Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans.
BACKGROUND
Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and different patterns of disease association. This study examined the genome arrangement of A. actinomycetemcomitans using the genome sequences of serotypes a-c strains. The genome alignment and rearrangement were analyzed by the MAUVE and the GRIMM algorithms. The distribution patterns of genes along the leading/lagging strands were investigated. The occurrence and the location of repeat sequences relative to the genome rearrangement breakpoints were also determined.


RESULTS
The genome arrangement of the serotype a strain D7S-1 is markedly different from the serotype b strain HK1651 or the serotype c strain D11S-1. Specific genome arrangements appear to be conserved among strains of the same serotypes. The reversal distance between D7S-1 and HK1651 by GRIMM analysis is also higher than the within-species comparisons of 7 randomly selected bacterial species. The locations of the orthologous genes are largely preserved between HK1651 and D11S-1 but not between D7S-1 and HK1651 (or D11S-1), irrespective of whether the genes are categorized as essential/nonessential or highly/nonhighly expressed. However, genome rearrangement did not disrupt the operons of the A. actinomycetemcomitans strains. A higher proportion of the genome in strain D7S-1 is occupied by repeat sequences than in strains HK1651 or D11S-1.


CONCLUSIONS
The results suggest a significant evolutionary divergence between serotype a strains and serotypes b/c strains of A. actinomycetemcomitans. The distinct patterns of genome arrangement may suggest phenotypic differences between serotype a and serotypes b/c strains.
Kittichotirat
Weerayuth
W
Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA, USA.
Bumgarner
Roger
R
Chen
Casey
C
D000188:Actinobacillus / Q000145:classification* / Q000235:genetics*; D000465:Algorithms; D020029:Base Pairing / Q000235:genetics; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D009876:Operon / Q000235:genetics; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D018741:Replication Origin / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012703:Serotyping
Curr Opin Microbiol. 2004 Oct;7(5):519-27
15451508
Nucleic Acids Res. 2004 Jul 16;32(13):3781-91
15258248
Oral Microbiol Immunol. 1995 Apr;10(2):65-8
7675520
Mol Biol Evol. 2006 Feb;23(2):365-71
16237205
Proc Natl Acad Sci U S A. 1981 Nov;78(11):7069-72
6273909
Genome Res. 2004 Jul;14(7):1394-403
15231754
Infect Immun. 2003 May;71(5):2384-93
12704108
Periodontol 2000. 1994 Jun;5:26-51
9673161
J Clin Microbiol. 2002 Apr;40(4):1181-7
11923328
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13579-84
14593200
Bioinformatics. 2000 Jun;16(6):560-1
10980154
Bioinformatics. 2007 Mar 15;23(6):673-9
17237039
Methods Mol Biol. 2000;132:365-86
10547847
J Clin Microbiol. 1996 Jun;34(6):1576-8
8735124
Mol Microbiol. 1997 Mar;23(6):1089-97
9106201
J Clin Periodontol. 1998 Feb;25(2):134-44
9495612
Science. 2003 Aug 8;301(5634):790-3
12907788
Bioinformatics. 2003 Nov 1;19(16):2005-15
14594704
EMBO Rep. 2001 May;2(5):376-81
11375927
Clin Infect Dis. 1997 Sep;25 Suppl 2:S227-9
9310687
J Periodontol. 2005 Nov;76(11 Suppl):2052-60
16277576
Annu Rev Genet. 2008;42:211-33
18605898
PLoS Genet. 2008 Jul 18;4(7):e1000128
18650965
BMC Bioinformatics. 2005 Feb 15;6:31
15713233
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
9023104
Oral Microbiol Immunol. 2004 Oct;19(5):340-2
15327649
Lancet. 2008 Jan 19;371(9608):237-42
18207019
Mol Biol Evol. 2006 Mar;23(3):513-22
16280545
Mol Oral Microbiol. 2010 Jun;25(3):207-14
20536748
J Clin Microbiol. 1997 Dec;35(12):3037-42
9399490
Genome Biol. 2000;1(6):RESEARCH0011
11178265
Genome Biol. 2000;1(6):REVIEWS0006
11380986
J Bacteriol. 2002 Jul;184(13):3442-9
12057937
Mol Biol Evol. 1996 May;13(5):660-5
8676740
J Clin Microbiol. 1994 Jan;32(1):75-81
7907346
Infect Immun. 1994 Aug;62(8):3058-65
7913695
J Bacteriol. 2009 Dec;191(23):7378-9
19820097
Microbiology (Reading). 2005 Oct;151(Pt 10):3371-3379
16207919
Nat Genet. 2000 Oct;26(2):195-7
11017076
Science. 1995 Jul 28;269(5223):496-512
7542800
J Bacteriol. 2010 May;192(10):2643-4
20348265
Oral Microbiol Immunol. 1991 Apr;6(2):115-8
1945486
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
19855009
Mol Biol Evol. 2005 Jun;22(6):1456-67
15772379
Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
17062412
Curr Opin Microbiol. 2002 Oct;5(5):506-12
12354559
Nucleic Acids Res. 2009 Jan;37(Database issue):D459-63
18988623
Bioinformatics. 2002 Mar;18(3):492-3
11934753
J Clin Periodontol. 2008 Sep;35(8 Suppl):346-61
18724862
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Environ Microbiol. 2006 Feb;8(2):353-61
16423021
J Clin Microbiol. 1995 Feb;33(2):395-401
7714199