Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Ternan, Nigel G ^a   Jain, Shailesh ^a   Srivastava, Malay ^a   McMullan, Geoff ^a  

^a UNIVERSITY OF ULSTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; FLAGELLIN; PROTEIN DNAK; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ADHERENCE; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; DNAK GENE; DOWN REGULATION; EPITHELIUM CELL; FLAGELLUM; FLIC GENE; GENE EXPRESSION; GENETIC TRANSCRIPTION; GROEL GENE; HEAT SHOCK RESPONSE; HEAT STRESS; HEAT TOLERANCE; INTRON; MUCUS; NONHUMAN; OPERON; TRANSPOSON; UPREGULATION;

CLOSTRIDIUM DIFFICILE; HEAT-SHOCK RESPONSE; INTRONS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM DIFFICILE 630;

EID: 84864467124     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042410     Document Type: Article

References (61)

1. Rupnik M, Wilcox MH, Gerding DN, (2009) Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nature Rev Microbiology 7: 526-536.
2. Stabler RA, He M, Dawson L, Martin M, Valiente E, et al. (2009) Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. BMC Genome Biol 10: R102 doi:10.1186/gb-2009-10-9-r102.
3. Kuehne SA, Cartman ST, Heap JT, Kelly ML, Cockayne A, et al. (2010) The role of toxin A and toxin B in Clostridium difficile infection. Nature 467: 711-713.
4. Voth DE, Ballard JD, (2005) Clostridium difficile toxins: Mechanism of action and role in disease. Clin Microbiol Rev 18: 247-263.
5. Bartlett JG, (2006) Narrative review: The new epidemic of Clostridium difficile-associated enteric disease. Ann Intern Med 145: 758-764.
6. Bartlett JG, (2008) Historical perspectives on studies of Clostridium difficile and C. difficile infection. Clin Infect Dis (Suppl 1): pp. s4-s11.
7. McFarland LV, (2008) Update on the changing epidemiology of Clostridium difficile-associated disease. Nat Clin Practice Gastroenterology & Hepatology 5: 40-48.
8. Miyajimal F, Roberts P, Swale A, Price V, Jones M, et al. (2011) Characterisation and carriage ratio of Clostridium difficile strains isolated from a community-dwelling elderly population in the United Kingdom. PLoS ONE 6 (8): e22804 doi:10.1371/journal.pone.0022804.
9. Clostridium difficile ribotyping network for England and Northern Ireland 2009/10 report. London; 2009. Available at: http://www.hpa.org.uk/webc/HPAwebFile/HPAweb_C/1296681523205 Accessed 20 March 2012.
10. Freeman J, Bauer MP, Baines SD, Corver J, Fawley WN, et al. (2010) The changing epidemiology of Clostridium difficile infections. Clin Microbiol Rev 23 (3): 529-549.
11. Burns DA, Heeg D, Cartman ST, Minton NP, (2011) Reconsidering the sporulation characteristics of hypervirulent Clostridium difficile BI/NAP1/027. PLoS ONE 6 (9): e24894 doi:10.1371/journal.pone.0024894.
12. Brouwer MSM, Warburton PJ, Roberts AP, Mullany P, Allan E, (2011) Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS ONE 6 (8): e23014 doi:10.1371/journal.pone.0023014.
13. Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton NP, et al. (2006) The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38: 779-786.
14. Janvilisri T, Scaria J, Thompson AD, Nicholson A, Limbago BM, et al. (2009) Microarray identification of Clostridium difficile core components and divergent regions associated with host origin. J Bacteriol 191: 3881-3891.
15. He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, et al. (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A 107: 7527-7532.
16. Forgetta V, Oughton MT, Marquis P, Brukner I, Blanchette R, et al. (2011) Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile. J Clin Microbiol 49 (6): 2230-2238.
17. Marsden GL, Davis IJ, Wright VJ, Sebaihia M, Kuijper EJ, et al. (2010) Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile. BMC Genomics 11: 389 doi:10.1186/1471-2164-11-389.
