Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression.
BACKGROUND
Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro.


RESULTS
To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).


CONCLUSIONS
The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods.
Han
Yanping
Y
State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, 20, Dongdajie, Fengtai, Beijing 100071, China. yanpinghan@gmail.com
Qiu
Jingfu
J
Guo
Zhaobiao
Z
Gao
He
H
Song
Yajun
Y
Zhou
Dongsheng
D
Yang
Ruifu
R
D001483:Base Sequence; D024202:Electrophoretic Mobility Shift Assay; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic; D037521:Virulence Factors / Q000235:genetics / Q000502:physiology; D015010:Yersinia pestis / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology
D037521:Virulence Factors