1
|
Qin J, Qi X, Li Y, Tang Z, Zhang X, Ru S, Xiong JQ. Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134149. [PMID: 38554512 DOI: 10.1016/j.jhazmat.2024.134149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.
Collapse
Affiliation(s)
- Jingyu Qin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Qi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuejiao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhuyun Tang
- School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xiaona Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
2
|
Li J, Peng W, Yin X, Wang X, Liu Z, Liu Q, Deng Z, Lin S, Liang R. Identification of an efficient phenanthrene-degrading Pseudarthrobacter sp. L1SW and characterization of its metabolites and catabolic pathway. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133138. [PMID: 38086304 DOI: 10.1016/j.jhazmat.2023.133138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/25/2023] [Accepted: 11/28/2023] [Indexed: 02/08/2024]
Abstract
Phenanthrene, a typical chemical of polycyclic aromatic hydrocarbons (PAHs) pollutants, severely threatens health of wild life and human being. Microbial degradation is effective and environment-friendly for PAH removal, while the phenanthrene-degrading mechanism in Gram-positive bacteria is unclear. In this work, one Gram-positive strain of plant growth-promoting rhizobacteria (PGPR), Pseudarthrobacter sp. L1SW, was isolated and identified with high phenanthrene-degrading efficiency and great stress tolerance. It degraded 96.3% of 500 mg/L phenanthrene in 72 h and kept stable degradation performance with heavy metals (65 mg/L of Zn2+, 5.56 mg/L of Ni2+, and 5.20 mg/L of Cr3+) and surfactant (10 CMC of Tween 80). Strain L1SW degraded phenanthrene mainly through phthalic acid pathway, generating intermediate metabolites including cis-3,4-dihydrophenanthrene-3,4-diol, 1-hydroxy-2-naphthoic acid, and phthalic acid. A novel metabolite (m/z 419.0939) was successfully separated and identified as an end-product of phenanthrene, suggesting a unique metabolic pathway. With the whole genome sequence alignment and comparative genomic analysis, 19 putative genes associated with phenanthrene metabolism in strain L1SW were identified to be distributed in three gene clusters and induced by phenanthrene and its metabolites. These findings advance the phenanthrene-degrading study in Gram-positive bacteria and promote the practical use of PGPR strains in the bioremediation of PAH-contaminated environments.
Collapse
Affiliation(s)
- Junlan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xianqi Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhixiang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qinchen Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| |
Collapse
|
3
|
Xu L, Wei HM, Sun YN, Wu Q, Gao XY, Shen B, Sun JQ. Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil. Syst Appl Microbiol 2024; 47:126488. [PMID: 38278082 DOI: 10.1016/j.syapm.2024.126488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/01/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Four vanillic acid-degrading bacterial strains, named LR5S13T, LR5S20, and M4R5S39T and LN1S58, were isolated from Kalidium cuspidatum rhizosphere and bulk soils, respectively. Phylogenetic analysis based on 16S rRNA gene as well as core genome revealed that LR5S13T and LR5S20 clustered closely with each other and with Halomonas ventosae Al12T, and that the two strains shared the highest similarities (both 99.3 %) with H. ventosae Al12T, in contrast, M4R5S39T and LN1S58 clustered together and with Halomonas heilongjiangensis 9-2T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with H. heilongjiangensis 9-2T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13T to LR5S20, and M4R5S39T to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel Halomonas species. Therefore, Halomonas rhizosphaerae sp. nov. (type strain LR5S13T = KCTC 8016T = CGMCC 1.62049T) and Halomonas kalidii (type strain M4R5S39T = KCTC 8015T = CGMCC 1.62047T) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.
Collapse
Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China; Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Hua-Mei Wei
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Ye-Nan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Qi Wu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Xiao-Yan Gao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
| |
Collapse
|
4
|
Bhattacharyya M, Dhar R, Basu S, Das A, Reynolds DM, Dutta TK. Molecular evaluation of the metabolism of estrogenic di(2-ethylhexyl) phthalate in Mycolicibacterium sp. Microb Cell Fact 2023; 22:82. [PMID: 37101185 PMCID: PMC10134610 DOI: 10.1186/s12934-023-02096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Di(2-ethylhexyl) phthalate (DEHP) is a widely detected plasticizer and a priority pollutant of utmost concern for its adverse impact on humans, wildlife and the environment. To eliminate such toxic burden, biological processes are the most promising ways to combat rampant environmental insults under eco-friendly conditions. The present study investigated the biochemical and molecular assessment of the catabolic potential of Mycolicibacterium sp. strain MBM in the assimilation of estrogenic DEHP. RESULTS A detailed biochemical study revealed an initial hydrolytic pathway of degradation for DEHP followed by the assimilation of hydrolyzed phthalic acid and 2-ethylhexanol to TCA cycle intermediates. Besides the inducible nature of DEHP-catabolic enzymes, strain MBM can efficiently utilize various low- and high-molecular-weight phthalate diesters and can grow under moderately halotolerant conditions. Whole genome sequence analysis exhibited a genome size of 6.2 Mb with a GC content of 66.51% containing 6,878 coding sequences, including multiple genes, annotated as relevant to the catabolism of phthalic acid esters (PAEs). Substantiating the annotated genes through transcriptome assessment followed by RT-qPCR analysis, the possible roles of upregulated genes/gene clusters in the metabolism of DEHP were revealed, reinforcing the biochemical pathway of degradation at the molecular level. CONCLUSIONS A detailed co-relation of biochemical, genomic, transcriptomic and RT-qPCR analyses highlights the PAE-degrading catabolic machineries in strain MBM. Further, due to functional attributes in the salinity range of both freshwater and seawater, strain MBM may find use as a suitable candidate in the bioremediation of PAEs.
Collapse
Affiliation(s)
- Mousumi Bhattacharyya
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Rinita Dhar
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Suman Basu
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Avijit Das
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India
| | - Darren M Reynolds
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Bristol, BS16 1QY, UK
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, EN-80, Sector V, Salt Lake, Kolkata, West Bengal, 700091, India.
| |
Collapse
|
5
|
Huang M, He P, He P, Wu Y, Munir S, He Y. Novel Virulence Factors Deciphering Klebsiella pneumoniae KpC4 Infect Maize as a Crossing-Kingdom Pathogen: An Emerging Environmental Threat. Int J Mol Sci 2022; 23:ijms232416005. [PMID: 36555647 PMCID: PMC9785288 DOI: 10.3390/ijms232416005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Klebsiella pneumoniae is not only a human and animal opportunistic pathogen, but a food-borne pathogen. Cross-kingdom infection has been focused on since K. pneumoniae was identified as the pathogen of maize, banana, and pomegranate. Although the pathogenicity of K. pneumoniae strains (from ditch water, maize, and human) on plant and mice has been confirmed, there are no reports to explain the molecular mechanisms of the pathogen. This study uncovered the K. pneumoniae KpC4 isolated from maize top rot for the determination of various virulence genes and resistance genes. At least thirteen plant disease-causing genes are found to be involved in the disruption of plant defense. Among them, rcsB is responsible for causing disease in both plants and animals. The novel sequence types provide solid evidence that the pathogen invades plant and has robust ecological adaptability. It is imperative to perform further studies on the verification of these KpC4 genes’ functions to understand the molecular mechanisms involved in plant−pathogen interactions.
