Transcriptome analysis of organisms with food safety relevance

Foodborne Pathogens and Disease

Volumn 5, Issue 4, 2008, Pages 517-529

  Puttamreddy, Supraja ^a   Carruthers, Michael D ^a   Madsen, Melissa L ^a   Minion, F Chris ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; COMPLEMENTARY DNA; DRINKING WATER; NITRIC OXIDE; OLIGONUCLEOTIDE;

BACTERIAL COLONIZATION; BACTERIAL FLORA; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL VIRULENCE; BACTERIUM CONTAMINATION; BIOFILM; CAMPYLOBACTER JEJUNI; DEVICE; DNA MICROARRAY; ENTEROBACTER INFECTION; ENTEROCOLITIS; ENVIRONMENTAL FACTOR; ESCHERICHIA COLI O157; FOOD CONTAMINATION; FOOD PROCESSING; FOOD SAFETY; FOOD SPOILAGE; GENE EXPRESSION; GRAM NEGATIVE INFECTION; HEAT SHOCK; HOST PATHOGEN INTERACTION; HUMAN; INFECTIOUS DIARRHEA; INFORMATION TECHNOLOGY; INTESTINE FLORA; LISTERIA MONOCYTOGENES; LISTERIOSIS; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA TYPHIMURIUM; SALMONELLOSIS; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; WATER CONTAMINATION; YERSINIA ENTEROCOLITICA; YERSINIOSIS;

BACTERIA; BIOFILMS; COMPUTATIONAL BIOLOGY; CONSUMER PRODUCT SAFETY; FOOD MICROBIOLOGY; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VIRULENCE;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER JEJUNI; ESCHERICHIA COLI; LISTERIA MONOCYTOGENES; SALMONELLA; YERSINIA ENTEROCOLITICA;

EID: 49949091440     PISSN: 15353141     EISSN: None     Source Type: Journal    
DOI: 10.1089/fpd.2008.0112     Document Type: Review

References (78)

