Reclassification of a reveromycin-producer and the proposals of Actinacidiphila reveromycinica sp. nov. and Actinacidiphila acidipaludis comb. nov.

Streptomyces sp. SN-593, a reveromycin producer, was previously thought to belong to the genus Streptomyces based on its morphological and chemotaxonomic characteristics. In this paper, we re-considered its taxonomic position according to the current criteria. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain belongs to the genus Actinacidiphila. In multilocus sequence and phylogenomic analyses, the strain SN-593 represented a distinct evolutionary lineage within this genus, and its closest neighbor was A. yanglinensis. Digital DNA-DNA hybridization indicated that the strain shares less than 32% DNA-DNA relatedness with the type strains of closely related species, confirming this strain is a novel genomospecies. According to its phenotypic distinctiveness from the closest neighbor, we propose Actinacidiphila reveromycinica sp. nov. for the strain SN-593T. Additionally, as Streptomyces acidipaludis belonged to the genus Actinacidiphila in these analyses, it should be transferred to the genus, for which Actinacidiphila acidipaludis comb. nov. is proposed.

Phytohabitans aurantiacus sp. nov., an actinomycete isolated from soil.

A novel actinomycete, designated RD004123T, was isolated from a soil sample collected in Hokkaido, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain RD004123T fell within the cluster of the family Micromonosporaceae but did not form a reliable cluster with any member of the family. The similarity values between strain RD004123T and the type species of 29 genera in the family Micromonosporaceae were 91.7-97.7 %. Meanwhile, phylogenomic analyses indicated that strain RD004123T was closely related to members of the genus Phytohabitans. Strain RD004123T contained both meso-diaminopimelic acid and l-lysine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinones were MK-10(H8) and MK-10(H6), and the major fatty acids were anteiso-C17 :  0, iso-C16 :  0, iso-C15 :  0 and C17 :  0. The detected polar lipids were phosphatidylinositol mannosides, phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol. These chemotaxonomic features corresponded to those of the genus Phytohabitans. Meanwhile, the results of genome comparison analyses and phenotypic characterizations distinguished strain RD004123T from the other members of the genus Phytohabitans. Therefore, strain RD004123T should be assigned as representing a novel species of the genus Phytohabitans, for which the name Phytohabitans aurantiacus sp. nov. is proposed. The type strain is RD004123T (=NBRC 114997T=DSM 114330T).

Recent Progress of Reclassification of the Genus Streptomyces.

The genus Streptomyces is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale. This review introduces reclassifications of the genus Streptomyces reported in the past decade. Appropriately 34 Streptomyces species were transferred to the other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus and recently proposed new genera. As a result of reclassifications of 14 subspecies, the genus Streptomyces includes only four subspecies at present in practice. A total of 63 species were reclassified as later heterotypic synonyms of previously recognized species in 24 published reports. As strong relationships between species and the secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications of this genus will not only contribute to systematics, but also provide significant information when searching for useful bioactive substances.

Taxonomic Positions and Secondary Metabolite-Biosynthetic Gene Clusters of Akazaoxime- and Levantilide-Producers.

Micromonospora sp. AKA109 is a producer of akazaoxime and A-76356, whereas Micromonospora sp. AKA38 is that of levantilide C. We aimed to clarify their taxonomic positions and identify biosynthetic gene clusters (BGCs) of these compounds. In 16S rRNA gene and DNA gyrase subunit B gene (gyrB) sequence analyses, strains AKA109 and AKA38 were the most closely related to Micromonospora humidisoli MMS20-R2-29T and Micromonospora schwarzwaldensis HKI0641T, respectively. Although Micromonospora sp. AKA109 was identified as M. humidisoli by the gyrB sequence similarity and DNA-DNA relatedness based on whole genome sequences, Micromonospora sp. AKA38 was classified to a new genomospecies. M. humidisoli AKA109 harbored six type-I polyketide synthase (PKS), one type-II PKS, one type-III PKS, three non-ribosomal peptide synthetase (NRPS) and three hybrid PKS/NRPS gene clusters, among which the BGC of akazaoxime and A-76356 was identified. These gene clusters are conserved in M. humidisoli MMS20-R2-29T. Micromonospora sp. AKA38 harbored two type-I PKS, one of which was responsible for levantilide C, one type-II PKS, one type-III PKS, two NRPS and five hybrid PKS/NRPS gene clusters. We predicted products derived from these gene clusters through bioinformatic analyses. Consequently, these two strains are revealed to be promising sources for diverse non-ribosomal peptide and polyketide compounds.

Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber.

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus Streptomyces. Gene sequences of atpD, gyrB, recA, rpoB and trpB are generally used in MLSA for Streptomyces species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of atpD gene sequences was not necessarily able to distinguish closely related species. In contrast, trpB gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in trpB gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that Streptomyces anthocyanicus and Streptomyces tricolor are synonyms of Streptomyces violaceoruber.

Taxonomic Positions of a Nyuzenamide-Producer and Its Closely Related Strains.

Streptomyces sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis. Streptomyces sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to Streptomyces hygroscopicus NBRC 13472T and Streptomyces demainii NRRL B-1478T, respectively. Although these members formed a clade in a phylogenetic tree based on 16S rRNA gene sequences, the clade split into two closely related subclades in multilocus sequence analysis (MLSA). One included Streptomyces sp. N11-34, S. demainii NRRL B-1478T, S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867 and the other comprised S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although Streptomyces sp. N11-34 was classified to S. hygroscopicus at the species level based on MLSA evolutionary distances and DNA-DNA relatedness, these distances and relatedness of members between the two subclades were comparatively far (0.004-0.006) and low (75.4-76.4%), respectively. Streptomyces sp. N11-34 possessed six NRPS, seven PKS and four hybrid PKS/NRPS gene clusters in the genome. Among the seventeen, ten were identified to be biosynthetic gene clusters (BGCs) of nyuzenamide, echoside, coelichelin, geldanamycin, mediomycin, nigericin, azalomycin, spore pigment, alchivemycin and totopotensamide, whereas the remaining seven were orphan in our bioinformatic analysis. All seventeen are conserved in S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867. In contrast, S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859 lacked the BGCs of alchivemycin, totopotensamide, a nonribosomal peptide and a hybrid polyketide/nonribosomal peptide compound. This difference was in a good accordance with the abovementioned phylogenetic relationship. Based on phenotypic differences in addition to phylogenetic relationship, DNA-DNA relatedness and BGCs, strains of S. hygroscopicus should be reclassified to two subspecies: S. hygroscopicus subsp. hygroscopicus and a new subspecies, for which we proposed S. hygroscopicus subsp. sporocinereus subsp. nov. The type strain is NBRC 100766T (=ATCC 43692T = DSM 41460T = INMI 32T = JCM 9093T = NRRL B-16376T = VKM Ac-312T). S. demainii was classified in this subspecies.

In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov.

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.

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes.

A genome mining survey combined with metabolome analysis of publicly available strains identified Couchioplanes sp. RD010705, a strain belonging to an underexplored genus of rare actinomycetes, as a producer of new metabolites. HPLC-DAD-guided fractionation of its fermentation extracts resulted in the isolation of five new methyl-branched unsaturated fatty acids, (2E,4E)-2,4-dimethyl-2,4-octadienoic acid (1), (2E,4E)-2,4,7-trimethyl-2,4-octadienoic acid (2), (R)-(-)-phialomustin B (3), (2E,4E)-7-hydroxy-2,4-dimethyl-2,4-octadienoic acid (4), (2E,4E)-7-hydroxy-2,4,7-trimethyl-2,4-octadienoic acid (5), and one prenylated tryptophan derivative, 6-(3,3-dimethylallyl)-N-acetyl-ʟ-tryptophan (6). The enantiomer ratio of 4 was determined to be approximately S/R = 56:44 by a recursive application of Trost's chiral anisotropy analysis and chiral HPLC analysis of its methyl ester. Compounds 1-5 were weakly inhibitory against Kocuria rhizophila at MIC 100 µg/mL and none were cytotoxic against P388 at the same concentration.

