Identify promoters and ECF sigma factors that control expression of known and suspected virulence factors in Pseudomonas syringae.
Characterize the subset of the transcriptome related to growth in defined medium, induction of virulence factors, and response to iron bioavailability
Elucidate mechanisms leading to iron-dependent expression of operons encoding virulence factors and regulators.
This research employs an interdisciplinary approach involving computational biology and laboratory methods for high-throughput functional
genomics and genetics. Expression studies including the use of microarrays and high-throughput reporter screens are being used to
characterize the components and behavior of virulence-related pathways, especially those related to iron homeostasis.
Chris Myers - Computational Biology Service Unit, Cornell University
Filiatrault et al, 2011. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.. PMID: 22216251
Markel et al, 2011. An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. PMID: 21840980
Butcher et al, 2011. Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. PMID: 21784947
Filiatrault et al, 2010. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity. PMID: 20190049
Associated changes to the Pto DC3000 annotation record:
/experiment ="RNA sequencing"
denotes loci coinciding with sequenced transcripts
denotes loci coinciding with sequenced peptides
/inference="ab initio prediction:Easygene 1.2"
denotes locus predictions made by Easygene
/note="see PMID:20190049 for expression data"
denotes source publication for inference and experiment data
/product="protein of unknown function"
denotes previously hypothetical proteins for which expression has been confirmed
/product="conserved protein of unknown function"
denotes previously conserved hypothetical proteins for which expression has been confirmed
Swingle et al, 2008. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals
regulon members and insights regarding PvdS function in other pseudomonads. PMID: 18363796
PvdS box models (gff format, readable with Artemis) for pseudomonads with available genome sequences Go to View genomes in Artemis for instructions on viewing sequences of a specified accession number in Artemis