A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes

BMC Microbiology

Volumn 8, Issue , 2008, Pages

  Seo, Young Su ^a   Sriariyanun, Malinee ^a   Wang, Li ^b,d   Pfeiff, Janice ^a   Phetsom, Jirapa ^a   Lin, Ye ^c   Jung, Ki Hong ^a   Chou, Hui Hsien ^b,c   Bogdanove, Adam ^b   Ronald, Pamela ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c Iowa State University   (United States)

^d MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL STRAIN; CORRELATION COEFFICIENT; DNA MICROARRAY; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENOME; HYBRIDIZATION; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; XANTHOMONAS; XANTHOMONAS ORAYZAE; BACTERIAL GENOME; CLASSIFICATION; EVALUATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PLANT DISEASE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE;

BACTERIA (MICROORGANISMS); XANTHOMONAS ORYZAE; XANTHOMONAS ORYZAE PV. ORYZAE;

BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT DISEASES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; XANTHOMONAS;

EID: 47649093163     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-8-99     Document Type: Article

References (59)

1. Xanthomonas oryzae pathovars: model pathogens of a model crop. DO Nĩo-Liu PC Ronald AJ Bogdanove, Molecular Plant Pathology 2006 7 303 324 10.1111/j.1364-3703.2006.00344.x
2. Rice disease. S Ou, Commonwealth Agricultural Bureau, Kew, Surrey 2nd 1985
3. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. H Ochiai Y Inoue M Takeya A Sasaki H Kaku, Jpn Agri Res Quart 2005 39 275 287
4. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. BM Lee YJ Park DS Park HW Kang JG Kim ES Song IC Park UH Yoon JH Hahn BS Koo GB Lee H Kim HS Park KO Yoon JH Kim C Jung NH Koh JS Seo SJ Go, Nucleic Acids Res 2005 33 2 577 586 15673718 10.1093/nar/gki206
5. Comprehensive Microbial Resource. http://cmr.jcvi.org/tigr-scripts/CMR/ CmrHomePage.cgi
6. Expression profiling using cDNA microarrays. DJ Duggan M Bittner Y Chen P Meltzer JM Trent, Nature genetics 1999 21 1 Suppl 10 14 10.1038/4434 9915494
7. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. TR Hughes M Mao AR Jones J Burchard MJ Marton KW Shannon SM Lefkowitz M Ziman JM Schelter MR Meyer S Kobayashi C Davis H Dai YD He SB Stephaniants G Cavet WL Walker A West E Coffey DD Shoemaker R Stoughton AP Blanchard SH Friend PS Linsley, Nature biotechnology 2001 19 4 342 347 10.1038/86730 11283592
8. Exploring the metabolic and genetic control of gene expression on a genomic scale. JL DeRisi VR Iyer PO Brown, Science 1997 278 680 686 10.1126/science.278.5338.680 9381177
9. Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae. NC Hauser M Vingron M Scheideler B Krems K Hellmuth KD Entian JD Hoheisel, Yeast (Chichester, England) 1998 14 13 1209 1221 10.1002/(SICI)1097- 0061(19980930)14:13〈1209::AID-YEA311〉3.0.CO;2-N 9791892
10. Expression profiling of virulence and pathogenicity genes of Xanthomonas axonopodis pv. citri. G Astua-Monge J Freitas-Astua G Bacocina J Roncoletta SA Carvalho MA Machado, Journal of bacteriology 2005 187 3 1201 1205 15659697 10.1128/JB.187.3.1201-1205.2005
11. Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis. A Guidot P Prior J Schoenfeld S Carrere S Genin C Boucher, Journal of bacteriology 2007 189 2 377 387 17085551 10.1128/JB.00999-06
12. Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris: identification of novel cell-cell communication-dependent genes and functions. YW He M Xu K Lin YJ Ng CM Wen LH Wang ZD Liu HB Zhang YH Dong JM Dow LH Zhang, Molecular microbiology 2006 59 2 610 622 10.1111/j.1365-2958.2005.04961.x 16390454
13. Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa. T Koide RZ Vencio SL Gomes, Journal of bacteriology 2006 188 16 5821 5830 16885450 10.1128/JB.00182-06
14. Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae. SE Lu N Wang J Wang ZJ Chen DC Gross, Mol Plant Microbe Interact 2005 18 4 324 333 10.1094/MPMI-18-0324 15828684
15. Integrated regulation of the type III secretion system and other virulence determinants in Ralstonia solanacearum. M Valls S Genin C Boucher, PLoS pathogens 2006 2 8 e82 16933989 10.1371/journal.ppat.0020082
