The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

Abstract

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.

Proteomic Analysis of the Burkholderia pseudomallei Type II Secretome Reveals Hydrolytic Enzymes, Novel Proteins, and the Deubiquitinase TssM

“…teins) or in minimal medium (9 proteins), which likely reflects gene expression differences of the exported products under these distinct growth conditions (42). Taken together, the results show that the MSHR668 T2SS secretome in rich and minimal media is composed of 48 distinct proteins with an array of putative enzymatic activities.…”

Cross-Species Comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei Quorum-Sensing Regulons

“…Two groups identified QS-1-controlled factors in different B. pseudomallei isolates (Bp008 and PP844) (49,50), and a third group used microarrays to study yet another B. pseudomallei strain (K96243) (unpublished data, available at http://www.melioidosis .info/about.aspx). Nearly half, 97, of the 216 B. pseudomallei QScontrolled genes we identified were also identified in other studies.…”

Immunisation with proteins expressed during chronic murine melioidosis provides enhanced protection against disease

“…The level of expression of these genes was measured relative to two housekeeping genes (aceA and gltB), in RNA isolated from spleen or lung tissues taken from chronically infected mice. We selected these housekeeping genes because we had previously shown that they were not differentially regulated in bacteria taken from acutely infected mice, compared to bacteria grown in broth cultures [18]. Using RNA isolated from chronically infected spleens, the relative levels of expression of the chronic stage antigen genes were similar when compared to the level of expression either aceA or gltB.…”

“…pseudomallei transcriptional profiles from in vitro conditions thought to reflect the environment inside a granuloma were obtained [18]. Transcriptome data was referenced to the transcriptome profile of B. pseudomallei grown in LB broth at 37 • C. Transcriptional responses from B. pseudomallei grown in low pH, peroxide, low oxygen and low nutrient (water) were interfaced and evaluated, and genes that were upregulated in at least three of the four granuloma mimicking conditions were selected.…”

“…Recently, the B. pseudomallei transcriptional response to a range of in vitro conditions reflecting the diversity of niches occupied by the bacterium was reported [18]. Evaluation of the transcriptional response of B. pseudomallei in conditions mimicking the environment inside the granuloma, including hypoxia and nutrient starvation, has provided clues to the repertoire of antigens expressed by the pathogen as it adapts to long-term persistence in the host.…”