title: Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen.
abstract: Moraxella catarrhalis is an emerging human-restricted respiratory tract pathogen that is a common cause of childhood otitis media and exacerbations of chronic obstructive pulmonary disease in adults. Here, we report the first completely assembled and annotated genome sequence of an isolate of M. catarrhalis, strain RH4, which originally was isolated from blood of an infected patient. The RH4 genome consists of 1,863,286 nucleotides that form 1,886 protein-encoding genes. Comparison of the RH4 genome to the ATCC 43617 contigs demonstrated that the gene content of both strains is highly conserved. In silico phylogenetic analyses based on both 16S rRNA and multilocus sequence typing revealed that RH4 belongs to the seroresistant lineage. We were able to identify almost the entire repertoire of known M. catarrhalis virulence factors and mapped the members of the biosynthetic pathways for lipooligosaccharide, peptidoglycan, and type IV pili. Reconstruction of the central metabolic pathways suggested that RH4 relies on fatty acid and acetate metabolism, as the genes encoding the enzymes required for the glyoxylate pathway, the tricarboxylic acid cycle, the gluconeogenic pathway, the nonoxidative branch of the pentose phosphate pathway, the beta-oxidation pathway of fatty acids, and acetate metabolism were present. Moreover, pathways important for survival under challenging in vivo conditions, such as the iron-acquisition pathways, nitrogen metabolism, and oxidative stress responses, were identified. Finally, we showed by microarray expression profiling that approximately 88% of the predicted coding sequences are transcribed under in vitro conditions. Overall, these results provide a foundation for future research into the mechanisms of M. catarrhalis pathogenesis and vaccine development.
authors.affiliation: Laboratory of Pediatric Infectious Diseases, Radboud University Nijmegen Medical Centre, P.O. Box 9101 (Route 224), 6500 HB Nijmegen, The Netherlands.
authors.forename: Stefan P W
authors.initials: SP
authors.lastname: de Vries
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schueler
authors.forename: Kristian
authors.initials: K
authors.lastname: Riesbeck
authors.forename: John P
authors.initials: JP
authors.lastname: Hays
authors.forename: Peter W M
authors.initials: PW
authors.lastname: Hermans
authors.forename: Hester J
authors.initials: HJ
authors.lastname: Bootsma
mesh_terms: D001426:Bacterial Proteins; D002876:Chromosomes, Bacterial; D004734:Energy Metabolism / Q000502:physiology; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D007501:Iron / Q000378:metabolism; D008969:Molecular Sequence Data; D001936:Moraxella catarrhalis / Q000235:genetics*; D018384:Oxidative Stress; D021381:Protein Transport; D037521:Virulence Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D037521:Virulence Factors; D007501:Iron
references.citation: Proteins. 2006 Aug 15;64(3):643-51
references.pmid: 16752418
references.citation: J Mol Biol. 2006 Sep 29;362(4):640-55
references.pmid: 16934839
references.citation: Annu Rev Biochem. 2008;77:643-67
references.pmid: 18078384
references.citation: Trends Biochem Sci. 2003 Jan;28(1):32-40
references.pmid: 12517450
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7
references.pmid: 17537822
references.citation: Expert Rev Vaccines. 2009 Jun;8(6):655-8
references.pmid: 19485745
references.citation: Infect Immun. 2001 Jun;69(6):3576-80
references.pmid: 11349016
references.citation: Microbiology (Reading). 2005 Apr;151(Pt 4):1151-1158
references.pmid: 15817782
references.citation: Annu Rev Microbiol. 2000;54:881-941
references.pmid: 11018148
references.citation: BMC Bioinformatics. 2008 Mar 27;9:173
references.pmid: 18371216
references.citation: Infect Immun. 2008 Apr;76(4):1599-607
references.pmid: 18227159
references.citation: BMC Biotechnol. 2009 Nov 25;9:97
references.pmid: 19939278
references.citation: FEMS Microbiol Lett. 1994 Jun 1;119(1-2):155-9
references.pmid: 8039655
references.citation: Curr Opin Cell Biol. 2000 Aug;12(4):420-30
references.pmid: 10873830
references.citation: Annu Rev Microbiol. 2006;60:373-95
references.pmid: 16756481
references.citation: J Bacteriol. 2001 Mar;183(5):1540-51
references.pmid: 11160084
references.citation: J Bacteriol. 2007 Jul;189(14):5130-41
references.pmid: 17496104
references.citation: Infect Immun. 2008 Nov;76(11):5330-40
references.pmid: 18678659
references.citation: Microb Pathog. 1993 Dec;15(6):433-45
references.pmid: 8007816
references.citation: Infect Immun. 2005 Apr;73(4):2400-10
references.pmid: 15784586
