A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes
<p>Abstract</p> <p>Background</p> <p><it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>) and <it>X. oryzae </it>pv. <it>oryzicola </it>(<it>Xoc</it>) are bacterial pathogens of the worldw...
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| Format: | Article |
| Language: | English |
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BMC
2008-06-01
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| Series: | BMC Microbiology |
| Online Access: | http://www.biomedcentral.com/1471-2180/8/99 |
| _version_ | 1818482077826285568 |
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| author | Lin Ye Phetsom Jirapa Pfeiff Janice Wang Li Sriariyanun Malinee Seo Young-Su Jung Ki-Hong Chou Hui Hsien Bogdanove Adam Ronald Pamela |
| author_facet | Lin Ye Phetsom Jirapa Pfeiff Janice Wang Li Sriariyanun Malinee Seo Young-Su Jung Ki-Hong Chou Hui Hsien Bogdanove Adam Ronald Pamela |
| author_sort | Lin Ye |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>) and <it>X. oryzae </it>pv. <it>oryzicola </it>(<it>Xoc</it>) are bacterial pathogens of the worldwide staple and grass model, rice. <it>Xoo </it>and <it>Xoc </it>are closely related but <it>Xoo </it>invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and <it>Xoc </it>colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on <it>hrp </it>genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for <it>Xoo </it>and <it>Xoc </it>and compared gene expression in <it>Xoo </it>strains PXO99<sup>A </sup>and <it>Xoc </it>strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce <it>hrp </it>genes in <it>Xoo </it>strain T7174.</p> <p>Results</p> <p>Three biological replicates of the microarray experiment to compare global gene expression in representative strains of <it>Xoo </it>and <it>Xoc </it>grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of <it>Xoo </it>and 39 genes of <it>Xoc </it>were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for <it>Xoo </it>and <it>Xoc </it>selected for validation. The differentially expressed genes represent 17 functional categories.</p> <p>Conclusion</p> <p>We describe here the construction and validation of a two-genome microarray for the two pathovars of <it>X. oryzae</it>. Microarray analysis revealed that using representative strains, a greater number of <it>Xoo </it>genes than <it>Xoc </it>genes are differentially expressed in XOM2 relative to PSB, and that these include <it>hrp </it>genes and other genes important in interactions with rice. An exception was the <it>rax </it>genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.</p> |
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| spelling | doaj.art-16cbbe04c5db4d25960c97df686e50022022-12-22T01:50:10ZengBMCBMC Microbiology1471-21802008-06-01819910.1186/1471-2180-8-99A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genesLin YePhetsom JirapaPfeiff JaniceWang LiSriariyanun MalineeSeo Young-SuJung Ki-HongChou Hui HsienBogdanove AdamRonald Pamela<p>Abstract</p> <p>Background</p> <p><it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>) and <it>X. oryzae </it>pv. <it>oryzicola </it>(<it>Xoc</it>) are bacterial pathogens of the worldwide staple and grass model, rice. <it>Xoo </it>and <it>Xoc </it>are closely related but <it>Xoo </it>invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and <it>Xoc </it>colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on <it>hrp </it>genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for <it>Xoo </it>and <it>Xoc </it>and compared gene expression in <it>Xoo </it>strains PXO99<sup>A </sup>and <it>Xoc </it>strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce <it>hrp </it>genes in <it>Xoo </it>strain T7174.</p> <p>Results</p> <p>Three biological replicates of the microarray experiment to compare global gene expression in representative strains of <it>Xoo </it>and <it>Xoc </it>grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of <it>Xoo </it>and 39 genes of <it>Xoc </it>were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for <it>Xoo </it>and <it>Xoc </it>selected for validation. The differentially expressed genes represent 17 functional categories.</p> <p>Conclusion</p> <p>We describe here the construction and validation of a two-genome microarray for the two pathovars of <it>X. oryzae</it>. Microarray analysis revealed that using representative strains, a greater number of <it>Xoo </it>genes than <it>Xoc </it>genes are differentially expressed in XOM2 relative to PSB, and that these include <it>hrp </it>genes and other genes important in interactions with rice. An exception was the <it>rax </it>genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.</p>http://www.biomedcentral.com/1471-2180/8/99 |
| spellingShingle | Lin Ye Phetsom Jirapa Pfeiff Janice Wang Li Sriariyanun Malinee Seo Young-Su Jung Ki-Hong Chou Hui Hsien Bogdanove Adam Ronald Pamela A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes BMC Microbiology |
| title | A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes |
| title_full | A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes |
| title_fullStr | A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes |
| title_full_unstemmed | A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes |
| title_short | A two-genome microarray for the rice pathogens <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>and <it>X. oryzae </it>pv. <it>oryzicola </it>and its use in the discovery of a difference in their regulation of <it>hrp </it>genes |
| title_sort | two genome microarray for the rice pathogens it xanthomonas oryzae it pv it oryzae it and it x oryzae it pv it oryzicola it and its use in the discovery of a difference in their regulation of it hrp it genes |
| url | http://www.biomedcentral.com/1471-2180/8/99 |
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