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Phylogenomics of Prokaryotic Ribosomal Proteins

Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of thei...

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Autores principales: Yutin, Natalya, Puigbò, Pere, Koonin, Eugene V., Wolf, Yuri I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353972/
https://www.ncbi.nlm.nih.gov/pubmed/22615861
http://dx.doi.org/10.1371/journal.pone.0036972
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author Yutin, Natalya
Puigbò, Pere
Koonin, Eugene V.
Wolf, Yuri I.
author_facet Yutin, Natalya
Puigbò, Pere
Koonin, Eugene V.
Wolf, Yuri I.
author_sort Yutin, Natalya
collection PubMed
description Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.
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spelling pubmed-33539722012-05-21 Phylogenomics of Prokaryotic Ribosomal Proteins Yutin, Natalya Puigbò, Pere Koonin, Eugene V. Wolf, Yuri I. PLoS One Research Article Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies. Public Library of Science 2012-05-16 /pmc/articles/PMC3353972/ /pubmed/22615861 http://dx.doi.org/10.1371/journal.pone.0036972 Text en This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Yutin, Natalya
Puigbò, Pere
Koonin, Eugene V.
Wolf, Yuri I.
Phylogenomics of Prokaryotic Ribosomal Proteins
title Phylogenomics of Prokaryotic Ribosomal Proteins
title_full Phylogenomics of Prokaryotic Ribosomal Proteins
title_fullStr Phylogenomics of Prokaryotic Ribosomal Proteins
title_full_unstemmed Phylogenomics of Prokaryotic Ribosomal Proteins
title_short Phylogenomics of Prokaryotic Ribosomal Proteins
title_sort phylogenomics of prokaryotic ribosomal proteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353972/
https://www.ncbi.nlm.nih.gov/pubmed/22615861
http://dx.doi.org/10.1371/journal.pone.0036972
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