Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora

R. R. McNally, G. W. Sundin, I. K. Toth, P. J.A. Cock, P. E. Hedley, Youfu Zhao

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Microarrays represent a powerful tool for the rapid and comprehensive identification of differentially-regulated genes within a genome. We developed an oligo microarray for the annotated genes of the fire blight pathogen E. amylovora Ea273, including plasmids pEA29 and plasmid 2, and including additional genes from plasmids pEL60 and pEU30 found in related strains. The microarray was validated through analysis of differential gene expression of a wild-type and ?hrpL mutant of E. amylovora Ea1189. HrpL is the cognate sigma factor of hypersensitive and pathogenicity (hrp) promoters, and the goal of this work was to define the HrpL regulon of E. amylovora. Both Ea1189 and Ea1189?hrpL were cultured in hrpinducing minimal medium, and total RNA was isolated after 6 and 18 h incubation. Results revealed that 24 genes were significantly and differentially regulated in Ea1189?hrpL with fold-change expression ratios greater than 1.5. Our analysis uncovered 19 genes that may be directly or indirectly under the positive regulation of HrpL and 5 genes that were negatively-regulated. The type III secretion system (T3SS) pilus subunit gene hrpA exhibited the largest expression fold-change and is part of a group of HrpL-regulated genes unveiled in our analysis with known roles in T3SS including hrpN, hrpW, dspA/E, and eopB. In addition to T3SS genes, we also discovered HrpL-dependent regulation of EAM-2938, a new gene located outside of the T3SS pathogenicity island. To uncover new hrp promoters important for the direct HrpL-mediated positive regulation of genes like EAM-2938, the genome of E. amylovora Ea273 was examined using a hidden Markov model assembled from known Erwinia spp. hrp promoters using T-coffee multiple alignment software and HMMer 2.3.2. Preliminary bioinformatic results support the existence of a novel hrp promoter upstream of EAM-2938 as well as additional new hrp promoters that may help reveal the broader HrpL regulon.

Original languageEnglish (US)
Title of host publicationXII International Workshop on Fire Blight
PublisherInternational Society for Horticultural Science
Pages263-270
Number of pages8
ISBN (Print)9789066051171
DOIs
StatePublished - May 13 2011

Publication series

NameActa Horticulturae
Volume896
ISSN (Print)0567-7572

Fingerprint

regulon
Erwinia amylovora
type III secretion system
pathogens
genes
pathogenicity
promoter regions
plasmids
pathogenicity islands
sigma factors
Erwinia
genome
fimbriae
bioinformatics
RNA

Keywords

  • Alternate sigma factor
  • Hrp box
  • Type III secretion

ASJC Scopus subject areas

  • Horticulture

Cite this

McNally, R. R., Sundin, G. W., Toth, I. K., Cock, P. J. A., Hedley, P. E., & Zhao, Y. (2011). Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora. In XII International Workshop on Fire Blight (pp. 263-270). (Acta Horticulturae; Vol. 896). International Society for Horticultural Science. https://doi.org/10.17660/ActaHortic.2011.896.36

Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora. / McNally, R. R.; Sundin, G. W.; Toth, I. K.; Cock, P. J.A.; Hedley, P. E.; Zhao, Youfu.

XII International Workshop on Fire Blight. International Society for Horticultural Science, 2011. p. 263-270 (Acta Horticulturae; Vol. 896).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

McNally, RR, Sundin, GW, Toth, IK, Cock, PJA, Hedley, PE & Zhao, Y 2011, Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora. in XII International Workshop on Fire Blight. Acta Horticulturae, vol. 896, International Society for Horticultural Science, pp. 263-270. https://doi.org/10.17660/ActaHortic.2011.896.36
McNally RR, Sundin GW, Toth IK, Cock PJA, Hedley PE, Zhao Y. Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora. In XII International Workshop on Fire Blight. International Society for Horticultural Science. 2011. p. 263-270. (Acta Horticulturae). https://doi.org/10.17660/ActaHortic.2011.896.36
McNally, R. R. ; Sundin, G. W. ; Toth, I. K. ; Cock, P. J.A. ; Hedley, P. E. ; Zhao, Youfu. / Microarray characterization of the hrpl regulon of the fire blight pathogen Erwinia amylovora. XII International Workshop on Fire Blight. International Society for Horticultural Science, 2011. pp. 263-270 (Acta Horticulturae).
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abstract = "Microarrays represent a powerful tool for the rapid and comprehensive identification of differentially-regulated genes within a genome. We developed an oligo microarray for the annotated genes of the fire blight pathogen E. amylovora Ea273, including plasmids pEA29 and plasmid 2, and including additional genes from plasmids pEL60 and pEU30 found in related strains. The microarray was validated through analysis of differential gene expression of a wild-type and ?hrpL mutant of E. amylovora Ea1189. HrpL is the cognate sigma factor of hypersensitive and pathogenicity (hrp) promoters, and the goal of this work was to define the HrpL regulon of E. amylovora. Both Ea1189 and Ea1189?hrpL were cultured in hrpinducing minimal medium, and total RNA was isolated after 6 and 18 h incubation. Results revealed that 24 genes were significantly and differentially regulated in Ea1189?hrpL with fold-change expression ratios greater than 1.5. Our analysis uncovered 19 genes that may be directly or indirectly under the positive regulation of HrpL and 5 genes that were negatively-regulated. The type III secretion system (T3SS) pilus subunit gene hrpA exhibited the largest expression fold-change and is part of a group of HrpL-regulated genes unveiled in our analysis with known roles in T3SS including hrpN, hrpW, dspA/E, and eopB. In addition to T3SS genes, we also discovered HrpL-dependent regulation of EAM-2938, a new gene located outside of the T3SS pathogenicity island. To uncover new hrp promoters important for the direct HrpL-mediated positive regulation of genes like EAM-2938, the genome of E. amylovora Ea273 was examined using a hidden Markov model assembled from known Erwinia spp. hrp promoters using T-coffee multiple alignment software and HMMer 2.3.2. Preliminary bioinformatic results support the existence of a novel hrp promoter upstream of EAM-2938 as well as additional new hrp promoters that may help reveal the broader HrpL regulon.",
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