Comparative pan genome analysis of oral Prevotella species implicated in periodontitis

Comparative pan genome analysis of oral Prevotella species implicated in periodontitis Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment. We identified the presence of type VI secretion system (T6SS) in P. fusca and P. intermedia strains. For some VgrG and Hcp proteins which were not part of the core T6SS loci, we used gene neighborhood analysis and identified putative effector proteins and putative polyimmunity loci in P. fusca and polymorphic toxin systems in P. intermedia strains. Earlier studies have identified the presence of Por secretion system (PorSS) in P. gingivalis, P. melaninogenica and P. intermedia. We noted the presence of their homologs in six other oral Prevotella studied here. We suggest that in Prevotella, PorSS is used to secrete cysteine proteases such as interpain and C-terminal domain containing proteins with a “Por_secre_tail” domain. We identified subtype I-B CRISPR-Cas system in P. enoeca. Putative CRISPR-Cas system subtypes for 37 oral Prevotella and 30 non-oral Prevotella species were also predicted. Further, we performed a BLASTp search of the Prevotella proteins which are also conserved in the red-complex pathogens, against the human proteome to identify potential broad-spectrum drug targets. In summary, the use of a pan genome approach enabled identification of secretion systems and defense mechanisms in Prevotella that confer adaptation to the oral cavity. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Functional & Integrative Genomics Springer Journals

Comparative pan genome analysis of oral Prevotella species implicated in periodontitis

Comparative pan genome analysis of oral Prevotella species implicated in periodontitis

Funct Integr Genomics (2017) 17:513–536 DOI 10.1007/s10142-017-0550-3 ORIGINAL ARTICLE Comparative pan genome analysis of oral Prevotella species implicated in periodontitis 1 1 1 Maziya Ibrahim & Ahalyaa Subramanian & Sharmila Anishetty Received: 18 October 2016 /Revised: 19 January 2017 /Accepted: 30 January 2017 /Published online: 24 February 2017 Springer-Verlag Berlin Heidelberg 2017 Abstract Prevotella is part of the oral bacterial community proteome to identify potential broad-spectrum drug targets. In implicated in periodontitis. Pan genome analyses of eight oral summary, the use of a pan genome approach enabled identifica- Prevotella species, P. dentalis, P. enoeca, P. fusca, tion of secretion systems and defense mechanisms in Prevotella P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia that confer adaptation to the oral cavity. 17-2 and P. sp. oral taxon 299 are presented in this study. . . . . Analysis of the Prevotella pan genome revealed features such Keywords Prevotella Periodontitis Pan genome T6SS as secretion systems, resistance to oxidative stress and clustered CRISPR PorSS regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment. We identified the presence of type VI secretion system (T6SS) in Introduction P. fusca and P. intermedia strains. For some VgrG and Hcp proteins which were not part of the core T6SS loci, we used gene The human oral cavity is a clinically important microbial habitat neighborhood analysis and identified putative effector proteins that is composed of bacteria, archaea, fungi and viruses, which is and putative polyimmunity loci in P. fusca and polymorphic referred to as the oral microbiota (He et al. 2015). Oral microbiota toxin systems in P. intermedia strains. Earlier studies have iden- inhabits the teeth, tongue, cheek, gingival sulcus, hard and soft tified the presence of Por secretion system (PorSS) in palates and...
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Publisher
Springer Berlin Heidelberg
Copyright
Copyright © 2017 by Springer-Verlag Berlin Heidelberg
Subject
Life Sciences; Cell Biology; Plant Genetics and Genomics; Microbial Genetics and Genomics; Biochemistry, general; Bioinformatics; Animal Genetics and Genomics
ISSN
1438-793X
eISSN
1438-7948
D.O.I.
10.1007/s10142-017-0550-3
Publisher site
See Article on Publisher Site

Abstract

Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment. We identified the presence of type VI secretion system (T6SS) in P. fusca and P. intermedia strains. For some VgrG and Hcp proteins which were not part of the core T6SS loci, we used gene neighborhood analysis and identified putative effector proteins and putative polyimmunity loci in P. fusca and polymorphic toxin systems in P. intermedia strains. Earlier studies have identified the presence of Por secretion system (PorSS) in P. gingivalis, P. melaninogenica and P. intermedia. We noted the presence of their homologs in six other oral Prevotella studied here. We suggest that in Prevotella, PorSS is used to secrete cysteine proteases such as interpain and C-terminal domain containing proteins with a “Por_secre_tail” domain. We identified subtype I-B CRISPR-Cas system in P. enoeca. Putative CRISPR-Cas system subtypes for 37 oral Prevotella and 30 non-oral Prevotella species were also predicted. Further, we performed a BLASTp search of the Prevotella proteins which are also conserved in the red-complex pathogens, against the human proteome to identify potential broad-spectrum drug targets. In summary, the use of a pan genome approach enabled identification of secretion systems and defense mechanisms in Prevotella that confer adaptation to the oral cavity.

Journal

Functional & Integrative GenomicsSpringer Journals

Published: Feb 24, 2017

References

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