Collapse
Affiliation(s)
- Min Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy and Life Sciences and Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, Kunming University, Kunming 650214, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
| |
Collapse
|
6
|
Whole genome sequencing exploitation analysis of dibutyl phthalate by strain Stenotrophomonas acidaminiphila BDBP 071. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
7
|
Góngora E, Chen YJ, Ellis M, Okshevsky M, Whyte L. Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119247. [PMID: 35390417 DOI: 10.1016/j.envpol.2022.119247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.
Collapse
Affiliation(s)
- Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Madison Ellis
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Mira Okshevsky
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| |
Collapse
|
8
|
Jiang C, Yan H, Shen X, Zhang Y, Wang Y, Sun S, Jiang H, Zang H, Zhao X, Hou N, Li Z, Wang L, Wang H, Li C. Genome Functional Analysis of the Psychrotrophic Lignin-Degrading Bacterium Arthrobacter sp. C2 and the Role of DyP in Catalyzing Lignin Degradation. Front Microbiol 2022; 13:921549. [PMID: 35910642 PMCID: PMC9327799 DOI: 10.3389/fmicb.2022.921549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
In the cold regions of China, lignin-rich corn straw accumulates at high levels due to low temperatures. The application of psychrotrophic lignin-degrading bacteria should be an effective means of overcoming the low-temperature limit for lignin degradation and promoting the utilization of corn straw. However, this application is limited by the lack of suitable strains for decomposition of lignin; furthermore, the metabolic mechanism of psychrotrophic lignin-degrading bacteria is unclear. Here, the whole genome of the psychrotrophic lignin-degrading bacterium Arthrobacter sp. C2, isolated in our previous work, was sequenced. Comparative genomics revealed that C2 contained unique genes related to lignin degradation and low-temperature adaptability. DyP may participate in lignin degradation and may be a cold-adapted enzyme. Moreover, DyP was proven to catalyze lignin Cα-Cβ bond cleavage. Deletion and complementation of the DyP gene verified its ability to catalyze the first-step reaction of lignin degradation. Comparative transcriptomic analysis revealed that the transcriptional expression of the DyP gene was upregulated, and the genetic compensation mechanism allowed C2ΔDyP to degrade lignin, which provided novel insights into the survival strategy of the psychrotrophic mutant strain C2ΔdyP. This study improved our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provided potential application options for energy-saving production using cold-adapted lignin-degrading enzymes.
Collapse
Affiliation(s)
- Cheng Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
| | - Haohao Yan
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaohui Shen
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
| | - Yuting Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Yue Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hanyi Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ziwei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Liwen Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hanjun Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| |
Collapse
|
9
|
Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr 2022; 10:e0234621. [PMID: 35579457 PMCID: PMC9241852 DOI: 10.1128/spectrum.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
Collapse
Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Jacob Ford
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Wing Yin Tam
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Meghan Whalen
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Marcel Huntemann
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alex Spunde
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - I-Min Chen
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T. B. K Reddy
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Ronan O’Malley
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos C. Kyrpides
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
10
|
Xu N, Qiu C, Yang Q, Zhang Y, Wang M, Ye C, Guo M. Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1. Front Microbiol 2021; 12:725755. [PMID: 34566929 PMCID: PMC8461059 DOI: 10.3389/fmicb.2021.725755] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading Acinetobacter lwoffii NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of A. lwoffii NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that A. lwoffii NL1 degraded phenol via the ortho-cleavage rather than the meta-cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in Escherichia coli and quantitative real-time PCR. A. lwoffii NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that A. lwoffii NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.
Collapse
Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chong Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qiyuan Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Yunzeng Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mingqi Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| |
Collapse
|
11
|
Elyamine AM, Kan J, Meng S, Tao P, Wang H, Hu Z. Aerobic and Anaerobic Bacterial and Fungal Degradation of Pyrene: Mechanism Pathway Including Biochemical Reaction and Catabolic Genes. Int J Mol Sci 2021; 22:ijms22158202. [PMID: 34360967 PMCID: PMC8347714 DOI: 10.3390/ijms22158202] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022] Open
Abstract
Microbial biodegradation is one of the acceptable technologies to remediate and control the pollution by polycyclic aromatic hydrocarbon (PAH). Several bacteria, fungi, and cyanobacteria strains have been isolated and used for bioremediation purpose. This review paper is intended to provide key information on the various steps and actors involved in the bacterial and fungal aerobic and anaerobic degradation of pyrene, a high molecular weight PAH, including catabolic genes and enzymes, in order to expand our understanding on pyrene degradation. The aerobic degradation pathway by Mycobacterium vanbaalenii PRY-1 and Mycobactetrium sp. KMS and the anaerobic one, by the facultative bacteria anaerobe Pseudomonas sp. JP1 and Klebsiella sp. LZ6 are reviewed and presented, to describe the complete and integrated degradation mechanism pathway of pyrene. The different microbial strains with the ability to degrade pyrene are listed, and the degradation of pyrene by consortium is also discussed. The future studies on the anaerobic degradation of pyrene would be a great initiative to understand and address the degradation mechanism pathway, since, although some strains are identified to degrade pyrene in reduced or total absence of oxygen, the degradation pathway of more than 90% remains unclear and incomplete. Additionally, the present review recommends the use of the combination of various strains of anaerobic fungi and a fungi consortium and anaerobic bacteria to achieve maximum efficiency of the pyrene biodegradation mechanism.
Collapse
Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni 269, Comoros
| | - Jie Kan
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
| | - Hui Wang
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou 515063, China; (A.M.E.); (J.K.); (S.M.); (P.T.); (H.W.)
