In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2

Ruth Nahurira,Yang Jia,Junhuan Wang,Ibatsam Khokhar,Adel Eltoukhy,Yanchun Yan,Shuanghu Fan

doi:10.1186/s13568-019-0733-5

Ruth Nahurira, Yang Jia + Show 5 more

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https://doi.org/10.1186/s13568-019-0733-5

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Journal: AMB Express	Publication Date: Feb 4, 2019
Citations: 10	License type: open-access

Affiliation: Chinese Academy of Agricultural Sciences

Abstract

Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd2+, Co2+, Cu2+, Ni2+, Zn2+, Mn2+ and Pb2+ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.

Highlights

Environmental pollution has become a global concern that requires concerted effort for monitoring, control and remediation plans across all sectors of society
Substrate utilization tests and intermediate analysis The ability of strain YC-RL2 to utilize diphenyl ether, naphthol, CHCl2, benzene, phenol, para-chlorobenzoic acid (PCBA), triphenyl phosphate (TPhP), o-xylene, hexane, tetra chlorobenzene, cholesterol, naphthalene, CHCl3 and phenyl phosphate, biphenyl and polychlorinated biphenyls (PCBs) was tested by inoculating the strain in trace element medium (TEM) medium supplemented with 50 ppm of each
Classification The strain was originally classified as G. alkanivorans strain YC-RL2 based on its partial 16S rRNA gene sequence (KR819397.1)

Summary

Introduction

Environmental pollution has become a global concern that requires concerted effort for monitoring, control and remediation plans across all sectors of society. Members of phylum Actinobacteria possess a great potential for remediation of contaminated environments through degradation of xenobiotics, sequestration of heavy metals and production of novel secondary metabolites. In the phylum Actinobacteria, the genus of Gordonia has recently gained attention due to the biotechnological potential of its members (Drzyzga 2012). Members of genus Gordonia are high G+C gram positive bacteria of the order Actinomycetales (Arenskötter et al 2004). Their ability includes but is not limited to degradation of various phthalic acid esters (PAEs), poly aromatic hydrocarbons (PAHs), alkylpyridines, 1,3,5-triazines and synthetic isoprene rubber (Drzyzga 2012). Most Gordonia species contain genes for polyketide and carotenoid biosynthesis and alkane degradation (Sowani et al 2018)

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