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Komaki H.,Chiba Institute of Technology | Ichikawa N.,NBRC | Hosoyama A.,NBRC | Fujita N.,NBRC | Igarashi Y.,Toyama Prefectural University
FEMS Microbiology Letters | Year: 2015

We report the draft genome sequence of marine-derived Streptomyces sp. TP-A0882, a producer of buryrolactol, an antifungal γ-lactone-containing polyketide. The genome harbored at least three type I polyketide synthase (PKS), three type II PKS, four nonribosomal peptide synthetase (NRPS) and two hybrid PKS/NRPS gene clusters. Annotation of gene functions enabled us to identify the type I PKS gene cluster for butyrolactol biosynthesis and propose a plausible biosynthetic pathway for this unique polyketide. © FEMS 2015. All rights reserved. Source


Komaki H.,Chiba Institute of Technology | Ichikawa N.,NBRC | Hosoyama A.,NBRC | Fujita N.,NBRC | Igarashi Y.,Toyama Prefectural University
Standards in Genomic Sciences | Year: 2015

Streptomycessp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners TPU-0037-A, −B, −C, and –D. We herein report the 8 Mb draft genome sequence of this strain, together with classification and features of the organism and generation, annotation and analysis of the genome sequence. The genome encodes 7,240 putative ORFs, of which 4,450 ORFs were assigned with COG categories. Also, 66 tRNA genes and one rRNA operon were identified. The genome contains eight gene clusters involved in the production of polyketides and nonribosomal peptides. Among them, a PKS/NRPS gene cluster was assigned to be responsible for lydicamycin biosynthesis and a plausible biosynthetic pathway was proposed on the basis of gene function prediction. This genome sequence data will facilitate to probe the potential of secondary metabolism in marine-derivedStreptomyces. © 2015 Komaki et al. Source


Komaki H.,Chiba Institute of Technology | Ichikawa N.,NBRC | Oguchi A.,NBRC | Hamada M.,Chiba Institute of Technology | And 2 more authors.
BMC Research Notes | Year: 2015

Background: The genus Herbidospora comprises actinomycetes belonging to the family Streptosporangiaceae and currently contains five recognized species. Although other genera of this family often produce bioactive secondary metabolites, Herbidospora strains have not yet been reported to produce secondary metabolites. In the present study, to assess their potential as secondary metabolite producers, we sequenced the whole genomes of the five type strains and searched for the presence of their non-ribosomal peptide synthetase (NRPS) and type-I polyketide synthase (PKS) gene clusters. These clusters are involved in the major secondary metabolite-synthetic pathways in actinomycetes. Results: The genome sizes of Herbidospora cretacea NBRC 15474T, Herbidospora mongoliensis NBRC 105882T, Herbidospora yilanensis NBRC 106371T, Herbidospora daliensis NBRC 106372T and Herbidospora sakaeratensis NBRC 102641T were 8.3, 9.0, 7.9, 8.5 and 8.6 Mb, respectively. They contained 15-18 modular NRPS and PKS gene clusters. Thirty-two NRPS and PKS pathways were identified, among which 9 pathways were conserved in all 5 strains, 8 were shared in 2-4 strains, and the remaining 15 were strain-specific. We predicted the chemical backbone structures of non-ribosomal peptides and polyketides synthesized by these gene clusters, based on module number and domain organization of NRPSs and PKSs. The relationship between 16S rRNA gene sequence-based phylogeny of the five strains and the distribution of their NRPS and PKS gene clusters were also discussed. Conclusions: The genomes of Herbidospora strains carry as many NRPS and PKS gene clusters, whose products are yet to be isolated, as those of Streptomyces. Herbidospora members should synthesize large and diverse metabolites, many of whose chemical structures are yet to be reported. In addition to those conserved within this genus, each strain possesses many strain-specific gene clusters, suggesting the diversity of these pathways. This diversity could be accounted for by genus-level vertical inheritance and recent acquisition of these gene clusters during evolution. This genome analysis suggested that Herbidospora strains are an untapped and attractive source of novel secondary metabolites. © 2015 Komaki et al. Source


Komaki H.,Chiba Institute of Technology | Ichikawa N.,NBRC | Hosoyama A.,NBRC | Takahashi-Nakaguchi A.,Chiba University | And 4 more authors.
BMC Genomics | Year: 2014

Background: Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology.Results: Draft genome sequences of Nocardia asteroides NBRC 15531T, Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402T, and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text.Conclusion: We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites. © 2014 Komaki et al.; licensee BioMed Central Ltd. Source

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