Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer

Abstract

Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. 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 9.9 Mb genome of Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were assigned with COG categories. We successfully identified a hybrid polyketide synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway. The alchivemycin biosynthetic gene cluster is also present in Streptomyces rapamycinicus NRRL 5491T, Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556, and Streptomyces ascomycinicus NBRC 13981T, which are taxonomically highly close to strain TP-A0867. This study shows a representative example that distribution of secondary metabolite genes is correlated with evolution within the genus Streptomyces.

Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains

“…The 16S rRNA genes were amplified using two universal primers, 9F and 1541R, and sequenced according to an established method 26 . EzTaxon-e was used for basic local alignment search tool (BLAST) analysis of the sequences 27 .…”

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

“…TP-A0468 were isolated as previously reported [ 3 , 4 ] and were deposited onto the NBRC culture collection as NBRC 110038 and NBRC 110461, respectively. The 16S rRNA gene sequences were determined by the same method used in our previous report [ 32 ]. The EzBioCloud web server [ 33 ] was used to search closely related type strains and calculate 16S rRNA gene sequence similarities.…”

“…MLSA was conducted by autoMLST [ 34 ] using the DNA sequences of 85 housekeeping genes: gatB , gatA , amino acid biosynthesis phosphoglycerate dehydrogenase (PGDH) gene, amino acid biosynthesis acetolactate synthase, small subunit (acolac_sm) gene, imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (IMP_synth_hisH) gene, nuoF , phosphoribosylformylglycinamidine synthase II (FGAM_synth_II) gene, rsmG, typA/bipA, ilvD , phosphoribosylformylglycinamidine synthase I (FGAM_synth_I) gene, hutU, yjeE , fructose-bisphosphate aldolase, class II (FruBisAldo_II_A) gene, histidinol-phosphatase (his_9_HisN) gene, recQ, nth, whiA , transketolase (tktlase_bact) gene, polyphosphate kinase 1 (poly_P_kin) gene, atpD, rplA, hrcA, glpX, rpe, lipA, purH , translation initiation factor IF-2 gene, pdx2 , SUF system FeS assembly protein, NifU family (SUF_scaf_2) gene, ung, rplM, atpA, secA, gyrA , preprotein translocase, SecY subunit (3a0501s007) gene, prfA, rpsC, truB, rplS , cystathionine beta-synthase (cysta_beta) gene, pth, pyrG , ribonuclease PH (RNasePH) gene, clpX , hypoxanthine phosphoribosyltransferase (HGPRTase) gene, ftsZ, ftsY, rlmN, cgtA, ftsE, trmU, prfB, radA, rpoC , CCA tRNA nucleotidyltransferase gene, ksgA, era , 1,4-alpha-glucan branching enzyme gene, ruvB, purS, pyrF, recA, dxs, gyrB, pdx1, engA, ffh, recR, dnaA, sufB, dxr, trmD, rplB, pyrH, mfd, rplV, mraZ, purA , nicotinate (nicotinamide) nucleotide adenylyltransferase gene, aspS, rpoZ , phosphopantothenoylcysteine decarboxylase/phosphopantothenate—cysteine ligase (coaBC_dfp) gene, purF , and rpsB . Whole genome sequencing and analyses of PKS and NRPS gene clusters in the genome sequences were conducted in the same manner of our previous reports [ 32 , 35 , 36 , 37 ]. These gene clusters and their domain were detected and determined, respectively, using antiSMASH [ 38 ].…”

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

“…As it did not show similarities to BGCs of known compounds, the product could not be predicted. Among the hybrid PKS/NRPS gene clusters in this strain, pks/nrps-1 and -2 were BGCs of alchivemycin [18] and totopotensamide, respectively, whose NRPSs and PKSs correspond to the biosynthetic enzymes (Table 4). In contrast, pks/nrps-3 and -4 were orphan gene clusters.…”

“…As S. hygroscopicus has two heterotypic synonyms, Streptomyces endus and Streptomyces sporocinereus [17], we included their type strains in the tree. S. hygroscopicus TP-A0867 is an alchivemycin producer [18]. S. hygroscopicus NBRC 16556 is a strain for which we reported the whole genome sequence [19].…”