Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  O'Loughlin, Jason L ^a   Eucker, Tyson P ^a   Chavez, Juan D ^b   Samuelson, Derrick R ^a   Neal McKinney, Jason ^a   Gourley, Christopher R ^a   Bruce, James E ^b   Konkel, Michael E ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RESTRICTION ENDONUCLEASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CAMPYLOBACTER JEJUNI; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; DNA RESTRICTION; GENE LOCATION; GENE SEQUENCE; GENETIC PROCEDURES; GENOME ANALYSIS; HUMAN; HUMAN CELL; NONHUMAN; PROTEOMICS; SINGLE MOLECULE REAL TIME SEQUENCING; ALGORITHM; BINDING SITE; DNA SEQUENCE; GENETICS; METABOLISM; NUCLEOTIDE MOTIF;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER JEJUNI;

ALGORITHMS; BINDING SITES; CAMPYLOBACTER JEJUNI; DNA RESTRICTION-MODIFICATION ENZYMES; GENOME, BACTERIAL; NUCLEOTIDE MOTIFS; SEQUENCE ANALYSIS, DNA;

EID: 84923164025     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118533     Document Type: Article

References (46)

1. Sebald M, Veron M. Base DNA Content and Classification of Vibrios. Annales de l'Institut Pasteur. 1963; 105:897-910. PMID: 14098102
2. Dekeyser P, Gossuin-Detrain M, Butzler JP, Sternon J. Acute enteritis due to related vibrio: first positive stool cultures. The Journal of infectious diseases. 1972; 125(4):390-2. PMID: 4553081
3. Black RE, Levine MM, Clements ML, Hughes TP, Blaser MJ. Experimental Campylobacter jejuni infection in humans. The Journal of infectious diseases. 1988; 157(3):472-9. Epub 1988/03/01 PMID: 3343522
4. Blaser MJ, Berkowitz ID, LaForce FM, Cravens J, Reller LB, Wang WL. Campylobacter enteritis: clinical and epidemiologic features. Ann Intern Med. 1979; 91(2):179-85. Epub 1979/08/01. PMID: 380433
5. Crushell E, Harty S, Sharif F, Bourke B. Enteric Campylobacter: purging its secrets? Pediatric research. 2004; 55(1):3-12. doi: 10.1203/01.PDR.0000099794.06260.71 PMID: 14605259
6. Schwerer B. Antibodies against gangliosides: a link between preceding infection and immunopathogenesis of Guillain-Barre syndrome. Microbes Infect. 2002; 4(3):373-84. Epub 2002/03/23. PMID: 11909748
7. Zhang M, Yang X, Liu H, Liu X, Huang Y, He L, et al. Genome Sequences of the Guillain-Barre Syndrome Outbreak-Associated Campylobacter jejuni Strains ICDCCJ07002 and ICDCCJ07004. Genome announcements. 2013; 1(3). doi: 10.1128/genomeA.00256-13
8. Yuki N, Taki T, Inagaki F, Kasama T, Takahashi M, Saito K, et al. A bacterium lipopolysaccharide that elicits Guillain-Barre syndrome has a GM1 ganglioside-like structure. The Journal of experimental medicine. 1993; 178(5):1771-5. PMID: 8228822
9. Biggs PJ, Fearnhead P, Hotter G, Mohan V, Collins-Emerson J, Kwan E, et al. Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PloS one. 2011; 6(11):e27121. doi: 10.1371/journal.pone.0027121 PMID: 22096527
10. Cooper KK, Cooper MA, Zuccolo A, Law B, Joens LA. Complete genome sequence of Campylobacter jejuni strain S3. Journal of bacteriology. 2011; 193(6):1491-2. doi: 10.1128/JB.01475-10 PMID: 21217004
11. Champion OL, Gaunt MW, Gundogdu O, Elmi A, Witney AA, Hinds J, et al. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102 (44):16043-8. doi: 10.1073/pnas.0503252102 PMID: 16230626
12. Wilson DJ, Gabriel E, Leatherbarrow AJ, Cheesbrough J, Gee S, Bolton E, et al. Tracing the source of campylobacteriosis. PLoS genetics. 2008; 4(9):e1000203. doi: 10.1371/journal.pgen.1000203 PMID: 18818764
13. Kramer JM, Frost JA, Bolton FJ, Wareing DR. Campylobacter contamination of raw meat and poultry at retail sale: identification of multiple types and comparison with isolates from human infection. Journal of food protection. 2000; 63(12):1654-9. PMID: 11131886
