1887

Chapter 4 : Comparative Genomics of

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Comparative Genomics of , Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815554/9781555814373_Chap04-1.gif /docserver/preview/fulltext/10.1128/9781555815554/9781555814373_Chap04-2.gif

Abstract:

The use of comparative genomics combined with robust methods for data analysis will continue and will form the basis for the development of rational intervention strategies to reduce in the food chain. This chapter reviews the salient comparative features of the four fully sequenced genomes and reveals highlights from selected whole-genome microarray studies. The publication of the first genome paved the way for comparative genomics of this species. The relative genome diversity of bacterial species varies from clonal (genetically uniform) to genetically highly variable. The majority of genes on CJIE3 are of unknown function, although 23% share homology with ATCC 51449 genomic island (HHGI1). Recent comparative phylogenomics studies have been undertaken on increasingly large collections of strains from defined origins. The chapter discusses case studies of genomic comparisons by microarray. More recently, the authors studied over 230 strains from diverse origin and have further demonstrated the split of strains into two clades. Approximately half of the human isolates from this study are not associated with the livestock clade. DNA microarrays represent a powerful enabling technology for the whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. The next challenge for microbiologists in this postgenomic era is to correlate genome to phenome. This will provide a clear and more comprehensive understanding of the biology of .

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4

Key Concept Ranking

Type IV Secretion Systems
0.4255062
0.4255062
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Venn diagram of the genome content of the three sequenced human isolates (NCTC 11168, CG8486, and 81-176) (adapted from ). The gene content of 81-176 is based on the results of . These estimations exclude the capsule, LOS, and flagellin posttranslational modification loci.

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Comparative phylogenomics pipeline. Graphical representation of steps involved in production of a phylogenetic tree. Genomic DNA from each member of the strain collection was hybridized to a BμGS 11168 microarray with 11168 gDNA as control. Florescent intensities were calculated by BlueFuse. GeneSpring calculated intensity ratios and removed low-quality data points. GACK was used to convert ratio data to binary present/absent data. MrBayes used the binary data to construct a putative phylogeny by means of a Bayesian algorithm. The resulting tree was statistically tested for robustness. Further strains can be fed into the pipeline, and selection may be influenced by current phylogeny prediction.

