The condition-dependent transcriptional landscape of Burkholderia pseudomallei.
Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes--Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes--quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an "accidental pathogen", where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.
Genome Institute of Singapore, Singapore, Republic of Singapore.
Wen Fong
WF
Ooi
Catherine
C
Ong
Tannistha
T
Nandi
Jason F
JF
Kreisberg
Hui Hoon
HH
Chua
Guangwen
G
Sun
Yahua
Y
Chen
Claudia
C
Mueller
Laura
L
Conejero
Majid
M
Eshaghi
Roy Moh Lik
RM
Ang
Jianhua
J
Liu
Bruno W
BW
Sobral
Sunee
S
Korbsrisate
Yunn Hwen
YH
Gan
Richard W
RW
Titball
Gregory J
GJ
Bancroft
Eric
E
Valade
Patrick
P
Tan
D016957:Burkholderia pseudomallei / Q000235:genetics* / Q000472:pathogenicity; D002875:Chromosomes / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006790:Host-Parasite Interactions / Q000235:genetics*; D006801:Humans; D008554:Melioidosis / Q000235:genetics* / Q000382:microbiology / Q000473:pathology; D014158:Transcription, Genetic; D014774:Virulence / Q000235:genetics