- Correspondence:
| |
Collapse
|
12
|
Liu T, Li J, Qiu L, Zhang F, Linhardt RJ, Zhong W. Combined genomic and transcriptomic analysis of the dibutyl phthalate metabolic pathway in
Arthrobacter
sp. ZJUTW. Biotechnol Bioeng 2020; 117:3712-3726. [DOI: 10.1002/bit.27524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Tengfei Liu
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Jun Li
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Lequan Qiu
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy New York
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy New York
| | - Weihong Zhong
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| |
Collapse
|
13
|
Schieferdecker S, Shabuer G, Letzel AC, Urbansky B, Ishida-Ito M, Ishida K, Cyrulies M, Dahse HM, Pidot S, Hertweck C. Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria. ACS Chem Biol 2019; 14:1490-1497. [PMID: 31243958 DOI: 10.1021/acschembio.9b00228] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metabolic profiling and genome mining revealed that anaerobic bacteria have the potential to produce acyloin natural products. In addition to sattazolin A and B, three new sattazolin congeners and a novel acyloin named clostrocyloin were isolated from three strains of Clostridium beijerinckii, a bacterium used for industrial solvent production. Bioactivity profiling showed that the sattazolin derivatives possess antimicrobial activities against mycobacteria and pseudomonads with only low cytotoxicity. Clostrocyloin was found to be mainly active against fungi. The thiamine diphosphate (ThDP)-dependent sattazolin-producing synthase was identified in silico and characterized both in vivo and in in vitro enzyme assays. A related acyloin synthase from the clostrocyloin producer was shown to be responsible for the production of the acyloin core of clostrocyloin. The biotransformation experiments provided first insights into the substrate scope of the clostrocyloin synthase and revealed biosynthetic intermediates.
Collapse
Affiliation(s)
- Sebastian Schieferdecker
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gulimila Shabuer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Barbara Urbansky
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Michael Cyrulies
- BioPilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sacha Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Victoria 3010, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| |
Collapse
|
14
|
Thelusmond JR, Strathmann TJ, Cupples AM. Carbamazepine, triclocarban and triclosan biodegradation and the phylotypes and functional genes associated with xenobiotic degradation in four agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:1138-1149. [PMID: 30677881 DOI: 10.1016/j.scitotenv.2018.12.145] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Pharmaceuticals and personal care products (PPCPs) are released into the environment due to their poor removal during wastewater treatment. Agricultural soils subject to irrigation with wastewater effluent and biosolids application are possible reservoirs for these chemicals. This study examined the impact of the pharmaceutical carbamazepine (CBZ), and the antimicrobial agents triclocarban (TCC) and triclosan (TCS) on four soil microbial communities using shotgun sequencing (HiSeq Illumina) with the overall aim of determining possible degraders as well as the functional genes related to general xenobiotic degradation. The biodegradation of CBZ and TCC was slow, with ≤50% decrease during the 80-day incubation period. In contrast, TCS biodegradation was rapid, with ~80% removal in 25 days. For each chemical, when all four soils were considered together, between three and ten phylotypes (from multiple phyla) were more abundant in the soil samples compared to the live controls. The genera of a number of previously reported CBZ, TCC or TCS degrading isolates were present; Rhodococcus (CBZ), Streptomyces (CBZ), Pseudomonas (CBZ, TCC, TCS), Sphingomonas (TCC, TCS), Methylobacillus (TCS) and Stenotrophomonas (TCS) were among the most abundant (chemical previously reported to be degraded is shown in parenthesis). From the analysis of xenobiotic degrading pathways, genes from five KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology pathways were the most dominant, including those associated with aminobenzoate, benzoate (most common), chlorocyclohexane/chlorobenzene, dioxin and nitrotoluene biodegradation. Several phylotypes including Bradyrhizobium, Mycobacterium, Rhodopseudomonas, Pseudomonas, Cupriavidus, and Streptomyces were common genera associated with these pathways. Overall, the data suggest several phylotypes are likely involved in the biodegradation of these PPCPs with Pseudomonas being an important genus.
Collapse
Affiliation(s)
- Jean-Rene Thelusmond
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy J Strathmann
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
15
|
Sengupta K, Swain MT, Livingstone PG, Whitworth DE, Saha P. Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1. Front Microbiol 2019; 9:3209. [PMID: 30662435 PMCID: PMC6328493 DOI: 10.3389/fmicb.2018.03209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/11/2018] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other Rhodococcus sp. A novel 4-NP catabolic 43 gene cluster “nph” was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many nph cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the nph cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the nph gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the nph cluster, for potential exploitation in bioremediation.
Collapse
Affiliation(s)
- Kriti Sengupta
- Department of Microbiology, Burdwan University, Bardhaman, India
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Paul G Livingstone
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Pradipta Saha
- Department of Microbiology, Burdwan University, Bardhaman, India
| |
Collapse
|
16
|
Yuan K, Xie X, Wang X, Lin L, Yang L, Luan T, Chen B. Transcriptional response of Mycobacterium sp. strain A1-PYR to multiple polycyclic aromatic hydrocarbon contaminations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:824-832. [PMID: 30243191 DOI: 10.1016/j.envpol.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Cometabolism mechanisms of organic pollutants in environmental microbes have not been fully understood. In this study, a global analysis of Mycobacterium sp. strain A1-PYR transcriptomes on different PAH substrates (single or binary of pyrene (PYR) and phenanthrene (PHE)) was conducted. Comparative results demonstrated that expression levels of 23 PAH degradation enzymes were significantly higher in the binary substrate than in the PYR-only one. These enzymes constituted an integrated enzymatic system to actualize all transformation steps of PYR, and most of their encoded genes formed a novel gene cascade in the genome of strain A1-PYR. The roles of different genotypes of enzymes in PYR cometabolism were also discriminated even though all of their gene sequences were presented in the genome of this strain. NidAB and PdoA2B2 instead of NidA3B3 served the initial oxidization of PAHs, and PcaL replaced PcaCD to catalyze the formation of 3-oxoadipate. Novel genes associated with PYR cometabolism was also predicted by the relationships between their transcription profiles and PYR removal. The results showed that ABC-type transporters probably played important roles in the transport of PAHs and their metabolites through cell membrane, and [4Fe-4S] ferredoxin might be essential for dioxygenases (NidAB and PdoA2B2) to achieve oxidative activities. This study provided molecular insight in that microbial degrader subtly cometabolized recalcitrant PAHs with relatively more degradable ones.
