESTHOF
@article{B2020b,
title = {Advances in RNA 3D Structure Modeling Using Experimental Data},
author = {B Li and Y Cao and E Westhof and Z Miao},
doi = {https://doi.org/10.3389/fgene.2020.574485},
year = {2020},
date = {2020-11-23},
journal = {Front Genet .},
volume = {11},
number = {574485},
abstract = {RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.},
keywords = {3D shape, chemical probing, RNA structure, RNA-puzzles, structure prediction, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.
Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea Journal Article
In: RNA, vol. 26, no. 12, pp. 1957-1975, 2020.
Abstract | Links | BibTeX | Tags: (hyper)thermophiles Archaea mass spectrometry modifications tRNA, ARN-MS, ENNIFAR, Unité ARN, WESTHOF
@article{,
title = {Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea},
author = {P Wolff and C Villette and J Zumsteg and D Heintz and L Antoine and B Chane-Woon-Ming and L Droogmans and H Grosjean and E Westhof},
url = {https://pubmed.ncbi.nlm.nih.gov/32994183/},
doi = {10.1261/rna.077537.120},
year = {2020},
date = {2020-09-29},
journal = {RNA},
volume = {26},
number = {12},
pages = {1957-1975},
abstract = {To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale) and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius. Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.},
keywords = {(hyper)thermophiles Archaea mass spectrometry modifications tRNA, ARN-MS, ENNIFAR, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale) and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius. Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
Westhof E, Liang S, Tong X, Ding X, Zheng L, Dai F
Unusual tertiary pairs in eukaryotic tRNA-Ala Journal Article
In: RNA, vol. 26, no. 11, pp. 1519-1529, 2020.
Abstract | Links | BibTeX | Tags: Ala Gly insects mammals tRNA, Unité ARN, WESTHOF
@article{,
title = {Unusual tertiary pairs in eukaryotic tRNA-Ala},
author = {E Westhof and S Liang and X Tong and X Ding and L Zheng and F Dai},
url = {https://pubmed.ncbi.nlm.nih.gov/32737189/},
doi = {10.1261/rna.076299.120},
year = {2020},
date = {2020-07-31},
journal = {RNA},
volume = {26},
number = {11},
pages = {1519-1529},
abstract = {tRNA molecules have well-defined sequence conservations that reflect the conserved tertiary pairs maintaining their architecture and functions during the translation processes. An analysis of aligned tRNA sequences present in the GtRNAdb data base (The Lowe Lab, University of California, Santa Cruz) led to surprising conservations on some cytosolic tRNAs specific for Alanine compared to other tRNA species, including tRNAs specific for Glycine. First, besides the well-known G3oU70 base pair in the amino acid stem, there is the frequent occurrence of a second wobble pair at G30oU40, a pair overwhelmingly observed as a Watson-Crick pair throughout phylogeny. Secondly, the tertiary pair R15/Y48 occurs as a purine-purine R15/A48 pair. Finally, the conserved T54/A58 pair maintaining the fold of the T-loop is observed as a purine-purine A54/A58 pair. The R15/A48 and A54/A58 pairs always occur together. The G30oU40 pair occurs alone or together with these other two pairs. The pairing variations are observed to variable extent depending on phylogeny. Among eukaryotes, insects display simultaneously all variations, while mammals present either the G30oU40 pair or both R15/A48 and A54/A58. tRNAs with the anticodon 34A(I)GC36 are the most prone to display all those pair variations in mammals and insects. tRNAs with anticodon Y34GC36 have preferentially G30oU40 only. These unusual pairs are not observed in bacterial, or archaeal tRNAs, probably because of the avoidance of A34-containing anticodons in 4-codon boxes. Among eukaryotes, these unusual pairing features were not observed in fungi and nematodes. These unusual structural features may affect transcription rates (e.g. 54/58) or ribosomal translocation (30/40).},
keywords = {Ala Gly insects mammals tRNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
tRNA molecules have well-defined sequence conservations that reflect the conserved tertiary pairs maintaining their architecture and functions during the translation processes. An analysis of aligned tRNA sequences present in the GtRNAdb data base (The Lowe Lab, University of California, Santa Cruz) led to surprising conservations on some cytosolic tRNAs specific for Alanine compared to other tRNA species, including tRNAs specific for Glycine. First, besides the well-known G3oU70 base pair in the amino acid stem, there is the frequent occurrence of a second wobble pair at G30oU40, a pair overwhelmingly observed as a Watson-Crick pair throughout phylogeny. Secondly, the tertiary pair R15/Y48 occurs as a purine-purine R15/A48 pair. Finally, the conserved T54/A58 pair maintaining the fold of the T-loop is observed as a purine-purine A54/A58 pair. The R15/A48 and A54/A58 pairs always occur together. The G30oU40 pair occurs alone or together with these other two pairs. The pairing variations are observed to variable extent depending on phylogeny. Among eukaryotes, insects display simultaneously all variations, while mammals present either the G30oU40 pair or both R15/A48 and A54/A58. tRNAs with the anticodon 34A(I)GC36 are the most prone to display all those pair variations in mammals and insects. tRNAs with anticodon Y34GC36 have preferentially G30oU40 only. These unusual pairs are not observed in bacterial, or archaeal tRNAs, probably because of the avoidance of A34-containing anticodons in 4-codon boxes. Among eukaryotes, these unusual pairing features were not observed in fungi and nematodes. These unusual structural features may affect transcription rates (e.g. 54/58) or ribosomal translocation (30/40).
