Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin

Engineered CRISPR-Cas9 for Streptomyces sp. genome editing to improve specialized metabolite production

The CRISPR-Cas9 system has frequently been used for genome editing in Streptomyces; however, cytotoxicity, caused by off-target cleavage, limits its application. In this study, we implement innovative modification to Cas9, strategically addressing challenges encountered during gene manipulation using Cas9 within strains possessing high GC content genome. The Cas9-BD, a modified Cas9 with the addition of polyaspartate to its N- and C-termini, is developed with decreased off-target binding and cytotoxicity compared with wild-type Cas9. Cas9-BD and similarly modified dCas9-BD have been successfully employed for simultaneous biosynthetic gene cluster (BGC) refactoring, multiple BGC deletions, or multiplexed gene expression modulations in Streptomyces. We also demonstrate improved secondary metabolite production using multiplexed genome editing with multiple single guide RNA libraries in several Streptomyces strains. Cas9-BD is also used to capture large BGCs using a developed in vivo cloning method. The modified CRISPR-Cas9 system is successfully applied to many Streptomyces sp., providing versatile and efficient genome editing tools for strain engineering of actinomycetes with high GC content genome.

Insights into the roles of exogenous phenylalanine and tyrosine in improving rapamycin production of Streptomyces rapamycinicus with transcriptome analysis

Rapamycin is an important natural macrolide antibiotic with antifungal, immunosuppressive and antitumor activities produced by Streptomyces rapamycinicus. However, their prospective applications are limited by low fermentation units. In this study, we found that the exogenous aromatic amino acids phenylalanine and tyrosine could effectively increase the yield of rapamycin in industrial microbial fermentation. To gain insight into the mechanism of rapamycin overproduction, comparative transcriptomic profiling was performed between media with and without phenylalanine and tyrosine addition. The results showed that the addition of phenylalanine and tyrosine upregulated the transcription levels of genes involved in rapamycin biosynthesis, precursor production, and transporters. In addition, the transcription levels of many carbohydrate metabolism-related genes were down-regulated, leading to a decrease in growth, suggesting that balancing cell growth and rapamycin biosynthesis may be important to promote efficient biosynthesis of rapamycin in Streptomyces rapamycinicus. These results provide a basis for understanding physiological roles of phenylalanine and tyrosine, and a new way to increase rapamycin production in Streptomyces cultures.

Identification and Application of Streptomyces rapamycinicus CQUSh011 against Potato Late Blight

Using chemical fungicides is the main strategy for controlling potato late blight (PLB), a devastating pre- and postharvest disease caused by Phytophthora infestans, resulting in environmental pollution and health risks. It is of great importance to develop a biofungicide from microorganisms. Through isolating potato rhizosphere microorganisms, CQUSh011 was found to have antioomycete activity with strong inhibition on vegetative growth and virulence of P. infestans. Morphological and molecular identification indicated that CQUSh011 belongs to Streptomyces rapamycinicus. Based on genome, metabolome, and HPLC quantification, rapamycin and salicylic acid were found to be the two active metabolites against P. infestans. Continuous field trials showed that CQUSh011 has sustainable control efficiency against PLB, and the efficiency was better when combined with Infinito, along with an increased endophytic microbial community and biodiversity in potato roots. The results demonstrated the potential of CQUSh011 as a biofungicide against PLB and provided an alternative strategy for reducing the application of chemical fungicides.

Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus

Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis to instruct rational strain improvement, using Streptomyces rimosus, the producer of the important antibiotic oxytetracycline (OTC) as a model system. Sequencing of the genomes of two industrial strains M4018 and R6-500, developed independently from a common ancestor, identified large DNA rearrangements located at the chromosome end. We evaluated the effect of these genome deletions on the parental S. rimosus Type Strain (ATCC 10970) genome where introduction of a 145 kb deletion close to the OTC BGC in the Type Strain resulted in massive OTC overproduction, achieving titers that were equivalent to M4018 and R6-500. Transcriptome data supported the hypothesis that the reason for such an increase in OTC biosynthesis was due to enhanced transcription of the OTC BGC and not due to enhanced substrate supply. We also observed changes in the expression of other cryptic BGCs; some metabolites, undetectable in ATCC 10970, were now produced at high titers. This study demonstrated for the first time that the main force behind BGC overexpression is genome rearrangement. This new approach demonstrates great potential to activate cryptic gene clusters of yet unexplored natural products of medical and industrial value.IMPORTANCEThere is a critical need to develop novel antibiotics to combat antimicrobial resistance. Streptomyces species are very rich source of antibiotics, typically encoding 20-60 biosynthetic gene clusters (BGCs). However, under laboratory conditions, most are either silent or poorly expressed so that their products are only detectable at nanogram quantities, which hampers drug development efforts. To address this subject, we used comparative genome analysis of industrial Streptomyces rimosus strains producing high titers of a broad spectrum antibiotic oxytetracycline (OTC), developed during decades of industrial strain improvement. Interestingly, large-scale chromosomal deletions were observed. Based on this information, we carried out targeted genome deletions in the native strain S. rimosus ATCC 10970, and we show that a targeted deletion in the vicinity of the OTC BGC significantly induced expression of the OTC BGC, as well as some other silent BGCs, thus suggesting that this approach may be a useful way to identify new natural products.