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Actinomadura sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of Actinomadura sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene (t1pks) clusters, a large t1pks cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.

The 16S rRNA gene sequence of ‘Streptomyces hyalinum’ NBRC 13850T shows 99.7 % similarity to that of Embleya scabrispora DSM 41855T; however, it shows Streptomyces spp. Phylogenetic analysis based on 16S rRNA gene sequences clearly suggests that ‘S. hyalinum’ belongs to the genus Embleya rather than to Streptomyces . The strain possesses ll-diaminopimelic acid in the cell wall. The major menaquinone observed is MK-9(H6), and MK-9(H4) and MK-9(H8) are minor components. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. In this study, the whole genome of strain NBRC 13850T was sequenced, and digital DNA–DNA hybridisation between ‘S. hyalinum’ NBRC 13850T and E. scabrispora DSM 41855T demonstrated 31.2 % of relatedness value between the two genomes. Morphological, chemotaxonomic, biochemical and physiological data also revealed that ‘S. hyalinum’ can be easily differentiated from E. scabrispora (the only the valid species of the genus Embleya ) and that it merits separate species status. This phenotypic and genetic evidence reveals that ‘S. hyalinum’ represents a novel species of the genus Embleya ; the name Embleya hyalina sp. nov. is proposed for this species. The type strain is NBRC 13850T (=ATCC 29817T=MB 891-A1T). We also emended the description of the genus Embleya considering the feature of E. hyalina.

Acrocarpospora is a rare, recently established actinomycete genus of the family Streptosporangiaceae. In the present study, we sequenced whole genomes of the type strains of Acrocarpospora corrugate, Acrocarpospora macrocephala, and Acrocarpospora pleiomorpha to assess their potency as secondary metabolite producers; we then surveyed their nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. The genome sizes of A. corrugate NBRC 13972T, A. macrocephala NBRC 16266T, and A. pleiomorpha NBRC 16267T were 9.3 Mb, 12.1 Mb, and 11.8 Mb, respectively. Each genome contained 12-17 modular NRPS and PKS gene clusters. Among the 23 kinds of NRPS and PKS gene clusters identified from the three strains, eight clusters were conserved in all the strains, six were shared between A. macrocephala and A. pleiomorpha, and the remaining nine were strain-specific. We predicted the chemical structures of the products synthesized by these gene clusters based on bioinformatic analyses. Since the chemical structures are diverse, Acrocarpospora strains are considered an attractive source of diverse nonribosomal peptide and polyketide compounds.

Acrocarpospora is a rare, recently established actinomycete genus of the family Streptosporangiaceae. In the present study, we sequenced whole genomes of the type strains of Acrocarpospora corrugate, Acrocarpospora macrocephala, and Acrocarpospora pleiomorpha to assess their potency as secondary metabolite producers; we then surveyed their nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. The genome sizes of A. corrugate NBRC 13972

The 16S rRNA gene sequence of '

Certain methanogens deteriorate steel surfaces through a process called microbiologically influenced corrosion (MIC). However, the mechanisms of MIC, whereby methanogens oxidize zerovalent iron (Fe0), are largely unknown. In this study, Fe0-corroding Methanococcus maripaludis strain OS7 and its derivative (strain OS7mut1) defective in Fe0-corroding activity were isolated. Genomic analysis of these strains demonstrated that the strain OS7mut1 contained a 12-kb chromosomal deletion. The deleted region, termed “MIC island”, encoded the genes for the large and small subunits of a [NiFe] hydrogenase, the TatA/TatC genes necessary for the secretion of the [NiFe] hydrogenase, and a gene for the hydrogenase maturation protease. Thus, the [NiFe] hydrogenase may be secreted outside the cytoplasmic membrane, where the [NiFe] hydrogenase can make direct contact with Fe0, and oxidize it, generating hydrogen gas: Fe0 + 2 H+ → Fe2+ + H2. Comparative analysis of extracellular and intracellular proteomes of strain OS7 supported this hypothesis. The identification of the MIC genes enables the development of molecular tools to monitor epidemiology, and to perform surveillance and risk assessment of MIC-inducing M. maripaludis.

Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468 are producers of arisostatin and kosinostatin, respectively. Micromonospora sp. TP-A0316 showed a 16S rRNA gene sequence similarity of 100% to Micromonosporaoryzae CP2R9-1T whereas Micromonospora sp. TP-A0468 showed a 99.3% similarity to Micromonospora haikouensis 232617T. A phylogenetic analysis based on gyrB sequences suggested that Micromonospora sp. TP-A0316 is closely related to Micromonospora oryzae whereas Micromonospora TP-A0468 is an independent genomospecies. As Micromonospora sp. TP-A0468 showed some phenotypic differences to its closely related species, it was classified as a novel species, for which the name Micromonospora okii sp. nov. is proposed. The type strain is TP-A0468T (= NBRC 110461T). Micromonospora sp. TP-A0316 and M. okii TP-A0468T were both found to harbor 15 gene clusters for secondary metabolites such as polyketides and nonribosomal peptides in their genomes. Arisostatin-biosynthetic gene cluster (BGC) of Micromonospora sp. TP-A0316 closely resembled tetrocarcin A-BGC of Micromonospora chalcea NRRL 11289. A large type-I polyketide synthase gene cluster was present in each genome of Micromonospora sp. TP-A0316 and M. okii TP-A0468T. It was an ortholog of quinolidomicin-BGC of M. chalcea AK-AN57 and widely distributed in the genus Micromonospora.

A sponge-derived Brevibacillus sp. TP-B0800 produces new polycyclic thiazoline derivatives designated ulbactins F and G which possess inhibitory activity against tumor cell migration. To elucidate the biosynthetic pathway of ulbactins, we read the genome sequence of this strain. The genome harbors six gene clusters related to nonribosomal peptides, one of which was identified to be responsible for ulbactin biosynthesis. We propose the putative ulbactin-biosynthetic pathway based on bioinformatics analysis. The genome information reported here also suggested potential of this strain to produce edeine, tyrocidin, and unidentified secondary metabolites.

Genome-based survey of nonribosomal peptide synthetase and polyketide synthase gene clusters in type strains of the genus Microtetraspora

Streptomyces hyaluromycini MB-PO13T (=NBRC 110483T = DSM 100105T) is type strain of the species, which produces a hyaluronidase inhibitor, hyaluromycin. Here, we report the draft genome sequence of this strain together with features of the organism and generation, annotation and analysis of the genome sequence. The 11.5 Mb genome of Streptomyces hyaluromycini MB-PO13T encoded 10,098 putative ORFs, of which 5317 were assigned with COG categories. The genome harbored at least six type I PKS clusters, three type II PKS gene clusters, two type III PKS gene clusters, six NRPS gene clusters, and one hybrid PKS/NRPS gene cluster. The type II PKS gene cluster including 2-amino-3-hydroxycyclopent-2-enone synthetic genes was identified to be responsible for hyaluromycin synthesis. We propose the biosynthetic pathway based on bioinformatic analysis.

Genome-based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in a novel strain taxonomically close to the genus Salinispora

The incorporation pattern of biosynthetic precursors into two structurally unique polyketides, akaeolide and lorneic acid A, was elucidated by feeding experiments with 13C-labeled precursors. In addition, the draft genome sequence of the producer, Streptomyces sp. NPS554, was performed and the biosynthetic gene clusters for these polyketides were identified. The putative gene clusters contain all the polyketide synthase (PKS) domains necessary for assembly of the carbon skeletons. Combined with the 13C-labeling results, gene function prediction enabled us to propose biosynthetic pathways involving unusual carbon-carbon bond formation reactions. Genome analysis also indicated the presence of at least ten orphan type I PKS gene clusters that might be responsible for the production of new polyketides.

Type strains of 72 validated Nocardia species were phylogenetically analyzed based on the multilocus sequence analysis (MLSA) concatenated atpD-groL1-groL2-recA-rpoA-secY-sodA-ychF. Furthermore, their similarity based on digital DNA-DNA hybridization (dDDH) was calculated. Nocardia soli, Nocardia cummidelens and Nocardia salmonicida, Nocardia nova and Nocardia elegans, Nocardia exalbida and Nocardia gamkensis, and Nocardia coubleae and Nocardia ignorata formed coherent clades, respectively. Moreover, each set showed over 70% relatedness by dDDH and shared common phenotypic characteristics. Therefore, we propose a reclassification of Nocardia soli and Nocardia cummidelens as a later heterotypic synonym of Nocardia salmonicida, Nocardia elegans as a later heterotypic synonym of Nocardia nova, Nocardia gamkensis as a later heterotypic synonym of Nocardia exalbida, and Nocardia coubleae as a later heterotypic synonym of Nocardia ignorata.