Trzaska C, Amand S, Bailly C, Leroy C, Marchand V, Duvernois-Berthet E, Saliou J M, Benhabiles H, Werkmeister E, Chassat T, Guilbert R, Hannebique D, Mouray A, Copin M C, Moreau P A, Adriaenssens E, Kulozik A, Westhof E, Tulasne D, Motorin Y, Rebuffat S, Lejeune F
2,6-Diaminopurine as a Highly Potent Corrector of UGA Nonsense Mutations Journal Article
In: Nat Commun, vol. 11, no. 1, pp. 1509, 2020, ISBN: 32198346.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {2,6-Diaminopurine as a Highly Potent Corrector of UGA Nonsense Mutations},
author = {C Trzaska and S Amand and C Bailly and C Leroy and V Marchand and E Duvernois-Berthet and J M Saliou and H Benhabiles and E Werkmeister and T Chassat and R Guilbert and D Hannebique and A Mouray and M C Copin and P A Moreau and E Adriaenssens and A Kulozik and E Westhof and D Tulasne and Y Motorin and S Rebuffat and F Lejeune},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32198346?dopt=Abstract},
doi = {10.1038/s41467-020-15140-z},
isbn = {32198346},
year = {2020},
date = {2020-01-01},
journal = {Nat Commun},
volume = {11},
number = {1},
pages = {1509},
abstract = {Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2'-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2'-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations.
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki J M, Westhof E, Szachniuk M, Miao Z
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools Journal Article
In: Nucleic Acids Res, vol. 48, no. 2, pp. 576-588, 2020, ISBN: 31799609.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools},
author = {M Magnus and M Antczak and T Zok and J Wiedemann and P Lukasiak and Y Cao and J M Bujnicki and E Westhof and M Szachniuk and Z Miao},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31799609},
doi = {10.1093/nar/gkz1108.},
isbn = {31799609},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {2},
pages = {576-588},
abstract = {Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.
Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F
In: Nucleic Acids Res, vol. 48, no. 11, pp. 6170-6183, 2020, ISBN: 32266934.
Abstract | Links | BibTeX | Tags: ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF
@article{,
title = {The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity},
author = {K Pernod and L Schaeffer and J Chicher and E Hok and C Rick and R Geslain and G Eriani and E Westhof and M Ryckelynck and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32266934?dopt=Abstract},
doi = {10.1093/nar/gkaa221},
isbn = {32266934},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {11},
pages = {6170-6183},
abstract = {Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.},
keywords = {ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
Miao Z, Adamiak R W, Antczak M, Boniecki M J, Bujnicki J M, Chen S J, Cheng C Y, Cheng Y, Chou F C, Das R, Dokholyan N V, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann T H, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins A M, Wiedemann J, Xiao Y, Xu X, Yesselman J D, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey R T, Golden B L, Huang L, Lilley D M, Liu Y, Patel D J, Westhof E
RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers Journal Article
In: RNA, vol. 26, no. 8, pp. 982-995, 2020, ISBN: 32371455.
Abstract | Links | BibTeX | Tags: RNA structure aptamer modeing prediction ribozyme, Unité ARN, WESTHOF
@article{,
title = {RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers},
author = {Z Miao and R W Adamiak and M Antczak and M J Boniecki and J M Bujnicki and S J Chen and C Y Cheng and Y Cheng and F C Chou and R Das and N V Dokholyan and F Ding and C Geniesse and Y Jiang and A Joshi and A Krokhotin and M Magnus and O Mailhot and F Major and T H Mann and P Piatkowski and R Pluta and M Popenda and J Sarzynska and L Sun and M Szachniuk and S Tian and J Wang and J Wang and A M Watkins and J Wiedemann and Y Xiao and X Xu and J D Yesselman and D Zhang and Y Zhang and Z Zhang and C Zhao and P Zhao and Y Zhou and T Zok and A Zyla and A Ren and R T Batey and B L Golden and L Huang and D M Lilley and Y Liu and D J Patel and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32371455?dopt=Abstract},
doi = {10.1261/rna.075341.120},
isbn = {32371455},
year = {2020},
date = {2020-01-01},
journal = {RNA},
volume = {26},
number = {8},
pages = {982-995},
abstract = {RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of six RNA sequences: four structures of nucleolytic ribozymes and two of riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss a) the comparison between the automated web server and human experts; b) the prediction of coaxial stacking; c) the prediction of structural details and ligand binding; d) the development of novel prediction methods; and e) the potential improvements to be made. It is illustrated that correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can be only predicted with low resolution and accurate ligand binding prediction still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.},
keywords = {RNA structure aptamer modeing prediction ribozyme, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of six RNA sequences: four structures of nucleolytic ribozymes and two of riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss a) the comparison between the automated web server and human experts; b) the prediction of coaxial stacking; c) the prediction of structural details and ligand binding; d) the development of novel prediction methods; and e) the potential improvements to be made. It is illustrated that correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can be only predicted with low resolution and accurate ligand binding prediction still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.
2019
Rozov A, Khusainov I, Omari K El, Duman R, Mykhaylyk V, Yusupov M, Westhof E, Wagner A, Yusupova G
Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction Journal Article
In: Nat Commun, vol. 10, no. 1, pp. 2519, 2019, ISBN: 31175275.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction},
author = {A Rozov and I Khusainov and K El Omari and R Duman and V Mykhaylyk and M Yusupov and E Westhof and A Wagner and G Yusupova},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31175275?dopt=Abstract},
doi = {10.1038/s41467-019-10409-4},
isbn = {31175275},
year = {2019},
date = {2019-01-01},
journal = {Nat Commun},
volume = {10},
number = {1},
pages = {2519},
abstract = {The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.
Westhof E, Yusupov M, Yusupova G
The multiple flavors of GoU pairs in RNA Journal Article
In: J Mol Recognit, pp. e2782, 2019, ISBN: 31033092.
