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2023
Giegé Richard, Eriani Gilbert
The tRNA identity landscape for aminoacylation and beyond Journal Article
In: Nucleic Acids Res, vol. 51, no. 4, pp. 1528–1570, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ERIANI, GIEGE, Unité ARN
@article{pmid36744444,
title = {The tRNA identity landscape for aminoacylation and beyond},
author = {Richard Giegé and Gilbert Eriani},
doi = {10.1093/nar/gkad007},
issn = {1362-4962},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Nucleic Acids Res},
volume = {51},
number = {4},
pages = {1528--1570},
abstract = {tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.},
keywords = {ERIANI, GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
2019
Florentz C, Giege R
History of tRNA research in Strasbourg Journal Article
In: IUBMB Life, vol. 71, no. 8, pp. 1066-1087, 2019, ISBN: 31185141.
Abstract | Links | BibTeX | Tags: FLORENTZ, GIEGE, Strasbourg epistemology evolution genetic code history structural biology transfer RNA translation, Unité ARN
@article{,
title = {History of tRNA research in Strasbourg},
author = {C Florentz and R Giege},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31185141?dopt=Abstract},
doi = {10.1002/iub.2079},
isbn = {31185141},
year = {2019},
date = {2019-01-01},
journal = {IUBMB Life},
volume = {71},
number = {8},
pages = {1066-1087},
abstract = {The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future.},
keywords = {FLORENTZ, GIEGE, Strasbourg epistemology evolution genetic code history structural biology transfer RNA translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future.
2016
Giege R, Springer M
Aminoacyl-tRNA Synthetases in the Bacterial World. Journal Article
In: EcoSal Plus, vol. 7, no. 1, pp. none, 2016, ISBN: 27223819.
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Aminoacyl-tRNA Synthetases in the Bacterial World.},
author = {R Giege and M Springer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27223819?dopt=Abstract},
doi = {10.1128/ecosalplus.ESP-0002-2016},
isbn = {27223819},
year = {2016},
date = {2016-01-01},
journal = {EcoSal Plus},
volume = {7},
number = {1},
pages = {none},
abstract = {Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined
2012
Giege R, Springer M
Aminoacyl-tRNA Synthetases in the Bacterial World. Journal Article
In: EcoSal Plus, vol. 5, no. 1, pp. none, 2012, ISBN: 26442825.
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Aminoacyl-tRNA Synthetases in the Bacterial World.},
author = {R Giege and M Springer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26442825},
doi = {10.1128/ecosalplus.4.2.1},
isbn = {26442825},
year = {2012},
date = {2012-01-01},
journal = {EcoSal Plus},
volume = {5},
number = {1},
pages = {none},
abstract = {Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
2006
Sauter C, Lorber B, Théobald-Dietrich A, Giege R, Khan-Malek C, Gauthier-Manuel B, Thuillier G, Ferrigno R
Dispositif microfluidique pour la cristallisation et l'analyse cristallographique de molécules. Miscellaneous
2006, ISBN: EP 2040809 A2.
BibTeX | Tags: FRUGIER, GIEGE, SAUTER, Unité ARN
@misc{,
title = {Dispositif microfluidique pour la cristallisation et l'analyse cristallographique de molécules.},
author = {C Sauter and B Lorber and A Théobald-Dietrich and R Giege and C Khan-Malek and B Gauthier-Manuel and G Thuillier and R Ferrigno},
isbn = {EP 2040809 A2},
year = {2006},
date = {2006-01-01},
keywords = {FRUGIER, GIEGE, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
Leguay J J, Giege R, Menager M T, Ansoborlo E
Facets of environmental nuclear toxicology Journal Article
In: Biochimie, vol. 88, no. 11, pp. 1513-1514, 2006, ISBN: 17079066, (0300-9084 (Print) Editorial).
Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Facets of environmental nuclear toxicology},
author = {J J Leguay and R Giege and M T Menager and E Ansoborlo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17079066},
isbn = {17079066},
year = {2006},
date = {2006-01-01},
journal = {Biochimie},
volume = {88},
number = {11},
pages = {1513-1514},
note = {0300-9084 (Print)
Editorial},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R
Transfer RNAs and the RNA world Journal Article
In: Bol Inf Assoc Nac Bioquimicos (portuguais), vol. 8, pp. 5-8, 2006.
Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Transfer RNAs and the RNA world},
author = {R Giege},
url = {none},
year = {2006},
date = {2006-01-01},
journal = {Bol Inf Assoc Nac Bioquimicos (portuguais)},
volume = {8},
pages = {5-8},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R
The early history of tRNA recognition by aminoacyl-tRNA synthetases Journal Article
In: J Biosci, vol. 31, no. 4, pp. 477-488, 2006, ISBN: 17206068, (0250-5991 (Print) Journal Article).
Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {The early history of tRNA recognition by aminoacyl-tRNA synthetases},
author = {R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17206068},
isbn = {17206068},
year = {2006},
date = {2006-01-01},
journal = {J Biosci},
volume = {31},
number = {4},
pages = {477-488},
note = {0250-5991 (Print)
Journal Article},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2005
Lorber B
Perspectives for pure and applied protein crystallogenesis studies Journal Article
In: Crystal Growth & Design, vol. 5, no. 1, pp. 17-19, 2005.
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Perspectives for pure and applied protein crystallogenesis studies},
author = {B Lorber},
url = {http://pubs.acs.org/doi/abs/10.1021/cg030065o},
year = {2005},
date = {2005-01-01},
journal = {Crystal Growth & Design},
volume = {5},
number = {1},
pages = {17-19},
abstract = {The unpredictability of protein crystallization is essentially due to our ignorance of the correlations existing between architectural features of these macromolecules and physical chemical properties of the crystallization medium in which their crystals nucleate and grow. Some ideas are suggested to guide crystal growth and bioinformatics specialists in their quest of relationships that might help to rationalize the general approach of protein crystal growth.},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The unpredictability of protein crystallization is essentially due to our ignorance of the correlations existing between architectural features of these macromolecules and physical chemical properties of the crystallization medium in which their crystals nucleate and grow. Some ideas are suggested to guide crystal growth and bioinformatics specialists in their quest of relationships that might help to rationalize the general approach of protein crystal growth.
Kadri A, Lorber B, Charron C, Robert M C, Capelle B, Damak M, Jenner G, Giege R
Crystal quality and differential crystal-growth behaviour of three proteins crystallized in gel at high hydrostatic pressure Journal Article
In: Acta Crystallogr D Biol Crystallogr, vol. 61, no. Pt 6, pp. 784-788, 2005, ISBN: 15930640, (0907-4449 Journal Article).