An alicyclic epoxy resin was modified with a copolymer having both a perfluoroalkyl side chain and a cyclohexenoxide-terminated side chain. The copolymer had a good solubility in the epoxy matrix during the reaction of the alicyclic epoxy groups on the terminal end of the side chains. Thus, the cured epoxy resin had a homogeneous phase structure and was a colorless material with excellent transparency. The fluorinated side chains were highly self-segregated in the air-side surface (thickness: less than 8 nm) to minimize the interfacial free energy between the air and cured epoxy resin. The surface of the epoxy coatings had a significantly low surface free energy (ca. 20 mJ/m2) and revealed both high hydro- and oleo-phobicities. In addition, the surface had a gradient in the refractive index due to the self-stratification of the C–F bond that has a low polarizability.

Bacterial strains YM16-303T and YM16-304T were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303T and YM16-304T were most similar to that of Ilumatobacter fluminis YM22-133T, and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter . Ilumatobacter fluminis YM22-133T and strains YM16-303T and YM16-304T should be classified as distinct species in the genus Ilumatobacter , however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303T = NBRC 109120T = KCTC 29139T) and Ilumatobacter coccineum sp. nov. (type strain YM16-304T = NBRC 103263T = KCTC 29153T), are proposed. The order Acidimicrobiales , which contains the genus Ilumatobacter , currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303T and YM16-304T clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133T, suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales .

The aim of this study was to reclarify the taxonomic relationship among Streptomyces hygroscopicus subsp. hygroscopicus, Streptomyces endus and Streptomyces sporocinereus. Whole genome shotgun sequencing was performed for the type strains of these three taxa. Average nucleotide identity and digital DNA-DNA hybridization values among the three taxa were greater than the thresholds for bacterial species delineation, indicating that they belong to the same genomospecies. In addition, the phenotypic data previously reported also support the synonymy. Therefore, S. endus and S. sporocinereus should be reclassified as later heterotypic synonyms of S. hygroscopicus subsp. hygroscopicus.

Here, we report the draft genome sequence of Bacillus subtilis TP-B0611, which produces the isocoumarin-type compounds bacilosarcin and amicoumacin. The genome encodes three nonribosomal peptide synthetase (NRPS) gene clusters and one hybrid polyketide synthase (PKS)/NRPS gene cluster. The hybrid PKS/NRPS gene cluster was identified to be responsible for the biosynthesis of bacilosarcins and amicoumacins.

We report the draft genome sequence of Streptomyces sp. TP-A0874 isolated from compost. This strain produces catechoserine, a new catecholate-type inhibitor of tumor cell invasion. The genome harbors at least six gene clusters for polyketide and nonribosomal peptide biosyntheses. The biosynthetic gene cluster for catechoserines was identified by bioinformatic analysis.

We report here the draft genome sequence of Streptomyces sp. SPMA113 isolated from soil in Thailand. This strain produces a new modified peptide, prajinamide, which has adipocyte differentiation activity. The genome harbors at least 30 gene clusters for synthases of polyketide and nonribosomal peptide, suggesting its potential to produce diverse secondary metabolites.

Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces hygroscopicus subsp. hygroscopicus into the NBRC culture collection. An average nucleotide identity analysis confirmed that the taxonomic identification is correct. The genome sequence will serve as a valuable reference for genome mining to search new secondary metabolites.

Tropolone, a phytotoxin produced by Burkholderia plantarii , causes rice seedling blight. To identify genes involved in tropolone synthesis, we systematically constructed mutations in the genes encoding 55 histidine kinases and 72 response regulators. From the resulting defective strains, we isolated three mutants, KE1, KE2, and KE3, in which tropolone production was repressed. The deleted genes of these mutants were named troR1 , troK , and troR2 , respectively. The mutant strains did not cause rice seedling blight, and complementation experiments indicated that TroR1, TroK, and TroR2 were involved in the synthesis of tropolone in B. plantarii . However, tropolone synthesis was repressed in the TroR1 D52A, TroK H253A, and TroR2 D46A site-directed mutants. These results suggest that the putative sensor kinase (TroK) and two response regulators (TroR1 and TroR2) control the production of tropolone in B. plantarii . IMPORTANCE A two-component system is normally composed of a sensor histidine kinase (HK) and a cognate response regulator (RR) pair. In this study, HK (TroK) and two RRs (TroR1 and TroR2) were found to be involved in controlling tropolone production in B. plantarii . These three genes may be part of a bacterial signal transduction network. Such networks are thought to exist in other bacteria to regulate phytotoxin production, as well as environmental adaptation and signal transduction.

Actinoplanes missouriensis Couch 1963 is a well-characterized member of the genus Actinoplanes, which is of morphological interest because its members typically produce sporangia containing motile spores. The sporangiospores are motile by means of flagella and exhibit chemotactic properties. It is of further interest that members of Actinoplanes are prolific sources of novel antibiotics, enzymes, and other bioactive compounds. Here, we describe the features of A. missouriensis 431(T), together with the complete genome sequence and annotation. The 8,773,466 bp genome contains 8,125 protein-coding and 79 RNA genes.