Abstract | Links | BibTeX | Tags: GoU pair anticodon codon mRNA miscoding ribosome tRNA tautomer, Unité ARN, WESTHOF
@article{,
title = {The multiple flavors of GoU pairs in RNA},
author = {E Westhof and M Yusupov and G Yusupova},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31033092?dopt=Abstract},
doi = {10.1002/jmr.2782},
isbn = {31033092},
year = {2019},
date = {2019-01-01},
journal = {J Mol Recognit},
pages = {e2782},
abstract = {Wobble GU pairs (or GoU) occur frequently within double-stranded RNA helices interspersed within the standard G═C and A─U Watson-Crick pairs. However, other types of GoU pairs interacting on their Watson-Crick edges have been observed. The structural and functional roles of such alternative GoU pairs are surprisingly diverse and reflect the various pairings G and U can form by exploiting all the subtleties of their electronic configurations. Here, the structural characteristics of the GoU pairs are updated following the recent crystallographic structures of functional ribosomal complexes and the development in our understanding of ribosomal translation.},
keywords = {GoU pair anticodon codon mRNA miscoding ribosome tRNA tautomer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Wobble GU pairs (or GoU) occur frequently within double-stranded RNA helices interspersed within the standard G═C and A─U Watson-Crick pairs. However, other types of GoU pairs interacting on their Watson-Crick edges have been observed. The structural and functional roles of such alternative GoU pairs are surprisingly diverse and reflect the various pairings G and U can form by exploiting all the subtleties of their electronic configurations. Here, the structural characteristics of the GoU pairs are updated following the recent crystallographic structures of functional ribosomal complexes and the development in our understanding of ribosomal translation.
Westhof E
Pseudouridines or how to draw on weak energy differences Journal Article
In: Biochem Biophys Res Commun, vol. 520, no. 4, pp. 702-704, 2019, ISBN: 31761086.
Abstract | Links | BibTeX | Tags: RNA, Unité ARN, WESTHOF
@article{,
title = {Pseudouridines or how to draw on weak energy differences},
author = {E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31761086},
doi = {10.1016/j.bbrc.2019.10.009},
isbn = {31761086},
year = {2019},
date = {2019-01-01},
journal = {Biochem Biophys Res Commun},
volume = {520},
number = {4},
pages = {702-704},
abstract = {In many RNA molecules, pseudouridines occur at conserved positions in functional sites. A great diversity of pseudouridine synthases guarantees the insertion of the modified base at precise locations. The accepted structural role of pseudouridines is a reduction of the RNA flexibility around the modification site. However, experiments rarely yield clear-cut evidence. The article "Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites" published in 2019 in Biochemical and Biophysical Research Communication by Kennedy et al. constitute a provocative case [1]. This example illustrates how a definite conformational state can be selected through small energy differences in a constrained environment.},
keywords = {RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
In many RNA molecules, pseudouridines occur at conserved positions in functional sites. A great diversity of pseudouridine synthases guarantees the insertion of the modified base at precise locations. The accepted structural role of pseudouridines is a reduction of the RNA flexibility around the modification site. However, experiments rarely yield clear-cut evidence. The article "Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites" published in 2019 in Biochemical and Biophysical Research Communication by Kennedy et al. constitute a provocative case [1]. This example illustrates how a definite conformational state can be selected through small energy differences in a constrained environment.
Shcherbakov D, Teo Y, Boukari H, Cortes-Sanchon A, Mantovani M, Osinnii I, Moore J, Juskeviciene R, Brilkova M, Duscha S, Kumar H S, Laczko E, Rehrauer H, Westhof E, Akbergenov R, Böttger E C
Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis Journal Article
In: Commun Biol, vol. 2, pp. 381, 2019, ISBN: 31637312.
Abstract | Links | BibTeX | Tags: Protein folding Protein transport Transcriptomics, Unité ARN, WESTHOF
@article{,
title = {Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis},
author = {D Shcherbakov and Y Teo and H Boukari and A Cortes-Sanchon and M Mantovani and I Osinnii and J Moore and R Juskeviciene and M Brilkova and S Duscha and H S Kumar and E Laczko and H Rehrauer and E Westhof and R Akbergenov and E C Böttger},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31637312},
doi = {10.1038/s42003-019-0626-9},
isbn = {31637312},
year = {2019},
date = {2019-01-01},
journal = {Commun Biol},
volume = {2},
pages = {381},
abstract = {Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the random error rate of mRNA decoding. Here, we present a global and comprehensive picture of the cellular changes in response to translational accuracy in mammalian ribosomes impaired by genetic manipulation. In addition to affecting established protein quality control pathways, such as elevated transcript levels for cytosolic chaperones, activation of the ubiquitin-proteasome system, and translational slowdown, ribosomal mistranslation led to unexpected responses. In particular, we observed increased mitochondrial biogenesis associated with import of misfolded proteins into the mitochondria and silencing of the unfolded protein response in the endoplasmic reticulum.},
keywords = {Protein folding Protein transport Transcriptomics, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the random error rate of mRNA decoding. Here, we present a global and comprehensive picture of the cellular changes in response to translational accuracy in mammalian ribosomes impaired by genetic manipulation. In addition to affecting established protein quality control pathways, such as elevated transcript levels for cytosolic chaperones, activation of the ubiquitin-proteasome system, and translational slowdown, ribosomal mistranslation led to unexpected responses. In particular, we observed increased mitochondrial biogenesis associated with import of misfolded proteins into the mitochondria and silencing of the unfolded protein response in the endoplasmic reticulum.
Antoine L, Wolff P, Westhof E, Romby P, Marzi S
Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS Journal Article
In: Biochimie, vol. 164, pp. 60-69, 2019, ISBN: 31295507.
Abstract | Links | BibTeX | Tags: 2D gel isolation Staphylococcus aureus nanoLC/MSMS post-transcriptional tRNA modifications, ARN-MS, ENNIFAR, ROMBY, Unité ARN, WESTHOF
@article{,
title = {Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS},
author = {L Antoine and P Wolff and E Westhof and P Romby and S Marzi},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31295507?dopt=Abstract},
doi = {10.1016/j.biochi.2019.07.003},
isbn = {31295507},
year = {2019},
date = {2019-01-01},
journal = {Biochimie},
volume = {164},
pages = {60-69},
abstract = {RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.},
keywords = {2D gel isolation Staphylococcus aureus nanoLC/MSMS post-transcriptional tRNA modifications, ARN-MS, ENNIFAR, ROMBY, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.
