DeoR regulates lincomycin production in Streptomyces lincolnensis

Application of multiple genomic-editing technologies in Streptomyces fungicidicus for improved enduracidin yield

Streptomyces fungicidicus, an industrial strain for enduracidin production, shows significant potential as a cellular chassis for the synthesis of novel small peptides. Targeted deletion of secondary metabolite gene clusters offers a promising strategy to enhance strain performance, but is often hampered by the lack of efficient gene editing tools. In this study, we optimized the traditional homologous recombination method by integrating selection and counter-selection markers to streamline the gene editing process, and successfully deleted gene clusters of up to 54.4 kb. Recognizing the significant potential of CRISPR/Cas-based systems in Streptomyces, we evaluated the base editing efficiency of the CRISPR/cBEST system in S. fungicidicus, which enabled stop codon insertions in the targeted gene with different mutation rates depending on the applied sgRNA. Additionally, we established a CRISPR/Cas9 system in S. fungicidicus while incorporating a counter-selection marker for efficient screening, which greatly shortened the gene editing cycle. The resulting mutants with single and cumulative gene cluster deletions exhibited improved growth characteristics, including a prolonged logarithmic phase and increased biomass. Although cumulative deletions did not result in consistent yield improvements, the mutants with improved growth characteristics show potential for further strain optimization in the future. The optimized gene editing systems developed in this study provide a valuable foundation for engineering other Streptomyces species.

The protocatechuic acid catabolism regulator PcaV inhibits lincomycin biosynthesis either directly or indirectly through the control of the expression of other regulatory or metabolic genes

Lincomycin, synthesized by Streptomyces lincolnensis, is extensively utilized in clinical settings to treat infections caused by Gram-positive pathogenic bacteria. Understanding the regulatory mechanism of lincomycin biosynthesis is crucial for improving its production. This study identified PcaV, a conserved regulator of protocatechuic acid catabolic genes, as a repressor of lincomycin biosynthesis. Knocking out the pcaV gene enhanced lincomycin production by up to 9.8-fold, and slowed cellular growth. Quantitative real-time PCR and electrophoretic mobility shift assays reconfirmed that PcaV binds to two 12-bp sites within a bidirectional promoter, repressing the expression of the pcaV gene and the pcaIJFHGBL operon. The pcaIJFHGBL operon, in turn, promoted lincomycin biosynthesis. Besides, PcaV directly represses the expression of lmbA, lmbV, lmbW, lmrA, and lmrC from the lincomycin biosynthesis gene cluster, thereby inhibiting lincomycin biosynthesis. It also directly activates the expression of adpA, aflQ1, bldD, glnR, lcbR1, and ramR, known regulators of lincomycin biosynthesis. Additionally, PcaV influences the expression of genes related to phosphorus metabolism, the shikimate pathway, sulfur metabolism, protocatechuic acid anabolism, amino acid metabolism, and nitrogen metabolism, indirectly impacting lincomycin production. This study thus broadens PcaV's regulon and redefines it as a novel pleiotropic regulator and a promising target for engineering antibiotic-producing strains.

SbhR, a DeoR family regulator, modulates secondary metabolism via the atypical two-component system AtcK/R in Streptomyces bingchenggensis

DeoR family transcriptional regulators are widely distributed in Streptomyces genomes, but their precise functions and regulatory mechanisms in secondary metabolite biosynthesis remain poorly understood. In Streptomyces bingchenggensis, an industrial producer of milbemycins and nanchangmycin, we identified the DeoR-type regulator SbhR as a key regulator of the atypical two-component system AtcK/R. CRISPR interference-mediated inhibition of sbhR significantly decreased milbemycin production but enhanced nanchangmycin production. SbhR was shown to activate atcK expression, thereby initiating the AtcK/R-KelR cascade that regulates both milbemycin and nanchangmycin biosynthesis. In strains with inhibited sbhR or atcK, AtcR was found to exert a positive effect on nanchangmycin production, in contrast to its inhibitory role observed in BC04. Through integrated overexpression of atcR and the cluster-situated activators nanR1 and nanR2 in sbhR- and atcK-repressed strains, nanchangmycin production was enhanced from 1060 mg/L to 8812 mg/L and 9675 mg/L, respectively, and the fermentation time required to reach maximum titer was reduced from 9 to 6 days. Cross-species genetic analyses further demonstrated that SbhR functions as a global regulatory switch for secondary metabolism in Streptomyces species. These results expand our understanding of the regulatory networks governing secondary metabolism and provide novel strategies for enhancing the yield of valuable metabolites in Streptomyces.

