Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381

Johnson, Shannon L.

Withers, T. Ryan

Yu, Hongwei D.

English

PubMed

Marshall University

Marshall UniversityMarshall Digital ScholarBiochemistry and Microbiology Faculty Research12-2012Draft Genome Sequence for Pseudomonasaeruginosa Strain PAO579, a Mucoid Derivative ofPAO381T. Ryan WithersMarshall University, withers19@marshall.eduShannon L. JohnsonHongwei D. YuMarshall University, yuh@marshall.eduFollow this and additional works at: http://mds.marshall.edu/sm_bmPart of the Biological Phenomena, Cell Phenomena, and Immunity Commons, GenomicsCommons, and the Medical Genetics CommonsThis Article is brought to you for free and open access by the Faculty Research at Marshall Digital Scholar. It has been accepted for inclusion inBiochemistry and Microbiology by an authorized administrator of Marshall Digital Scholar. For more information, please contactzhangj@marshall.edu.Recommended CitationWithers, T. R., Johnson, S. L., & Yu, H. D. (2012). Draft genome sequence for Pseudomonas aeruginosa strain PAO579, a mucoidderivative of PAO381. Journal of Bacteriology, 194(23), 6617.  2012, 194(23):6617. DOI: 10.1128/JB.01406-12. J. Bacteriol. T. Ryan Withers, Shannon L. Johnson and Hongwei D. Yu Derivative of PAO381aeruginosa Strain PAO579, a Mucoid Draft Genome Sequence for Pseudomonashttp://jb.asm.org/content/194/23/6617Updated information and services can be found at: These include:REFERENCEShttp://jb.asm.org/content/194/23/6617#ref-list-1This article cites 5 articles, 3 of which can be accessed free at: CONTENT ALERTS more»articles cite this article), Receive: RSS Feeds, eTOCs, free email alerts (when newhttp://journals.asm.org/site/misc/reprints.xhtmlInformation about commercial reprint orders: http://journals.asm.org/site/subscriptions/To subscribe to to another ASM Journal go to:  on April 25, 2014 by MARSHALL UNIV SCHOOL OF MEDhttp://jb.asm.org/Downloaded from  on April 25, 2014 by MARSHALL UNIV SCHOOL OF MEDhttp://jb.asm.org/Downloaded from Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579,a Mucoid Derivative of PAO381T. Ryan Withers,a Shannon L. Johnson,d and Hongwei D. Yua,b,cDepartments of Biochemistry and Microbiologya and Pediatrics,b Joan C. Edwards School of Medicine at Marshall University, Huntington, West Virginia, USA; ProgenesisTechnologies, LLC, Huntington, West Virginia, USAc; and Genome Science Group (B6), Los Alamos National Laboratory, Los Alamos, New Mexico, USAdPseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cys-tic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strainPAO381.Pseudomonas aeruginosa is a ubiquitous, opportunistic patho-gen and the leading cause of mortality with individuals af-flictedwith cystic fibrosis (CF).P. aeruginosauses the overproduc-tion of an exopolysaccharide, called alginate, to form mucoidbiofilms. Biofilm formation is responsible for the development ofchronic infections, as well as increased resistance to antibiotictreatment (2), and reduced phagocytosis by macrophages (4). P.aeruginosa strain PAO579 was first isolated as a mucoid, alginate-overproducing variant of PAO381, a derivative of the nonmucoidreference strain PAO1 (3, 5). Both PAO579 and PAO381 have awild-type mucA gene (mucA), and both strains are leucine auxot-rophic (leu38) and streptomycin resistant (strA2).Genomic DNA from P. aeruginosa strain PAO579 was isolatedusing phenol-chloroform extraction and ethanol precipitation;paired-end sequencing libraries were generated using vendor pro-tocols (Illumina, San Diego, CA); and genome sequencing wasperformed on an Illumina GAIIX with 60-bp-length sequencinggenerating 54,496,482 raw reads covering a total of 3,269,788,920bp. Data were generated and assembled using Illumina Pipelineversion SCS 2.8.0 paired with OLB 1.8.0 and aligned with the P.aeruginosa strain PAO1 reference genome (GenBank accessionno. NC_2516.2) using NovoAlign version 2.07.10. All specificsregarding aligner algorithms can be obtained from Novocraft,Selangor, Malaysia. The total number of base