2018
Tosar J P, Gámbaro F, Darré L, Pantano S, Westhof E, Cayota A
Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs Journal Article
In: Nucleic Acids Res, vol. 46, no. 17, pp. 9081-9093, 2018, ISBN: 29893896.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs},
author = {J P Tosar and F Gámbaro and L Darré and S Pantano and E Westhof and A Cayota},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29893896?dopt=Abstract},
doi = {10.1093/nar/gky495},
isbn = {29893896},
year = {2018},
date = {2018-01-01},
journal = {Nucleic Acids Res},
volume = {46},
number = {17},
pages = {9081-9093},
abstract = {We have previously shown that 5' halves from tRNAGlyGCC and tRNAGluCUC are the most enriched small RNAs in the extracellular space of human cell lines, and especially in the non-vesicular fraction. Extracellular RNAs are believed to require protection by either encapsulation in vesicles or ribonucleoprotein complex formation. However, deproteinization of non-vesicular tRNA halves does not affect their retention in size-exclusion chromatography. Thus, we considered alternative explanations for their extracellular stability. In-silico analysis of the sequence of these tRNA-derived fragments showed that tRNAGly 5' halves can form homodimers or heterodimers with tRNAGlu 5' halves. This capacity is virtually unique to glycine tRNAs. By analyzing synthetic oligonucleotides by size exclusion chromatography, we provide evidence that dimerization is possible in vitro. tRNA halves with single point substitutions preventing dimerization are degraded faster both in controlled nuclease digestion assays and after transfection in cells, showing that dimerization can stabilize tRNA halves against the action of cellular nucleases. Finally, we give evidence supporting dimerization of endogenous tRNAGlyGCC 5' halves inside cells. Considering recent reports have shown that 5' tRNA halves from Ala and Cys can form tetramers, our results highlight RNA intermolecular structures as a new layer of complexity in the biology of tRNA-derived fragments.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
We have previously shown that 5' halves from tRNAGlyGCC and tRNAGluCUC are the most enriched small RNAs in the extracellular space of human cell lines, and especially in the non-vesicular fraction. Extracellular RNAs are believed to require protection by either encapsulation in vesicles or ribonucleoprotein complex formation. However, deproteinization of non-vesicular tRNA halves does not affect their retention in size-exclusion chromatography. Thus, we considered alternative explanations for their extracellular stability. In-silico analysis of the sequence of these tRNA-derived fragments showed that tRNAGly 5' halves can form homodimers or heterodimers with tRNAGlu 5' halves. This capacity is virtually unique to glycine tRNAs. By analyzing synthetic oligonucleotides by size exclusion chromatography, we provide evidence that dimerization is possible in vitro. tRNA halves with single point substitutions preventing dimerization are degraded faster both in controlled nuclease digestion assays and after transfection in cells, showing that dimerization can stabilize tRNA halves against the action of cellular nucleases. Finally, we give evidence supporting dimerization of endogenous tRNAGlyGCC 5' halves inside cells. Considering recent reports have shown that 5' tRNA halves from Ala and Cys can form tetramers, our results highlight RNA intermolecular structures as a new layer of complexity in the biology of tRNA-derived fragments.
Reinharz V, Soulé A, Westhof E, Waldispühl J, Denise A
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families Journal Article
In: Nucleic Acids Res, vol. 46, no. 8, pp. 3841-3851, 2018, ISBN: 29608773.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families},
author = {V Reinharz and A Soulé and E Westhof and J Waldispühl and A Denise},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29608773?dopt=Abstract},
doi = {10.1093/nar/gky197},
isbn = {29608773},
year = {2018},
date = {2018-01-01},
journal = {Nucleic Acids Res},
volume = {46},
number = {8},
pages = {3841-3851},
abstract = {The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.
Patel D, Westhof E
In: Curr Opin Struct Biol, vol. 53, pp. vi-viii, 2018, ISBN: 30553297.
Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Editorial overview: Protein nucleic acid interactions: order, ambiguities and disorder in recognition and complex formation between proteins and nucleic acids},
author = {D Patel and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30553297?dopt=Abstract},
doi = {10.1016/j.sbi.2018.11.009},
isbn = {30553297},
year = {2018},
date = {2018-01-01},
journal = {Curr Opin Struct Biol},
volume = {53},
pages = {vi-viii},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Hoernes T P, Faserl K, Juen M A, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher M D
Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions Journal Article
In: Nat Commun, vol. 9, no. 1, pp. 4865, 2018, ISBN: 30451861.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions},
author = {T P Hoernes and K Faserl and M A Juen and J Kremser and C Gasser and E Fuchs and X Shi and A Siewert and H Lindner and C Kreutz and R Micura and S Joseph and C Höbartner and E Westhof and A Hüttenhofer and M D Erlacher},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30451861?dopt=Abstract},
doi = {10.1038/s41467-018-07321-8},
isbn = {30451861},
year = {2018},
date = {2018-01-01},
journal = {Nat Commun},
volume = {9},
number = {1},
pages = {4865},
abstract = {The precise interplay between the mRNA codon and the tRNA anticodon is crucial for ensuring efficient and accurate translation by the ribosome. The insertion of RNA nucleobase derivatives in the mRNA allowed us to modulate the stability of the codon-anticodon interaction in the decoding site of bacterial and eukaryotic ribosomes, allowing an in-depth analysis of codon recognition. We found the hydrogen bond between the N1 of purines and the N3 of pyrimidines to be sufficient for decoding of the first two codon nucleotides, whereas adequate stacking between the RNA bases is critical at the wobble position. Inosine, found in eukaryotic mRNAs, is an important example of destabilization of the codon-anticodon interaction. Whereas single inosines are efficiently translated, multiple inosines, e.g., in the serotonin receptor 5-HT2C mRNA, inhibit translation. Thus, our results indicate that despite the robustness of the decoding process, its tolerance toward the weakening of codon-anticodon interactions is limited.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The precise interplay between the mRNA codon and the tRNA anticodon is crucial for ensuring efficient and accurate translation by the ribosome. The insertion of RNA nucleobase derivatives in the mRNA allowed us to modulate the stability of the codon-anticodon interaction in the decoding site of bacterial and eukaryotic ribosomes, allowing an in-depth analysis of codon recognition. We found the hydrogen bond between the N1 of purines and the N3 of pyrimidines to be sufficient for decoding of the first two codon nucleotides, whereas adequate stacking between the RNA bases is critical at the wobble position. Inosine, found in eukaryotic mRNAs, is an important example of destabilization of the codon-anticodon interaction. Whereas single inosines are efficiently translated, multiple inosines, e.g., in the serotonin receptor 5-HT2C mRNA, inhibit translation. Thus, our results indicate that despite the robustness of the decoding process, its tolerance toward the weakening of codon-anticodon interactions is limited.