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Crystal quality and differential crystal-growth behaviour of three proteins crystallized in gel at high hydrostatic pressure},
author = {A Kadri and B Lorber and C Charron and M C Robert and B Capelle and M Damak and G Jenner and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15930640},
isbn = {15930640},
year = {2005},
date = {2005-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {61},
number = {Pt 6},
pages = {784-788},
abstract = {Pressure is a non-invasive physical parameter that can be used to control and influence protein crystallization. It is also found that protein crystals of superior quality can be produced in gel. Here, a novel crystallization strategy combining hydrostatic pressure and agarose gel is described. Comparative experiments were conducted on hen and turkey egg-white lysozymes and the plant protein thaumatin. Crystals could be produced under up to 75-100 MPa (lysozymes) and 250 MPa (thaumatin). Several pressure-dependent parameters were determined, which included solubility and supersaturation of the proteins, number, size and morphology of the crystals, and the crystallization volume. Exploration of three-dimensional phase diagrams in which pH and pressure varied identified growth conditions where crystals had largest size and best morphology. As a general trend, nucleation and crystal-growth kinetics are altered and nucleation is always enhanced under pressure. Further, solubility of the lysozymes increases with pressure while that of thaumatin decreases. Likewise, changes in crystallization volumes at high and atmospheric pressure are opposite, being positive for the lysozymes and negative for thaumatin. Crystal quality was estimated by analysis of Bragg reflection profiles and X-ray topographs. While the quality of lysozyme crystals deteriorates as pressure increases, that of thaumatin crystals improves, with more homogeneous crystal morphology suggesting that pressure selectively dissociates ill-formed nuclei. Analysis of the thaumatin structure reveals a less hydrated solvent shell around the protein when pressure increases, with approximately 20% less ordered water molecules in crystals grown at 150 MPa when compared with those grown at atmospheric pressure (0.1 MPa). Noticeably, the altered water distribution is seen in depressurized crystals, indicating that pressure triggers a stable structural alteration on the protein surface while its polypeptide backbone remains essentially unaltered.},
note = {0907-4449
Journal Article},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pressure is a non-invasive physical parameter that can be used to control and influence protein crystallization. It is also found that protein crystals of superior quality can be produced in gel. Here, a novel crystallization strategy combining hydrostatic pressure and agarose gel is described. Comparative experiments were conducted on hen and turkey egg-white lysozymes and the plant protein thaumatin. Crystals could be produced under up to 75-100 MPa (lysozymes) and 250 MPa (thaumatin). Several pressure-dependent parameters were determined, which included solubility and supersaturation of the proteins, number, size and morphology of the crystals, and the crystallization volume. Exploration of three-dimensional phase diagrams in which pH and pressure varied identified growth conditions where crystals had largest size and best morphology. As a general trend, nucleation and crystal-growth kinetics are altered and nucleation is always enhanced under pressure. Further, solubility of the lysozymes increases with pressure while that of thaumatin decreases. Likewise, changes in crystallization volumes at high and atmospheric pressure are opposite, being positive for the lysozymes and negative for thaumatin. Crystal quality was estimated by analysis of Bragg reflection profiles and X-ray topographs. While the quality of lysozyme crystals deteriorates as pressure increases, that of thaumatin crystals improves, with more homogeneous crystal morphology suggesting that pressure selectively dissociates ill-formed nuclei. Analysis of the thaumatin structure reveals a less hydrated solvent shell around the protein when pressure increases, with approximately 20% less ordered water molecules in crystals grown at 150 MPa when compared with those grown at atmospheric pressure (0.1 MPa). Noticeably, the altered water distribution is seen in depressurized crystals, indicating that pressure triggers a stable structural alteration on the protein surface while its polypeptide backbone remains essentially unaltered.
Giege R, Rees B
Aspartyl-tRNA synthetases Book Chapter
In: Ibba, M; Francklyn, C; Cusack, S (Ed.): The Aminoacyl-tRNA Synthetases, pp. 1-26, Landes Biosciences, 2005.
