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Genome Sequence of Kitasatospora Setae NBRC 14216T: an Evolutionary Snapshot of the Family Streptomycetaceae

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Genome Sequence of Kitasatospora Setae NBRC 14216T: an Evolutionary Snapshot of the Family Streptomycetaceae DNA RESEARCH 17, 393–406, (2010) doi:10.1093/dnares/dsq026 Advance Access publication on November 8, 2010 Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae NATSUKO Ichikawa1,AKIO Oguchi 1,HARUO Ikeda 2,JUN Ishikawa3,SHIGERU Kitani 4,YUMI Watanabe 1, SANAE Nakamura 1,YOKO Katano 1,EMI Kishi 1,MACHI Sasagawa1,AKIHO Ankai 5,SHIGEHIRO Fukui5, YOSHIMI Hashimoto 1,SACHI Kamata1,MISA Otoguro 6,SATOSHI Tanikawa1,TAKUYA Nihira 4, SUEHARU Horinouchi 7,YASUO Ohnishi7,MASAYUKI Hayakawa8,TOMOHISA Kuzuyama 9,AKIRA Arisawa10, FUMIKI Nomoto 11,HIROMI Miura 12,YOKO Takahashi 12, and NOBUYUKI Fujita1,* NITE Bioresource Information Center, Department of Biotechnology, National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan1; Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 252-0373, Japan2; Department of Bioactive Molecules, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan3; International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan4; Tohoku Regional Office, National Institute of Technology and Evaluation, 4-5-18 Higashisendai, Miyagino-ku, Sendai, Miyagi 983-0833, Japan5; NITE Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan6; Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan7; Division of Applied Biological Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Takeda-4, Kofu, Yamanashi 400-8511, Japan8; Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan9; Bioresource Laboratories, Mercian Corp., 1808 Nakaizumi, Iwata, Shizuoka 438-0078, Japan10; Nagase & Co. Ltd, Research and Development Center, 2-2-3 Murotani, Nishi- ku, Kobe, Hyogo 651-2241, Japan11 and Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan12 *To whom correspondence should be addressed. Tel. þ81 3-3481-1933. Fax. þ81 3-3481-8424. E-mail: [email protected] Edited by Katsumi Isono (Received 15 July 2010; accepted 30 September 2010; published online 8 November 2010) Abstract Kitasatospora setae NBRC 14216T (5KM-6054T) is known to produce setamycin (bafilomycin B1) pos- sessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the genus Streptomyces, although they are distinguishable from each other on the basis of cell wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of K. setae NBRC 14216T as the first Streptomycetaceae genome other than Streptomyces. The genome is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp, predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes. Although these features resemble those of Streptomyces, genome-wide comparison of orthologous genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the Streptomyces genus. Although many of the genes related to morphological differentiation identified in Streptomyces were highly conserved in K. setae, there were some differences such as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the copy number and variation of paralogous components involved in cell wall synthesis. Key words: Kitasatospora setae; complete genome; Streptomyces # The Author 2010. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 394 Complete Genome Sequence of Kitasatospora setae [Vol. 17, 1. Introduction of Kitasatospora, in contrast, contains both LL- and meso-DAP.16 In K. setae NBRC 14216T, aerial spores Among many filamentous bacteria belonging to the on solid culture and submerged spores in liquid phylum Actinobacteria, Streptomyces species have been culture both contain exclusively LL-DAP, whereas extensively studied because of the ability to produce mycelia in both cultures contain mainly meso- various bioactive secondary metabolites and the DAP.14,15,17 This suggests that the composition of complex process of morphological differentiation. cell wall peptidoglycan would be regulated in The life cycle of Streptomyces is initiated by the germi- Kitasatospora depending on differentiation stages. nation of spores that develop into vegetative mycelia. Many of the genes involved in the formation of In response to environmental signals, aerial mycelia aerial mycelium (bld genes and others) and sporula- emerge from the colony surface and differentiate