Rozov A, Wolff P, Grosjean H, Yusupov M, Yusupova G, Westhof E
Tautomeric G*U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria Journal Article
In: Nucleic Acids Res, vol. 46, no. 14, pp. 7425-7435, 2018, ISBN: 29931292.
Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN, WESTHOF
@article{,
title = {Tautomeric G*U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria},
author = {A Rozov and P Wolff and H Grosjean and M Yusupov and G Yusupova and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29931292?dopt=Abstract},
doi = {10.1093/nar/gky547},
isbn = {29931292},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {Nucleic Acids Res},
volume = {46},
number = {14},
pages = {7425-7435},
abstract = {We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick GC and miscoding GU pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding GU pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by GU pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a GU pair in the tRNA/mRNA complex and very rarely from a G = C to a GU pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool.},
keywords = {ARN-MS, ENNIFAR, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick GC and miscoding GU pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding GU pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by GU pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a GU pair in the tRNA/mRNA complex and very rarely from a G = C to a GU pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool.
Hosseini M, Roy P, Sissler M, Zirbel C L, Westhof E, Leontis N
How to fold and protect mitochondrial ribosomal RNA with fewer guanines Journal Article
In: Nucleic Acids Res, vol. 46, no. 20, pp. 10946-10968, 2018, ISBN: 30215760.
Abstract | Links | BibTeX | Tags: SISSLER, Unité ARN, WESTHOF
@article{,
title = {How to fold and protect mitochondrial ribosomal RNA with fewer guanines},
author = {M Hosseini and P Roy and M Sissler and C L Zirbel and E Westhof and N Leontis},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30215760?dopt=Abstract},
doi = {10.1093/nar/gky762},
isbn = {30215760},
year = {2018},
date = {2018-01-01},
journal = {Nucleic Acids Res},
volume = {46},
number = {20},
pages = {10946-10968},
abstract = {Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA-RNA or RNA-protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA-RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid-RNA interactions.},
keywords = {SISSLER, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA-RNA or RNA-protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA-RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid-RNA interactions.
Akbergenov R, Duscha S, Fritz A K, Juskeviciene R, Oishi N, Schmitt K, Shcherbakov D, Teo Y, Boukari H, Freihofer P, Isnard-Petit P, Oettinghaus B, Frank S, Thiam K, Rehrauer H, Westhof E, Schacht J, Eckert A, Wolfer D, Böttger E C
Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations Journal Article
In: EMBO Rep, vol. 19, no. 11, pp. e46193, 2018, ISBN: 30237157.
Abstract | Links | BibTeX | Tags: aging disease misreading mitochondria protein synthesis, Unité ARN, WESTHOF
@article{,
title = {Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations},
author = {R Akbergenov and S Duscha and A K Fritz and R Juskeviciene and N Oishi and K Schmitt and D Shcherbakov and Y Teo and H Boukari and P Freihofer and P Isnard-Petit and B Oettinghaus and S Frank and K Thiam and H Rehrauer and E Westhof and J Schacht and A Eckert and D Wolfer and E C Böttger},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30237157?dopt=Abstract},
doi = {10.15252/embr.201846193},
isbn = {30237157},
year = {2018},
date = {2018-01-01},
journal = {EMBO Rep},
volume = {19},
number = {11},
pages = {e46193},
abstract = {The 1555 A to G substitution in mitochondrial 12S A-site rRNA is associated with maternally transmitted deafness of variable penetrance in the absence of otherwise overt disease. Here, we recapitulate the suggested A1555G-mediated pathomechanism in an experimental model of mitoribosomal mistranslation by directed mutagenesis of mitoribosomal protein MRPS5. We first establish that the ratio of cysteine/methionine incorporation and read-through of mtDNA-encoded MT-CO1 protein constitute reliable measures of mitoribosomal misreading. Next, we demonstrate that human HEK293 cells expressing mutant V336Y MRPS5 show increased mitoribosomal mistranslation. As for immortalized lymphocytes of individuals with the pathogenic A1555G mutation, we find little changes in the transcriptome of mutant V336Y MRPS5 HEK cells, except for a coordinated upregulation of transcripts for cytoplasmic ribosomal proteins. Homozygous knock-in mutant Mrps5 V338Y mice show impaired mitochondrial function and a phenotype composed of enhanced susceptibility to noise-induced hearing damage and anxiety-related behavioral alterations. The experimental data in V338Y mutant mice point to a key role of mitochondrial translation and function in stress-related behavioral and physiological adaptations.},
keywords = {aging disease misreading mitochondria protein synthesis, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The 1555 A to G substitution in mitochondrial 12S A-site rRNA is associated with maternally transmitted deafness of variable penetrance in the absence of otherwise overt disease. Here, we recapitulate the suggested A1555G-mediated pathomechanism in an experimental model of mitoribosomal mistranslation by directed mutagenesis of mitoribosomal protein MRPS5. We first establish that the ratio of cysteine/methionine incorporation and read-through of mtDNA-encoded MT-CO1 protein constitute reliable measures of mitoribosomal misreading. Next, we demonstrate that human HEK293 cells expressing mutant V336Y MRPS5 show increased mitoribosomal mistranslation. As for immortalized lymphocytes of individuals with the pathogenic A1555G mutation, we find little changes in the transcriptome of mutant V336Y MRPS5 HEK cells, except for a coordinated upregulation of transcripts for cytoplasmic ribosomal proteins. Homozygous knock-in mutant Mrps5 V338Y mice show impaired mitochondrial function and a phenotype composed of enhanced susceptibility to noise-induced hearing damage and anxiety-related behavioral alterations. The experimental data in V338Y mutant mice point to a key role of mitochondrial translation and function in stress-related behavioral and physiological adaptations.