1. Andersen MT, Brøndsted L, Pearson BM, Mulholland F, Parker M, Pin C, Wells JM, and Ingmer H. Diverse roles for HspR in Campylobacter jejuni revealed by the proteome, transcriptome and phenotypic characterization of an hspR mutant. Microbiology 2005;151:905-915.
2. Bansal T, Englert D, Lee J, Hegde M, Wood TK, and Jayaraman A. Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression. Infect. Immun. 2007;75:4597-4607.
3. Bottone EJ. Yersinia enterocolitica: overview and epidemiologic correlates. Microbes Infect. 1999;1:323-333.
4. Bowman JP, Bittencourt CR, and Ross T. Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing. Microbiology 2008;154:462-475.
5. Brown PO and Botstein D. Exploring the new world of the genome with DNA microarrays. Nat. Gen. 1999;21:33-37.
6. Burnens AP, Frey A, and Nicolet J. Association between clinical presentation, biogroups and virulence attributes of Yersinia enterocolitica strains in human diarrhoeal disease. Epidemiol. Infect. 1996;116:27-34.
7. Campellone KG, Roe AJ, Løbner-Olesen A, Murphy KC, Magoun L, Brady MJ, Donohue-Rolfe A, Tzipori S, Gally DL, Leong JM, and Marinus MG. Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7. Mol. Microbiol. 2007;63:1468-1481.
8. CDC. Preliminary FoodNet data on the incidence of infection with pathogens transmitted commonly through food - 10 states, 2007. MMWR 2008;57:366-370.
9. Chan YC, Raengpradub S, Boor KJ, and Wiedmann M. Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells. Appl. Environ. Microbiol. 2007;73:6484-6498.
10. Chatterjee SS, Hossain H, Otten S, Kuenne C, Kuchmina K, Machata S, Domann E, Chakraborty T, and Hain T. Intracellular gene expression profile of Listeria monocytogenes. Infect. Immun. 2006;74:1323-1338.
11. Churchill GA. Fundamentals of experimental design for cDNAmicroarrays. Nat. Genet. 2002;32 (Suppl):490-495.
12. Clements MO, Eriksson S, Thompson A, Lucchini S, Hinton JC, Normark S, and Rhen M. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc. Natl. Acad. Sci. U. S. A. 2002;99:8784-8789.
13. Dahan S, Knutton S, Shaw RK, Crepin VF, Dougan G, and Frankel G. Transcriptome of enterohemorrhagic Escherichia coli O157 adhering to eukaryotic plasma membranes. Infect. Immun. 2004;72:5452-5459.
14. De Keersmaecker SC, Marchal K, Verhoeven TL, Engelen K, Vanderleyden J, and Detweiler CS. Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself. J. Bacteriol. 2005;187:4381-4391.
15. DeRisi JL, Iyer VR, and Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997;278:680-686.
16. Eisen MB, Spellman PT, Brown PO, and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 1998;95:14863-14868.
17. Ekins, R. Multi-analyte immunoassay. J. Pharm. Biomed. Anal. 1989;7:155-168.
18. Ekins R, Chu F, and Micallef J. High specific activity chemiluminescent and fluorescent markers: their potential application to high sensitivity and 'multi-analyte' immunoassays. J. Biolumin. Chemilumin. 1989;4:59-78.
19. Elvers KT, Turner SM, Wainwright LM, Marsden G, Hinds J, Cole JA, Poole RK, Penn CW, and Park SF. NssR, a member of the Crp-Fnr superfamily from Campylobacter jejuni, regulates a nitrosative stress-responsive regulon that includes both a single-domain and a truncated haemoglobin. Mol. Microbiol. 2005;57:735-750.
20. Fitzhenry R, Dahan S, Torres AG, Chong Y, Heuschkel R, Murch SH, Thomson M, Kaper JB, Frankel G, and Phillips AD. Long polar fimbriae and tissue tropism in Escherichia coli O157:H7. Microbes Infect. 2006;8: 1741-1749.
21. Friis LM, Pin C, Taylor DE, Pearson BM, and Wells JM. A role for the tet(O) plasmid in maintaining Campylobacter plasticity. Plasmid 2007;57:18-28.
22. Frye J, Karlinsey JE, Felise HR, Marzolf B, Dowidar N, McClelland M, and Hughes KT. Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J. Bacteriol. 2006;188:2233-2243.
23. Gaynor EC, Wells DH, MacKichan JK, and Falkow S. The Campylobacter jejuni stringent response controls specific stress survival and virulence-associated phenotypes. Mol. Microbiol. 2005;56:8-27.
24. Guo B, Wang Y, Shi F, Barton YW, Plummer P, Reynolds DL, Nettleton D, Grinnage-Pulley T, Lin J, and Zhang Q. CmeR functions as a pleiotropic regulator and is required for optimal colonization of Campylobacter jejuni in vivo. J. Bacteriol. 2008;190:1879-1890.
25. Hain T, Hossain H, Chatterjee SS, Machata S, Volk U, Wagner S, Brors B, Haas S, Kuenne CT, Billion A, Otten S, Pane-Farre J, Engelmann S, and Chakraborty T. Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e sigmaB regulon. BMC Microbiol. 2008;8:20.
26. Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, and Fuqua SA. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl. Cancer Inst. 1999;91:453-459.
