Cited by 126RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

Phylogenetic distribution of translational GTPases in bacteria

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Margus, Tõnu, Remm, Maido, Tenson, Tanel·2007·BMC Genomics

Abstract

Background: Translational GTPases are a family of proteins in which GTPase activity is stimulated by the large ribosomal subunit. Conserved sequence features allow members of this family to be identified. Results: To achieve accurate protein identification and grouping we have developed a method combining searches with Hidden Markov Model profiles and tree based grouping. We found all the genes for translational GTPases in 191 fully sequenced bacterial genomes. The protein sequences were grouped into nine subfamilies. Analysis of the results shows that three translational GTPases, the translation factors EF-Tu, EF-G and IF2, are present in all organisms examined. In addition, several copies of the genes encoding EF-Tu and EF-G are present in some genomes. In the case of multiple genes for EF-Tu, the gene copies are nearly identical; in the case of multiple EF-G genes, the gene copies have been considerably diverged. The fourth translational GTPase, LepA, the function of which is currently unknown, is also nearly universally conserved in bacteria, being absent from only one organism out of the 191 analyzed. The translation regulator, TypA, is also present in most of the organisms examined, being absent only from bacteria with small genomes. Surprisingly, some of the well studied translational GTPases are present only in a very small number of bacteria. The translation termination factor RF3 is absent from many groups of bacteria with both small and large genomes. The specialized translation factor for selenocysteine incorporation – SelB – was found in only 39 organisms. Similarly, the tetracycline resistance proteins (Tet) are present only in a small number of species. Proteins of the CysN/NodQ subfamily have acquired functions in sulfur metabolism and production of signaling molecules. The genes coding for CysN/NodQ proteins were found in 74 genomes. This protein subfamily is not confined to Proteobacteria, as suggested previously but present also in many other groups of bacteria. Conclusion: Four of the translational GTPase subfamilies (IF2, EF-Tu, EF-G and LepA) are represented by at least one member in each bacterium studied, with one exception in LepA. This defines the set of translational GTPases essential for basic cell functions.

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  • Tet(O) protects the bacterial ribosome from binding the antibiotic tetracycline.

    “Tetracycline resistance protein Tet(O), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational GTPase with significant similarity in both sequence and structure to the elongation factor EF-G.”
  • Tet(O) is a translational GTPase with significant sequence and structural similarity to EF-G.

    “Tetracycline resistance protein Tet(O), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational GTPase with significant similarity in both sequence and structure to the elongation factor EF-G.”
  • Tet(M) and Tet(O) are paralogs of the translational GTPase EF-G and actively remove Tc from the ribosome in a GTP-hydrolysis-dependent fashion.

    “Several of these proteins–the best-known being Tet(M) and Tet(O) – are paralogs of the translational GTPase EF-G 6 and actively remove Tc from the ribosome in a GTP-hydrolysis-dependent fashion 7,8.”

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  1. Garrity GM Bell, J. A., Lilburn, T. G. Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition 2004 5 Springer-Verlag

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Authors
Margus, T., Remm, M., & Tenson, T.
Affiliations
University of Tartu (EE)
Corresponding author
Tenson, Tanel
Venue
BMC Genomics
Published
2007-01-10
Volume
8
Issue
1
Pages
15-15
ISSN
1471-2164 (ISSN-L)
OpenAlex
W1939105798
Cited by
115
References
114
Citations by year
2026: 1 · 2025: 5 · 2024: 2 · 2023: 3 · 2022: 5 · 2021: 14 · 2020: 8 · 2019: 1 · 2018: 5 · 2017: 7 · 2016: 11 · 2015: 8 · 2014: 6 · 2013: 8 · 2012: 4
FWCI
2.51
Type
journal article
Language
en
Open access
Locations
  • BMC Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Wellcome Trust (070210)
  • Eesti Teadusfondi
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
translational GTPases, bacterial phylogeny, elongation factor Tu, elongation factor G, initiation factor 2, Lepas, Rf3, Selb, selenocysteine incorporation, essential genes, gene family evolution
MeSH terms
Amino Acid Sequence, Bacteria, Base Sequence, DNA, Bacterial, Markov Chains, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid, Protein Biosynthesis, Genome, Bacterial, GTP Phosphohydrolases

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