Cargando…
Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa
Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, he...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372532/ https://www.ncbi.nlm.nih.gov/pubmed/30787911 http://dx.doi.org/10.3389/fmicb.2019.00053 |
_version_ | 1783394760265826304 |
---|---|
author | Sood, Utkarsh Hira, Princy Kumar, Roshan Bajaj, Abhay Rao, Desiraju Lakshmi Narsimha Lal, Rup Shakarad, Mallikarjun |
author_facet | Sood, Utkarsh Hira, Princy Kumar, Roshan Bajaj, Abhay Rao, Desiraju Lakshmi Narsimha Lal, Rup Shakarad, Mallikarjun |
author_sort | Sood, Utkarsh |
collection | PubMed |
description | Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, hence we scaled up the analyses to understand the differences in environmental and clinical outlier strains. We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. The outliers had the complete operon for the production of vibrioferrin, a siderophore present in plant growth promoting bacteria. The competence to acquire multidrug resistance and new virulence factors makes these strains a potential threat. However, we identified major regulatory hubs that can be used as drug targets against both the classical and outlier groups. |
format | Online Article Text |
id | pubmed-6372532 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-63725322019-02-20 Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa Sood, Utkarsh Hira, Princy Kumar, Roshan Bajaj, Abhay Rao, Desiraju Lakshmi Narsimha Lal, Rup Shakarad, Mallikarjun Front Microbiol Microbiology Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, hence we scaled up the analyses to understand the differences in environmental and clinical outlier strains. We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. The outliers had the complete operon for the production of vibrioferrin, a siderophore present in plant growth promoting bacteria. The competence to acquire multidrug resistance and new virulence factors makes these strains a potential threat. However, we identified major regulatory hubs that can be used as drug targets against both the classical and outlier groups. Frontiers Media S.A. 2019-02-06 /pmc/articles/PMC6372532/ /pubmed/30787911 http://dx.doi.org/10.3389/fmicb.2019.00053 Text en Copyright © 2019 Sood, Hira, Kumar, Bajaj, Rao, Lal and Shakarad. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Sood, Utkarsh Hira, Princy Kumar, Roshan Bajaj, Abhay Rao, Desiraju Lakshmi Narsimha Lal, Rup Shakarad, Mallikarjun Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title | Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title_full | Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title_fullStr | Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title_full_unstemmed | Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title_short | Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa |
title_sort | comparative genomic analyses reveal core-genome-wide genes under positive selection and major regulatory hubs in outlier strains of pseudomonas aeruginosa |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372532/ https://www.ncbi.nlm.nih.gov/pubmed/30787911 http://dx.doi.org/10.3389/fmicb.2019.00053 |
work_keys_str_mv | AT soodutkarsh comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT hiraprincy comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT kumarroshan comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT bajajabhay comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT raodesirajulakshminarsimha comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT lalrup comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa AT shakaradmallikarjun comparativegenomicanalysesrevealcoregenomewidegenesunderpositiveselectionandmajorregulatoryhubsinoutlierstrainsofpseudomonasaeruginosa |