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815554.ch04
1. Bacon, D. J.,, R. A. Alm,, D. H. Burr,, L. Hu,, D. J. Kopecko,, C. P. Ewing,, T. J. Trust, and, P. Guerry. 2000. Involvement of a plasmid in virulence of Campylobacter jejuni 81-176. Infect. Immun. 68:43844390.
2. Bacon, D. J.,, R. A. Alm,, L. Hu,, T. E. Hickey,, C. P. Ewing,, R. A. Batchelor,, T. J. Trust, and, P. Guerry. 2002. DNA sequence and mutational analyses of the pVir plasmid of Campylobacter jejuni 81-176. Infect. Immun. 70:62426250.
3. Bacon, D. J.,, C. M. Szymanski,, D. H. Burr,, R. P. Silver,, R. A. Alm, and, P. Guerry. 2001. A phase-variable capsule is involved in virulence of Campylobacter jejuni 81-176. Mol. Microbiol. 40:769777.
4. Batchelor, R. A.,, B. M. Pearson,, L. M. Friis,, P. Guerry, and, J. M. Wells. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150:35073517.
5. Black, R. E.,, M. M. Levine,, M. L. Clements,, T. P. Hughes, and, M. J. Blaser. 1988. Experimental Campylobacter jejuni infection in humans. J. Infect. Dis. 157:472479.
6. Champion, O. L.,, M. W. Gaunt,, O. Gundogdu,, A. Elmi,, A. A. Witney,, J. Hinds,, N. Dorrell, and, B. W. Wren. 2005. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc. Natl. Acad. Sci. USA 102:1604316048.
7. Desiere, F.,, W. M. McShan,, D. van Sinderen,, J. J. Ferretti, and, H. Brussow. 2001. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions. Virology 288:325341.
8. Dorrell, N.,, J. A. Mangan,, K. G. Laing,, J. Hinds,, D. Linton,, H. Al-Ghusein,, B. G. Barrell,, J. Parkhill,, N. G. Stoker,, A. V. Karlyshev,, P. D. Butcher, and, B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome. Res. 11:17061715.
9. Fouts, D. E.,, E. F. Mongodin,, R. E. Mandrell,, W. G. Miller,, D. A. Rasko,, J. Ravel,, L. M. Brinkac,, R. T. DeBoy,, C. T. Parker,, S. C. Daugherty,, R. J. Dodson,, A. S. Durkin,, R. Madupu,, S. A. Sullivan,, J. U. Shetty,, M. A. Ayodeji,, A. Shvartsbeyn,, M. C. Schatz,, J. H. Badger,, C. M. Fraser, and, K. E. Nelson. 2005. Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species. PLoS. Biol. 3:e15.
10. Gilbert, M.,, M. F. Karwaski,, S. Bernatchez,, N. M. Young,, E. Taboada,, J. Michniewicz,, A. M. Cunningham and, W. W. Wakarchuk. 2002. The genetic bases for the variation in the lipooligosaccharide of the mucosal pathogen, Campylobacter jejuni. Biosynthesis of sialylated ganglioside mimics in the core oligosaccharide. J. Biol. Chem. 277:327337.
11. Goon, S.,, C. P. Ewing,, M. Lorenzo,, D. Pattarini,, G. Majam, and, P. Guerry. 2006. A sigma28-regulated nonflagella gene contributes to virulence of Campylobacter jejuni 81-176. Infect. Immun. 74:769772.
12. Gundogdu, O.,, S. D. Bentley,, M. T. Holden,, J. Parkhill,, N. Dorrell, and, B. W. Wren. 2007. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics 8:162.
13. Hendrix, R. W. 2002. Bacteriophages: evolution of the majority. Theoretical Population Biol. 61:471480.
14. Hinchliffe, S. J.,, K. E. Isherwood,, R. A. Stabler,, M. B. Prentice,, A. Rakin,, R. A. Nichols,, P. C. Oyston,, J. Hinds,, R. W. Titball, and, B. W. Wren. 2003. Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 13:20182029.
15. Hofreuter, D.,, J. Tsai,, R. O. Watson,, V. Novik,, B. Altman,, M. Benitez,, C. Clark,, C. Perbost,, T. Jarvie,, L. Du, and, J. E. Galan. 2006. Unique features of a highly pathogenic Campylobacter jejuni strain. Infect. Immun. 74:46944707.
16. Howard, S. L.,, W., Gaunt,, J. Hinds,, A. A. Witney,, R. Stabler, and, B. W. Wren. 2006. Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J. Bacteriol. 188:36453653.
17. Hu, L., and, D. J. Kopecko. 1999. Campylobacter jejuni 81-176 associates with microtubules and dynein during invasion of human intestinal cells. Infect. Immun. 67:41714182.
18. Karlyshev, A. V.,, O. L. Champion,, C. Churcher,, J. R. Brisson,, H. C. Jarrell,, M. Gilbert,, D. Brochu,, F. St Michael,, J. Li,, W. W. Wakarchuk,, I. Goodhead,, M. Sanders,, K. Stevens,, B. Stevens,, J. Parkhill,, B. W. Wren, and, C. M. Szymanski. 2005. Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses. Mol. Microbiol. 55:90103.
19. Karlyshev, A. V., and, B. W. Wren. 2001. Detection and initial characterization of novel capsular polysaccharide among diverse Campylobacter jejuni strains using Alcian blue dye. J. Clin. Microbiol. 39:279284.
20. Leonard, E. E., II,, T. Takata,, M. J. Blaser,, S. Falkow,, L. S. Tompkins, and, E. C. Gaynor. 2003. Use of an open-reading frame-specific Campylobacter jejuni DNA microarray as a new genotyping tool for studying epidemiologically related isolates. J. Infect. Dis. 187:691694.
21. Leonard, E. E., II,, L. S. Tompkins,, S. Falkow, and, I. Nachamkin. 2004. Comparison of Campylobacter jejuni isolates implicated in Guillain-Barré syndrome and strains that cause enteritis by a DNA microarray. Infect. Immun. 72:11991203.