references.citation: Microbes Infect. 2000 Apr;2(5):547-59
references.pmid: 10865200
references.citation: JAMA. 2006 Jul 12;296(2):202-11
references.pmid: 16835426
references.citation: Infect Immun. 2007 Jan;75(1):314-24
references.pmid: 17088358
references.citation: Mol Microbiol. 1999 Apr;32(2):403-14
references.pmid: 10231495
references.citation: Infect Immun. 1998 Aug;66(8):3656-65
references.pmid: 9673246
references.citation: Am J Respir Crit Care Med. 2005 Jul 15;172(2):195-9
references.pmid: 15805178
references.citation: Infect Immun. 2004 Apr;72(4):1906-13
references.pmid: 15039309
references.citation: Microbiology (Reading). 2008 Apr;154(Pt 4):1178-1184
references.pmid: 18375810
references.citation: Microbiology (Reading). 2006 Aug;152(Pt 8):2207-2219
references.pmid: 16849788
references.citation: Microbiol Mol Biol Rev. 2009 Sep;73(3):389-406, Table of Contents
references.pmid: 19721084
references.citation: Vaccine. 2008 Dec 23;26 Suppl 7:G5-10
references.pmid: 19094935
references.citation: J Bacteriol. 1996 Oct;178(20):5853-9
references.pmid: 8830678
references.citation: J Infect Dis. 1994 Oct;170(4):867-72
references.pmid: 7523537
references.citation: J Bacteriol. 2008 Dec;190(23):7762-72
references.pmid: 18820017
references.citation: Microbiol Rev. 1991 Dec;55(4):561-85
references.pmid: 1779927
references.citation: Arch Microbiol. 2004 Sep;182(1):1-6
references.pmid: 15221203
references.citation: Infect Immun. 2007 Dec;75(12):5559-64
references.pmid: 17908808
references.citation: Infect Immun. 1996 Jun;64(6):2024-30
references.pmid: 8675303
references.citation: Mol Microbiol. 2008 May;68(4):827-37
references.pmid: 18399938
references.citation: Infect Immun. 2007 Oct;75(10):4959-71
references.pmid: 17620351
references.citation: Clin Microbiol Rev. 1990 Oct;3(4):293-320
references.pmid: 2121328
references.citation: J Clin Microbiol. 2005 Dec;43(12):6139-43
references.pmid: 16333114
references.citation: J Bacteriol. 2000 Mar;182(5):1364-73
references.pmid: 10671460
references.citation: Curr Opin Infect Dis. 2009 Jun;22(3):279-85
references.pmid: 19405217
references.citation: Infect Immun. 2003 Nov;71(11):6426-34
references.pmid: 14573664
references.citation: Infect Immun. 2003 Apr;71(4):1843-8
references.pmid: 12654799
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W470-4
references.pmid: 18487625
references.citation: Infect Immun. 2005 Jun;73(6):3758-63
references.pmid: 15908408
references.citation: Infect Immun. 2004 Nov;72(11):6426-32
references.pmid: 15501773
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: BMC Microbiol. 2005 Oct 07;5:58
references.pmid: 16212653
references.citation: Infect Immun. 2007 Jun;75(6):2929-36
references.pmid: 17420235
references.citation: Trends Microbiol. 2001 Aug;9(8):397-403
references.pmid: 11514223
references.citation: PLoS Comput Biol. 2005 Nov;1(6):e60
references.pmid: 16292354
references.citation: Mol Microbiol. 2006 Aug;61(4):847-60
references.pmid: 16879643
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W181-4
references.pmid: 18411202
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
references.pmid: 18077471
references.citation: Infect Immun. 2003 Jun;71(6):3302-9
references.pmid: 12761112
references.citation: Infect Immun. 2007 Jun;75(6):2765-75
references.pmid: 17371858
references.citation: Mol Microbiol. 2007 Nov;66(4):829-39
references.pmid: 17919287
references.citation: BMC Bioinformatics. 2008 Feb 01;9:79
references.pmid: 18237442
references.citation: J Infect Dis. 2000 Apr;181(4):1376-87
references.pmid: 10762569
references.citation: Protein Sci. 2003 Aug;12(8):1652-62
references.pmid: 12876315
references.citation: Annu Rev Biochem. 2007;76:295-329
references.pmid: 17362200
references.citation: Vaccine. 2009 Nov 23;27(50):7065-72
references.pmid: 19786139
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9
references.pmid: 15215418
references.citation: J Bacteriol. 2003 Apr;185(7):2285-95
references.pmid: 12644500
references.citation: EMBO J. 2003 May 1;22(9):1959-68
references.pmid: 12727864
references.citation: Clin Microbiol Rev. 2002 Jan;15(1):125-44
references.pmid: 11781271
references.citation: Infect Immun. 2003 Aug;71(8):4341-50
references.pmid: 12874311
references.citation: Genome Res. 2007 Nov;17(11):1647-56
references.pmid: 17895425
references.citation: J Bacteriol. 1987 Jan;169(1):42-52
references.pmid: 3025185
references.citation: Antimicrob Agents Chemother. 1996 Apr;40(4):966-72
references.pmid: 8849261
references.citation: N Engl J Med. 2008 Nov 27;359(22):2355-65
references.pmid: 19038881
references.citation: Carbohydr Res. 2006 Nov 6;341(15):2600-6
references.pmid: 16934238