16. The expression of genes encoding lipodepsipeptide phytotoxins by Pseudomonas syringae pv. syringae is coordinated in response to plant signal molecules. N Wang SE Lu J Wang ZJ Chen DC Gross, Mol Plant Microbe Interact 2006 19 3 257 269 10.1094/MPMI-19-0257 16570656
17. Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris. YQ He L Zhang BL Jiang ZC Zhang RQ Xu DJ Tang J Qin W Jiang X Zhang J Liao JR Cao SS Zhang XX Liang ML Wei GT Lu JX Feng B Chen J Cheng JL Tang, Genome Biol 2007 8 10 R218 17927820 10.1186/gb-2007-8-10-r218
18. Expression of Xanthomonas oryzae pv. oryzae hrp Genes in XOM2, a Novel Synthetic Medium. S Tsuge F Ayako F Rie OKU Takashi T Kazunori O Hirokazu I Yasuhiro K Hisatoshi K Yasuyuki, J Gen Plant Path 2002 V68 4 363 10.1007/PL00013104
19. Gene involved in transcriptional activation of the hrp regulatory gene hrpG in Xanthomonas oryzae pv. oryzae. S Tsuge T Nakayama S Terashima H Ochiai A Furutani T Oku K Tsuno Y Kubo H Kaku, Journal of bacteriology 2006 188 11 4158 4162 16707710 10.1128/JB.00006-06
20. A Xanthomonas Pathogenicity Locus Is Induced by Sucrose and Sulfur-Containing Amino Acids. R Schulte U Bonas, Plant Cell 1992 4 1 79 86 12297631 10.1105/tpc.4.1.79
21. Inhibition of resistance gene mediated defense in rice by Xanthomonas oryzae pv. oryzicola. S Makino Sugio, A., White, F.F., and Bogdanove, A.J., Mol Plant-Microbe Interact 2006 19 240 249 10.1094/MPMI-19-0240 16570654
22. Identification of two novel hrp-associated genes in the hrp gene cluster of Xanthomonas oryzae pv. oryzae. W Zhu MaGbanua, M., and White, F., J Bacteriol 2000 182 7 1844 1853 10714988 10.1128/JB.182.7.1844-1853.2000
23. Plant and environmental sensory signals control the expression of hrp genes in Pseudomonas syringae pv. phaseolicola. LG Rahme MN Mindrinos NJ Panopoulos, Journal of bacteriology 1992 174 11 3499 3507 1592805
24. Expression of Erwinia amylovora hrp genes in response to environmental stimuli. ZM Wei Sneath, B. J., Beer, S. V., J Bacteriol 1992 174 1875 1882 1372313
25. Unique characteristics of Xanthomonas oryzae pv. oryzae AvrXa21 and implications for plant innate immunity. SW Lee SW Han LE Bartley PC Ronald, PNAS 2006 103 49 18395 18400 17082309 10.1073/pnas.0605508103
26. RaxH/RaxR: a two-component regulatory system in Xanthomonas oryzae pv. oryzae required for AvrXa21 activity. S Burdman Y Shen SW Lee Q Xue P Ronald, Mol Plant Microbe Interact 2004 17 6 602 612 10.1094/MPMI.2004.17.6.602 15195943
27. Bacterial genes involved in type I secretion and sulfation are required to elicit the rice Xa21-mediated innate immune response. FG da Silva Y Shen C Dardick S Burdman RC Yadav AL de Leon PC Ronald, Molecular Plant-Microbe Interactions 2004 17 6 593 601 10.1094/MPMI.2004.17.6.593 15195942
28. The Xanthomonas oryzae pv. oryzae raxP and raxQ genes encode an ATP sulfurylase and adenosine-5'-phosphosulphate kinase that are required for AvrXa21 avirulence activity. Y Shen P Sharma FG da Silva PC Ronald, Mol Microbiol 2002 44 37 38 10.1046/j.1365-2958.2002.02862.x 11967067
29. Design and analysis of experiments with high throughput biological assay data. DM Rocke, Semin Cell Dev Biol 2004 15 6 703 713 15561590
30. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. B Yao SN Rakhade Q Li S Ahmed R Krauss S Draghici JA Loeb, BMC bioinformatics 2004 5 99 15272935 10.1186/1471-2105-5-99
31. Systems biology of bacterial chemotaxis. M Baker P Wolanin J Stock, Current Opinion in Microbiology 2006 9 187 192 10.1016/j.mib.2006.02.007 16529985
32. The protein network of bacterial motility. S Rajagopala B Titz J Goll J Parrish K Wohlbold M MacKevitt T Palzkill H Mori R Finley P Uetz, Mol Systems Biol 2007 3 128
33. Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor. R Barak M Eisenbach, Biochemistry 1992 31 6 1821 1826 10.1021/bi00121a034 1737035
34. The cytoplasmic component of the bacterial flagellar motor. IH Khan TS Reese S Khan, PNAS 1992 89 13 5956 5960 1631080 10.1073/pnas.89.13.5956
35. Diversity in chemotaxismechanisms among the bacteria and archeae. H Szurmant and Ordal, G., Microbiology and Molecular Biology Reviews 2004 68 2 301 319 10.1128/MMBR.68.2.301-319.2004
36. Mutational analysis reveals novel candidate virulence factors in the rice pathogen Xanthomonas oryzae pv. oryzicola. L Wang S Makino A Subedee AJ Bogdanove, Appl Environ Microbiol 2008 73 8023 8027 10.1128/AEM.01414-07
