Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria
In Gram-negative bacteria, type IV pili (TFP) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and DNA transfer, with significant consequences for pathogenicity. More recently it became apparent that Gram-positive bacteria also express...
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| description | In Gram-negative bacteria, type IV pili (TFP) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and DNA transfer, with significant consequences for pathogenicity. More recently it became apparent that Gram-positive bacteria also express type IV pili; however, little is known about the diversity and abundance of these structures in Gram-positives. Computational tools for automated identification of type IV pilins are not currently available.
To assess TFP diversity in Gram-positive bacteria and facilitate pilin identification, we compiled a comprehensive list of putative Gram-positive pilins encoded by operons containing highly conserved pilus biosynthetic genes (pilB, pilC). A surprisingly large number of species were found to contain multiple TFP operons (pil, com and/or tad). The N-terminal sequences of predicted pilins were exploited to develop PilFind, a rule-based algorithm for genome-wide identification of otherwise poorly conserved type IV pilins in any species, regardless of their association with TFP biosynthetic operons (http://signalfind.org). Using PilFind to scan 53 Gram-positive genomes (encoding >187,000 proteins), we identified 286 candidate pilins, including 214 in operons containing TFP biosynthetic genes (TBG+ operons). Although trained on Gram-positive pilins, PilFind identified 55 of 58 manually curated Gram-negative pilins in TBG+ operons, as well as 53 additional pilin candidates in operons lacking biosynthetic genes in ten species (>38,000 proteins), including 27 of 29 experimentally verified pilins. False positive rates appear to be low, as PilFind predicted only four pilin candidates in eleven bacterial species (>13,000 proteins) lacking TFP biosynthetic genes.
We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins. |
| doi_str_mv | 10.1371/journal.pone.0028919 |
| format | Article |
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To assess TFP diversity in Gram-positive bacteria and facilitate pilin identification, we compiled a comprehensive list of putative Gram-positive pilins encoded by operons containing highly conserved pilus biosynthetic genes (pilB, pilC). A surprisingly large number of species were found to contain multiple TFP operons (pil, com and/or tad). The N-terminal sequences of predicted pilins were exploited to develop PilFind, a rule-based algorithm for genome-wide identification of otherwise poorly conserved type IV pilins in any species, regardless of their association with TFP biosynthetic operons (http://signalfind.org). Using PilFind to scan 53 Gram-positive genomes (encoding >187,000 proteins), we identified 286 candidate pilins, including 214 in operons containing TFP biosynthetic genes (TBG+ operons). Although trained on Gram-positive pilins, PilFind identified 55 of 58 manually curated Gram-negative pilins in TBG+ operons, as well as 53 additional pilin candidates in operons lacking biosynthetic genes in ten species (>38,000 proteins), including 27 of 29 experimentally verified pilins. False positive rates appear to be low, as PilFind predicted only four pilin candidates in eleven bacterial species (>13,000 proteins) lacking TFP biosynthetic genes.
We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0028919</identifier><identifier>PMID: 22216142</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Amino Acid Sequence ; Amino acids ; Bacteria ; Bacterial proteins ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biology ; Biosynthesis ; Cellular structure ; Cholera ; Computation ; Computer applications ; Deoxyribonucleic acid ; DNA ; DNA methylation ; E coli ; Escherichia coli ; Fimbriae, Bacterial ; Genes ; Genomes ; Genomics ; Gram-negative bacteria ; Gram-positive bacteria ; Gram-Positive Bacteria - genetics ; Gram-Positive Bacteria - metabolism ; Localization ; Molecular Sequence Data ; Motility ; Neisseria gonorrhoeae ; Operon ; Operons ; Pathogenicity ; Pathogens ; Peptides ; Pili ; Pilin ; Proteins ; Pseudomonas aeruginosa ; Sequence Homology, Amino Acid ; Software ; Species ; Vibrio cholerae</subject><ispartof>PloS one, 2011-12, Vol.6 (12), p.e28919-e28919</ispartof><rights>2011 Imam et al.</rights><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Imam et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Imam et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c757t-8520206783a22c0fc9f5ec41ccce111e753442b99ca3e25707b0373965e5c02b3</citedby><cites>FETCH-LOGICAL-c757t-8520206783a22c0fc9f5ec41ccce111e753442b99ca3e25707b0373965e5c02b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244431/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244431/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22216142$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Imam, Saheed</creatorcontrib><creatorcontrib>Chen, Zhongqiang</creatorcontrib><creatorcontrib>Roos, David S</creatorcontrib><creatorcontrib>Pohlschröder, Mechthild</creatorcontrib><title>Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>In Gram-negative bacteria, type IV pili (TFP) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and DNA transfer, with significant consequences for pathogenicity. More recently it became apparent that Gram-positive bacteria also express type IV pili; however, little is known about the diversity and abundance of these structures in Gram-positives. Computational tools for automated identification of type IV pilins are not currently available.