Streptomyces sp. TP-A0871 produces the polyene macrolactam heronamide C. Here, we report its draft genome sequence to get insight into heronamide biosynthesis and genome-mining for novel secondary metabolites of polyketide and nonribosomal peptide classes. The genome encodes over nine orphan gene clusters for polyketide and/or nonribosomal peptide syntheses.

Nonomuraea sp. TP-A0861 produces the nonribosomal peptide myxochelin A, which is known as a microbial siderophore. Here, we report its draft genome sequence. The genome contains at least three nonribosomal peptide synthetase gene clusters, one of which is proposed to be responsible for the biosynthesis of myxochelin A.

Here, we report the draft genome sequence of Streptomyces sp. TP-A0356, a producer of a potent antitumor antibiotic, yatakemycin, to evaluate potential for secondary metabolite production. The genome sequence data suggest the presence of at least nine gene clusters for polyketide synthases and nonribosomal peptide synthetases in this strain.

Here, we report the draft genome sequence of an anthracimycin producer, Streptomyces sp. TP-A0875. The genome contains at least two type I polyketide synthase (PKS) gene clusters, two type II PKS gene clusters, and three nonribosomal peptide synthetase gene clusters. The gene cluster for anthracimycin biosynthesis was identified based on the PKS domain organization.

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.

Here, we report the draft genome sequence of Streptomyces sp. TP-A0890, a producer of FR-900452 and A-74863a. The genome was found to contain at least eight polyketide synthase and nonribosomal peptide synthetase gene clusters. A prediction of gene functions based on the sequence similarity allowed us to assign the biosynthetic gene clusters for FR-900452 and A-74863a.

Thirteen novel Gram-stain-positive bacteria were isolated from various samples collected from mangrove forests in Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence comparisons showed that the 13 isolates formed a single clade with Lysinimicrobium mangrovi HI08-69T, with a similarity range of 97.6–99.5 %. The peptidoglycan of the isolates was of the A4α type with an interpeptide bridge comprising Ser–Glu and an l-Ser residue at position 1 of the peptide subunit. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. These chemotaxonomic characteristics corresponded to those of the genus Lysinimicrobium. On the basis of the phenotypic and phylogenetic data, along with average nucleotide identity values among the isolates, we concluded that the 13 isolates should be assigned to the following nine novel species of the genus Lysinimicrobium: Lysinimicrobium aestuarii sp. nov. (type strain HI12-104T = NBRC 109392T = DSM 28144T), Lysinimicrobium flavum sp. nov. (type strain HI12-45T = NBRC 109391T = DSM 28150T), Lysinimicrobium gelatinilyticum sp. nov. (type strain HI12-44T = NBRC 109390T = DSM 28149T), Lysinimicrobium iriomotense sp. nov. (type strain HI12-143T = NBRC 109399T = DSM 28146T), Lysinimicrobium luteum sp. nov. (type strain HI12-123T = NBRC 109395T = DSM 28147T), Lysinimicrobium pelophilum sp. nov. (type strain HI12-111T = NBRC 109393T = DSM 28148T), Lysinimicrobium rhizosphaerae sp. nov. (type strain HI12-135T = NBRC 109397T = DSM 28152T), Lysinimicrobium soli sp. nov. (type strain HI12-122T = NBRC 109394T = DSM 28151T) and Lysinimicrobium subtropicum sp. nov. (type strain HI12-128T = NBRC 109396T = DSM 28145T). In addition, an emended description of the genus Lysinimicrobium is proposed.

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.

Selenomonas ruminantium subsp. lactilytica, a strictly anaerobic ruminal bacterium, possesses typical Gram-negative cell surface structure comprising cytoplasmic membrane, peptidoglycan layer and outer membrane, whereas its 16S rRNA-based taxonomy shows that the bacteria belongs to Gram-positive Firmicutes. Complete genome analysis showed that genes or gene clusters involved in Gram-negative cell structure were scattered in the S. ruminantium genome, and might provide the new insight of phylogenetic relationship between the bacterium and other bacterial species.

Here, we report the draft genome sequences of the type strains of Demequina aestuarii , Demequina aurantiaca , Demequina flava , Demequina globuliformis , Demequina lutea , Demequina oxidasica , Demequina salsinemoris , and Demequina sediminicola . The genome sequences presented here will facilitate taxonomical, ecological, and functional studies of members of the genus Demequina .