Reclassification of four subspecies in the genus Streptomyces to Streptomyces rubradiris sp. nov., Streptomyces asoensis sp. nov., Streptomyces fructofermentans sp. nov. and Streptomyces ossamyceticus sp. nov.

The genus Streptomyces includes, at the time of writing, eight subspecies with validly published names. Streptomyces thermoviolaceus subsp. apingens NBRC 15459T and Streptomyces lavendulae subsp. grasserius NBRC 13045T show 16S rRNA gene sequence similarities of >99.7% to their parent species Streptomyces thermoviolaceus subsp. thermoviolaceus NBRC 13905T and Streptomyces lavendulae subsp. lavendulae NRRL B-2774T, respectively. In contrast, the type strains of the remaining six subspecies, Streptomyces achromogenes subsp. rubradiris, Streptomyces albosporeus subsp. labilomyceticus , Streptomyces cacaoi subsp. asoensis , Streptomyces chrysomallus subsp. fumigatus , Streptomyces cinereoruber subsp. fructofermentans and Streptomyces hygroscopicus subsp. ossamyceticus, do not show >99.0% 16S rRNA gene sequence similarity to that of each parent species. Although S. chrysomallus subsp. fumigatus and S. hygroscopicus subsp. ossamyceticus were respectively reclassified to 'Kitasatospora fumigata' and 'Streptomyces ossamyceticus', these names have not been validly published yet. In this study, we investigated the taxonomic positions of S. achromogenes subsp. rubradiris, S. cacaoi subsp. asoensis, S. cinereoruber subsp. fructofermentans, S. hygroscopicus subsp. ossamyceticus and S. thermoviolaceus subsp. apingens given that their whole genome sequences are available. Except for S. thermoviolaceus subsp. apingens, these subspecies were discriminated from the parent and closely related species based on phylogenetic, genomic and phenotypic differences. Thus, we reclassify S. achromogenes subsp. rubradiris, S. cacaoi subsp. asoensis , S. cinereoruber subsp. fructofermentans and S. hygroscopicus subsp. ossamyceticus as Streptomyces rubradiris sp. nov., Streptomyces asoensis sp. nov., Streptomyces fructofermentans sp. nov. and Streptomyces ossamyceticus sp. nov., respectively. Multilocus sequence and 16S rRNA gene sequence analyses suggested that S. albosporeus subsp. labilomyceticus and S. lavendulae subsp. grasserius may also be reclassified as independent species.

Reclassification of Streptomyces cinnamonensis as a later heterotypic synonym of Streptomyces virginiae.

We studied the taxonomic relationship between Streptomyces cinnamonensis and Streptomyces virginiae. These type strains shared the same 16S rRNA gene sequence. Phylogenomic analysis supported them being closely related. Digital DNA-DNA relatedness and average nucleotide identity using whole genome sequences indicated that the two species represent the same genomospecies. They shared similar phenotypic characteristics and harboured the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides in the genomes. Therefore, according to Rule 24b of the Bacteriological Code, S. cinnamonensis Okami 1952, 572AL (Approved Lists 1980) should be reclassified as a later heterotypic synonym of S. virginiae Grundy et al. 1952, 399AL (Approved Lists 1980) emend. Nouioui et al. 2018. Although 16S rRNA gene sequences were identical among type strains of Streptomyces xanthophaeus, Streptomyces spororaveus and Streptomyces nojiriensis and between those of Streptomyces vinaceus and Streptomyces cirratus, respectively, digital DNA-DNA relatedness indicated that these species are not synonymous.

Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus.

