Characterization of plasmid pXL100 fromAmycolatopsis orientalisHCCB10007 and construction of a shuttle vector

High-Yield Natural Vanillin Production by Amycolatopsis sp. after CRISPR-Cas12a-Mediated Gene Deletion

Vanillin is an aromatic compound, which is widely used in food flavoring, beverages, perfumes, and pharmaceuticals. Amycolatopsis sp. is considered a good strain for the production of vanillin from ferulic acid by fermentation; however, its high genomic guanine-cytosine (GC) content (>70%) and low transformation and recombination efficiency limit its genetic modification potential to improve vanillin production. Efficient genome editing of Amycolatopsis sp. has been challenging, but this study developed a CRISPR-Cas12a system for efficient, markerless, and scarless genome editing of Amycolatopsis sp. CCTCC NO: M2011265. A mutant, ΔvdhΔphdB, was obtained by the deletion of two genes coding byproduct enzymes from the vanillin biosynthetic pathway. The gene deletion increased vanillin production from 10.60 g/L (wild-type) to 20.44 g/L and reduced byproduct vanillic acid from 2.45 to 0.15 g/L in a 3 L fed-batch fermentation, markedly enhancing vanillin production and reducing byproduct formation; the mutant has great potential for industrial application.

CRISPR/Cas9-mediated genome editing in vancomycin-producing strain Amycolatopsis keratiniphila

Amycolatopsis is an important source of diverse valuable bioactive natural products. The CRISPR/Cas-mediated gene editing tool has been established in some Amycolatopsis species and has accomplished the deletion of single gene or two genes. The goal of this study was to develop a high-efficient CRISPR/Cas9-mediated genome editing system in vancomycin-producing strain A. keratiniphila HCCB10007 and enhance the production of vancomycin by deleting the large fragments of ECO-0501 BGC. By adopting the promoters of gapdhp and ermE*p which drove the expressions of scocas9 and sgRNA, respectively, the all-in-one editing plasmid by homology-directed repair (HDR) precisely deleted the single gene gtfD and inserted the gene eGFP with the efficiency of 100%. Furthermore, The CRISPR/Cas9-mediated editing system successfully deleted the large fragments of cds13-17 (7.7 kb), cds23 (12.7 kb) and cds22-23 (21.2 kb) in ECO-0501 biosynthetic gene cluster (BGC) with high efficiencies of 81%-97% by selecting the sgRNAs with a suitable PAM sequence. Finally, a larger fragment of cds4-27 (87.5 kb) in ECO-0501 BGC was deleted by a dual-sgRNA strategy. The deletion of the ECO-0501 BGCs revealed a noticeable improvement of vancomycin production, and the mutants, which were deleted the ECO-0501 BGCs of cds13-17, cds22-23 and cds4-27, all achieved a 30%-40% increase in vancomycin yield. Therefore, the successful construction of the CRISPR/Cas9-mediated genome editing system and its application in large fragment deletion in A. keratiniphila HCCB10007 might provide a powerful tool for other Amycolatopsis species.

Marker-Free Genome Engineering in Amycolatopsis Using the pSAM2 Site-Specific Recombination System

Actinobacteria of the genus Amycolatopsis are important for antibiotic production and other valuable biotechnological applications such as bioconversion or bioremediation. Despite their importance, tools and methods for their genetic manipulation are less developed than in other actinobacteria such as Streptomyces. We report here the use of the pSAM2 site-specific recombination system to delete antibiotic resistance cassettes used in gene replacement experiments or to create large genomic deletions. For this purpose, we constructed a shuttle vector, replicating in Escherichia coli and Amycolatopsis, expressing the integrase and the excisionase from the Streptomyces integrative and conjugative element pSAM2. These proteins are sufficient for site-specific recombination between the attachment sites attL and attR. We also constructed two plasmids, replicative in E. coli but not in Amycolatopsis, for the integration of the attL and attR sites on each side of a large region targeted for deletion. We exemplified the use of these tools in Amycolatopsis mediterranei by obtaining with high efficiency a marker-free deletion of one single gene in the rifamycin biosynthetic gene cluster or of the entire 90-kb cluster. These robust and simple tools enrich the toolbox for genome engineering in Amycolatopsis.