14. Tock MR, Dryden DT. The biology of restriction and anti-restriction. Current opinion in microbiology. 2005; 8(4):466-72. doi: 10.1016/j.mib.2005.06.003 PMID: 15979932
15. Miller WG, Pearson BM, Wells JM, Parker CT, Kapitonov VV, Mandrell RE. Diversity within the Campylobacter jejuni type I restriction-modification loci. Microbiology. 2005; 151(Pt 2):337-51. doi: 10.1099/mic.0.27327-0
16. Casadesus J, Low D. Epigenetic gene regulation in the bacterial world. Microbiology and molecular biology reviews: MMBR. 2006; 70(3):830-56. doi: 10.1128/MMBR.00016-06 PMID: 16959970
17. Raphael RH, Monteville MR, Klena JD, Joens LA, Konkel ME. Interactions of Campylobacter jejuni with non-professional phagocytic cells. In: JM K, ME K, editors. Campylobacter molecular and cellular biology. Norfolk: Horizon Bioscience; 2005. p. 397-413.
18. Samuelson DR, Eucker TP, Bell JA, Dybas L, Mansfield LS, Konkel ME. The Campylobacter jejuni CiaD effector protein activates MAP kinase signaling pathways and is required for the development of disease. Cell communication and signaling: CCS. 2013; 11:79. doi: 10.1186/1478-811X-11-79 PMID: 24144181
19. Konkel ME, Monteville MR, Rivera-Amill V, Joens LA. The pathogenesis of Campylobacter jejuni-mediated enteritis. Curr Issues Intest Microbiol. 2001; 2(2):55-71. PMID: 11721281
20. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005; 21(4):537-9. doi: 10.1093/bioinformatics/bti054 PMID: 15479716
21. Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008; 24(23):2672-6. doi: 10.1093/bioinformatics/btn529 PMID: 18845581
22. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome research. 2004; 14(6):1188-90. doi: 10.1101/gr.849004 PMID: 15173120
23. Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE. Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research. Journal of proteomics. 2013; 88:109-19. doi: 10.1016/j.jprot.2013.04.009 PMID: 23590889
24. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, et al. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 2005; 21(5):617-23. doi: 10.1093/bioinformatics/bti057 PMID: 15501914
25. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic acids research. 2006; 34(Database issue):D187-91. doi: 10.1093/nar/gkj161
26. Konkel ME, Corwin MD, Joens LA, Cieplak W. Factors that influence the interaction of Campylobacter jejuni with cultured mammalian cells. Journal of medical microbiology. 1992; 37(1):30-7. PMID: 1625313
27. Christensen JE, Pacheco SA, Konkel ME. Identification of a Campylobacter jejuni-secreted protein required for maximal invasion of host cells. Mol Microbiol. 2009; 73(4):650-62. Epub 2009/07/25. doi: 10.1111/j.1365-2958.2009.06797.x PMID: 19627497
28. Malik-Kale P, Raphael BH, Parker CT, Joens LA, Klena JD, Quinones B, et al. Characterization of genetically matched isolates of Campylobacter jejuni reveals that mutations in genes involved in flagellar biosynthesis alter the organism's virulence potential. Applied and environmental microbiology. 2007; 73(10):3123-36. doi: 10.1128/AEM.01399-06 PMID: 17369342
29. Konkel ME, Gray SA, Kim BJ, Garvis SG, Yoon J. Identification of the enteropathogens Campylobacter jejuni and Campylobacter coli based on the cadF virulence gene and its product. Journal of clinical microbiology. 1999; 37(3):510-7. PMID: 9986804
30. Arakawa K, Tomita M. Measures of compositional strand bias related to replication machinery and its applications. Current genomics. 2012; 13(1):4-15. doi: 10.2174/138920212799034749 PMID: 22942671