37. Chemotaxis Is Required for Virulence and Competitive Fitness of the Bacterial Wilt Pathogen Ralstonia solanacearum. J Yao C Allen, J Bacteriol 2006 188 10 3697 3708 16672623 10.1128/JB.188.10.3697-3708.2006
38. Regulation of bacterial virulence by two-component systems. D Beier and Gross, R., Current Opinion in Microbiology 2006 9 143 152 10.1016/j.mib.2006.01. 005 16481212
39. Histidine kinases and response regulator proteins in two-component signaling systems. AH West AM Stock, Trends Biochem Sci 2001 26 369 376 10.1016/S0968-0004(01)01852-7 11406410
40. Molecular characterization of the Mg2+ responsive PhoP-PhoQ regulon in Salmonella enterica. S Lejona Aguirre, A., Cabeza, M., Ve'scovi, E., and Soncini, F., J Bacteriol 2003 185 21 6287-6294 10.1128/JB.185.21.6287-6294.2003
41. Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. I Zwir D Shin A Kato K Nishino T Latifi F Solomon J Hare H Huang E Groisman, Proc Natl Acad Sci 2005 102 8 2862- 2867 10.1073/pnas.0408238102
42. The PhoP/Q two-component system is required for AvrXA21 activity, activation of hrp gene expression, and virulence in Xanthomonas oryzae pv. oryzae. SW Lee SW Han KS Park PC Ronald, J Bacteriology 2007
43. Cell-cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover. R Ryan Y Fouhy J Lucey L Crossman S Spiro YW He LH Zhang S Heeb M Cámara P Williams M Dow, PNAS 2006 13 17
44. Establishment of the hrp-inducing systems for the expression of the hrp genes of Xanthomonas oryzae pv. oryzicola. YL Xiao YR Li ZY Liu Y Xiang GY Chen, Wei Sheng Wu Xue Bao 2007 47 396 401 17672294
45. HrpG, a key hrp regulatory protein of Xanthomonas campestris pv. vesicatoria is homologous to two-component response regulators. K Wengelnik G Ackerveken U Bonas, Mol Plant-Microbe Interact 1996 9 704-712
46. HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria. K Wengelnik U Bonas, J Bacteriol 1996 178 3462 3469 8655542
47. Domain structure of HrpE, the Hrp pilus subunit of Xanthomonas campestris pv. vesicatoria. E Weber R Koebnik, Journal of bacteriology 2005 187 17 6175 6186 16109959 10.1128/JB.187.17.6175-6186.2005
48. Hpa1 secretion via type III secretion system in Xanthomonas oryzae pv. oryzae. TS Furutani A. Oku T, Tsuno K, Inoue Y, Ochiai H, Kaku H, Kubo Y, J Gen Plant Path 2003 69 271 275 10.1007/s10327-003-0042-2
49. The Pseudomonas syringae pv. tomato HrpW protein has domains similar to harpins and pectate lyases and can elicit the plant hypersensitive response and bind to pectate. AO Charkowski JR Alfano G Preston J Yuan SY He A Collmer, J Bacteriol 1998 180 5211 5217 9748456
50. cDNA-AFLP analysis unravels a genomic-wide hrpG-regulon in the plant pathogen Xanthomonas campestris pv. vesicatoria. L Noël F Thieme D Nennstiel U Bonas, Molecular microbiology 2001 41 6 1271 1281 10.1046/j.1365-2958.2001.02567.x 11580833
51. Bacterial infection as assessed by in vivo gene expression. D Heithoff Conner, C, Hanna, P, Julio, S, Hentschel, U, and Mahan, M, PNAS 1997 94 934 939 9023360 10.1073/pnas.94.3.934
52. In vivo expression technology strategies: valuable tools for biotechnology. P Rainey and Preston, G., Current Opinion in Biotechnology 2000 11 440 444 10.1016/S0958-1669(00)00132-4 11024360
53. Identification of genes in Xanthomonas campestris pv. vesicatoria induced during its interaction with tomato. D Tamir-Ariel Navon, N., and Burdman, S., J Bacteriol 2007 189 17 6359 6371 17573477 10.1128/JB.00320-07
54. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. K Le Brigand R Russell C Moreilhon JM Rouillard B Jost FV Amiot C Bole-Feysot P Rostagno V Virolle V Defamie P Dessen G Williams P Lyons G Rios B Mari E Gulari P Kastner X Gidrol TC Freeman P Barbry, Nucleic Acids Res 2006 34 e87 16855282 10.1093/nar/gkl485
55. Picky: oligo microarray design for large genomes. HH Chou AP Hsia DL Mooney PS Schnable, Bioinformatics (Oxford, England) 2004 20 17 2893 2902 10.1093/bioinformatics/bth347 15180932
56. Integrated DNA Technology. http://www.idtdna.com
57. ArrayCore Microarray Facility at the University of California, Davis. http://array.ucdavis.edu/home/contact.php
58. Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride. N Raghavachari YO Bao G Li X Xie UR Muller, Anal Biochem 2003 312 101 105 10.1016/S0003-2697(02)00440-2 12531193
59. Primer3. http://frodo.wi.mit.edu