Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q

Authors
Li, Jun
Qian, Shulan
Xiong, Lie
Zhu, Chengyun
Shu, Ming
Wang, Jie
Jiao, Yang
He, Houlong
Zhang, Fuming
Linhardt, Robert J.
ORCID
https://orcid.org/0000-0003-2219-5833
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Issue Date
2017-10-31
Keywords
Biology , Chemistry and chemical biology , Chemical and biological engineering , Biomedical engineering
Degree
Terms of Use
Attribution 3.0 United States
CC BY : this license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. Credit must be given to the authors and the original work must be properly cited.
Full Citation
Comparative genomics reveals specific genetic architectures in nicotine metabolism of Pseudomonas sp. JY-Q, J. Li, S. Qian, L. Xiong, C. Zhu, J. Wang, Y. Jiao, H. He, F. Zhang, R. J. Linhardt, W. Zhong, Frontiers in Microbiology, 8, 2085, 2017.
Abstract
Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l−1 nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l−1) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations. Comparative genomic analysis indicated that JY-Q degrades nicotine through putative novel mechanisms. Two candidate gene cluster duplications located separately at distant loci were predicted to be responsible for nicotine degradation. These two nicotine (Nic) degradation-related loci (AA098_21325—AA098_21340, AA098_03885—AA098_03900) exhibit nearly completely consistent gene organization and component synteny. The nicotinic acid (NA) degradation gene cluster (AA098_17770–AA098_17790) and Nic-like clusters were both predicted to be flanked by mobile genetic elements (MGE). Furthermore, we analyzed the regions of genomic plasticity (RGP) in the JY-Q strain and found a dynamic genome carrying a type VI secretion system (T6SS) that promotes nicotine metabolism and tolerance based on transcriptomics and used in silico methods to identify the T6SS effector protein. Thus, a novel nicotine degradation mechanism was elucidated for Pseudomonas sp. JY-Q, suggesting its potential application in the bioremediation of nicotine-contaminated environments, such as TWEs.
Description
Comparative genomics reveals specific genetic architectures in nicotine metabolism of Pseudomonas sp. JY-Q
Department
The Linhardt Research Labs.
The Shirley Ann Jackson, Ph.D. Center for Biotechnology and Interdisciplinary Studies (CBIS)
Publisher
Frontiers Media SA
Relationships
The Linhardt Research Labs Online Collection
Rensselaer Polytechnic Institute, Troy, NY
Frontiers in Microbiology
https://harc.rpi.edu/
Access
Open Access
CC BY — Creative Commons Attribution