β-carboline chemical signals induce reveromycin production through a LuxR family regulator in Streptomyces sp. SN-593

Abstract

Actinomycetes bacteria produce diverse bioactive molecules that are useful as drug seeds. to improve their yield, researchers often optimize the fermentation medium. However, exactly how the extracellular chemicals present in the medium activate secondary metabolite gene clusters remains unresolved. BR-1, a β-carboline compound, was recently identified as a chemical signal that enhanced reveromycin A production in Streptomyces sp. SN-593. Here we show that BR-1 specifically bound to the transcriptional regulator protein RevU in the reveromycin A biosynthetic gene cluster, and enhanced RevU binding to its promoter. RevU belongs to the LuxR family regulator that is widely found in bacteria. Interestingly, BR-1 and its derivatives also enhanced the production of secondary metabolites in other Streptomyces species. Although LuxR-N-acyl homoserine lactone systems have been characterized in Gram-negative bacteria, we revealed LuxR-β-carboline system in Streptomyces sp. SN-593 for the production of secondary metabolites. This study might aid in understanding hidden chemical communication by β-carbolines. Microorganisms utilize a variety of communication systems that enable them to send and receive chemical signals to one another 1. Quorum sensing is one cell-cell communication mechanism. Gram-negative bacteria produce hormone-like signals, such as the release of acyl-homoserine lactones, to control cellular responses 2,3. Streptomyces, a soil-dwelling gram-positive bacteria, utilize autoregulatory hormones to produce a variety of secondary metabolites (SMs) 4. The classical example of such hormone is A-factor in Streptomyces griseus 5 , and the structurally diverse autoregulators such as 2-alkyl-4-hydroxymethylfuran-3-carboxylic acids in Streptomyces coelicolor 6 , PI factor in Streptomyces natalensis 7 , avenolide in Streptomyces avermitilis 8 , VB-A in Streptomyces virginiae 9 , IM-2 in Streptomyces sp. FRI-5 10 , SCB1 in Streptomyces coelicolor 11 , and SRB1 in Streptomyces rochei 12 are also known to promote morphological development and regulating secondary metabolism. These have been extensively reviewed elsewhere 13-15. On the other hand, chemical signals derived from extra-species/environmental stimuli such as hormaomycin 16 , goadsporin 17 , promomycin 18 , antibiotic-remodeling compounds (ARCs) 19 , and rare earth elements 20 also induce morphogenesis and SM production in Streptomyces species at higher concentration range compared to autoregulators. Co-culturing Streptomyces with mycolic acid-containing bacteria was found to also induce SM production 21. Except for some ARCs, which inhibit fatty acid biosynthesis, the mechanisms of how extracellular chemical signals activate SM biosynthesis have not been clarified. Reveromycin (RM) A was identified from Streptomyces sp. SN-593 as an inhibitor of the mitogenic activity of epidermal growth factor 22. It also inhibits bone resorption specifically in osteoclast 23. The RM biosynthetic gene cluster consists of 21 genes, including three transcriptional regulators 24...

Comparative genomic and functional analysis of Arthrobacter sp. UMCV2 reveals the presence of luxR-related genes inducible by the biocompound N, N-dimethylhexadecilamine

“…Aliivibrio fischeri LuxR ( Fuqua et al, 1994 ) and Pseudomonas sp. GM79 PipR ( Coutinho et al, 2018 ) were included in the analysis as references for canonical experimentally characterized LuxR proteins, Streptomyces purpurogeneiscleroticus NRRL B-2952 LuxR ( Rajput and Kumar, 2017 ) as a canonical in silico characterized LuxR protein from actinobacteria, and Streptomyces SN-593 RevU ( Panthee et al, 2020 ) as an experimentally characterized LuxR-related protein from actinobacteria. All four reference proteins presented a characteristic DNA-binding domain at the C-terminal end (IPR000792).…”

Dihydromaniwamycin E, a Heat-Shock Metabolite from Thermotolerant Streptomyces sp. JA74, Exhibiting Antiviral Activity against Influenza and SARS-CoV-2 Viruses

“…Several methods have been developed to activate these SMBGCs in actinomycete strains. For instance, chemical elicitors that activate secondary metabolism have been identified from libraries of chemical compounds . Alternatively, genetic-engineering-based strategies, such as heterologous expression and cluster-situated regulator engineering, also have been used to obtain novel secondary metabolites.…”

“…For instance, chemical elicitors that activate secondary metabolism have been identified from libraries of chemical compounds. 7 Alternatively, genetic-engineering-based strategies, such as heterologous expression 8 and cluster-situated regulator engineering, 9 also have been used to obtain novel secondary metabolites. In one example, the coculture of a pathogenic actinomycete with mouse macrophage-like cells was reported to activate secondary metabolism.…”

Dihydrolucilactaene, a Potent Antimalarial Compound from Fusarium sp. RK97-94

“…SN-593. 19,20 This approach can be easily employed in any microbial culture, does not require genetic manipulation, and is readily scalable to high-throughput, all of which are advantages over the genetic approach. As a part of our fungal secondary metabolism activation project, our group recently identified NPD938 (Figure S1) as a fungal secondary metabolism inducer via elicitor screening of a pilot library, which contains 376 small molecules [representing the chemical space of approximately 40 000 compounds available in the RIKEN Natural Products Depository (NPDepo) at RIKEN].…”

“…Another example of chemical elicitation is the use of a β-carboline compound (BR-1), which successfully induced reveromycin production in Streptomyces sp. SN-593. , This approach can be easily employed in any microbial culture, does not require genetic manipulation, and is readily scalable to high-throughput, all of which are advantages over the genetic approach.…”