22. Louwen, R. P.,, A. van Belkum,, J. A. Wagenaar,, Y. Doorduyn,, R. Achterberg, and, H. P. Endtz. 2006. Lack of association between the presence of the pVir plasmid and bloody diarrhea in Campylobacter jejuni enteritis. J. Clin. Microbiol. 44:18671868.
23. McGovern, K. J.,, T. G. Blanchard,, J. A. Gutierrez,, S. J. Czinn,, S. Krakowka, and, P. Youngman. 2001. Gamma-glutamyltransferase is a Helicobacter pylori virulence factor but is not essential for colonization. Infect. Immun. 69:41684173.
24. Miller, W. G.,, B. M. Pearson,, J. M. Wells,, C. T. Parker,, V. V. Kapitonov, and, R. E. Mandrell. 2005. Diversity within the Campylobacter jejuni type I restriction-modification loci. Microbiology 151:337351.
25. Morgan, G. J.,, G. F. Hatfull,, S. Casjens, and, R. W. Hendrix. 2002. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317:337359.
26. Oelschlaeger, T. A.,, P. Guerry, and, D. J. Kopecko. 1993. Unusual microtubule-dependent endocytosis mechanisms triggered by Campylobacter jejuni and Citrobacter freundii. Proc. Natl. Acad. Sci. USA 90:68846888.
27. On, S. L.,, N. Dorrell,, L. Petersen,, D. D. Bang,, S. Morris,, S. J. Forsythe, and, B. W. Wren. 2006. Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses. Int. J. Med. Microbiol. 296:353363.
28. Parkhill, J.,, B. W. Wren,, K. Mungall,, J. M. Ketley,, C. Churcher,, D. Basham,, T. Chillingworth,, R. M. Davies,, T. Feltwell,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Moule,, M. J. Pallen,, C. W. Penn,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, A. H. van Vliet,, S. Whitehead, and, B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403:665668.
29. Pearson, B. M.,, C. Pin,, J. Wright,, K. I’Anson,, T. Humphrey, and, J. M. Wells. 2003. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS. Lett. 554:224230.
30. Poly, F.,, T. Read,, D. R. Tribble,, S. Baqar,, M. Lorenzo, and, P. Guerry. 2007. Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand. Infect. Immun. 75:34253433.
31. Prendergast, M. M.,, D. R. Tribble,, S. Baqar,, D. A. Scott,, J. A. Ferris,, R. I. Walker, and, A. P. Moran. 2004. In vivo phase variation and serologic response to lipooligosaccharide of Campylobacter jejuni in experimental human infection. Infect. Immun. 72:916922.
32. Russell, R. G.,, M. J. Blaser,, J. I. Sarmiento, and, J. Fox. 1989. Experimental Campylobacter jejuni infection in Macaca nemestrina. Infect. Immun. 57:14381444.
33. Stabler, R. A.,, D. N. Gerding,, J. G. Songer,, D. Drudy,, J. S. Brazier,, H. T. Trinh,, A. A. Witney,, J. Hinds, and, B. W. Wren. 2006. Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J. Bacteriol. 188:72977305.
34. Suerbaum, S.,, C. Josenhans,, T. Sterzenbach,, B. Drescher,, P. Brandt,, M. Bell,, M. Droge,, B. Fartmann,, H. P. Fischer,, Z. Ge,, A. Horster,, R. Holland,, K. Klein,, J. Konig,, L. Macko,, G. L. Mendz,, G. Nyakatura,, D. B. Schauer,, Z. Shen,, J. Weber,, M. Frosch, and, J. G. Fox. 2003. The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus. Proc. Natl. Acad. Sci. USA 100:79017906.
35. Taboada, E. N.,, R. R. Acedillo,, C. D. Carrillo,, W. A. Findlay,, D. T. Medeiros,, O. L. Mykytczuk,, M. J. Roberts,, C. A. Valencia,, J. M. Farber, and, J. H. Nash. 2004. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J. Clin. Microbiol. 42:45664576.
36. Tholema, N.,, M. Vor der Bruggen,, P. Maser,, T. Nakamura,, J. I. Schroeder,, H. Kobayashi,, N. Uozumi, and, E. P. Bakker. 2005. All four putative selectivity filter glycine residues in KtrB are essential for high affinity and selective K+ uptake by the KtrAB system from Vibrio alginolyticus. J. Biol. Chem. 280:4114641154.
37. Tracz, D. M.,, M. Keelan,, J. Ahmed-Bentley,, A. Gibreel,, K. Kowalewska-Grochowska, and, D. E. Taylor. 2005. pVir and bloody diarrhea in Campylobacter jejuni enteritis. Emerg. Infect. Dis. 11:838843.
38. van Belkum, A.,, S., Scherer,, L. van Alphen, and, H. Verbrugh. 1998. Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62:275293.
39. Wagner, D.,, J. Maser,, B. Lai,, Z. Cai,, C. E. Barry III,, K. Honer Zu Bentrup,, D. G. Russell, and, L. E. Bermudez. 2005. Elemental analysis of Mycobacterium avium–, Mycobacterium tuberculosis–, and Mycobacterium smegmatis–containing phagosomes indicates pathogen-induced microenvironments within the host cell’s endosomal system. J. Immunol. 174:14911500.
40. Wagner, P. L., and, M. K. Waldor. 2002. Bacteriophage control of bacterial virulence. Infect. Immun. 70:39853993.
41. Yao, R.,, D. H. Burr, and, P. Guerry. 1997. CheY-mediated modulation of Campylobacter jejuni virulence. Mol. Microbiol. 23:10211031.

Tables

Generic image for table
Table 1.

Summary of genomes sequenced to date and comparison to

Citation: Champion O, Al-Jaberi S, Stabler R, Wren B. 2008. Comparative Genomics of , p 63-71. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch4

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error