Collapse
Affiliation(s)
- Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China; School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiuqin Xie
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiaowei Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Lin
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lihua Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China; School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| |
Collapse
|
17
|
Liu S, Du MZ, Wen QF, Kang J, Dong C, Xiong L, Huang J, Guo FB. Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization. Environ Microbiol 2018; 20:3836-3850. [PMID: 30187624 DOI: 10.1111/1462-2920.14399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022]
Abstract
To better understand the mechanisms of bacterial adaptation in oxygen environments, we explored the aerobic living-associated genes in bacteria by comparing Clusters of Orthologous Groups of proteins' (COGs) frequencies and gene expression analyses and 38 COGs were detected at significantly higher frequencies (p-value less than 1e-6) in aerobes than in anaerobes. Differential expression analyses between two conditions further narrowed the prediction to 27 aerobe-specific COGs. Then, we annotated the enzymes associated with these COGs. Literature review revealed that 14 COGs contained enzymes catalysing oxygen-involved reactions or products involved in aerobic pathways, suggesting their important roles for survival in aerobic environments. Additionally, protein-protein interaction analyses and step length comparisons of metabolic networks suggested that the other 13 COGs may function relevantly with the 14 enzymes-corresponding COGs, indicating that these genes may be highly associated with oxygen utilization. Phylogenetic and evolutionary analyses showed that the 27 COGs did not have similar trees, and all suffered purifying selection pressures. The divergent times of species containing or lacking aerobic COGs validated that the appearing time of oxygen-utilizing gene was approximately 2.80 Gyr ago. In addition to help better understand oxygen adaption, our method may be extended to identify genes relevant to other living environments.
Collapse
Affiliation(s)
- Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qing-Feng Wen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Juanjuan Kang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lifeng Xiong
- Department of Microbiology, University of Hong Kong, Special Administrative Region, Hong Kong, 999077, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| |
Collapse
|
18
|
Cabral L, Pereira de Sousa ST, Júnior GVL, Hawley E, Andreote FD, Hess M, de Oliveira VM. Microbial functional responses to long-term anthropogenic impact in mangrove soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:231-239. [PMID: 29807296 DOI: 10.1016/j.ecoenv.2018.04.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery.
Collapse
Affiliation(s)
- Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sanderson Tarciso Pereira de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB) - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Erik Hawley
- Washington State University, Pullman, WA, USA
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| |
Collapse
|
19
|
Fan S, Wang J, Li K, Yang T, Jia Y, Zhao B, Yan Y. Complete genome sequence of Gordonia sp. YC-JH1, a bacterium efficiently degrading a wide range of phthalic acid esters. J Biotechnol 2018; 279:55-60. [DOI: 10.1016/j.jbiotec.2018.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/29/2018] [Accepted: 05/09/2018] [Indexed: 02/05/2023]
|
20
|
New Findings on Aromatic Compounds’ Degradation and Their Metabolic Pathways, the Biosurfactant Production and Motility of the Halophilic Bacterium Halomonas sp. KHS3. Curr Microbiol 2018; 75:1108-1118. [DOI: 10.1007/s00284-018-1497-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/19/2018] [Indexed: 11/26/2022]
|
21
|
Dada N, Sheth M, Liebman K, Pinto J, Lenhart A. Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors. Sci Rep 2018; 8:2084. [PMID: 29391526 PMCID: PMC5794770 DOI: 10.1038/s41598-018-20367-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/17/2018] [Indexed: 02/04/2023] Open
Abstract
In light of the declining global malaria burden attained largely due to insecticides, a deeper understanding of the factors driving insecticide resistance is needed to mitigate its growing threat to malaria vector control programs. Following evidence of microbiota-mediated insecticide resistance in agricultural pests, we undertook a comparative study of the microbiota in mosquitoes of differing insecticide resistance status. The microbiota of wild-caught Anopheles albimanus, an important Latin American malaria vector, that were resistant (FEN_Res) or susceptible (FEN_Sus) to the organophosphate (OP) insecticide fenitrothion were characterized and compared using whole metagenome sequencing. Results showed differing composition of the microbiota and its functions between FEN_Res and FEN_Sus, with significant enrichment of OP-degrading bacteria and enzymes in FEN_Res compared to FEN_Sus. Lower bacterial diversity was observed in FEN_Res compared to FEN_Sus, suggesting the enrichment of bacterial taxa with a competitive advantage in response to insecticide selection pressure. We report and characterize for the first time whole metagenomes of An. albimanus, revealing associations between the microbiota and phenotypic resistance to the insecticide fenitrothion. This study lays the groundwork for further investigation of the role of the mosquito microbiota in insecticide resistance.
Collapse
Affiliation(s)
- Nsa Dada
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, 1600 Clifton RD. NE. MS G-49, Atlanta, GA 30329, United States of America
- American Society for Microbiology, 1752 N Street, N. W. Washington, D. C., 20036, United States of America
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging & Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, 1600 Clifton RD. NE, Atlanta, GA 30329, United States of America
| | - Kelly Liebman
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, 1600 Clifton RD. NE. MS G-49, Atlanta, GA 30329, United States of America
- Vector-Borne Disease Section, Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, United States of America
| | - Jesus Pinto
- Instituto Nacional de Salud, Avenida Defensores del Morro (Ex-Huaylas) 2268, Chorrillos, Lima, Peru
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, 1600 Clifton RD. NE. MS G-49, Atlanta, GA 30329, United States of America.
| |
Collapse
|
22
|
Morales LT, González-García LN, Orozco MC, Restrepo S, Vives MJ. The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. Stand Genomic Sci 2017; 12:71. [PMID: 29225727 PMCID: PMC5716253 DOI: 10.1186/s40793-017-0287-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/23/2017] [Indexed: 01/04/2023] Open
Abstract
Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum. The assembly consisted of 178 high-quality DNA scaffolds with 1.93% of sequence repeats identified. A total of 11,195 protein-coding genes were predicted including a diverse group of gene families involved in hydrocarbon degradation pathways like dioxygenases and cytochrome P450. The metabolic pathways identified in the genome can potentially degrade hydrocarbons like chloroalkane/alkene, chorocyclohexane, and chlorobenzene, benzoate, aminobenzoate, fluorobenzoate, toluene, caprolactam, geraniol, naphthalene, styrene, atrazine, dioxin, xylene, ethylbenzene, and polycyclic aromatic hydrocarbons. The comparison analysis between this strain and the previous sequenced clinical strain showed important differences in terms of annotated genes involved in the hydrocarbon degradation process.