MarR family regulator LcbR2 activates lincomycin biosynthesis in multiple ways

Lincomycin, produced by the actinomycete Streptomyces lincolnensis, is highly effective against Gram-positive bacteria and protozoans, making it widely used in clinical settings. This study identified LcbR2, a MarR family transcriptional regulator, as an activator of lincomycin biosynthesis. Knocking out the lcbR2 gene reduced lincomycin production by 63.0 % without affecting growth or morphology. Quantitative real-time PCR, electrophoretic mobility shift assays, and XylE reporter assays demonstrated that LcbR2 binds to a 13-bp imperfect palindromic sequence -TTGCCnnnnnCAA-, repressing the expression of lcbR2 Further analysis revealed that LcbR2 directly activates the expression of lincomycin biosynthesis genes (lmbD, lmbJ, lmbK, lmbV, and lmbW), enhancing lincomycin production. It also regulates lincomycin resistance genes (lmrA and lmrB), increasing the self-tolerance of S. lincolnensis to lincomycin. Additionally, LcbR2 modulates other regulatory genes (lmbU, adpA, aflQ1, bldD, and lcbR1), affecting lincomycin production in a cascade manner. LcbR2 also influences the expression of genes related to carbon, nitrogen, phosphorus, and sulfur metabolism, indirectly impacting lincomycin production. Moreover, the binding of LcbR2 to DNA can be attenuated by apramycin. This study thus characterized LcbR2 as a novel transcriptional regulator with a broad regulatory scope.

The DeoR-like pleiotropic regulator SCO1897 controls specialised metabolism, sporulation, spore germination, and phosphorus accumulation in Streptomyces coelicolor

Streptomycetes are bacteria of significant biotechnological interest due to their production of bioactive specialised metabolites used in medicine and agriculture. In these bacteria, specialised metabolism and morphological differentiation are linked and typically repressed under high phosphate conditions. This study characterises a DeoR-like transcriptional regulator, SCO1897, in Streptomyces coelicolor, whose expression increases during sporulation. Disruption of sco1897 results in reduced biosynthesis of specialised metabolites, delayed sporulation, higher spore phosphate content, and impaired germination. Transcriptomic analysis revealed 1420 genes differentially expressed in the sco1897 mutant compared to the S. coelicolor wild-type strain. The sco1897 gene is located upstream and transcribed in the same direction as six genes, including sco1898-1900 encoding sub-units of an ABC transporter annotated as involved in carbohydrate transport. SCO1897 negatively regulates its own expression, that of the sco1898-1900 ABC transporter, and sco4142, encoding the PstS phosphate-binding protein. The overexpression of sco1898-1900 in the S. coelicolor wild-type strain leads to a significant increase in intracellular spore phosphate levels, similar to those observed in the sco1897 mutant. These findings suggest a complex regulatory network involving the sco1897-sco1900 region. Hypotheses are proposed to explain the various phenotypes of the sco1897 mutant and the complex regulation of the genes of the sco1897-sco1900 region.

Transcriptional regulators of secondary metabolite biosynthesis in Streptomyces

In the post-genome era, great progress has been made in metabolic engineering using recombinant DNA technology to enhance the production of high-value products by Streptomyces. With the development of microbial genome sequencing techniques and bioinformatic tools, a growing number of secondary metabolite (SM) biosynthetic gene clusters in Streptomyces and their biosynthetic logics have been uncovered and elucidated. In order to increase our knowledge about transcriptional regulators in SM of Streptomyces, this review firstly makes a comprehensive summary of the characterized factors involved in enhancing SM production and awakening SM biosynthesis. Future perspectives on transcriptional regulator engineering for new SM biosynthesis by Streptomyces are also provided.