2017
Sissler M, González-Serrano L E, Westhof E
Recent Advances in Mitochondrial Aminoacyl-tRNA Synthetases and Disease Journal Article
In: Trends Mol Med, vol. 23, no. 8, pp. 693-708, 2017, ISBN: 28716624.
Abstract | Links | BibTeX | Tags: aminoacyl-tRNA synthetase central nervous system mitochondrial disease mitochondrial translation moonlighting proteins unfolded protein response, SISSLER, Unité ARN, WESTHOF
@article{,
title = {Recent Advances in Mitochondrial Aminoacyl-tRNA Synthetases and Disease},
author = {M Sissler and L E González-Serrano and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28716624?dopt=Abstract},
doi = {10.1016/j.molmed.2017.06.002},
isbn = {28716624},
year = {2017},
date = {2017-01-01},
journal = {Trends Mol Med},
volume = {23},
number = {8},
pages = {693-708},
abstract = {Dysfunctions in mitochondria - the powerhouses of the cell - lead to several human pathologies. Because mitochondria integrate nuclear and mitochondrial genetic systems, they are richly intertwined with cellular activities. The nucleus-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are key components of the mitochondrial translation apparatus. Mutations in these enzymes predominantly affect the central nervous system (CNS) but also target other organs. Comparable mutations in mt-aaRSs can lead to vastly diverse diseases, occurring at different stages in life, and within different tissues; this represents a confounding issue. With newer information available, we propose that the pleiotropy and tissue-specificity of mt-aaRS-associated diseases result from the molecular integration of mitochondrial translation events within the cell; namely, through specific crosstalk between the cellular program and the energy demands of the cell. We place particular focus on neuronal cells.},
keywords = {aminoacyl-tRNA synthetase central nervous system mitochondrial disease mitochondrial translation moonlighting proteins unfolded protein response, SISSLER, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Dysfunctions in mitochondria - the powerhouses of the cell - lead to several human pathologies. Because mitochondria integrate nuclear and mitochondrial genetic systems, they are richly intertwined with cellular activities. The nucleus-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are key components of the mitochondrial translation apparatus. Mutations in these enzymes predominantly affect the central nervous system (CNS) but also target other organs. Comparable mutations in mt-aaRSs can lead to vastly diverse diseases, occurring at different stages in life, and within different tissues; this represents a confounding issue. With newer information available, we propose that the pleiotropy and tissue-specificity of mt-aaRS-associated diseases result from the molecular integration of mitochondrial translation events within the cell; namely, through specific crosstalk between the cellular program and the energy demands of the cell. We place particular focus on neuronal cells.
Miao Z, Westhof E
RNA Structure: Advances and Assessment of 3D Structure Prediction. Journal Article
In: Annu Rev Biophys, vol. 46, pp. 483-503, 2017, ISBN: 28375730.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {RNA Structure: Advances and Assessment of 3D Structure Prediction.},
author = {Z Miao and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28375730},
doi = {10.1146/annurev-biophys-070816-034125},
isbn = {28375730},
year = {2017},
date = {2017-01-01},
journal = {Annu Rev Biophys},
volume = {46},
pages = {483-503},
abstract = {Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Miao Z, Adamiak R W, Antczak M, Batey R T, Becka A J, Biesiada M, Boniecki M J, Bujnicki J, Chen S J, Cheng C Y, Chou F C, Ferré-D'Amaré A R, Das R, Dawson W K, Feng D, Dokholyan N V, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach G E, Major F, Mann T H, Magnus M, Pachulska-Wieczorek K, Patel D J, Piccirilli J A, Popenda M, Purzycka K J, Ren A, Rice G M, Santalucia Jr. J, Sarzynska J, Szachniuk M, Tandon A, Trausch J J, Tian S, Wang J, Weeks K M, 2nd. B Williams, Xiao Y, Xu X, Zhang D, Zok T, Westhof E
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Journal Article
In: RNA, vol. 23, no. 5, pp. 655-672, 2017, ISBN: 28138060.
Abstract | Links | BibTeX | Tags: 3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF
@article{,
title = {RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.},
author = {Z Miao and R W Adamiak and M Antczak and R T Batey and A J Becka and M Biesiada and M J Boniecki and J Bujnicki and S J Chen and C Y Cheng and F C Chou and A R Ferré-D'Amaré and R Das and W K Dawson and D Feng and N V Dokholyan and S Dunin-Horkawicz and C Geniesse and K Kappel and W Kladwang and A Krokhotin and G E Lach and F Major and T H Mann and M Magnus and K Pachulska-Wieczorek and D J Patel and J A Piccirilli and M Popenda and K J Purzycka and A Ren and G M Rice and Jr. J Santalucia and J Sarzynska and M Szachniuk and A Tandon and J J Trausch and S Tian and J Wang and K M Weeks and 2nd. B Williams and Y Xiao and X Xu and D Zhang and T Zok and E Westhof},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28138060?dopt=Abstract},
doi = {10.1261/rna.060368.116},
isbn = {28138060},
year = {2017},
date = {2017-01-01},
journal = {RNA},
volume = {23},
number = {5},
pages = {655-672},
abstract = {RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.},
keywords = {3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.