Collapse
Affiliation(s)
- Laura T Morales
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura N González-García
- Laboratorio de Micología y Fitopatología Uniandes, Universidad de los Andes, Bogotá, Colombia
| | - María C Orozco
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes, Universidad de los Andes, Bogotá, Colombia
| | - Martha J Vives
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| |
Collapse
|
23
|
Acinetobacter sp. DW-1 immobilized on polyhedron hollow polypropylene balls and analysis of transcriptome and proteome of the bacterium during phenol biodegradation process. Sci Rep 2017; 7:4863. [PMID: 28687728 PMCID: PMC5501837 DOI: 10.1038/s41598-017-04187-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/03/2017] [Indexed: 02/07/2023] Open
Abstract
Phenol is a hazardous chemical known to be widely distributed in aquatic environments. Biodegradation is an attractive option for removal of phenol from water sources. Acinetobacter sp. DW-1 isolated from drinking water biofilters can use phenol as a sole carbon and energy source. In this study, we found that Immobilized Acinetobacter sp. DW-1cells were effective in biodegradation of phenol. In addition, we performed proteome and transcriptome analysis of Acinetobacter sp. DW-1 during phenol biodegradation. The results showed that Acinetobacter sp. DW-1 degrades phenol mainly by the ortho pathway because of the induction of phenol hydroxylase, catechol-1,2-dioxygenase. Furthermore, some novel candidate proteins (OsmC-like family protein, MetA-pathway of phenol degradation family protein, fimbrial protein and coenzyme F390 synthetase) and transcriptional regulators (GntR/LuxR/CRP/FNR/TetR/Fis family transcriptional regulator) were successfully identified to be potentially involved in phenol biodegradation. In particular, MetA-pathway of phenol degradation family protein and fimbrial protein showed a strong positive correlation with phenol biodegradation, and Fis family transcriptional regulator is likely to exert its effect as activators of gene expression. This study provides valuable clues for identifying global proteins and genes involved in phenol biodegradation and provides a fundamental platform for further studies to reveal the phenol degradation mechanism of Acinetobacter sp.
Collapse
|
24
|
Jin J, Yao J, Zhang Q, Liu J. Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses. CHEMOSPHERE 2016; 164:379-386. [PMID: 27596825 DOI: 10.1016/j.chemosphere.2016.08.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
In this study, a pyrene-degrading bacterial strain Pseudomonas sp. JPN2 was isolated from crude oil in Dagang Oilfield, China. The degrading percent of the strain JPN2 to pyrene was increased with the extension of culture time and achieved a maximum of 82.88% after 25 d culture. Meanwhile, four metabolites 4,5-dihydroxy-4,5-dihydropyrene, 4-phenanthrol, 1-hydroxy-2-naphthoic acid and phthalate were detected in the culture solution by GC-MS analysis. In addition, DNA fragments of nahAc gene, encoding α subunit of naphthalene dioxygenase, were amplified by PCR program and sequenced. As a result, it was presumed that the initial cleavage of the aromatic rings on pyrene was occurred at C4 and C5 positions and formed the intermediate 4,5-dihydroxy-4,5-dihydropyrene. This issue had been verified by the interaction analysis between pyrene and the active site of naphthalene dioxygenase in the strain JPN2 by molecular docking. Meanwhile, the differences of the amino acid residues in the active sites of template and target enzymes may be a factor leading to the different biological activity between the strain JPN2 and the other bacteria from the genus Pseudomonas. Additionally, the microcalorimetry analysis displayed that the strain JPN2 had high tolerance for pyrene, and the effect could be negligible under the experimental concentration (100 mg L-1). Consequently, the strain JPN2 was considered as an excellent candidate for the further bioremediation study of pyrene and the other aromatic contaminants.
Collapse
Affiliation(s)
- Jingnan Jin
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jun Yao
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; State Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education, and Sino-Hungarian Joint Laboratory of Environmental Science and Health, China University of Geoscience, Wuhan 430074, China.
| | - Qingye Zhang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianli Liu
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| |
Collapse
|
25
|
Shahbaaz M, Ahmad F, Imtaiyaz Hassan M. Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. 3 Biotech 2015; 5:317-336. [PMID: 28324295 PMCID: PMC4434415 DOI: 10.1007/s13205-014-0231-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 05/28/2014] [Indexed: 12/20/2022] Open
Abstract
Haemophilus influenzae is a small pleomorphic Gram-negative bacteria which causes several chronic diseases, including bacteremia, meningitis, cellulitis, epiglottitis, septic arthritis, pneumonia, and empyema. Here we extensively analyzed the sequenced genome of H. influenzae strain Rd KW20 using protein family databases, protein structure prediction, pathways and genome context methods to assign a precise function to proteins whose functions are unknown. These proteins are termed as hypothetical proteins (HPs), for which no experimental information is available. Function prediction of these proteins would surely be supportive to precisely understand the biochemical pathways and mechanism of pathogenesis of Haemophilus influenzae. During the extensive analysis of H. influenzae genome, we found the presence of eight HPs showing lyase activity. Subsequently, we modeled and analyzed three-dimensional structure of all these HPs to determine their functions more precisely. We found these HPs possess cystathionine-β-synthase, cyclase, carboxymuconolactone decarboxylase, pseudouridine synthase A and C, D-tagatose-1,6-bisphosphate aldolase and aminodeoxychorismate lyase-like features, indicating their corresponding functions in the H. influenzae. Lyases are actively involved in the regulation of biosynthesis of various hormones, metabolic pathways, signal transduction, and DNA repair. Lyases are also considered as a key player for various biological processes. These enzymes are critically essential for the survival and pathogenesis of H. influenzae and, therefore, these enzymes may be considered as a potential target for structure-based rational drug design. Our structure–function relationship analysis will be useful to search and design potential lead molecules based on the structure of these lyases, for drug design and discovery.
Collapse
Affiliation(s)
- Mohd Shahbaaz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
26
|
Chemical intervention in bacterial lignin degradation pathways: Development of selective inhibitors for intradiol and extradiol catechol dioxygenases. Bioorg Chem 2015; 60:102-9. [DOI: 10.1016/j.bioorg.2015.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/28/2015] [Accepted: 05/01/2015] [Indexed: 11/23/2022]
|
27
|
Baker E, Tang Y, Chu F, Tisa LS. Molecular responses of Frankia sp. strain QA3 to naphthalene. Can J Microbiol 2015; 61:281-92. [PMID: 25742598 DOI: 10.1139/cjm-2014-0786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Frankia-actinorhizal plant symbiosis plays a significant role in plant colonization in soils contaminated with heavy metals and toxic aromatic hydrocarbons. The molecular response of Frankia upon exposure to soil contaminants is not well understood. To address this issue, we subjected Frankia sp. strain QA3 to naphthalene stress and showed that it could grow on naphthalene as a sole carbon source. Bioinformatic analysis of the Frankia QA3 genome identified a potential operon for aromatic compound degradation as well as several ring-hydroxylating dioxygenases. Under naphthalene stress, the expression of these genes was upregulated. Proteome analysis showed a differential protein profile for cells under naphthalene stress. Several protein spots were analyzed and used to identify proteins involved in stress response, metabolism, and energy production, including a lignostilbene dioxygenase. These results provide a model for understanding the molecular response of Frankia to common soil pollutants, which may be required for survival and proliferation of the bacterium and their hosts in polluted environments.
