Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites

Abstract

Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is commercially important in human and veterinary medicine. The major interest in this genus Streptomyces is the diversity of its production of secondary metabolites as an industrial microorganism. A major factor in its prominence as a producer of the variety of secondary metabolites is its possession of several metabolic pathways for biosynthesis. Here we report sequence analysis of S. avermitilis, covering 99% of its genome. At least 8.7 million base pairs exist in the linear chromosome; this is the largest bacterial genome sequence, and it provides insights into the intrinsic diversity of the production of the secondary metabolites of Streptomyces. Twenty-five kinds of secondary metabolite gene clusters were found in the genome of S. avermitilis. Four of them are concerned with the biosyntheses of melanin pigments, in which two clusters encode tyrosinase and its cofactor, another two encode an ochronotic pigment derived from homogentiginic acid, and another polyketide-derived melanin. The gene clusters for carotenoid and siderophore biosyntheses are composed of seven and five genes, respectively. There are eight kinds of gene clusters for type-I polyketide compound biosyntheses, and two clusters are involved in the biosyntheses of type-II polyketide-derived compounds. Furthermore, a polyketide synthase that resembles phloroglucinol synthase was detected. Eight clusters are involved in the biosyntheses of peptide compounds that are synthesized by nonribosomal peptide synthetases. These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome.

Figure 1

Linear physical map of the chromosome of S. avermitilis ATCC31267 showing the position of known genes (cysD, recA, proA, and argA), six rrn operons, region around the replication origin, and secondary metabolite clusters. Vertical lines in boxes indicate recognition sites of the restriction enzyme AseI. All rrn regions have a unique AseI site between Q and V; G1 and H; R and I; I and B; S and G2; and T and D. Abbreviations of biosynthetic gene cluster symbols: ave, avermectin; crt, carotenoid; hpd, ochronotic pigment; melC and melC′, melanin; nrps1–8, peptide; olm, oligomycin; pks1–10, polyketide; pte, polyene macrolide; sid, siderophore; spp, spore pigment. Both AseI-W and -D contain telomere sequences.

Figure 2

Gene clusters for pigment and siderophore biosyntheses. Melanin pigments gene clusters are under A, carotenoid gene cluster is under B, and siderophore gene cluster is under C. Four melanin gene clusters are classified into three types: (i) melanin pigment formation involving tyrosinase, (ii) hydroxyphenylpyruvate dioxygenase, and (iii) type-II PKS. Abbreviations of gene symbols: acp, acyl carrier protein; alcA, monooxygenase; alcB, acetyltransferase; alcC, urease homolog; clf, chain-length factor; crtE, geranylgeranyl pyrophosphate synthase; crtI, phytoene synthetase; crtT, methyltransferase; crtU, β-carotene desaturase; crtV, methyltransferase; crtY, lycopene cyclase; cyc, cyclase; dbd, L-2,4-diaminobutyrate decarboxylase; fot, formyl transferase; hpd, 4-hydroxyphenylpyrucate dioxygenase; hyd, hydroxylase; ks, β-ketoacyl synthase; melC1, tyrosinase cofactor; melC2, tyrosinase; omt, O-methyltransferase; reg, regulatory protein.

Figure 3

Gene clusters for polyketide biosyntheses. Structures of metabolites assembled by type-I PKSs are characterized (A) and uncharacterized (B). Clusters contain type-II PKSs (C) and other types of PKSs (D). Open-boxed ORFs indicate type-I, -II, and other type PKS genes; shadowed-boxed ORFs are probably involved in the postpolyketide modification; and hatched-boxed ORFs would not be involved in the biosynthesis. abc, ABC transporter; acd, acyl-CoA dehydrogenase; acp, acyl carrier protein; aro, aromatase; ave, avermectin PKS; clf, chain-length factor; clp, ATP-dependent protease homolog; cyc, cyclase; dh, dehydratase; hyd, hydroxylase; kr, ketoreductase; ks, β-ketoacyl synthase; mt, methyltransferase; p450, cytochrome P450; olm, oligomycin PKS; omt, O-methyltransferase; oxy, oxidoreductase; pte, polyene macrolide PKS; reg, regulatory protein.

Figure 4

Gene clusters for peptide biosyntheses. Open-boxed ORFs indicate NRPS genes, shadowed-boxed ORFs are probably involved in the postpeptide modification, and hatched-boxed ORFs would not be involved in biosynthesis.