18. Emerson JE, Stabler RA, Wren BW, Fairweather NF, (2008) Microarray analysis of the transcriptional responses of Clostridium difficile to environmental and antibiotic stress. J Med Microbiol 57: 757-764.
19. Janvilisri T, Scaria J, Chang Y-F, (2010) Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection. J Infect Dis 202 (2): 282-290.
20. Scaria J, Janvilisri T, Fubini S, Gleed RD, McDonough SP, et al. (2011) Clostridium difficile transcriptome analysis using pig ligated loop model reveals modulation of pathways not modulated in vitro. J Infect Dis 203: 1613-1620.
21. Jain S, Graham C, Graham RLJ, McMullan G, Ternan NG, (2011) A quantitative proteomic analysis of the heat stress response in Clostridium difficile strain 630. J Proteome Res 10 (9): 3880-3890.
22. Lemeé L, Dhalluin A, Pestel-Caron M, Lemeland JF, Pons JL, (2004) Multilocus sequence typing analysis of human and animal Clostridium difficile isolates of various toxigenic types. J Clin Microbiol 42: 2609-2617.
23. Do JH, Choi DK, (2007) cDNA Labeling Strategies for Microarrays Using Fluorescent Dyes. Eng Life Sci 7 (1): 26-34.
24. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucl Acid Res 30 (1): 207-210.
25. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55 (4): 611-622.
26. Moszer I, Glaser P, Danchin A, (1995) SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141: 261-268.
27. Graham RLJ, Sharma MK, Ternan NG, Weatherly DB, Tarleton RL, et al. (2007) A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi. BMC Genome Biol 8: R110.
28. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucl Acid Res 39(Database issue): D561-568.
29. Donovan M, Schumuke JJ, Fonzi WA, Bonar SL, Gheesling-Mullis K, et al. (2001) Virulence of a phosphoribosylaminoimidazole carboxylase-deficient Candida albicans strain in an immunosuppressed murine model of systemic candidiasis. Infect Immun 69 (4): 2542-2548.
30. Propst KL, Mima T, Choi KH, Dow SW, Schweizer HP, (2010) A Burkholderia pseudomallei delta purM mutant is avirulent in immunocompetent and immunodeficient animals: candidate strain for exclusion from select-agent lists. Inf Immun 78 (7): 3136-3143.
31. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. (2011) Enterotypes of the human gut microbiome. Nature 474: 174-180.
32. Chen Y, Indurthi DC, Jones SW, Papoutsakis ET, (2011) Small RNAs in the genus Clostridium. MBio 2 (1): e00340-10 doi:10.1128/mBio.00340-10.
33. Ternan NG, Quinn JP, (1998) Phosphate starvation-independent 2-aminoethylphosphonic acid biodegradation in a newly isolated strain of Pseudomonas putida, NG2. Syst Appl Microbiol 21: 346-352.
34. Ternan NG, McGrath JW, McMullan G, Quinn JP, (1998) Organophosphonates: occurrence, synthesis and biodegradation by microorganisms. World J Microbiol Biotechnol 14: 635-647.
35. Helmann JD, Wu MF, Kobel PA, Gamo FJ, Wilson M, et al. (2001) Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183 (24): 7318-7328.
36. Hecker M, Reder A, Fuchs S, Pagels M, Engelmann S, (2009) Physiological proteomics and stress/starvation responses in Bacillus subtilis and Staphylococcus aureus. Res Microbiol 160 (4): 245-258.
37. Schumann W, (2003) The Bacillus subtilis heat shock stimulon. Cell Stress Chaperones 8: 207-217.
38. Versteeg S, Escher A, Wende A, Schumann W, (2003) Regulation of the Bacillus subtilis heat shock gene htpG is under positive control. J Bacteriol 185 (2): 466-474.
39. Nielsen AK, Breüner A, Krzystanek M, Andersen JT, Poulsen TA, et al. (2010) Global transcriptional analysis of Bacillus licheniformis reveals an overlap between heat shock and iron limitation stimulon. Mol Microbiol Biotechnol 18: 162-173.
