Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichi
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ORIGINAL PAPER
Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC‑6 Minggen Cheng1 · Xin Yan1 · Jian He1 · Jiguo Qiu1 · Qing Chen1,2 Received: 1 February 2019 / Revised: 11 April 2019 / Accepted: 12 April 2019 / Published online: 17 April 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019
Abstract The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CHdegrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization. Keywords Chloroacetanilide herbicide · Genome comparison · Mineralizing pathway · Sphingomonads · Sphingomonas wittichii DC-6
Introduction
Communicated by Erko Stackebrandt. * Jiguo Qiu [email protected] * Qing Chen [email protected] 1
Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
College of Life Sciences, Zaozhuang University, Zaozhuang 277160, Shandong, China
2
Chloroacetanilide herbicides (CH) are a class of agrochemicals with significant pre-emergence control efficacy of annual grass and broadleaf weeds in soybean, cotton, or maize fields. Over the past decades, CH has become one of the most popular herbicides in the USA, Europe, and many developing countries (Yang and Holmen 2008), and their widespread use has caused nonpo
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