Strategy for Producing the High-Quality Glycopeptide Antibiotic A82846B in Amycolatopsis orientalis Based on the CRISPR-Cas12a System

Oritavancin is a new-generation semisynthetic lipoglycopeptide antibiotic used to prevent the spread of vancomycin-resistant Gram-positive bacteria. The glycopeptide A82846B is the direct precursor of oritavancin. Considering the structural similarity between A82846B and vancomycin, the vancomycin producer Amycolatopsis orientalis was used as a chassis for the construction of a strain producing high-quality A82846B. To construct the A82846B synthetic pathway, we established a highly efficient CRISPR-Cas12a system by optimizing the conditions of conjugation and by screening the regulatory elements in the A. orientalis, which is difficult to be genetically manipulated. The efficiency of gene knockout was almost 100%. The glycosyltransferases module (gtfDE) and glycosyl synthesis module (vcaAEBD) in the vancomycin gene cluster were replaced with the corresponding glycosyltransferases module (gtfABC) and glycosyl synthesis module (evaAEBD) in the A82846B cluster, respectively. A82846B was successfully produced by the artificially constructed synthetic pathway. Moreover, the titer of A82846B was increased 80% by expressing the pathway-specific regulatory strR. This strategy has excellent potential for remodification of natural products to solve antibiotic resistance.

Role of two 5-aminolevulinic acid biosynthetic pathways in heme and secondary metabolite biosynthesis in Amycolatopsis orientalis

Analysis of the Amycolatopsis orientalis genome revealed that two genes, hemA1 and hemA2, belonging to divergent pathways, were involved in the biosynthesis of 5-aminolevulinic acid. The roles of hemA1 and hemA2 were elucidated via genetic manipulation and metabolite analysis. The disruption of hemA1, encoding the glutamyl-tRNA^Glu reductase of the C₅ pathway, was essential for cell growth and is used for heme synthesis. Overexpression of hemA1 resulted in elevated vancomycin and ECO-0501 production in Amycolatopsis orientalis, and it was also effective in increasing the production of daptomycin and natamycin in other Streptomycetes. The disruption of hemA2 indicated that it encodes the 5-aminolevulinic acid synthase of the Shemin pathway, serving as a key enzyme for the synthesis of the precursor aminohydroxycyclopentenone unit of ECO-0501. However, hemA2 disruption could not be complemented by the addition of 5-aminolevulinic acid or by the expression of hemA2 outside of the ECO-0501 gene cluster. The synthesis of ECO-0501 was only restored by the insertion of hemA2 at its original locus. The hemA2 gene could partly complement the hemA1 deficiency. Overexpression of hemA1, a key gene from the heme biosynthetic pathway, is proposed here as a new approach to improve the production of secondary metabolites in bacteria, whereas hemA2 plays different roles depending on its pattern of expression.

Complete genome sequence of Amycolatopsis orientalis CPCC200066, the producer of norvancomycin

Amycolatopsis orientalis CPCC200066 is an actinomycete exploited commercially in China for the production of norvancomycin, an important glycopeptide antibiotic structurally close to the well-known vancomycin. The availability of the complete genome sequence of CPCC200066 would greatly strengthen our understanding of the regulation pattern of norvancomycin biosynthesis and ultimately improve its production, as well as potentiate discoveries of novel bioactive compounds. Here we report the complete genome sequence of A. orientalis CPCC200066, a circular chromosome consisting of 9,490,992bp. Forty putative secondary metabolite biosynthetic gene clusters, including norvancomycin, were predicted, covering 20.3% of the whole genome. To facilitate genetic manipulation of this strain, an efficient transformation system was established by constructing a novel integrative vector pIMBT1, which could be transferred into CPCC200066 by electroporation with high efficiency. ΦBT1 attB sites were also identified in other known Amycolatopsis genomes, indicating pIMBT1's prospect to be a novel vector for genus Amycolatopsis.

Genetics and Genomics of the Genus Amycolatopsis

Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies.