Whole-genome sequencing and sequence analysis of Streptomyces anulatus 89-2-2

Abstract:

[Background] Streptomyces anulatus 89-2-2, a moderately halophilic actinomycete strain, can produce secondary metabolites capable of inhibiting the tyrosinase activity in mushrooms and the melanin synthesis and tyrosinase activity in mouse melanoma B16 cells. Few studies report the genome sequence of S.anulatus 89-2-2, which limits the studies on the biosynthesis and regulation of tyrosinase inhibitors, melanin synthesis inhibitors and other secondary metabolites in the strain. [Objective] This study sequenced the genome of S.anulatus 89-2-2 and mined the genetic resources of secondary metabolites, aiming to lay a foundation for deciphering the mechanisms of tyrosinase inhibitor production and biosynthesis regulation in this strain. [Methods] Nanopore sequencing platform was used to uncover the genome sequence of S. anulatus 89-2-2. Bioinformatics tools were used for sequence assembly, gene prediction, functional annotation, phylogenetic analysis, synteny analysis, and prediction of the gene clusters for biosynthesis of secondary metabolites. The genomes of different Streptomyces spp. were compared, and the secondary metabolic potential and the evolutionary relationship of different Streptomyces spp. were studied. [Results] The genome of strain 89-2-2 was a single linear chromosome with a length of 8 117 999 bp and the G+C content of 71.52%. The sequence has been submitted to the GenBank of the NCBI, with the accession number CP137002. The genome of the strain contained 7 088 coding sequences. The annotation against COG, GO, KEGG, and NR predicted 5 300, 4 176, 2 513, and 7 013 genes, respectively. The antiSMASH predicted 34 gene clusters for the biosynthesis of secondary metabolites in the genome of 89-2-2, and these gene clusters were involved in the biosynthesis of a variety of natural products, such as terpenoids, non-ribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides. Eleven clusters showed low similarities to the gene clusters for the biosynthesis of known compounds, which suggested that strain 89-2-2 had the potential to produce a variety of novel secondary metabolites. The genome of S.anulatus 89-2-2 presented high synteny with that of Streptomyces sp. AM2-1-1, which indicated their high homology. It showed large inversions compared with that of S.microflavus DSM40593, which suggested their low homology. Strain 89-2-2 had 51 specific gene families and 1 235 specific genes. The results indicated that Streptomyces spp. had strong ability to adapt to diverse environments, and partial fluctuations in the genomes occurred between species during the long-term adaptation. Further studies remain to be carried out to reveal the relationship between specific genes and adaptability of strain 89-2-2 to different environments. [Conclusion] This study analyzed the whole-genome sequence of S.anulatus 89-2-2, laying a foundation for further studies about the strain in terms of the association between the tyrosinase-inhibiting activity and the genome, the structures of gene clusters for the biosynthesis of secondary metabolites, and the secondary metabolic potential of Streptomyces spp. This study provides basic data for the discovery of novel compounds and new drugs.

Key words:moderately halophilic Streptomyces spp.;tyrosinase inhibitor;whole-genome sequencing;gene cluster for biosynthesis