Caillet J, Nogueira T, Masquida B, Winter F, Graffe M, Dock-Bregeon A C, Torres-Larios A, Sankaranarayanan R, Westhof E, Ehresmann B, Ehresmann C, Romby P, Springer M
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression Journal Article
In: Mol Microbiol, vol. 47, no. 4, pp. 961-974, 2003, ISBN: 12581352, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF
@article{,
title = {The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression},
author = {J Caillet and T Nogueira and B Masquida and F Winter and M Graffe and A C Dock-Bregeon and A Torres-Larios and R Sankaranarayanan and E Westhof and B Ehresmann and C Ehresmann and P Romby and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12581352},
isbn = {12581352},
year = {2003},
date = {2003-01-01},
journal = {Mol Microbiol},
volume = {47},
number = {4},
pages = {961-974},
abstract = {In addition to its role in tRNA aminoacylation, Escherichia coli threonyl-tRNA synthetase is a regulatory protein which binds a site, called the operator, located in the leader of its own mRNA and inhibits translational initiation by competing with ribosome binding. This work shows that the two essential steps of regulation, operator recognition and inhibition of ribosome binding, are performed by different domains of the protein. The catalytic and the C-terminal domain of the protein are involved in binding the two anticodon arm-like structures in the operator whereas the N-terminal domain of the enzyme is responsible for the competition with the ribosome. This is the first demonstration of a modular structure for a translational repressor and is reminiscent of that of transcriptional regulators. The mimicry between the operator and tRNA, suspected on the basis of previous experiments, is further supported by the fact that identical regions of the synthetase recognize both the operator and the tRNA anticodon arm. Based on these results, and recent structural data, we have constructed a computer-derived molecular model for the operator-threonyl-tRNA synthetase complex, which sheds light on several essential aspects of the regulatory mechanism.},
note = {0950-382x
Journal Article},
keywords = {Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Tishchenko S V, Vassilieva J M, Platonova O B, Serganov A A, Fomenkova N P, Mudrik E S, Piendl W, Ehresmann C, Ehresmann B, Garber M B
Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin Journal Article
In: Biochemistry (Mosc), vol. 66, no. 9, pp. 948-953, 2001, ISBN: 11703173, (0006-2979 Journal Article).
Abstract | Links | BibTeX | Tags: Archaeal/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Binding Sites Crystallization Magnesium/chemistry/metabolism Methanococcus/chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus/chemistry/genetics, Ribosomal/*chemistry/*metabolism Ribosomal Proteins/*chemistry/isolation & purification/*metabolism Support, Unité ARN
@article{,
title = {Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin},
author = {S V Tishchenko and J M Vassilieva and O B Platonova and A A Serganov and N P Fomenkova and E S Mudrik and W Piendl and C Ehresmann and B Ehresmann and M B Garber},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11703173},
isbn = {11703173},
year = {2001},
date = {2001-01-01},
journal = {Biochemistry (Mosc)},
volume = {66},
number = {9},
pages = {948-953},
abstract = {The core ribosomal protein S8 binds to the central domain of 16S rRNA independently of other ribosomal proteins and is required for assembling the 30S subunit. It has been shown with E. coli ribosomes that a short rRNA fragment restricted by nucleotides 588-602 and 636-651 is sufficient for strong and specific protein S8 binding. In this work, we studied the complexes formed by ribosomal protein S8 from Thermus thermophilus and Methanococcus jannaschii with short rRNA fragments isolated from the same organisms. The dissociation constants of the complexes of protein S8 with rRNA fragments were determined. Based on the results of binding experiments, rRNA fragments of different length were designed and synthesized in preparative amounts in vitro using T7 RNA-polymerase. Stable S8-RNA complexes were crystallized. Crystals were obtained both for homologous bacterial and archaeal complexes and for hybrid complexes of archaeal protein with bacterial rRNA. Crystals of the complex of protein S8 from M. jannaschii with the 37-nucleotide rRNA fragment from the same organism suitable for X-ray analysis were obtained.},
note = {0006-2979
Journal Article},
keywords = {Archaeal/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Binding Sites Crystallization Magnesium/chemistry/metabolism Methanococcus/chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus/chemistry/genetics, Ribosomal/*chemistry/*metabolism Ribosomal Proteins/*chemistry/isolation & purification/*metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Auxilien S, Englisch U, Cramer F, Fasiolo F
The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase Journal Article
In: Biochemistry, vol. 36, no. 27, pp. 8269-8275, 1997, ISBN: 9204872, (0006-2960 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Anticodon Base Sequence Escherichia coli/genetics Inosine/*chemistry/metabolism Isoleucine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Fungal/chemistry/metabolism RNA, Ile/*chemistry/metabolism Saccharomyces cerevisiae/*genetics Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase},
author = {B Senger and S Auxilien and U Englisch and F Cramer and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9204872},
isbn = {9204872},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {27},
pages = {8269-8275},
abstract = {Earlier work by two independent groups has established the fact that anticodons GAU and LAU of Escherichia coli tRNAIle isoacceptors play a critical role in the tRNA identity. Yeast possesses two isoleucine transfer RNAs, a major one with anticodon IAU and a minor one with anticodon PsiAPsi which are derived from the post-transcriptional modification of AAU and UAU gene sequences, respectively. We present direct evidence which reveals that inosine is a positive determinant for yeast isoleucyl-tRNA synthetase. We also show that yeast tRNAMet with guanosine at the wobble position becomes aminoacylated with isoleucine while methionine acceptance is lost. As inosine and guanosine share the 6-keto and the N-1 hydrogen groups, this suggests that these hydrogen donor and acceptor groups are determinants for isoleucine specificity. The role of the minor tRNAIle anticodon pseudouridines in tRNA isoleucylation could not be tested directly but was deduced from a 40-fold decrease in the activity of the unmodified transcript. The presence of the NHCO structure in guanosine, inosine, pseudouridine, and lysidine suggests a unifying model of wobble base recognition by the yeast and E. coli isoleucyl-tRNA synthetase. In contrast to lysidine which switches the identity of the tRNA from methionine to isoleucine [Muramatsu, T., Nishikawa, K., Nemoto, F., Kuchino, Y., Nishimura, S., Miyazawa, T., & Yokoyama, S. (1988) Nature 336, 179-181], pseudouridine-34 does not modify the specificity of the yeast minor tRNAIle since U-34 is a strong negative determinant for yeast MetRS. Therefore, the major role of Psi-34 (in combination with Psi-36 or not) is likely in isoleucine AUA codon specificity and translational fidelity.},
note = {0006-2960
Journal Article},
keywords = {Acylation Anticodon Base Sequence Escherichia coli/genetics Inosine/*chemistry/metabolism Isoleucine-tRNA Ligase/*metabolism Molecular Sequence Data Nucleic Acid Conformation Pseudouridine/chemistry/metabolism RNA, Bacterial/chemistry/metabolism RNA, Fungal/chemistry/metabolism RNA, Ile/*chemistry/metabolism Saccharomyces cerevisiae/*genetics Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Malmgren C, Engdahl H M, Romby P, Wagner E G
In: RNA, vol. 2, no. 10, pp. 1022-1032, 1996, ISBN: 8849778, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1},
author = {C Malmgren and H M Engdahl and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8849778},
isbn = {8849778},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {10},
pages = {1022-1032},
abstract = {Antisense RNAs in prokaryotic systems often inhibit translation of mRNAs. In some cases, this involves sequestration of Shine-Dalgarno (SD) sequences and start codons. In other cases, antisense/target RNA duplexes do not overlap these signals, but form upstream. We have performed toeprinting analyses on repA mRNA of plasmid R1, both free and in duplex with the antisense RNA, CopA. An intermolecular RNA duplex 2 nt upstream of the tap SD prevents ribosome binding. An intrastrand stem-loop at this location yields the same inhibition. Thus, stable secondary structures immediately upstream of the tap SD sequence inhibit translation, as shown by toeprinting in vitro and repA-lacZ expression in vivo. Previous work showed that repA (initiator protein) expression requires tap (leader peptide) translation. Toeprinting data confirm that the tap ribosome binding site (RBS) is accessible, whereas the repA RBS, which is sequestered by a stable stem-loop, is weakly recognized by the ribosome. Truncated CopA RNA (CopI) is unable to pair completely with target RNA, but proceeds normally to a kissing intermediate. This mutant RNA species inhibits repA expression in vivo. By a kinetic toeprint inhibition protocol, we have shown that the structure of the kissing complex is sufficient to sterically prevent ribosome binding. These results are discussed in comparison with the effect of RNA structures elsewhere in the ribosome-binding region of an mRNA.},
note = {1355-8382
Journal Article},
keywords = {Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}