Streptomyces albus is the type species of the genus Streptomyces. Here, we report the draft genome sequence of S. albus strain NBRC 13014 T . The genome contains at least seven orphan polyketide synthase and nonribosomal peptide synthetase gene clusters. The genome sequence will also serve as a valuable reference for Streptomyces taxonomy.

Streptomyces sp. TP-A0873, isolated from deep-sea water, produces three different classes of secondary metabolites: antimycin, bohemamine, and alkylated butenolides. In order to assess the biosynthetic potential of this strain, draft genome sequencing was carried out. The genome contained at least 14 gene clusters for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS).

Streptomyces sp. 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-derived Streptomyces.

Members of the genus Streptacidiphilus are acidophilic actinomycetes with streptomycete-like features. Here, we report the draft genome sequences of the type strains of Streptacidiphilus albus , Streptacidiphilus anmyonensis , Streptacidiphilus carbonis , Streptacidiphilus jiangxiensis , Streptacidiphilus melanogenes , and Streptacidiphilus neutrinimicus . These genome sequences will serve as valuable references for understanding their taxonomic relationships, genetic characteristics, and potentials for industry.

Background: CIA, an interactor of the CCG1 histone acetyltransferase subunit of TFIID, was identified as a human histone chaperone. The Saccharomyces cerevisiae orthologue ASF1, when it was over-expressed, was reported to cause de-repression of silent loci; however, the involvement of Asf1p in the alteration of nucleosomal structures remained unknown. Curiously, there is a polyanionic stretch, a structural motif characteristic of histone chaperones, in S. cerevisiae Asf1p, but not in human CIA. We investigated how CIA/Asf1p utilizes its domain(s) for the alteration of nucleosomal structure. Results: To characterize the relationships between the domain structures and nuclear functions of CIA, we isolated the gene for the CIA counterpart in Schizosaccharomyces pombe, designated cia1+, whose putative product contains a polyanionic stretch. Gene disruption of cia1+ was lethal, which is the distinct phenotype of viable S. cerevisiae asf1. The cia1− lethality was rescued by the introduction of S. cerevisiae ASF1, but not by the introduction of human CIA cDNA. To our surprise, the construct that produces Asf1p, lacking the polyanionic stretch, is capable of rescuing the lethality caused by the cia1+ deletion, while the highly conserved N-terminal region of Asf1p is essential for the complementation of cia1− growth defects. The polyanionic stretch-deleted Asf1p is sufficient both for interaction with histones H3/H4 and for nucleosome assembly in vitro, as well as for telomeric de-repression in vivo. Conclusion: These findings suggest that the areas responsible for both the conserved and species-specific functions of CIA/cia1/Asf1p are within their highly conserved regions and that the yeast-specific polyanionic stretch of cia1/Asf1p is not necessary for viability, histone binding, nucleosome assembly, or anti-silencing.

Here, we report the draft genome sequence of the only species of the genus Lysinimicrobium , Lysinimicrobium mangrovi NBRC 105856 T , isolated from the rhizosphere of a mangrove. The first genomic sequence of this genus and species presented here will facilitate taxonomical, ecological, and functional studies of this rare actinobacterial group.

Here we report the draft genome sequence of Nocardiopsis sp. strain TP-A0876, isolated from marine sediment, which produces polyketide-derived pyrones called nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters, one of which was proposed to be responsible for nocapyrone biosynthesis. This genome sequence will facilitate the study of the potential for secondary metabolism in Nocardiopsis strains.

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. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-323) contains supplementary material, which is available to authorized users.

Although members of the genus Streptomyces are useful producers of secondary metabolites, Streptomyces turgidiscabies, a cause of potato scab, has not been investigated for this purpose. To examine the potential of S. turgidiscabies as a secondary metabolite producer, its polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters, conferring major biosynthetic pathways in actinomycetes, were surveyed using whole genome analysis of S. turgidiscabies NBRC 16081. This strain possessed seventeen PKS and NRPS gene clusters composed of two type-I PKS, two type-II PKS, seven NRPS, and six PKS/NRPS hybrid clusters. Abundance of these gene clusters was not only comparable to those of industrially useful strains such as S. avermitilis MA-4680 and S. griseus subsp. griseus NBRC 13350, but also superior to those of genetically well-studied S. coelicolor A3(2) and potato scab-causing S. scabiei 87.22. Remarkably, its PKS/NRPS gene clusters were more diverse in their module organization than those of other Streptomyces strains, although it possessed the lowest number of type-I PKS gene clusters. Our results suggest that S. turgidiscabies, unlike S. scabiei, harbors considerable genetic potential for producing diverse polyketide and peptide compounds.

Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1(T) (NBRC 101784(T)), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.