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@inbook{,
title = {Aspartyl-tRNA synthetases},
author = {R Giege and B Rees},
editor = {M Ibba and C Francklyn and S Cusack},
url = {http://makeover.landesbioscience.com/curie/chapter/1877},
year = {2005},
date = {2005-01-01},
booktitle = {The Aminoacyl-tRNA Synthetases},
pages = {1-26},
publisher = {Landes Biosciences},
abstract = {Aspartyl-tRNA synthetases (AspRSs) belong to subclass IIb of synthetases. The subunits of these dimeric proteins have a conserved modular architecture in the three kingdoms of life, comprising a C-terminal active site domain linked by a short hinge domain to an N-terminal anticodon-binding domain. An additional flexible domain is appended at the N-terminus of eukaryotic AspRSs that helps to better anchor the tRNA on the synthetase body. Eubacterial AspRSs are characterized by an insertion module in the active site domain, while archaeal AspRSs display the smallest structures. Sequence and especially three-dimensional structure comparisons indicate mimicries between AspRS modules and various other proteins. X-ray structures of AspRSs complexed with their ligands, separately or in combination, and results of site directed mutagenesis on tRNA and synthetase provide a detailed mechanistic understanding of the tRNA aspartylation reaction. In this process, accompanied by conformational changes in the synthetase and the interacting tRNAAsp, AspRS conserved residues and class and subclass defining motifs, together with identity determinants in tRNAAsp, play crucial roles.},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Aspartyl-tRNA synthetases (AspRSs) belong to subclass IIb of synthetases. The subunits of these dimeric proteins have a conserved modular architecture in the three kingdoms of life, comprising a C-terminal active site domain linked by a short hinge domain to an N-terminal anticodon-binding domain. An additional flexible domain is appended at the N-terminus of eukaryotic AspRSs that helps to better anchor the tRNA on the synthetase body. Eubacterial AspRSs are characterized by an insertion module in the active site domain, while archaeal AspRSs display the smallest structures. Sequence and especially three-dimensional structure comparisons indicate mimicries between AspRS modules and various other proteins. X-ray structures of AspRSs complexed with their ligands, separately or in combination, and results of site directed mutagenesis on tRNA and synthetase provide a detailed mechanistic understanding of the tRNA aspartylation reaction. In this process, accompanied by conformational changes in the synthetase and the interacting tRNAAsp, AspRS conserved residues and class and subclass defining motifs, together with identity determinants in tRNAAsp, play crucial roles.
2004
Charron C, Roy H, Blaise M, Giege R, Kern D
Crystallization and preliminary X-ray diffraction data of an archaeal asparagine synthetase related to asparaginyl-tRNA synthetase Journal Article
In: Acta Crystallogr D Biol Crystallogr, vol. 60, no. Pt 4, pp. 767-769, 2004, ISBN: 15039580, (0907-4449 Journal Article).
Abstract | Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {Crystallization and preliminary X-ray diffraction data of an archaeal asparagine synthetase related to asparaginyl-tRNA synthetase},
author = {C Charron and H Roy and M Blaise and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15039580},
isbn = {15039580},
year = {2004},
date = {2004-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {60},
number = {Pt 4},
pages = {767-769},
abstract = {The archaebacterial-type asparagine synthetase A from Pyrococcus abyssi (AS-AR), which is related to asparaginyl-tRNA synthetase, was crystallized in two different conditions using the hanging-drop vapour-diffusion method. Crystals belonging to space group C2 with unit-cell parameters a = 103.6},
note = {0907-4449
Journal Article},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The archaebacterial-type asparagine synthetase A from Pyrococcus abyssi (AS-AR), which is related to asparaginyl-tRNA synthetase, was crystallized in two different conditions using the hanging-drop vapour-diffusion method. Crystals belonging to space group C2 with unit-cell parameters a = 103.6
2003
Giege R, Lorber B
In memorium Jean Witz: the contrbution of Jean Witz to the early study of transfer ribonucleic acids Journal Article
In: Biochimie, vol. 85, no. 12, pp. 1235, 2003.
Links | BibTeX | Tags: GIEGE, Unité ARN
@article{,
title = {In memorium Jean Witz: the contrbution of Jean Witz to the early study of transfer ribonucleic acids},
author = {R Giege and B Lorber},
url = {http://www.sciencedirect.com/science/article/pii/S0300908403002074},
year = {2003},
date = {2003-01-01},
journal = {Biochimie},
volume = {85},
number = {12},
pages = {1235},
keywords = {GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2002
Francklyn C., Perona J. J., Putz J., Hou Y. M.
Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation Journal Article
In: RNA, vol. 8, no. 11, pp. 1363-1372, 2002.