27. Horne SM and Pruss BM. Global gene regulation in Yersinia enterocolitica: effect of FliA on the expression levels of flagellar and plasmid-encoded virulence genes. Arch. Microbiol. 2006;185:115-126.
28. Hu Y, Oliver HF, Raengpradub S, Palmer ME, Orsi RH, Wiedmann M, and Boor KJ. Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes. Appl. Environ. Microbiol. 2007a;73:7981-7991.
29. Hu Y, Raengpradub S, Schwab U, Loss C, Orsi RH, Wiedmann M, and Boor KJ. Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes. Appl. Environ. Microbiol. 2007b;73:7967-7980.
30. Joseph B, Przybilla K, Stühler C, Schauer K, Slaghuis J, Fuchs TM, and Goebel W. Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening. J. Bacteriol. 2006;188:556-568.
31. Kallipolitis BH and Ingmer H. Listeria monocytogenes response regulators important for stress tolerance and pathogenesis. FEMS Microbiol. Lett. 2001;204:111-115.
32. Kapatral V, Campbell JW, Minnich SA, Thomson NR, Matsumura P, and Prüss BM. Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate. Microbiology 2004;150:2289-2300.
33. Kazmierczak MJ, Mithoe SC, Boor KJ, and Wiedmann M. Listeria monocytogenes sigma B regulates stress response and virulence functions. J. Bacteriol. 2003;185:5722-5734.
34. Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JC, and Dorman CJ. A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 2004;150:2037-2053.
35. Kerr MK, Martin M, and Churchill GA. Analysis of variance for gene expression microarray data. J. Comput. Biol. 2000;7:819-837.
36. Kim CC and Falkow S. Significance analysis of lexical bias in microarray data. BMC Bioinformatics 2003;4:12.
37. Lawhon SD, Frye JG, Suyemoto M, Porwollik S, McClelland M, and Altier C. Global regulation by CsrA in Salmonella typhimurium. Mol. Microbiol. 2003;48:1633-1645.
38. Lee J, Bansal T, Jayaraman A, Bentley WE, and Wood TK. Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin. Appl. Environ. Microbiol. 2007;73:4100-4109.
39. MacKichan JK, Gaynor EC, Chang C, Cawthraw S, Newell DG, Miller JF, and Falkow S. The Campylobacter jejuni dccRS two-component system is required for optimal in vivo colonization but is dispensable for in vitro growth. Mol. Microbiol. 2004;54:1269-1286.
40. Malik-Kale P, Parker CT, and Konkel ME. Culture of Campylobacter jejuni with sodium deoxycholate induces virulence gene expression. J. Bacteriol. 2008;190:2286-2297.
41. Malone AS, Chung YK, and Yousef AE. Genes of Escherichia coli O157:H7 that are involved in high-pressure resistance. Appl. Environ. Microbiol. 2006;72:2661-2671.
42. Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, and Tauxe RV. Food-related illness and death in the United States. Emerg. Infect. Dis. 1999;5:607-625.
43. Monsieurs P, De Keersmaecker S, Navarre WW, Bader MW, De Smet F, McClelland M, Fang FC, De Moor B, Vanderleyden J, and Marchal K. Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J. Mol. Evol. 2005;60:462-474.
44. Myers KM, Gaba J, and Al-Khaldi SF. Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization. Mol. Cell. Probes 2006;20:71-80.
45. Palyada K, Threadgill D, and Stintzi A. Iron acquisition and regulation in Campylobacter jejuni. J. Bacteriol. 2004;186:4714-4729.
46. Perna NT, Plunkett GI, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Pósfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, and Blattner FR. Genome sequence of enterohaemorrahgic Escherichia coli O157:H7. Nature 2001;409:529-533.
47. Prouty AM, Brodsky IE, Falkow S, and Gunn JS. Bilesalt-mediated induction of antimicrobial and bile resistance in Salmonella typhimurium. Microbiology 2004a;150:775-783.
48. Prouty AM, Brodsky IE, Manos J, Belas R, Falkow S, and Gunn JS. Transcriptional regulation of Salmonella enterica serovar Typhimurium genes by bile. FEMS Immunol. Med. Microbiol. 2004b;41:177-185.
49. Roe AJ, Tysall L, Dransfield T, Wang D, Fraser-Pitt D, Mahajan A, Constandinou C, Inglis N, Downing A, Talbot R, Smith DG, and Gally DL. Analysis of the expression, regulation and export of NleA-E in Escherichia coli O157:H7. Microbiology 2007;153:1350-1360.
50. Schena M. Microarray Analysis. Hoboken, NJ: John Wiley & Sons, Inc., 2003.
51. Schena M, Shalon D, Davis RW, and Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995;270:467-470.
52. Schena M, Shalon D, Heller R, Chai A, Brown PO, and Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. U. S. A. 1996;93:10614-10619.
53. Seo J, Savitzky DC, Ford E, and Darwin AJ. Global analysis of tolerance to secretin-induced stress in Yersinia enterocolitica suggests that the phage-shock-protein system may be a remarkably self-contained stress response. Mol. Microbiol. 2007;65:714-727.
54. Shen A and Higgins DE. The MogR transcriptional repressor regulates nonhierarchal expression of flagellar motility genes and virulence in Listeria monocytogenes. PLoS Pathog. 2006;2:e30.