Collapse
Affiliation(s)
- Ethan Baker
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | | | | | | |
Collapse
|
28
|
Hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides. J Bacteriol 2015; 197:1115-24. [PMID: 25583978 DOI: 10.1128/jb.02443-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The degradation mechanisms of natural and artificial hydrazides have been elucidated. Here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (HBPH) from soils. Physiological and phylogenetic studies identified one bacterium as Microbacterium sp. strain HM58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an Escherichia coli expression system. The Microbacterium sp. HM58-2 hydrazidase is a 631-amino-acid monomer that was 31% identical to indoleacetamide hydrolase isolated from Bradyrhizobium japonicum. Phylogenetic studies indicated that the Microbacterium sp. HM58-2 hydrazidase constitutes a novel hydrazidase group among amidase signature proteins that are distributed within proteobacteria, actinobacteria, and firmicutes. The hydrazidase stoichiometrically hydrolyzed the acylhydrazide residue of HBPH to the corresponding acid and hydrazine derivative. Steady-state kinetics showed that the enzyme hydrolyzes structurally related 4-hydrozybenzamide to hydroxybenzoic acid at a lower rate than HBPH, indicating that the hydrazidase prefers hydrazide to amide. The hydrazidase contains the catalytic Ser-Ser-Lys motif that is conserved among members of the amidase signature family; it shares a catalytic mechanism with amidases, according to mutagenesis findings, and another hydrazidase-specific mechanism must exist that compensates for the absence of the catalytic Ser residue. The finding that an environmental bacterium produces hydrazidase implies the existence of a novel bacterial mechanism of hydrazide degradation that impacts its ecological role.
Collapse
|
29
|
Gröning JAD, Eulberg D, Tischler D, Kaschabek SR, Schlömann M. Gene redundancy of two-component (chloro)phenol hydroxylases in Rhodococcus opacus 1CP. FEMS Microbiol Lett 2015; 361:68-75. [PMID: 25283988 DOI: 10.1111/1574-6968.12616] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/27/2014] [Accepted: 09/29/2014] [Indexed: 11/29/2022] Open
Abstract
Among other factors, a distinct gene redundancy is discussed to facilitate high metabolic versatility of rhodococci. Rhodococcus opacus 1CP is a typical member in that respect and degrades a multitude of (chlorinated) aromatic compounds. In contrast to the central pathways of aromatic degradation in strain 1CP, little is known about the degree of gene redundancy and to what extent this is reflected on protein level within the steps of peripheral degradation. By means of degenerated primers deduced from tryptic peptides of a purified phenol hydroxylase component and using the amplified fragment as a labelled probe against genomic 1CP-DNA, three gene sets encoding three different two-component phenol hydroxylases pheA1/pheA2(1-3) could be identified. One of them was found to be located on the megaplasmid p1CP, which confirms the role of these elements for metabolic versatility. Protein chromatography of phenol- and 4-chlorophenol-grown 1CP-biomass gave first evidences on a functional expression of these oxygenases, which could be initially characterised in respect of their substrate specificity.
Collapse
Affiliation(s)
- Janosch A D Gröning
- Environmental Microbiology, IÖZ, TU Bergakademie Freiberg, Freiberg, Germany
| | | | - Dirk Tischler
- Environmental Microbiology, IÖZ, TU Bergakademie Freiberg, Freiberg, Germany
| | - Stefan R Kaschabek
- Environmental Microbiology, IÖZ, TU Bergakademie Freiberg, Freiberg, Germany
| | - Michael Schlömann
- Environmental Microbiology, IÖZ, TU Bergakademie Freiberg, Freiberg, Germany
| |
Collapse
|
30
|
Yamanashi T, Kim SY, Hara H, Funa N. In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1. Biosci Biotechnol Biochem 2015; 79:830-5. [PMID: 25558786 DOI: 10.1080/09168451.2014.993915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The β-ketoadipate pathway is a major pathway involved in the catabolism of the aromatic compounds in microbes. The recent progress in genome sequencing has led to a rapid accumulation of genes from the β-ketoadipate pathway in the available genetic database, yet the functions of these genes remain uncharacterized. In this study, the protocatechuate branch of the β-ketoadipate pathway of Rhodococcus jostii was reconstituted in vitro. Analysis of the reaction products of PcaHG, PcaB, and PcaL was achieved by high-performance liquid chromatography. These reaction products, β-ketoadipate enol-lactone, 3-carboxy-cis,cis-muconate, γ-carboxymuconolactone, muconolactone, and β-ketoadipate, were further characterized using LC-MS and nuclear magnetic resonance. In addition, the in vitro reaction of PcaL, a bidomain protein consisting of γ-carboxy-muconolactone decarboxylase and β-ketoadipate enol-lactone hydrolase activities, was demonstrated for the first time. This work provides a basis for analyzing the catalytic properties of enzymes involved in the growing number of β-ketoadipate pathways deposited in the genetic database.
Collapse
Affiliation(s)
- Tomoya Yamanashi
- a Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , Shizuoka , Japan
| | | | | | | |
Collapse
|
31
|
Comparative genomics of the protocatechuate branch of the β-ketoadipate pathway in the Roseobacter lineage. Mar Genomics 2014; 17:25-33. [PMID: 24906178 DOI: 10.1016/j.margen.2014.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 11/23/2022]
Abstract
The protocatechuate branch of the β-ketoadipate pathway is the most common pathway for degradation of monoaromatic compounds in the Roseobacter lineage. We analyzed 43 Roseobacter genomes in order to determine if they possessed all genetic elements for this pathway and if there were common patterns in gene organization. The eight genes of the pathway (pcaG, -H, -B, -C, -D, -I, -J, and -F), possible regulators, and genes encoding for proteins with related function (i.e. catabolism of 4-hydroxybenzoate, catechol, and meta-cleavage of protocatechuate) were predicted by sequence homology analysis. Most of the Roseobacters studied had putatively a complete protocatechuate branch of the β-ketoadipate pathway while 11 of them would probably have an incomplete pathway. Thirty-one Roseobacters would be potentially able of transforming 4-hydroxybenzoate to protocatechuate, and 13 of them might transform catechol via ortho-cleavage, the starting reaction of the catechol branch of the β-ketoadipate pathway. We observed variability in gene organization, with no clear relationship between gene order and Roseobacter taxonomy. Genes were usually organized in several gene clusters. One of the clusters (pcaRIJF) was not reported previously in Roseobacters. The presence of the putative regulator pcaR in these bacteria was also a novel finding. The conserved ORF (chp), encoding for a protein of family DUF849 whose functional role has been proven recently, was detected in 34 genomes. Sequence homology confirmed that proteins encoded by chp corresponded to putative BKACE G4 proteins, which are able to transform β-ketoadipate. Therefore, most Roseobacters seemed to possess two different enzymes for transforming β-ketoadipate. We also report two possible regulation mechanisms of gene pobA (encoding for the enzyme transforming 4-hydroxybenzoate to protocatechuate): via PcaQ, the regulator commonly found with pca genes, and via an independent regulator (PobR). The results of this study evidence the relevance of 4-hydroxybenzoate, protocatechuate and β-ketoadipate degradation pathways in Roseobacters and provide a more complex view of possible regulation mechanisms.