To assess TFP diversity in Gram-positive bacteria and facilitate pilin identification, we compiled a comprehensive list of putative Gram-positive pilins encoded by operons containing highly conserved pilus biosynthetic genes (pilB, pilC). A surprisingly large number of species were found to contain multiple TFP operons (pil, com and/or tad). The N-terminal sequences of predicted pilins were exploited to develop PilFind, a rule-based algorithm for genome-wide identification of otherwise poorly conserved type IV pilins in any species, regardless of their association with TFP biosynthetic operons (http://signalfind.org). Using PilFind to scan 53 Gram-positive genomes (encoding >187,000 proteins), we identified 286 candidate pilins, including 214 in operons containing TFP biosynthetic genes (TBG+ operons). Although trained on Gram-positive pilins, PilFind identified 55 of 58 manually curated Gram-negative pilins in TBG+ operons, as well as 53 additional pilin candidates in operons lacking biosynthetic genes in ten species (>38,000 proteins), including 27 of 29 experimentally verified pilins. False positive rates appear to be low, as PilFind predicted only four pilin candidates in eleven bacterial species (>13,000 proteins) lacking TFP biosynthetic genes.
We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Bacteria</subject><subject>Bacterial proteins</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biology</subject><subject>Biosynthesis</subject><subject>Cellular structure</subject><subject>Cholera</subject><subject>Computation</subject><subject>Computer applications</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>E coli</subject><subject>Escherichia coli</subject><subject>Fimbriae, Bacterial</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Gram-negative bacteria</subject><subject>Gram-positive bacteria</subject><subject>Gram-Positive Bacteria - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Imam, Saheed</au><au>Chen, Zhongqiang</au><au>Roos, David S</au><au>Pohlschröder, Mechthild</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-12-21</date><risdate>2011</risdate><volume>6</volume><issue>12</issue><spage>e28919</spage><epage>e28919</epage><pages>e28919-e28919</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In Gram-negative bacteria, type IV pili (TFP) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and DNA transfer, with significant consequences for pathogenicity. More recently it became apparent that Gram-positive bacteria also express type IV pili; however, little is known about the diversity and abundance of these structures in Gram-positives. Computational tools for automated identification of type IV pilins are not currently available.
To assess TFP diversity in Gram-positive bacteria and facilitate pilin identification, we compiled a comprehensive list of putative Gram-positive pilins encoded by operons containing highly conserved pilus biosynthetic genes (pilB, pilC). A surprisingly large number of species were found to contain multiple TFP operons (pil, com and/or tad). The N-terminal sequences of predicted pilins were exploited to develop PilFind, a rule-based algorithm for genome-wide identification of otherwise poorly conserved type IV pilins in any species, regardless of their association with TFP biosynthetic operons (http://signalfind.org). Using PilFind to scan 53 Gram-positive genomes (encoding >187,000 proteins), we identified 286 candidate pilins, including 214 in operons containing TFP biosynthetic genes (TBG+ operons). Although trained on Gram-positive pilins, PilFind identified 55 of 58 manually curated Gram-negative pilins in TBG+ operons, as well as 53 additional pilin candidates in operons lacking biosynthetic genes in ten species (>38,000 proteins), including 27 of 29 experimentally verified pilins. False positive rates appear to be low, as PilFind predicted only four pilin candidates in eleven bacterial species (>13,000 proteins) lacking TFP biosynthetic genes.
We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22216142</pmid><doi>10.1371/journal.pone.0028919</doi><tpages>e28919</tpages><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1312160085 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Algorithms Amino Acid Sequence Amino acids Bacteria Bacterial proteins Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Biology Biosynthesis Cellular structure Cholera Computation Computer applications Deoxyribonucleic acid DNA DNA methylation E coli Escherichia coli Fimbriae, Bacterial Genes Genomes Genomics Gram-negative bacteria Gram-positive bacteria Gram-Positive Bacteria - genetics Gram-Positive Bacteria - metabolism Localization Molecular Sequence Data Motility Neisseria gonorrhoeae Operon Operons Pathogenicity Pathogens Peptides Pili Pilin Proteins Pseudomonas aeruginosa Sequence Homology, Amino Acid Software Species Vibrio cholerae |
| title | Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-20T14%3A16%3A53IST&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=Identification%20of%20surprisingly%20diverse%20type%20IV%20pili,%20across%20a%20broad%20range%20of%20gram-positive%20bacteria&rft.jtitle=PloS%20one&rft.au=Imam,%20Saheed&rft.date=2011-12-21&rft.volume=6&rft.issue=12&rft.spage=e28919&rft.epage=e28919&rft.pages=e28919-e28919&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0028919&rft_dat=%3Cgale_plos_%3EA476858254%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=1312160085&rft_id=info:pmid/22216142&rft_galeid=A476858254&rft_doaj_id=oai_doaj_org_article_a1ff6601c0774080a63fb76c93c8771e&rfr_iscdi=true |