The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria
The family of ribosomal proteins S1 contains about 20% of all bacterial proteins including the S1 domain. An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated ex...
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| creator | Machulin, Andrey V Deryusheva, Evgenia I Selivanova, Olga M Galzitskaya, Oxana V |
| description | The family of ribosomal proteins S1 contains about 20% of all bacterial proteins including the S1 domain. An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. The third and fourth domains for the most representative four- and six-domain S1 have the highest percentage of identity with the S1 domain from polynucleotide phosphorylase and S1 domains from one-domain S1. In addition, for these groups, the central part of S1 (the third domain) is more conserved than the terminal domains. |
| doi_str_mv | 10.1371/journal.pone.0221370 |
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An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. The third and fourth domains for the most representative four- and six-domain S1 have the highest percentage of identity with the S1 domain from polynucleotide phosphorylase and S1 domains from one-domain S1. In addition, for these groups, the central part of S1 (the third domain) is more conserved than the terminal domains.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0221370</identifier><identifier>PMID: 31437214</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Actinobacteria - classification ; Actinobacteria - genetics ; Actinomycetes ; Algorithms ; Amino Acid Sequence ; Analysis ; Automation ; Bacteria ; Bacterial proteins ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Biochemistry ; Biological research ; Biology and Life Sciences ; Biomarkers ; Computer and Information Sciences ; Conserved Sequence ; E coli ; Evolution ; Firmicutes - classification ; Firmicutes - genetics ; Gene Expression ; Genes ; Genomes ; Gram-positive bacteria ; Microorganisms ; Molecular biology ; Phosphorylase ; Phosphorylases ; Phylogenetics ; Phylogeny ; Polynucleotide phosphorylase ; Polyribonucleotide Nucleotidyltransferase - chemistry ; Polyribonucleotide Nucleotidyltransferase - genetics ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Domains ; Proteins ; Proteobacteria - classification ; Proteobacteria - genetics ; Research and Analysis Methods ; Ribonuclease ; Ribosomal protein S1 ; Ribosomal proteins ; Ribosomal Proteins - chemistry ; Ribosomal Proteins - genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequences</subject><ispartof>PloS one, 2019-08, Vol.14 (8), p.e0221370-e0221370</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Machulin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. 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An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. The third and fourth domains for the most representative four- and six-domain S1 have the highest percentage of identity with the S1 domain from polynucleotide phosphorylase and S1 domains from one-domain S1. In addition, for these groups, the central part of S1 (the third domain) is more conserved than the terminal domains.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31437214</pmid><doi>10.1371/journal.pone.0221370</doi><tpages>e0221370</tpages><orcidid>https://orcid.org/0000-0002-3962-1520</orcidid><orcidid>https://orcid.org/0000-0002-6213-2784</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Actinobacteria - classification Actinobacteria - genetics Actinomycetes Algorithms Amino Acid Sequence Analysis Automation Bacteria Bacterial proteins Bacterial Proteins - chemistry Bacterial Proteins - genetics Biochemistry Biological research Biology and Life Sciences Biomarkers Computer and Information Sciences Conserved Sequence E coli Evolution Firmicutes - classification Firmicutes - genetics Gene Expression Genes Genomes Gram-positive bacteria Microorganisms Molecular biology Phosphorylase Phosphorylases Phylogenetics Phylogeny Polynucleotide phosphorylase Polyribonucleotide Nucleotidyltransferase - chemistry Polyribonucleotide Nucleotidyltransferase - genetics Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Domains Proteins Proteobacteria - classification Proteobacteria - genetics Research and Analysis Methods Ribonuclease Ribosomal protein S1 Ribosomal proteins Ribosomal Proteins - chemistry Ribosomal Proteins - genetics Sequence Alignment Sequence Homology, Amino Acid Sequences |
| title | The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-13T00%3A45%3A12IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20number%20of%20domains%20in%20the%20ribosomal%20protein%20S1%20as%20a%20hallmark%20of%20the%20phylogenetic%20grouping%20of%20bacteria&rft.jtitle=PloS%20one&rft.au=Machulin,%20Andrey%20V&rft.date=2019-08-22&rft.volume=14&rft.issue=8&rft.spage=e0221370&rft.epage=e0221370&rft.pages=e0221370-e0221370&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0221370&rft_dat=%3Cgale_plos_%3EA597167834%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2278024234&rft_id=info:pmid/31437214&rft_galeid=A597167834&rft_doaj_id=oai_doaj_org_article_6159d73852e140948588cb735732d963&rfr_iscdi=true |