Collapse
|
32
|
Functional annotation of putative hypothetical proteins from Candida dubliniensis. Gene 2014; 543:93-100. [DOI: 10.1016/j.gene.2014.03.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 01/12/2023]
|
33
|
Wecke T, Halang P, Staroń A, Dufour YS, Donohue TJ, Mascher T. Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain. Microbiologyopen 2012; 1:194-213. [PMID: 22950025 PMCID: PMC3426412 DOI: 10.1002/mbo3.22] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 03/30/2012] [Indexed: 11/08/2022] Open
Abstract
Bacteria need signal transducing systems to respond to environmental changes. Next to one- and two-component systems, alternative σ factors of the extra-cytoplasmic function (ECF) protein family represent the third fundamental mechanism of bacterial signal transduction. A comprehensive classification of these proteins identified more than 40 phylogenetically distinct groups, most of which are not experimentally investigated. Here, we present the characterization of such a group with unique features, termed ECF41. Among analyzed bacterial genomes, ECF41 σ factors are widely distributed with about 400 proteins from 10 different phyla. They lack obvious anti-σ factors that typically control activity of other ECF σ factors, but their structural genes are often predicted to be cotranscribed with carboxymuconolactone decarboxylases, oxidoreductases, or epimerases based on genomic context conservation. We demonstrate for Bacillus licheniformis and Rhodobacter sphaeroides that the corresponding genes are preceded by a highly conserved promoter motif and are the only detectable targets of ECF41-dependent gene regulation. In contrast to other ECF σ factors, proteins of group ECF41 contain a large C-terminal extension, which is crucial for σ factor activity. Our data demonstrate that ECF41 σ factors are regulated by a novel mechanism based on the presence of a fused regulatory domain.
Collapse
Affiliation(s)
- Tina Wecke
- Department of Biology I, Ludwig-Maximilians-University MunichGermany
| | - Petra Halang
- Department of Biology I, Ludwig-Maximilians-University MunichGermany
| | - Anna Staroń
- Department of Biology I, Ludwig-Maximilians-University MunichGermany
| | - Yann S Dufour
- Department of Bacteriology, University of WisconsinMadison, Wisconsin
| | - Timothy J Donohue
- Department of Bacteriology, University of WisconsinMadison, Wisconsin
| | - Thorsten Mascher
- Department of Biology I, Ludwig-Maximilians-University MunichGermany
| |
Collapse
|
34
|
Comparative transcriptomic and proteomic analyses of Trichomonas vaginalis following adherence to fibronectin. Infect Immun 2012; 80:3900-11. [PMID: 22927047 DOI: 10.1128/iai.00611-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The morphological transformation of Trichomonas vaginalis from an ellipsoid form in batch culture to an adherent amoeboid form results from the contact of parasites with vaginal epithelial cells and with immobilized fibronectin (FN), a basement membrane component. This suggests host signaling of the parasite. We applied integrated transcriptomic and proteomic approaches to investigate the molecular responses of T. vaginalis upon binding to FN. A transcriptome analysis was performed by using large-scale expressed-sequence-tag (EST) sequencing. A total of 20,704 ESTs generated from batch culture (trophozoite-EST) versus FN-amoeboid trichomonad (FN-EST) cDNA libraries were analyzed. The FN-EST library revealed decreased amounts of transcripts that were of lower abundance in the trophozoite-EST library. There was a shift by FN-bound organisms to the expression of transcripts encoding essential proteins, possibly indicating the expression of genes for adaptation to the morphological changes needed for the FN-adhesive processes. In addition, we identified 43 differentially expressed proteins in the proteomes of FN-bound and unbound trichomonads. Among these proteins, cysteine peptidase, glyceraldehyde-3-phosphate dehydrogenase (an FN-binding protein), and stress-related proteins were upregulated in the FN-adherent cells. Stress-related genes and proteins were highly expressed in both the transcriptome and proteome of FN-bound organisms, implying that these genes and proteins may play critical roles in the response to adherence. This is the first report of a comparative proteomic and transcriptomic analysis after the binding of T. vaginalis to FN. This approach may lead to the discovery of novel virulence genes and affirm the role of genes involved in disease pathogenesis. This knowledge will permit a greater understanding of the complex host-parasite interplay.
Collapse
|
35
|
Kosa M, Ragauskas AJ. Bioconversion of lignin model compounds with oleaginous Rhodococci. Appl Microbiol Biotechnol 2011; 93:891-900. [PMID: 22159607 DOI: 10.1007/s00253-011-3743-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 11/02/2011] [Accepted: 11/16/2011] [Indexed: 11/24/2022]
Abstract
Although economically efficient biomass conversion depends on the utilization of the complete cell wall (biorefinery concept), including polysaccharides and lignin, current biofuels research concentrate mostly on cellulose conversion, while lignin is viewed as a side-product that is used primarily as a thermal resource. Microbiological conversion of lignin is almost exclusive to fungi, usually resulting in increased cell mass and lignolytic enzymes. Some bacteria can also degrade lignin-related compounds using the β-ketoadipate pathway; for example, Rhodococcus opacus DSM 1069 can degrade coniferyl alcohol and grow on it as sole carbon source. Moreover, this strain belongs to the actinomycetes group that is also known for oleaginous species with lipid accumulation over 20%. Present work shows that R. opacus DSM 1069 and PD630 strains under nitrogen limiting conditions can convert lignin model compounds into triacylglycerols, also known as neutral lipids. 4-Hydroxybenzoic and vanillic acid lignin model compounds were used as sole carbon sources, and after brief adaptation periods, the cells not only began growing but accumulated lipids to the level of oleaginicity. These lipids were extracted for transesterification and analysis of fatty acid methyl esters showed good composition for biodiesel applications with no aromatics. Furthermore, the two strains showed distinct substrate metabolism and product profiles.