31. Gundogdu O, Bentley SD, Holden MT, Parkhill J, Dorrell N, Wren BW. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC genomics. 2007; 8:162. doi: 10.1186/1471-2164-8-162 PMID: 17565669
32. Batchelor RA, Pearson BM, Friis LM, Guerry P, Wells JM. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology. 2004; 150(Pt 10):3507-17. doi: 10.1099/mic.0.27112-0 PMID: 15470128
33. Pearson BM, Pin C, Wright J, I'Anson K, Humphrey T, Wells JM. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS letters. 2003; 554(1-2):224-30. PMID: 14623122
34. Dorrell N, Mangan JA, Laing KG, Hinds J, Linton D, Al-Ghusein H, et al. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome research. 2001; 11(10):1706-15. doi: 10.1101/gr.185801 PMID: 11591647
35. Wilson MK, Lane AB, Law BF, Miller WG, Joens LA, Konkel ME, et al. Analysis of the pan genome of Campylobacter jejuni isolates recovered from poultry by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and repetitive sequence polymerase chain reaction (rep-PCR) reveals different discriminatory capabilities. Microbial ecology. 2009; 58(4):843-55. doi: 10.1007/s00248-009-9571-3 PMID: 19697077
36. Duong T, Konkel ME. Comparative studies of Campylobacter jejuni genomic diversity reveal the importance of core and dispensable genes in the biology of this enigmatic food-borne pathogen. Current opinion in biotechnology. 2009; 20(2):158-65. doi: 10.1016/j.copbio.2009.03.004 PMID: 19346123
37. Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, Boitano M, et al. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic acids research. 2012; 40(4):e29. doi: 10.1093/nar/gkr1146 PMID: 22156058
38. Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, et al. Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS computational biology. 2013; 9(3):e1002935. doi: 10.1371/journal.pcbi.1002935 PMID: 23516341
39. Krebes J, Morgan RD, Bunk B, Sproer C, Luong K, Parusel R, et al. The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic acids research. 2014; 42(4):2415-32. doi: 10.1093/nar/gkt1201 PMID: 24302578
40. Choe W, Chandrasegaran S, Ostermeier M. Protein fragment complementation in M.HhaI DNA methyltransferase. Biochemical and biophysical research communications. 2005; 334(4):1233-40. doi: 10.1016/j.bbrc.2005.07.017 PMID: 16040000
41. Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, et al. The methylomes of six bacteria. Nucleic acids research. 2012; 40(22):11450-62. doi: 10.1093/nar/gks891 PMID: 23034806
42. Poly F, Threadgill D, Stintzi A. Genomic diversity in Campylobacter jejuni: identification of C. jejuni 81-176-specific genes. Journal of clinical microbiology. 2005; 43(5):2330-8. doi: 10.1128/JCM.43.5. 2330-2338.2005 PMID: 15872262
43. Gilbert M, Mandrell RE, Parker CT, Li J, Vinogradov E. Structural analysis of the capsular polysaccharide from Campylobacter jejuni RM1221. Chembiochem: a European journal of chemical biology. 2007; 8(6):625-31. doi: 10.1002/cbic.200600508 PMID: 17335095
44. Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, et al. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000; 403 (6770):665-8. doi: 10.1038/35001088 PMID: 10688204
45. Ratel D, Ravanat JL, Charles MP, Platet N, Breuillaud L, Lunardi J, et al. Undetectable levels of N6-methyl adenine in mouse DNA: Cloning and analysis of PRED28, a gene coding for a putative mammalian DNA adenine methyltransferase. FEBS letters. 2006; 580(13):3179-84. doi: 10.1016/j.febslet. 2006.04.074 PMID: 16684535
46. Malik-Kale P, Parker CT, Konkel ME. Culture of Campylobacter jejuni with sodium deoxycholate induces virulence gene expression. Journal of bacteriology. 2008; 190(7):2286-97. Epub 2008/01/29. doi: 10.1128/JB.01736-07 PMID: 18223090