tion (whi genes and others) have been identified by into chains of spores. Many pioneering works about genetic analysis of Streptomyces species,1,2 but the the regulation of secondary metabolism and differen- genetic and molecular basis for the differential tiation of Streptomyces species were done using model incorporation of DAP isomers in Kitasatospora raises organisms such as S. coelicolor A3(2) and S. griseus IFO new questions. Considering the unique taxonomic 13350.1,2 The complete genome sequences of three position of Kitasatospora, as well as the common and Streptomyces species, S. coelicolor A3(2),3 S. avermitilis distinct features of Kitasatospora and Streptomyces, MA-4680T4 and S. griseus IFO 13350,5 have been Kitasatospora would be a key microorganism for reported and further accelerated the studies. further understanding of the evolution of not only Kitasatospora setae is a soil-habiting mycelial bacterium actinobacteria within the family Streptomycetaceae belonging to the same family Streptomycetaceae. All 23 but also other mycelial actinobacteria. validly published species belonging to the genus We determined the complete genome sequence of Kitasatospora exhibit a similar life style and mor- K. setae NBRC 14216T (¼KM-6054T) and compared phology with Streptomyces species. Kitasatospora may it with Streptomyces genomes. Although the overall also be comparable with Streptomyces in its capacity topology and gene organization of the K. setae NBRC to produce bioactive secondary metabolites. The type 14216T genome showed close resemblance to strain of K. setae, NBRC 14216T, is known to produce Streptomyces genomes, there are discriminative dis- setamycin (bafilomycin B1) and bafilomycin A1, tances between them. We established a robust phylo- specific inhibitors of vacuolar ATPase and commonly genetic position of the genus Kitasatospora by used as biochemical reagents for investigation of mol- multilocus phylogenetic analysis and confirmed the ecular transport in eukaryotic cells. This genus also previous results based on 16S rDNA sequences. We includes several other strains reported as producers also describe the conservation and variation of differ- of bioactive compounds including a proteasome inhibi- entiation-related genes predicted from the annota- tor and an anti-fungal agent.6,7 tion of K. setae NBRC 14216T genome, as well as After the first proposal of the genus Kitasatospora the possible coding capacity of the genome for bio- (originally Kitasatosporia) by Omura et al. in 1982,8 active secondary metabolites. the taxonomic position of Kitasatospora had been under a debate. It was once reclassified as a synonym of Streptomyces based on morphology and 2. Materials and methods partial 16S rDNA analysis reported by Wellington et al.9 and Ochi and Hiranuma.10 Afterward, Zhang 2.1. Genome sequencing, assembly and validation et al.11 reported that Streptomyces and Kitasatospora DNA shotgun libraries with average insert sizes of form distinct phyletic groups in the detailed inspec- 1.6 and 6.5 kb were constructed in pUC118 tion of the 16S rDNA and the 16S –23S rDNA internal (TaKaRa), whereas a fosmid library with average spacer region and proposed the revival of the genus insert size of 37 kb was constructed in pCC1FOS Kitasatospora. Such a history made Kitasatospora a (EPICENTRE) as described previously.18,19 A total of suitable model for the development of methods dis- 50 400 clones (34 560, 10 752 and 5088 clones tinguishing closely related species and genera based from libraries with 1.6, 6.5 and 37 kb inserts, respect- on the DNA sequence.12,13 Besides the molecular ively) were subjected to sequencing from both ends of phylogenetic approach, there are clear phenotypic cri- the inserts on either ABI 3730xl DNA Analyzer teria to distinguish Kitasatospora from Streptomyces,of (Applied Biosystems) or Base Station DNA Fragment which most notable is the chemical composition of Analyzer BST-0100 (MJ Research, Inc.). Sequence cell wall peptidoglycan.14,15 Cell wall peptidoglycan reads were trimmed at a threshold quality value of of streptomycetes contains the LL isomer of diamino- 20 by Phred and assembled by Phrap and CONSED pimelic acid (DAP), whereas many other sporoactino- assembly tools.20,21 For alignment and validation mycetes contain the meso isomer.
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