This study aimed to clarify the taxonomic relationships among Streptomyces costaricanus, Streptomyces graminearus, Streptomyces murinus and Streptomyces phaeogriseichromatogenes. These strains share the same 16S rRNA gene sequence. Multilocus sequence analysis revealed that S. costaricanus, S. murinus and S. phaeogriseichromatogenes belong to the same species, but S. graminearus does not. Digital DNA-DNA relatedness and average nucleotide identity among S. costaricanus, S. murinus and S. phaeogriseichromatogenes were 70.9-74.6% and 96.5-97.0 %, respectively. In addition to the previously reported phenotypic data, the presence of a similar set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides supported the similarity among the three species. Therefore, S. costaricanus and S. phaeogriseichromatogenes should be reclassified as later heterotypic synonyms of S. murinus.

Isolation and structure determination of new linear azole-containing peptides spongiicolazolicins A and B from Streptomyces sp. CWH03.

Linear azole-containing peptides are a class of ribosomally synthesized and post-translationally modified peptides. We performed a chemical investigation on marine actinomycetes, and new linear azole-containing peptides named spongiicolazolicins A and B were found in the MeOH extracts of a newly isolated strain Streptomyces sp. CWH03 (NBRC 114659) and two strains of S. spongiicola (strain HNM0071T: DSM 103383T and strain 531S: NBRC 113560). The strain Streptomyces sp. CWH03 was indicated to be a new species closely related to S. spongiicola by phylogenetic analysis using the genome sequence. The new peptides named spongiicolazolicins A and B were isolated from the cell of Streptomyces sp. CWH03. The partial structure of spongiicolazolicin A was determined by 2D NMR experiments. Based on data of MS/MS experiments, the chemical structures of spongiicolazolicins A and B were proposed using the amino acid sequence deduced from the precursor-encoding gene, which was found from whole-genome sequence data of Streptomyces sp. CWH03. The biosynthetic gene cluster of spongiicolazolicins was proposed based on comparative analysis with that of a known linear azole peptide goadsporin. KEY POINTS: • Streptomyces sp. CWH03 was a new species isolated from marine sediment. • New linear azole-containing peptides named spongiicolazolicins A and B were isolated. • Biosynthetic pathway of spongiicolazolicins was proposed.

Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters in the genus Acrocarpospora.

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.

Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans.

(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.

Reclassification of Streptomyces fulvissimus as a later heterotypic synonym of Streptomyces microflavus.

We investigated the taxonomic relationships among Streptomyces fulvissimus, Streptomyces fulvorobeus and Streptomyces microflavus. These type strains shared the same 16S rRNA gene sequence. Digital DNA-DNA relatedness and average nucleotide identity analyses using whole genome sequences suggested that S. fulvissimus and S. microflavus belong to the same genomospecies, whereas S. fulvorobeus does not. In addition to previously reported phenotypic data, the presence of almost the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides also supported the synonymy between S. fulvissimus and S. microflavus. Therefore, S. fulvissimus should be reclassified as a later heterotypic synonym of S. microflavus.

Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis.

We investigated the taxonomic relationships among Streptomyces diastaticus subsp. ardesiacus, Streptomyces diastaticus subsp. diastaticus, Streptomyces gougerotii and Streptomyces rutgersensis. The 16S rRNA gene sequence similarity between S. diastaticus subsp. ardesiacus and S. diastaticus subsp. diastaticus was 97.7 %, whereas S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis showed 100 % nucleotide sequence identity. In addition, S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis formed a single clade in the phylogenetic tree. Digital DNA-DNA relatedness between S. diastaticus subsp. diastaticus and S. diastaticus subsp. ardesiacus was only 22.8%, indicative of different species. In comparison, DNA-DNA relatedness values for S. diastaticus subsp. diastaticus, S. gougerotii and S. rutgersensis ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that S. diastaticus subsp. ardesiacus should be classified as an independent species, Streptomyces ardesiacus sp. nov. The type strain is NBRC 13412T (=ATCC 3315T=CBS 713.72T=DSM 40496T=ISP 5496T=JCM 4745T=NBRC 3714T=NRRL B-1241T=RIA 1373T). Our data also suggests that S. rutgersensis and S. gougerotii should be reclassified as later heterotypic synonyms of S. diastaticus.

Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis.

We investigated the taxonomic relationships among Streptomyces hygroscopicus subsp. glebosus, Streptomyces libani subsp. rufus and Streptomyces platensis. The three species formed a single clade in the phylogenetic trees based on 16S rRNA gene sequence and multilocus sequence analyses. Digital DNA-DNA hybridization using whole genome sequences suggested that S. hygroscopicus subsp. glebosus, S. libani subsp. rufus and S. platensis belong to the same genomospecies. Previously reported phenotypic data also supported this synonymy. Therefore, S. hygroscopicus subsp. glebosus and S. libani subsp. rufus should be reclassified as later heterotypic synonyms of S. platensis.

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium.

Aside from the well-studied conventional actinomycetes such as Streptomyces, the less investigated genera of actinomycetes also represent a promising source of natural products. Genome mining indicated that members of the underexplored genus Pseudosporangium, from which no secondary metabolites have been reported to date, may harbor the biosynthetic machinery for the formation of novel natural products. The strain RD062863, that is available at a public culture collection, was obtained and subjected to metabolite analysis, which resulted in the discovery of a novel cyclopeptide, pseudosporamide (1), along with three new oligomycin-class polyketides, pseudosporamicins A-C (2-4). The unusual structure of compound 1, featured by a biaryl-bond bridging across a tripeptide scaffold, N-acetyl-ʟ-Tyr-ʟ-Pro-ʟ-Trp, was determined by a combination of spectroscopic analyses, chemical derivatization, ECD calculation, and DFT-based theoretical chemical shift calculation, revealing the presence of an (S a)-axial chirality around the biaryl bond. Compounds 2-4 lacked hydroxylation on the side chain of the spiroacetal rings, which showed clear contrast to other oligomycin congeners and related polyketides with ring-truncation or expansion. The new macrolides 2-4 displayed potent antimicrobial activity against the Gram-positive bacterium Kocuria rhizohpila and the plant pathogenic fungus Glomerella cingulata. All compounds showed moderate cytotoxicity against P388 murine leukemia cells with IC50 values in the micromolar to submicromolar ranges. These results exemplified the validity of phylogeny-focused strain selection combined with biosynthetic gene-directed genome mining for the efficient discovery of new natural products.

Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway.

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.

Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds.

(1) Background: Streptomyces sp. TP-A0598 derived from seawater produces lydicamycin and its congeners. We aimed to investigate its taxonomic status; (2) Methods: A polyphasic approach and whole genome analysis are employed; (3) Results: Strain TP-A0598 contained ll-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6) and MK-9(H8), and the major fatty acids were C16:0, iso-C15:0, iso-C16:0, and anteiso-C15:0. Streptomyces sp. TP-A0598 showed a 16S rDNA sequence similarity value of 99.93% (1 nucleottide difference) to Streptomyces angustmyceticus NRRL B-2347T. The digital DNA-DNA hybridisation value between Streptomyces sp. TP-A0598 and its closely related type strains was 25%-46%. Differences in phenotypic characteristics between Streptomyces sp. TP-A0598 and its phylogenetically closest relative, S. angustmyceticus NBRC 3934T, suggested strain TP-A0598 to be a novel species. Streptomyces sp. TP-A0598 and S. angustmyceticus NBRC 3934T harboured nine and 13 biosynthetic gene clusters for polyketides and nonribosomal peptides, respectively, among which only five clusters were shared between them, whereas the others are specific for each strain; and (4) Conclusions: For strain TP-A0598, the name Streptomyces lydicamycinicus sp. nov. is proposed; the type strain is TP-A0598T (=NBRC 110027T).