Do Global Regulators Hold the Key to Production of Bacterial Secondary Metabolites?

Abstract

The emergence of multiple antibiotic resistant bacteria has pushed the available pool of antibiotics to the brink. Bacterial secondary metabolites have long been a valuable resource in the development of antibiotics, and the genus Burkholderia has recently emerged as a source of novel compounds with antibacterial, antifungal, and anti-cancer activities. Genome mining has contributed to the identification of biosynthetic gene clusters, which encode enzymes that are responsible for synthesis of such secondary metabolites. Unfortunately, these large gene clusters generally remain silent or cryptic under normal laboratory settings, which creates a hurdle in identification and isolation of these compounds. Various strategies, such as changes in growth conditions and antibiotic stress, have been applied to elicit the expression of these cryptic gene clusters. Although a number of compounds have been isolated from different Burkholderia species, the mechanisms by which the corresponding gene clusters are regulated remain poorly understood. This review summarizes the activity of well characterized secondary metabolites from Burkholderia species and the role of local regulators in their synthesis, and it highlights recent evidence for the role of global regulators in controlling production of secondary metabolites. We suggest that targeting global regulators holds great promise for the awakening of cryptic gene clusters and for developing better strategies for discovery of novel antibiotics.

Keywords: Burkholderia; MftR; ScmR; antibiotics; biosynthetic gene clusters; gene regulation; global transcriptional regulator; secondary metabolites.

Figure 1

Chemical structures of selected secondary metabolites. Two-dimensional structures were obtained from PubChem (Malleilactone under the name Burkholderic Acid), except for Burkholdac B, which was obtained from ChEMBL (under the name Thailandepsin A) and Capistruin, for which the three-dimensional structure represents its conformation in complex with RNA polymerase (PDB ID 6N61). The complete amino acid sequence of Capistruin is GTPGFQTPDARVISRFGFN, where bold letters denote residues linked by a backbone-sidechain lactam linkage to form the cyclic structure through which the C-terminal residues are threaded. Images were rendered with PyMol. C, yellow; O, red; N, blue; H, grey; S, orange; Cl, green.

Figure 2

Organization of biosynthetic gene clusters. (A) Malleilactone. (B) Bactobolin. (C) Capistruin. (D) Thailandamide. (E) Burkholdacs. (F) Pyoverdine. (G) Ornibactin. (H) Thailanstatin. Genomic loci and individual gene annotations correspond to B. thailandensis E264 and are obtained from the Burkholderia Genome Database (https://www.burkholderia.com), except for the Ornibactin biosynthetic gene cluster (B. cenocepacia J2315; Burkholderia Genome Database [22]) and the Thailanstatin gene cluster (B. thailandensis MSMB43; NCBI GenBank JX307851.1).

Figure 3

Regulation of biosynthetic gene clusters by Major Facilitator Transport Regulator (MftR) and Secondary Metabolite Regulator (ScmR). Cluster-specific regulators, where known, are identified in green. Repression is shown as lines, and activation as arrows. Deletion of mftR or scmR results in the greatest upregulation of Bactobolin and Burkholdac, respectively, as indicated by heavier lines. ScmR-mediated activation of Pyoverdine biosynthetic genes is marginal (dotted line). For ScmR-mediated regulation of the Bactobolin biosynthetic gene cluster, direct repression of btaI2 was inferred, with BtaR2 reciprocally activating scmR.