40. Hecker M, Völker U, (2001) General stress response of Bacillus subtilis and other bacteria. Adv Microb Physiol 44: 35-91.
41. Olivares-Hernandez R, Usaite R, Nielsen J, (2010) Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level. Biotech Bioengineering 107 (5): 865-875.
42. Olivares-Hernández R, Bordel S, Nielsen J, (2011) Codon usage variability determines the correlation between proteome and transcriptome fold changes. BMC Systems Biology 5: 33 doi:10.1186/1752-0509-5-33.
43. Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, et al. (2011) Proteomics and transcriptomics characterisation of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Proteomics 10 (2) DOI:10.1074/mcp.M110.002741.
44. Resch A, Leicht S, Saric M, Pásztor L, Jakob A, et al. (2006) Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling. Proteomics 6: 1867-1877.
45. Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, et al. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. Mol Microbiol 41: 1159-1172.
46. Darmon E, Noone D, Masson A, Bron S, Kuipers OP, et al. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated cssrs two-component system of Bacillus subtilis. J Bacteriol 184: 5661-5671.
47. Schumann W, (2007) Thermosensors in eubacteria: role and evolution. J. Biosci 32: 549-557.
48. Stabler RA, Gerding DN, Songer JG, Drudy D, Brazier JS, et al. (2006) Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 188: 7297-7305.
49. Twine SM, Reid CW, Aubry A, McMullin DR, Fulton KM, et al. (2009) Motility and flagellar glycosylation in Clostridium difficile. J Bacteriol 191 (22): 7050-7062.
50. Dingle TC, Mulvey GL, Armstrong GD, (2011) Mutagenic analysis of the Clostridium difficile flagellar proteins, FliC and FliD, and their contribution to virulence in hamsters. Inf Immun 79 (10): 4061-4067.
51. Karlsson S, Dupuy B, Mukherjee K, Norin E, Burman LG, et al. (2003) Expression of Clostridium difficile Toxins A and B and their sigma factor TcdD is controlled by temperature. Infect Immun 71: 1784-1793.
52. Kortmann J, Narberhaus F, (2012) Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Microbiol 10: 255-265.
53. van den Berg RJ, Schaap I, Templeton KE, Klaassen CHW, Kuijper EJ, (2006) Typing and subtyping of Clostridium difficile isolates by using multiple-locus variable-number tandem-repeat analysis. J Clin Microbiol 45 (3): 1024-1028.
54. Merrigan M, Venugopal A, Mallozzi M, Roxas B, Viswanathan VK, et al. (2010) Human Hypervirulent Clostridium difficile strains exhibit increased sporulation as well as robust toxin production. J Bacteriol 192 (19): 4904-4911.
55. Mullany P, Roberts AP, Wang H, (2002) Mechanism of integration and excision in conjugative transposons. Cell Mol Life Sci 59 (12): 2017-2022.
56. Lyras D, Rood JI (2005) Transposable genetic elements of Clostridia. In: Durre P, editor. Handbook on Clostridia. Taylor and Francis. CRC Press. Pp. 631-643.
57. Jasni AS, Mullany P, Hussain H, Roberts AP, (2010) Demonstration of conjugative transposon (Tn5397)-mediated horizontal gene transfer between Clostridium difficile and Enterococcus faecalis. Antimicrob Agents and Chemotherapy 54 (11): 4924-4926.
58. Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, et al. (2008) Group II intron protein localization and insertion sites are affected by polyphosphate. PLoS Biol 6 (6): e150 doi:10.1371/journal.pbio.0060150.
59. Coros CJ, Piazza CL, Chalamcharla VR, Smith D, Belfort M, (2009) Global regulators orchestrate group II intron retromobility. Mol Cell 34 (2): 250-256.
60. Storz G, Vogel J, Wassarman KM, (2011) Regulation by Small RNAs in Bacteria: Expanding Frontiers. Mol Cell 43 (6): 880-891.
61. Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, et al. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. PNAS 108 (50): 20172-20177.