Microbial Resources and Systematics
Online ISSN : 2759-2006
Print ISSN : 1342-4041
Volume 30, Issue 1
Displaying 1-5 of 5 articles from this issue
  • Hisayuki Komaki, Natsuko Ichikawa, Mitsuo Sekine, Yuko Kitahashi, Nobu ...
    2014 Volume 30 Issue 1 Pages 1-11
    Published: 2014
    Released on J-STAGE: December 25, 2024
    JOURNAL FREE ACCESS

    The complete genome sequence of Streptomyces avermitilis ATCC 31267T, known as an avermectin producer, was reported in 2001 (Omura et al., 2001), and is now published as that of S. avermitilis MA-4680T in GenBank/EMBL/DDBJ (Ikeda et al., 2003). In our PCR-based nonribosomal peptide synthetase (NRPS) gene analysis for actinomycetes, NRPS genes that are not present in the S. avermitilis complete genome sequence were unexpectedly amplified from S. avermitilis NBRC 14893T. To investigate the reason of this unexpected result, we sequenced the whole genome of S. avermitilis NBRC 14893T using Genome Sequencer FLX and Illumina HiSeq1000. Consequently, the genome size was estimated at approximately 10 Mb, and 92 contig/scaffold sequences were obtained. Some of the sequences were not present in the published S. avermitilis genome sequence. Approximately 40 kb of NRPS gene cluster and 65 kb NRPS/polyketide synthase hybrid gene cluster, previously unreported in S. avermitilis, were discovered in the NBRC 14893T-specific genome sequences. Bioinformatic analyses suggested that the two gene clusters were likely involved in the synthesis of demethylcomplestatin and a novel oxazolomycin analog, respectively. According to strain transfer histories among culture collections, the original type strain S. avermitilis MA-4680T had been deposited to Agricultural Research Service Culture Collection (NRRL), and the NRRL strain had been subsequently deposited to KCC Culture Collection of Actinomycetes, Kaken Pharmaceutical Co., Ltd. (KCC) and American Type Culture Collection (ATCC). NBRC 14893T is derived from the KCC strain, while the complete genome-elucidated strain is from ATCC 31267T. It is hard to imagine that pure culture stocks acquire additional DNA coding large biosynthetic gene clusters. Furthermore, plasmid loss and dynamic genome reconstitution frequently occur in the genus Streptomyces. Therefore, the deletion of the two gene clusters we discovered here had probably occurred after the type strain of S. avermitilis was transferred from NRRL to ATCC.

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  • Hiroyuki Sawada, Fukuhiro Yamasaki, Masaru Takeya, Takayuki Aoki
    2014 Volume 30 Issue 1 Pages 13-27
    Published: 2014
    Released on J-STAGE: December 25, 2024
    JOURNAL FREE ACCESS

    In the case of the genus Agrobacterium, which comprises crown gall bacteria and hairy root bacteria, the genus and species have been artificially defined based on pathogenic characters. For some species of the genus, several biovars, equivalent to the rank of variety level, have been established. Recently, based on the results of polyphasic taxonomic approaches, it was proposed that each biovar should be elevated to the species level (Sawada et al., IJSB 43: 694-702, 1993; Ophel & Kerr, IJSB 40: 236-241, 1990), and that the genera Agrobacterium and Rhizobium should be amalgamated into one single genus Rhizobium (Young et al., IJSEM 51: 89-103, 2001). Taking these changes in the taxonomic situation into consideration, strains belonging to the phytopathogenic Rhizobium species (formerly Agrobacterium species) preserved in the NIAS Genebank were re-identified based on phylogenetic analyses using 16S rDNA, atpD, glnA and recA, inoculation tests, PCR assays and so on, and some of them with typical characters for each species/pathogenic state/genomovar were selected as approved strains (reference strains for taxonomic studies). In addition, for every host plant, we chose pathogenic strains that were proved to harbor Ti or Ri plasmids, as approved strains (reference strains for inoculation tests). The DNA sequence data of the strains are provided by the NIAS Genebank database (http://www.gene.affrc.go.jp/databases-micro_search_en.php).

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