Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various streptomyces species - PubMed (original) (raw)

Comparative Study

Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various streptomyces species

Mikko Metsä-Ketelä et al. Appl Environ Microbiol. 2002 Sep.

Abstract

A 613-bp fragment of an essential ketosynthase gene from the biosynthetic pathway of aromatic polyketide antibiotics was sequenced from 99 actinomycetes isolated from soil. Phylogenetic analysis showed that the isolates clustered into clades that correspond to the various classes of aromatic polyketides. Additionally, sequencing of a 120-bp fragment from the gamma-variable region of 16S ribosomal DNA (rDNA) and subsequent comparative sequence analysis revealed incongruity between the ketosynthase and 16S rDNA phylogenetic trees, which strongly suggests that there has been horizontal transfer of aromatic polyketide biosynthesis genes. The results show that the ketosynthase tree could be used for DNA fingerprinting of secondary metabolites and for screening interesting aromatic polyketide biosynthesis genes. Furthermore, the movement of the ketosynthase genes suggests that traditional marker molecules like 16S rDNA give misleading information about the biosynthesis potential of aromatic polyketides, and thus only molecules that are directly involved in the biosynthesis of secondary metabolites can be used to gain information about the biodiversity of antibiotic production in different actinomycetes.

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Figures

FIG.1.

Phylogenetic tree constructed from partial 16S rDNA sequences. Bootstrap values greater than 60% are shown at the nodes (1,000 = 100%). Scale bar = 10% dissimilarity. Sequences marked with an asterisk were obtained from Ribosomal Database Project II (14). The numbers in front of the Ribosomal Database Project II Streptomyces strains (1 to 12) are the numbers used in the classification system (classes 6 and 7 were omitted as representatives of these classes contained only sequences that had ambiguous characters). The nucleotide sequence accession numbers for the reference strains are as follows: S. albus, X53163; S. thermodiastaticus, Z68101; S. albidoflavus, Z76685; S. coelicolor, Y00411; S. scabies, AB026206; S. setonii, D63872; S. bikiniensis, X79851; S. cinnamoneus, X53171; S. armeniacus, AB018094; S. mashuense, X79323; Amycolatopsis thermoflava, AF052390; and E. coli, AF233451.

FIG.2.

Phylogenetic tree constructed from KSα gene fragments. Bootstrap values greater than 70% are shown at the nodes (1,000 = 100%). Scale bar = 10% dissimilarity. Sequences marked with an asterisk were derived from the GenBank database. The sequences obtained from strains S. galilaeus, S. nogalater, S. coelicolor, S. argillaceus, and S. peucetius in this work were identical to the sequences deposited in the GenBank database. The nucleotide sequence accession numbers for the reference strains are as follows: S. galilaeus, AF257324; S. nogalater, AJ224512; S. coelicolor, X63449 (act) and X55942 (whiE); S. halstedii, L05390; S. avermitilis, AB070937 (spore pigment) and AB070947 (pks-9); S. collinus, AF293354 (PKSA ORF1) and AF293355 (rub); S. curacoi, M33704; S. roseofulvus, L26338; S. glaucescens, M80674; S. violaceoruber, X16144; S. arenae, AF098965; S. argillaceus, X89899; S. peucetius, L35560; S. rimosus, Z25538; S. griseus, X77865; S. fradiae, X87093; S. cinnamonensis, Z11511; S. venezuelae, L33245; and S. cyanogenus, AF080235.

FIG. 3.

Structures of compounds that represent different classes of aromatic polyketides. (A) Angucycline antibiotic rabelomycin; (B) naphthaquinone antibiotic actinorhodin; (C) anthracycline antibiotic daunomycin; (D) tetracycline antibiotic oxytetracycline; (E) tetracenomycin C; (F) aureolic acid antibiotic mithramycin; and (G) rubromycin β. R1, R2, and R3 refer to sugar moieties, which are not derived from the PKS pathway.

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Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various streptomyces species - PubMed (original) (raw)