Abstract | BibTeX | Tags: Aminoacyl-tRNA, Code, Genetic, GIEGE, synthetases
@article{,
title = {Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation},
author = { C. Francklyn and J.J. Perona and J. Putz and Y. M. Hou},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {11},
pages = {1363-1372},
abstract = {Aminoacyl-tRNA synthetases attach amino acids to the 3' termini of cognate tRNAs to establish the specificity of protein synthesis. A recent Asilomar conference (California, January 13-18, 2002) discussed new research into the structure-function relationship of these crucial enzymes, as well as a multitude of novel functions, including participation in amino acid biosynthesis, cell cycle control, RNA splicing, and export of tRNAs from nucleus to cytoplasm in eukaryotic cells. Together with the discovery of their role in the cellular synthesis of proteins to incorporate selenocysteine and pyrrolysine, these diverse functions of aminoacyl-tRNA synthetases underscore the flexibility and adaptability of these ancient enzymes and stimulate the development of new concepts and methods for expanding the genetic code.},
keywords = {Aminoacyl-tRNA, Code, Genetic, GIEGE, synthetases},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases attach amino acids to the 3' termini of cognate tRNAs to establish the specificity of protein synthesis. A recent Asilomar conference (California, January 13-18, 2002) discussed new research into the structure-function relationship of these crucial enzymes, as well as a multitude of novel functions, including participation in amino acid biosynthesis, cell cycle control, RNA splicing, and export of tRNAs from nucleus to cytoplasm in eukaryotic cells. Together with the discovery of their role in the cellular synthesis of proteins to incorporate selenocysteine and pyrrolysine, these diverse functions of aminoacyl-tRNA synthetases underscore the flexibility and adaptability of these ancient enzymes and stimulate the development of new concepts and methods for expanding the genetic code.
Kowal M., Roslinski J., Dmoszynska A., Borzecki A., Borzecka H., Keith G.
Genomic hypomethylation in patients with B-cell chronic lymphocytic leukemia Journal Article
In: Acta Haematol Pol, vol. 33, no. 3, pp. 323-330, 2002.
Abstract | BibTeX | Tags: Chronic, DNA, GIEGE, leukemia, lymphocytic, Methylation
@article{,
title = {Genomic hypomethylation in patients with B-cell chronic lymphocytic leukemia},
author = { M. Kowal and J. Roslinski and A. Dmoszynska and A. Borzecki and H. Borzecka and G. Keith},
year = {2002},
date = {2002-01-01},
journal = {Acta Haematol Pol},
volume = {33},
number = {3},
pages = {323-330},
abstract = {During the last few years, increasing attention has been paid to the relationship between DNA methylation and cancer. Hypo- or hypermethylation of DNA may result in up or down regulation of genes involved in the pathogenesis of leukemias. In this study we have analyzed DNA methylation in peripheral blood and bone marrow B (CD19+) and T (CD3+) lymphocytes from untreated patients with B-cell chronic lymphocytic leukemia.},
keywords = {Chronic, DNA, GIEGE, leukemia, lymphocytic, Methylation},
pubstate = {published},
tppubtype = {article}
}
During the last few years, increasing attention has been paid to the relationship between DNA methylation and cancer. Hypo- or hypermethylation of DNA may result in up or down regulation of genes involved in the pathogenesis of leukemias. In this study we have analyzed DNA methylation in peripheral blood and bone marrow B (CD19+) and T (CD3+) lymphocytes from untreated patients with B-cell chronic lymphocytic leukemia.
2001
Obrecht-Pflumio S., Dirheimer G.
Horseradish peroxidase mediates DNA and deoxyguanosine 3'-monophosphate adduct formation in the presence of ochratoxin A Journal Article
In: Arch Toxicol, vol. 75, no. 10, pp. 583-590, 2001.