Lai L B, Tanimoto A, Lai S M, Chen W Y, Marathe I A, Westhof E, Wysocki V H, Gopalan V
A novel double kink-turn module in euryarchaeal RNase P RNAs. Journal Article
In: Nucleic Acids Res, vol. 45, no. 12, pp. 7432-7440, 2017, ISBN: 28525600.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {A novel double kink-turn module in euryarchaeal RNase P RNAs.},
author = {L B Lai and A Tanimoto and S M Lai and W Y Chen and I A Marathe and E Westhof and V H Wysocki and V Gopalan},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28525600?dopt=Abstract},
doi = {10.1093/nar/gkx388},
isbn = {28525600},
year = {2017},
date = {2017-01-01},
journal = {Nucleic Acids Res},
volume = {45},
number = {12},
pages = {7432-7440},
abstract = {RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented 'double K-turn' module in type A and type M archaeal RPR variants.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented 'double K-turn' module in type A and type M archaeal RPR variants.
Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M
Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI Journal Article
In: RNA, vol. 23, no. 12, pp. 1788-1795, 2017, ISBN: 28939697.
Abstract | Links | BibTeX | Tags: DFHBI Spinach crystal structure fluorescence fluorogenic RNA aptamer, ENNIFAR, RYCKELYNCK, Unité ARN, WESTHOF
@article{,
title = {Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI},
author = {P Fernandez-Millan and A Autour and E Ennifar and E Westhof and M Ryckelynck},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28939697?dopt=Abstract},
doi = {10.1261/rna.063008},
isbn = {28939697},
year = {2017},
date = {2017-01-01},
journal = {RNA},
volume = {23},
number = {12},
pages = {1788-1795},
abstract = {Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach comprising five mutations whom the exact role was not deciphered yet. In this work, we co-crystallized a re-engineered version of iSpinach in complex with the DFHBI and solved the x-ray structure of the complex at 2 Å resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach allows shedding some light on the possible function of the different beneficial mutations carried by iSpinach.},
keywords = {DFHBI Spinach crystal structure fluorescence fluorogenic RNA aptamer, ENNIFAR, RYCKELYNCK, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach comprising five mutations whom the exact role was not deciphered yet. In this work, we co-crystallized a re-engineered version of iSpinach in complex with the DFHBI and solved the x-ray structure of the complex at 2 Å resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach allows shedding some light on the possible function of the different beneficial mutations carried by iSpinach.
Carapito R, Konantz M, Paillart J C, Miao Z, Pichot A, Leduc M S, Yang Y, Bergstrom K L, Mahoney D H, Shardy D L, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller J S, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho C S, Amati-Bonneau P, Procaccio V, Mosca-Boidron A L, Marle N, Osmani N, Lefebvre O, Goetz J G, Unal S, Akarsu N A, Radosavljevic M, Chenard M P, Rialland F, Grain A, Béné M C, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming M D, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, Bahram S
Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features Journal Article
In: J Clin Invest, vol. 127, no. 11, pp. 4090-4103, 2017, ISBN: 28972538.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features},
author = {R Carapito and M Konantz and J C Paillart and Z Miao and A Pichot and M S Leduc and Y Yang and K L Bergstrom and D H Mahoney and D L Shardy and G Alsaleh and L Naegely and A Kolmer and N Paul and A Hanauer and V Rolli and J S Müller and E Alghisi and L Sauteur and C Macquin and A Morlon and C S Sancho and P Amati-Bonneau and V Procaccio and A L Mosca-Boidron and N Marle and N Osmani and O Lefebvre and J G Goetz and S Unal and N A Akarsu and M Radosavljevic and M P Chenard and F Rialland and A Grain and M C Béné and M Eveillard and M Vincent and J Guy and L Faivre and C Thauvin-Robinet and J Thevenon and K Myers and M D Fleming and A Shimamura and E Bottollier-Lemallaz and E Westhof and C Lengerke and B Isidor and S Bahram},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28972538?dopt=Abstract},
doi = {10.1172/JCI92876},
isbn = {28972538},
year = {2017},
date = {2017-01-01},
journal = {J Clin Invest},
volume = {127},
number = {11},
pages = {4090-4103},
abstract = {Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.
2016
Westhof E
Perspectives and Pitfalls in Nucleic Acids Crystallography Book Chapter
In: Ennifar, E (Ed.): Nucleic Acid Crystallography: Methods and Protocols, vol. 1320, pp. 3-8, Humana Press, NY, 2016, ISBN: 26227033.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@inbook{,
title = {Perspectives and Pitfalls in Nucleic Acids Crystallography},
author = {E Westhof},
editor = {E Ennifar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26227033?dopt=Abstract},
doi = {10.1007/978-1-4939-2763-0_1},
isbn = {26227033},
year = {2016},
date = {2016-01-01},
booktitle = {Nucleic Acid Crystallography: Methods and Protocols},
volume = {1320},
pages = {3-8},
publisher = {Humana Press},
address = {NY},
series = {Methods in Molecular Biology},
abstract = {X-ray crystallography offers precious and striking knowledge on biomolecular architectures. Although safeguards do exist to guarantee the accuracy of the structures deposited in databases, they are not always applied, leading to the spread of inaccurate data. The importance of validation reports in the publication process is emphasized.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {inbook}
}
X-ray crystallography offers precious and striking knowledge on biomolecular architectures. Although safeguards do exist to guarantee the accuracy of the structures deposited in databases, they are not always applied, leading to the spread of inaccurate data. The importance of validation reports in the publication process is emphasized.
Rozov A, Westhof E, Yusupov M, Yusupova G
The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix. Journal Article
In: Nucleic Acids Res, vol. 44, no. 13, pp. 6434-6441, 2016, ISBN: 27174928.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.},
author = {A Rozov and E Westhof and M Yusupov and G Yusupova},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27174928?dopt=Abstract},
doi = {10.1093/nar/gkw431},
isbn = {27174928},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {13},
pages = {6434-6441},
abstract = {Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a GU base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical GC pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a GU base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical GC pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.
Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Journal Article
In: Nat Commun, vol. 21, no. 7, pp. 10457, 2016, ISBN: 26791911.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.},
author = {A Rozov and N Demeshkina and I Khusainov and E Westhof and M Yusupov and G Yusupova},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26791911?dopt=Abstract},
doi = {10.1038/ncomms10457},
isbn = {26791911},
year = {2016},
date = {2016-01-01},
journal = {Nat Commun},
volume = {21},
number = {7},
pages = {10457},
abstract = {Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)UUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)UUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.
Miao Z, Westhof E
RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database. Journal Article
In: Nucleic Acids Res, vol. 44, no. W1, pp. W562-W567, 2016, ISBN: 27084949.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.},
author = {Z Miao and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27084939?dopt=Abstract},
doi = {10.1093/nar/gkw251},
isbn = {27084949},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {W1},
pages = {W562-W567},
abstract = {RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on:http://ahsoka.u-strasbg.fr/rbscorenbench/.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on:http://ahsoka.u-strasbg.fr/rbscorenbench/.
Miao Z, Cao Y
Quantifying side-chain conformational variations in protein structure. Journal Article
In: Sci Rep, vol. 6, pp. 37024, 2016, ISBN: 27845406.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {Quantifying side-chain conformational variations in protein structure.},
author = {Z Miao and Y Cao},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27845406?dopt=Abstract},
doi = {10.1038/srep37024},
isbn = {27845406},
year = {2016},
date = {2016-01-01},
journal = {Sci Rep},
volume = {6},
pages = {37024},
abstract = {Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.
Grosjean H, Westhof E
An integrated, structure- and energy-based view of the genetic code. Journal Article
In: Nucleic Acids Res, vol. 44, no. 17, pp. 8020-8040, 2016, ISBN: 27448410.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{,
title = {An integrated, structure- and energy-based view of the genetic code.},
author = {H Grosjean and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27448410?dopt=Abstract},
doi = {10.1093/nar/gkw608},
isbn = {27448410},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {17},
pages = {8020-8040},
abstract = {The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon-anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well with the necessity to stabilize AU-rich codon-anticodon pairs and to avoid miscoding in split codon boxes. The evolution and expansion of the genetic code is viewed as being originally based on GC content with progressive introduction of A/U together with tRNA modifications. The representation we present should help the engineering of the genetic code to include non-natural amino acids.
D'Ascenzo L, Auffinger P
Anions in Nucleic Acid Crystallography Book Chapter
In: Ennifar, E (Ed.): Nucleic Acid Crystallography: Methods and Protocols, vol. 1320, pp. 337-351, Humana Press, NY, 2016, ISBN: 26227054.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@inbook{,
title = {Anions in Nucleic Acid Crystallography},
author = {L D'Ascenzo and P Auffinger},
editor = {E Ennifar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26227054?dopt=Abstract},
doi = {10.1007/978-1-4939-2763-0_22},
isbn = {26227054},
year = {2016},
date = {2016-01-01},
booktitle = {Nucleic Acid Crystallography: Methods and Protocols},
volume = {1320},
pages = {337-351},
publisher = {Humana Press},
address = {NY},
series = {Methods in Molecular Biology},
abstract = {Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {inbook}
}
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
Autour A, Westhof E, Ryckelynck M
iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Journal Article
In: Nucleic Acids Res, vol. 44, no. 6, pp. 2491-2500, 2016, ISBN: 26932363.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN, WESTHOF
@article{,
title = {iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications.},
author = {A Autour and E Westhof and M Ryckelynck},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26932363?dopt=Abstract},
doi = {10.1093/nar/gkw083},
isbn = {26932363},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {6},
pages = {2491-2500},
abstract = {Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.},
keywords = {RYCKELYNCK, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.
Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G
New Structural Insights into Translational Miscoding. Journal Article
In: Trends Biochem Sci, vol. 41, no. 9, pp. 798-814, 2016, ISBN: 27372401.
Abstract | Links | BibTeX | Tags: crystallography decoding ribosome structure translation, Unité ARN, WESTHOF
@article{,
title = {New Structural Insights into Translational Miscoding.},
author = {A Rozov and N Demeshkina and E Westhof and M Yusupov and G Yusupova},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27372401},
doi = {10.1016/j.tibs.2016.06.001},
isbn = {27372401},
year = {2016},
date = {2016-01-01},
journal = {Trends Biochem Sci},
volume = {41},
number = {9},
pages = {798-814},
abstract = {The fidelity of translation depends strongly on the selection of the correct aminoacyl-tRNA that is complementary to the mRNA codon present in the ribosomal decoding center. The ribosome occasionally makes mistakes by selecting the wrong substrate from the pool of aminoacyl-tRNAs. Here, we summarize recent structural advances that may help to clarify the origin of missense errors that occur during decoding. These developments suggest that discrimination between tRNAs is based primarily on steric complementarity and shape acceptance rather than on the number of hydrogen bonds between the molding of the decoding center and the codon-anticodon duplex. They strengthen the hypothesis that spatial mimicry, due either to base tautomerism or ionization, drives infidelity in ribosomal translation.},
keywords = {crystallography decoding ribosome structure translation, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The fidelity of translation depends strongly on the selection of the correct aminoacyl-tRNA that is complementary to the mRNA codon present in the ribosomal decoding center. The ribosome occasionally makes mistakes by selecting the wrong substrate from the pool of aminoacyl-tRNAs. Here, we summarize recent structural advances that may help to clarify the origin of missense errors that occur during decoding. These developments suggest that discrimination between tRNAs is based primarily on steric complementarity and shape acceptance rather than on the number of hydrogen bonds between the molding of the decoding center and the codon-anticodon duplex. They strengthen the hypothesis that spatial mimicry, due either to base tautomerism or ionization, drives infidelity in ribosomal translation.