pairs aligned withthe reference genome is 2,077,041,840 bp, representing an averageof 340 per target base pair aligned. The number of bases satu-rated at or above 8 is 6,016,396 (96.04%), and the number ofbases saturated below 8 is 248,008 (3.96%). The total number ofreference bases covered is 6,036,589 (96.36%) with the total num-ber of bases missed being 227,815 (3.64%). There are a total of 16contigs (ALOF01000001 to ALOF01000016). Further analysis ofthe genome was performed using Samtools version 0.1.16a for thegeneration of pileup after sorting and removing supplicate readsand then analysis pipeline software developed by CofactorGenomics (St. Louis, MO). The genome was annotated and pre-pared for submission using the NCBI Prokaryotic Genomes Au-tomatic Annotation Pipeline (PGAAP; http://www.ncbi.nlm.nih.gov.genomes/static/Pipeline.html) server at NCBI.Based upon this analysis, a total of 31 homozygous single nu-cleotide polymorphisms (SNPs), or point mutations, were calledwith a high confidence between the sequenced reads and thePAO1 reference genome and were tabulated for each genomicposition, as well as the total coverage of bases observed at thatlocation. Of particular interest is the substitution of thymine foradenine at genome position 4980548 in the DegS-like MucA pro-tease gene, algW (PA4446). This alteration results in a change inthe primary structure of AlgW, more specifically a substitution ofisoleucine for phenylalanine at amino acid position 239. This pre-dicted substitution is thought to affect the proteolytic activity ofAlgW (1). Also of note, we observed mutations in leuA (PA3792),the 2-isopropylmalate synthase gene, and rpsL (PA4268), the 30Sribosomal protein S12 gene. These mutations are contiguouslypart of the PAO381 lineage and are responsible for leucine auxot-rophy and streptomycin resistance, respectively.Nucleotide sequence accession number. The draft genomesequence of P. aeruginosa strain PAO579 has been deposited inGenBank under accession number ALOF00000000.ACKNOWLEDGMENTSWe thank Jian Gao and Cofactor Genomics for assistance in sequencingand data analysis.This project was funded through the National Aeronautics and SpaceAdministrationWest Virginia Space Grant Consortium (NASAWVSGC)and the Cystic Fibrosis Foundation (CFF-YU11G0). H.D.Y. was sup-ported by NIH P20RR016477 and P20GM103434 to the West VirginiaIDeA Network for Biomedical Research Excellence.REFERENCES1. Cezairliyan BO, Sauer RT. 2009. Control of Pseudomonas aeruginosaAlgW protease cleavage of MucA by peptide signals and MucB. Mol. Mi-crobiol. 72:368–379.2. Govan JR, Deretic V. 1996. Microbial pathogenesis in cystic fibrosis: mu-coid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol. Rev.60:539–574.3. Govan JR, Fyfe JA. 1978. Mucoid Pseudomonas aeruginosa and cysticfibrosis: resistance of the mucoid from to carbenicillin, flucloxacillin andtobramycin and the isolation of mucoid variants in vitro. J. Antimicrob.Chemother. 4:233–240.4. Leid JG, et al. 2005. The exopolysaccharide alginate protects Pseudomonasaeruginosa biofilm bacteria from IFN-gamma-mediated macrophage kill-ing. J. Immunol. 175:7512–7518.5. Stanisich V, Holloway BW. 1969. Conjugation in Pseudomonas aerugi-nosa. Genetics 61:327–339.Received 2 August 2012 Accepted 18 September 2012Address correspondence to Hongwei D. Yu, yuh@marshall.edu.Copyright © 2012, American Society for Microbiology. All Rights Reserved.doi:10.1128/JB.01406-12GENOME ANNOUNCEMENTDecember 2012 Volume 194 Number 23 Journal of Bacteriology p. 6617 jb.asm.org 6617 on April 25, 2014 by MARSHALL UNIV SCHOOL OF MEDhttp://jb.asm.org/Downloaded from 

Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381

ABSTRACT
          
            Pseudomonas aeruginosa
            is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of
            P. aeruginosa
            strain PAO579, an alginate-overproducing derivative of strain PAO381.
          </jats:p

Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381

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