55. Smyth GK and Speed T. Normalization of cDNA microarray data. Methods 2003;31:265-273.
56. Snyder LA, Davies JK, and Saunders NJ. Microarray _genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with minimal mobile elements. BMC Genomics 2004;5:23.
57. Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 1975;98:503-517.
58. Stintzi A. Gene expression profile of Campylobacter jejuni in response to growth temperature variation. J. Bacteriol. 2003;185:2009-2016.
59. Stintzi A, Marlow D, Palyada K, Naikare H, Panciera R, Whitworth L, and Clarke C. Use of genome-wide expression profiling and mutagenesis to study the intestinal lifestyle of Campylobacter jejuni. Infect. Immun. 2005;73:1797-1810.
60. Taboada EN, Acedillo RR, Carrillo CD, Findlay WA, Medeiros DT, Mykytczuk OL, Roberts MJ, Valencia CA, Farber JM, and Nash JH. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J. Clin. Microbiol. 2004;42:4566-4576.
61. Tanaka TS, Jaradat SA, Lim MK, Kargul GJ, Wang X, Grahovac MJ, Pantano S, Sano Y, Piao Y, Nagaraja R, Doi H, Wood WH 3rd, Becker KG, and Ko MS. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc. Natl. Acad. Sci. U. S. A. 2000;97:9127-9132.
62. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, et al. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc. Natl. Acad. Sci. U. S. A. 2002;99:12391-12396.
63. Thompson A, Rowley G, Alston M, Danino V, and Hinton JC. Salmonella transcriptomics: relating regulons, stimulons and regulatory networks to the process of infection. Curr. Opin. Microbiol. 2006;9:109-116.
64. Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T, Feltwell T, Abdellah Z, Hauser H, Jagels K, Maddison M, Moule S, Sanders M, Whitehead S, Quail MA, Dougan G, Parkhill J, and Prentice MB. The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet. 2006;2:e206.
65. van der Veen S, Hain T, Wouters JA, Hossain H, de Vos WM, Abee T, Chakraborty T, and Wells-Bennik MH. The heat-shock response of Listeria monocytogenes comprises genes involved in heat shock, cell division, cell wall synthesis, and the SOS response. Microbiology 2007;153:3593-3607.
66. Volokhov D, Chizhikov V, Chumakov K, and Rasooly A. Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis. J. Clin. Microbiol. 2003;41:4071-4080.
67. Wang Q, Frye JG, McClelland M, and Harshey RM. Gene expression patterns during swarming in Salmonella typhimurium: genes specific to surface growth and putative new motility and pathogenicity genes. Mol. Microbiol. 2004;52:169-187.
68. Wang Q, Zhao Y, McClelland M, and Harshey RM. The RcsCDB signaling system and swarming motility in Salmonella enterica serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J. Bacteriol. 2007;189:8447-8457.
69. Ward WO, Swartz CD, Porwollik S, Warren SH, Hanley NM, Knapp GW, McClelland M, and DeMarini DM. Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella. BMC Bioinformatics 2007;8:378.
70. Wauters G, Kandolo K, and Janssens M. Revised bio-grouping scheme of Yersinia enterocolitica. Contrib. Microbiol. Immunol. 1987;9:14-21.
71. Welford SM, Gregg J, Chen E, Garrison D, Sorensen PH, Denny CT, and Nelson SF. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res. 1998;26:3059-3065.
72. Wick LM, Qi W, Lacher DW, and Whittam TS. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J. Bacteriol. 2005;187:1783-1791.
73. Widmer KW, Jesudhasan PR, Dowd SE, and Pillai SD. Differential expression of virulence-related genes in a Salmonella enterica serotype typhimurium luxS mutant in response to autoinducer AI-2 and poultry meat-derived AI-2 inhibitor. Foodborne Pathog. Dis. 2007;4:5-15.
74. Williams T, Joseph B, Beier D, Goebel W, and Kuhn M. Response regulator DegU of Listeria monocytogenes regulates the expression of flagella-specific genes. FEMS Microbiol. Lett. 2005;252:287-298.
75. Wilson JW, Ott CM, Ramamurthy R, Porwollik S, McClelland M, Pierson DL, and Nickerson CA. Low-shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent manner. Appl. Environ. Microbiol. 2002a;68:5408-5416.
76. Wilson JW, Ott CM, Höner zu Bentrup K, Ramamurthy R, Quick L, Porwollik S, et al. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. Proc. Natl. Acad. Sci. U. S. A. 2007;104:16299-31604.
77. Wilson JW, Ramamurthy R, Porwollik S, McClelland M, Hammond T, Allen P, Ott CM, Pierson DL, and Nickerson CA. Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon. Proc. Natl. Acad. Sci. U. S. A. 2002b;99:13807-13812.
78. Wosten MM, Parker CT, van Mourik A, Guilhabert MR, van Dijk L, and van Putten JP. The Campylobacter jejuni PhosS/PhosR operon represents a non-classical phosphate-sensitive two-component system. Mol. Microbiol. 2006;62:278-291.