Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264

Abstract

Bacteria produce a diverse array of secondary metabolites that have been invaluable in the clinic and in research. These metabolites are synthesized by dedicated biosynthetic gene clusters (BGCs), which assemble architecturally complex molecules from simple building blocks. The majority of BGCs in a given bacterium are not expressed under normal laboratory growth conditions, and our understanding of how they are silenced is in its infancy. Here, we have addressed this question in the Gram-negative model bacterium Burkholderia thailandensis E264 using genetic, transcriptomic, metabolomic, and chemical approaches. We report that a previously unknown, quorum-sensing-controlled LysR-type transcriptional regulator, which we name ScmR (for secondary metabolite regulator), serves as a global gatekeeper of secondary metabolism and a repressor of numerous BGCs. Transcriptionally, we find that 13 of the 20 BGCs in B. thailandensis are significantly (threefold or more) upor down-regulated in a scmR deletion mutant (ΔscmR). Metabolically, the ΔscmR strain displays a hyperactive phenotype relative to wild type and overproduces a number of compound families by 18-to 210-fold, including the silent virulence factor malleilactone. Accordingly, the ΔscmR mutant is hypervirulent both in vitro and in a Caenorhabditis elegans model in vivo. Aside from secondary metabolism, ScmR also represses biofilm formation and transcriptionally activates ATP synthesis and stress response. Collectively, our data suggest that ScmR is a pleiotropic regulator of secondary metabolism, virulence, biofilm formation, and other stationary phase processes. A model for how the interplay of ScmR with pathwayspecific transcriptional regulators coordinately silences virulence factor production is proposed.biosynthetic gene clusters | natural products | Burkholderia thailandensis | regulation | virulence

Regulator LdhR and d -Lactate Dehydrogenase LdhA of Burkholderia multivorans Play Roles in Carbon Overflow and in Planktonic Cellular Aggregate Formation

“…Nevertheless, ldhA expression was increased when ldhR was overexpressed in the WT strain, giving additional support to the hypothesis that the ldhR and ldhA genes are in a polycistronic operon and confirming the direct or indirect involvement of the LdhR regulator in ldhA expression. Transcription data from B. thailandensis E264 show a 4.8-fold decreased expression of the ldhA gene when the upstream gene scmR was deleted (21), also supporting our observations in B. multivorans ATCC 17616.…”

“…2B). A comparison of the region upstream of ldhR with that of the characterized homolog scmR from Burkholderia thailandensis E264, whose expression is known to be induced by quorum sensing and has a lux-box (21), showed the absence of such a conserved region in B. multivorans (Fig. 2B).…”

“…A study of the sigma factor RpoH1 in the regulation of Sinorhizobium meliloti genes upon pH stress also identified the differential expression of several RpoH1-dependent genes, including the upregulation of genes encoding heat shock proteins, such as IbpA, GrpE, GroEL5, and Hsp20, and proteases, such as ClpA, ClpB, ClpS1, ClpP2, ClpX, DegP1, Lon, and HslV, as well as the downregulation of genes involved in translation and nitrogen metabolism, such as NarB, NirB, NirD, and GlnK (25). The upregulation of stress response genes in the WT B. thailandensis E264 is attributed to the adaptation to stationary-phase growth (21). Yet, it cannot be excluded that this induction of stress response gene expression might result from the presence of high concentrations of toxic secondary metabolites in the culture medium.…”

Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis

“…In B. ambifaria , inactivation of genes within this cluster resulted in increased AHL production, while the opposite was reported on inactivation of a structural gene in B. pseudomallei , reflecting a complex QS network. 12, 13 ScmR was reported to activate expression of genes encoding HMAQs; 7 the increased expression of the hmaq gene cluster in mftRΔ may therefore be a consequence of increased scmR expression.…”

“…In B. thailandensis , QS has been implicated in controlling expression of ScmR, a LysR-family transcription factor that in turn regulates expression of several biosynthetic gene clusters. 7 B. thailandensis and B. pseudomallei each encode three AHL-based QS systems, of which two are conserved in B. mallei . 8–10 In addition, two orphan LuxR homologs that lack a cognate LuxI have been identified in B. thailandensis , BtaR4 (also named MalR) and BtaR5.…”