Abstract | BibTeX | Tags: GIEGE
@article{,
title = {Horseradish peroxidase mediates DNA and deoxyguanosine 3'-monophosphate adduct formation in the presence of ochratoxin A},
author = { S. Obrecht-Pflumio and G. Dirheimer},
year = {2001},
date = {2001-01-01},
journal = {Arch Toxicol},
volume = {75},
number = {10},
pages = {583-590},
abstract = {Ochratoxin A (OTA) gives rise to DNA and deoxyguanosine-3'-monophosphate (dGMP) adducts in vitro using mice kidney microsomes in the presence of arachidonic acid. This result points to the involvement of prostaglandin H synthases, which are present at high levels in the kidney, urinary bladder and seminal vesicles, and/or of lipoxygenases in the metabolic activation of OTA to genotoxic compounds. These enzymes have peroxidase activities. Incubation of OTA with DNA in the presence of horseradish peroxidase (HRP) and cumene hydroperoxide at pH 7.4 led to the formation of one major and three minor adducts with a total adduct level of 42 per 10(9) nucleotides. Incubation with dGMP gave a total adduct level of 159 per 10(9) nucleotides. In the presence of H2O2 instead of cumene hydroperoxide, a lower level of adducts was obtained, both with DNA and dGMP. The concentrations of HRP and co-substrate used in this paper were higher than those used by other authors who obtained negative results when they sought DNA adducts of OTA in the presence of HRP and H2O2. The main adduct we obtained with DNA incubated with HRP and OTA had the same chromatographic behaviour as that obtained when DNA or dGMP were incubated with OTA, arachidonic acid and mice kidney microsomes. However, the main adduct obtained with dGMP incubated with HRP and OTA behaved differently. These results show that OTA can be metabolized by a peroxidase to metabolically activated species that bind covalently to DNA and dGMP; however, the main adduct obtained in vitro with HRP and dGMP cannot serve as a model for one of the adducts formed by OTA with DNA because it behaves differently in two chromatographic systems.},
keywords = {GIEGE},
pubstate = {published},
tppubtype = {article}
}
Ochratoxin A (OTA) gives rise to DNA and deoxyguanosine-3'-monophosphate (dGMP) adducts in vitro using mice kidney microsomes in the presence of arachidonic acid. This result points to the involvement of prostaglandin H synthases, which are present at high levels in the kidney, urinary bladder and seminal vesicles, and/or of lipoxygenases in the metabolic activation of OTA to genotoxic compounds. These enzymes have peroxidase activities. Incubation of OTA with DNA in the presence of horseradish peroxidase (HRP) and cumene hydroperoxide at pH 7.4 led to the formation of one major and three minor adducts with a total adduct level of 42 per 10(9) nucleotides. Incubation with dGMP gave a total adduct level of 159 per 10(9) nucleotides. In the presence of H2O2 instead of cumene hydroperoxide, a lower level of adducts was obtained, both with DNA and dGMP. The concentrations of HRP and co-substrate used in this paper were higher than those used by other authors who obtained negative results when they sought DNA adducts of OTA in the presence of HRP and H2O2. The main adduct we obtained with DNA incubated with HRP and OTA had the same chromatographic behaviour as that obtained when DNA or dGMP were incubated with OTA, arachidonic acid and mice kidney microsomes. However, the main adduct obtained with dGMP incubated with HRP and OTA behaved differently. These results show that OTA can be metabolized by a peroxidase to metabolically activated species that bind covalently to DNA and dGMP; however, the main adduct obtained in vitro with HRP and dGMP cannot serve as a model for one of the adducts formed by OTA with DNA because it behaves differently in two chromatographic systems.
2000
Jerzak M., Potawski K., Keith G., Jakowicki J. A., Baranovski W.
Genomic DNA methylation in the human trophoblast from recurrent spontaneous abortion-premilimary report Journal Article
In: Pol J Gyn Invest, vol. 3, pp. 9-12, 2000.
@article{,
title = {Genomic DNA methylation in the human trophoblast from recurrent spontaneous abortion-premilimary report},
author = { M. Jerzak and K. Potawski and G. Keith and J. A. Jakowicki and W. Baranovski},
year = {2000},
date = {2000-01-01},
journal = {Pol J Gyn Invest},
volume = {3},
pages = {9-12},
keywords = {ACL, GIEGE},
pubstate = {published},
tppubtype = {article}
}
