Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment.

Yongjun Wei,Lei Zhang,Xing Yan,Zhihua Zhou

doi:10.3389/fmicb.2018.00295

Abstract

Polyketides (PKs) and nonribosomal peptides (NRPs) are widely applied as drugs in use today, and one potential source for novel PKs and NRPs is the marine sediment microbes. However, the diversities of microbes and their PKs and NRPs biosynthetic genes in the marine sediment are rarely reported. In this study, 16S rRNA gene fragments of the Yellow Sea sediment were analyzed, demonstrating that Proteobacteria and Bacteroidetes accounted for 62% of all the bacterial species and Actinobacteria bacteria which were seen as the typical PKs and NRPs producers only accounted for 0.82% of all the bacterial species. At the same time, PKs and NRPs diversities were evaluated based on the diversity of gene fragments of type I polyketide synthase (PKS) ketosynthase domain (KS), nonribosomal peptide synthetase (NRPS) adenylation domain (AD), and dTDP-glucose-4,6-dehydratase (dTGD). The results showed that AD genes and dTGD genes were abundant and some of them had less than 50% identities with known ones; By contrast, only few KS genes were identified and most of them had more than 60% identities with known KS genes. Moreover, one 70,000-fosmid clone library was further constructed to screen for fosmid clones harboring PKS or NRPS gene clusters of the Yellow Sea sediment. Nine selected fosmid clones harboring KS or AD were sequenced, and three of the clones were assigned to Proteobacteria. Though only few Actinobacteria 16S rRNA gene sequences were detected in the microbial community, five of the screened fosmid clones were assigned to Actinobacteria. Further assembly of the 9 fosmid clones resulted in 11 contigs harboring PKS, NRPS or hybrid NPRS-PKS gene clusters. These gene clusters showed less than 60% identities with the known ones and might synthesize novel natural products. Taken together, we revealed the diversity of microbes in the Yellow Sea sediments and found that most of the microbes were uncultured. Besides, evaluation of PKS and NRPS biosynthetic gene clusters suggested that the marine sediment might have the ability to synthesize novel natural products and more NRPS gene clusters than PKS gene clusters distributed in this environment.

Highlights

Natural products of polyketides (PKs) and nonribosomal peptides (NRPs) are secondary metabolites of microbes, which can help microbes adapt to environment and resist to stressful natural conditions
0.3% of total 16S rRNA reads and 0.8% of the representative operational taxonomic units (OTUs) were assigned as Actinobacteria bacteria which was believed to synthesize more than 45% of the known microbial PKs and NRPs in nature (Bérdy, 2005)
The 16S rRNA gene analysis indicated that Proteobacteria was the most dominant phylum in the Yellow Sea sediment, which was similar with bacteria diversity distributed in the East China Sea and the South China Sea where Proteobacteria was the most dominant phylum (Lu et al, 2011; Zhu et al, 2013)

Summary

Introduction

Natural products of polyketides (PKs) and nonribosomal peptides (NRPs) are secondary metabolites of microbes, which can help microbes adapt to environment and resist to stressful natural conditions. Many previously identified PKs and NRPs were recovered from isolated bacteria of terrestrial environments (Handelsman et al, 1998; Daniel, 2004), especially from the phylum of Actinobacteria (Bérdy, 2005; Fenical and Jensen, 2006; Bull and Stach, 2007). 16S rRNA analysis showed that Actinobacteria bacteria were not the most abundant phyla in the marine sediment, suggesting there might be other potential PKs and NRPs producer which can produce novel PKs and NRPs (Zhu et al, 2013). Different natural product biosynthetic genes are distributed in phylogenetic similar microbial communities (Reddy et al, 2012), showing the unrevealed marine environments are the attractive starting points to recover novel bioactive compounds (Brady et al, 2002; Piel, 2011; Wilson and Piel, 2013)

Methods

Results

Conclusion