Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species.

Hisayuki Komaki,Ken-Ichiro Suzuki,Akira Hosoyama,Tetsuhiro Matsuzawa,Tohru Gonoi,Nobuyuki Fujita,Azusa Takahashi-Nakaguchi,Natsuko Ichikawa

doi:10.1186/1471-2164-15-323

Abstract

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

Highlights

Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they opportunistically infect the respiratory system, skin, and other organs of humans and animals
The complete genome sequences of N. cyriacigeorgica GUH-2, N. brasiliensis HUJEG-1 (=ATCC 700358), and N. farcinica IFM 10152 were downloaded from DDBJ [14], with accession numbers FO082843, CP0033876, and AP006618, respectively
We focused on Polyketide synthase (PKS)-I and nonribosomal peptide synthetase (NRPS) secondary metabolite clusters because their products usually have larger molecular weights with more

Summary

Introduction

Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they opportunistically infect the respiratory system, skin, and other organs of humans and animals. 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. Actinomycetous strains of the genus Nocardia usually live in soil or water and play saprophytic roles in the environment, and are opportunistic human pathogens, infecting the respiratory tract, skin, brain, and other organs of both immunocompromised and immunocompetent patients. More than 80 species have been established in the genus Nocardia, and approximately one-third to one-half of the species have been reported as human pathogens [1,2,3] Because of their medical importance, Nocardia strains have accumulated in microbial collections as a resource for clinical and scientific studies in the last few decades (e.g., [4,5,6,7]). It has been found that these clusters produce several medically and industrially important compounds, such as pathogenic factors, avermectin, erythromycin, and vancomycin

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