Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

Handle URI:
http://hdl.handle.net/10754/625054
Title:
Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853
Authors:
Cao, Huiluo; Lai, Yong; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Xu, Zeling; Yan, Aixin
Abstract:
Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome.Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the virulence genes lecA, lasB, quorum sensing regulators LasI/R, and the type I, III and VI secretion systems were observed in the two strains.The complete genome sequence of P. aeruginosa ATCC 27853 reveals the comprehensive genetic background of the strain, and provides genetic basis for several interesting findings about the functions of surface associated proteins, prophages, and genomic islands. Comparative transcriptome analysis of P. aeruginosa ATCC 27853 and PAO1 revealed several classes of differentially expressed genes in the two strains, underlying the genetic and molecular details of several known and yet to be explored morphological and physiological potentials of P. aeruginosa ATCC 27853.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Cao H, Lai Y, Bougouffa S, Xu Z, Yan A (2017) Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853. BMC Genomics 18. Available: http://dx.doi.org/10.1186/s12864-017-3842-z.
Publisher:
Springer Nature
Journal:
BMC Genomics
Issue Date:
12-Jun-2017
DOI:
10.1186/s12864-017-3842-z
Type:
Article
ISSN:
1471-2164
Sponsors:
This work was supported by the Hong Kong University Grants Council General Research Fund (HKU17142316) and Seed Funding for Basic Research Scheme of The University of Hong Kong (201411159065) to Dr. Aixin Yan and the postdoctoral fellowship from The University of Hong Kong to Dr. Huiluo Cao. We thank the Centre for Genomic Sciences at the University of Hong Kong for the sequencing and bioinformatics analysis assistance of the project. We thank Prof. Christopher Rensing (Fujian Agriculture & Forestry University) for proof-reading our manuscript.
Additional Links:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3842-z
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorCao, Huiluoen
dc.contributor.authorLai, Yongen
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorXu, Zelingen
dc.contributor.authorYan, Aixinen
dc.date.accessioned2017-06-19T09:21:45Z-
dc.date.available2017-06-19T09:21:45Z-
dc.date.issued2017-06-12en
dc.identifier.citationCao H, Lai Y, Bougouffa S, Xu Z, Yan A (2017) Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853. BMC Genomics 18. Available: http://dx.doi.org/10.1186/s12864-017-3842-z.en
dc.identifier.issn1471-2164en
dc.identifier.doi10.1186/s12864-017-3842-zen
dc.identifier.urihttp://hdl.handle.net/10754/625054-
dc.description.abstractPseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome.Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the virulence genes lecA, lasB, quorum sensing regulators LasI/R, and the type I, III and VI secretion systems were observed in the two strains.The complete genome sequence of P. aeruginosa ATCC 27853 reveals the comprehensive genetic background of the strain, and provides genetic basis for several interesting findings about the functions of surface associated proteins, prophages, and genomic islands. Comparative transcriptome analysis of P. aeruginosa ATCC 27853 and PAO1 revealed several classes of differentially expressed genes in the two strains, underlying the genetic and molecular details of several known and yet to be explored morphological and physiological potentials of P. aeruginosa ATCC 27853.en
dc.description.sponsorshipThis work was supported by the Hong Kong University Grants Council General Research Fund (HKU17142316) and Seed Funding for Basic Research Scheme of The University of Hong Kong (201411159065) to Dr. Aixin Yan and the postdoctoral fellowship from The University of Hong Kong to Dr. Huiluo Cao. We thank the Centre for Genomic Sciences at the University of Hong Kong for the sequencing and bioinformatics analysis assistance of the project. We thank Prof. Christopher Rensing (Fujian Agriculture & Forestry University) for proof-reading our manuscript.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3842-zen
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectPseudomonas aeruginosaen
dc.subjectColony morphologyen
dc.subjectprophageen
dc.subjectRna-seqen
dc.subjectGenomic islandsen
dc.subjectComparative Transcriptome Analysisen
dc.subjectSecretion Systemen
dc.titleComparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853en
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBMC Genomicsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSchool of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China. hcao@hku.hk.en
dc.contributor.institutionSchool of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.en
dc.contributor.institutionPresent address: Interdisciplinary research group in Infectious Diseases, The Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore.en
dc.contributor.institutionSchool of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China. ayan8@hku.hk.en
kaust.authorBougouffa, Salimen
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