Collapse
Affiliation(s)
- Matyas Kosa
- Department of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, 500 10th Street, NW, Atlanta, GA 30332, USA
| | | |
Collapse
|
36
|
Barbey C, Crépin A, Cirou A, Budin-Verneuil A, Orange N, Feuilloley M, Faure D, Dessaux Y, Burini JF, Latour X. Catabolic pathway of gamma-caprolactone in the biocontrol agent Rhodococcus erythropolis. J Proteome Res 2011; 11:206-16. [PMID: 22085026 DOI: 10.1021/pr200936q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gamma-caprolactone (GCL) is well-known as a food flavor and has been recently described as a biostimulant molecule promoting the growth of bacteria with biocontrol activity against soft-rot pathogens. Among these biocontrol agents, Rhodococcus erythropolis, characterized by a remarkable metabolic versatility, assimilates various γ-butyrolactone molecules with a branched-aliphatic chain, such as GCL. The assimilative pathway of GCL in R. erythropolis was investigated by two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) analysis. This analysis suggests the involvement of the lactonase QsdA in ring-opening, a feature confirmed by heterologous expression in Escherichia coli. According to proteome analysis, the open-chain form of GCL was degraded by β- and ω-oxidation coupled to the Krebs cycle and β-ketoadipate pathway. Ubiquity of qsdA gene among environmental R. erythropolis isolates was verified by PCR. In addition to a previous N-acyl homoserine lactone catabolic function, QsdA may therefore be involved in an intermediate degradative step of cyclic recalcitrant molecules or in synthesis of flavoring lactones.
Collapse
Affiliation(s)
- Corinne Barbey
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, EA 4312 Université de Rouen, IUT Evreux 55 rue Saint-Germain, 27000 Evreux, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
PcaO positively regulates pcaHG of the beta-ketoadipate pathway in Corynebacterium glutamicum. J Bacteriol 2010; 192:1565-72. [PMID: 20081038 DOI: 10.1128/jb.01338-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a new regulator, PcaO, which is involved in regulation of the protocatechuate (PCA) branch of the beta-ketoadipate pathway in Corynebacterium glutamicum. PcaO is an atypical large ATP-binding LuxR family (LAL)-type regulator and does not have a Walker A motif. A mutant of C. glutamicum in which pcaO was disrupted (RES167DeltapcaO) was unable to grow on PCA, and growth on PCA was restored by complementation with pcaO. Both an enzymatic assay of PCA 3,4-dioxygenase activity (encoded by pcaHG) and transcriptional analysis of pcaHG by reverse transcription-PCR revealed that PcaO positively regulated pcaHG. A promoter-LacZ transcriptional fusion assay suggested that PcaO interacted with the sequence upstream of pcaHG. Electrophoretic mobility shift assay (EMSA) analysis indicated that an imperfect palindromic sequence ((-78)AACCCCTGACCTTCGGGGTT(-59)) that was located upstream of the -35 region of the pcaHG promoter was essential for PcaO regulation. DNase I footprinting showed that this imperfect palindrome was protected from DNase I digestion. Site-directed mutation and EMSA tests revealed that this palindrome sequence was essential for PcaO binding to the DNA fragment. In vitro EMSA results showed that ATP weakened the binding between PcaO and its target sequence but ADP strengthened this binding, while the effect of protocatechuate on PcaO binding was dependent on the protocatechuate concentration.
Collapse
|
38
|
Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1. J Bacteriol 2010; 192:1543-52. [PMID: 20061479 DOI: 10.1128/jb.01208-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.
Collapse
|
39
|
Yam KC, van der Geize R, Eltis LD. Catabolism of Aromatic Compounds and Steroids by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
40
|
Identification of a novel self-sufficient styrene monooxygenase from Rhodococcus opacus 1CP. J Bacteriol 2009; 191:4996-5009. [PMID: 19482928 DOI: 10.1128/jb.00307-09] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of a 9-kb genomic fragment of the actinobacterium Rhodococcus opacus 1CP led to identification of an open reading frame encoding a novel fusion protein, StyA2B, with a putative function in styrene metabolism via styrene oxide and phenylacetic acid. Gene cluster analysis indicated that the highly related fusion proteins of Nocardia farcinica IFM10152 and Arthrobacter aurescens TC1 are involved in a similar physiological process. Whereas 413 amino acids of the N terminus of StyA2B are highly similar to those of the oxygenases of two-component styrene monooxygenases (SMOs) from pseudomonads, the residual 160 amino acids of the C terminus show significant homology to the flavin reductases of these systems. Cloning and functional expression of His(10)-StyA2B revealed for the first time that the fusion protein does in fact catalyze two separate reactions. Strictly NADH-dependent reduction of flavins and highly enantioselective oxygenation of styrene to (S)-styrene oxide were shown. Inhibition studies and photometric analysis of recombinant StyA2B indicated the absence of tightly bound heme and flavin cofactors in this self-sufficient monooxygenase. StyA2B oxygenates a spectrum of aromatic compounds similar to those of two-component SMOs. However, the specific activities of the flavin-reducing and styrene-oxidizing functions of StyA2B are one to two orders of magnitude lower than those of StyA/StyB from Pseudomonas sp. strain VLB120.
Collapse
|
41
|
Characterization of a gene cluster involved in 4-chlorocatechol degradation by Pseudomonas reinekei MT1. J Bacteriol 2009; 191:4905-15. [PMID: 19465655 DOI: 10.1128/jb.00331-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas reinekei MT1 has previously been reported to degrade 4- and 5-chlorosalicylate by a pathway with 4-chlorocatechol, 3-chloromuconate, 4-chloromuconolactone, and maleylacetate as intermediates, and a gene cluster channeling various salicylates into an intradiol cleavage route has been reported. We now report that during growth on 5-chlorosalicylate, besides a novel (chloro)catechol 1,2-dioxygenase, C12O(ccaA), a novel (chloro)muconate cycloisomerase, MCI(ccaB), which showed features not yet reported, was induced. This cycloisomerase, which was practically inactive with muconate, evolved for the turnover of 3-substituted muconates and transforms 3-chloromuconate into equal amounts of cis-dienelactone and protoanemonin, suggesting that it is a functional intermediate between chloromuconate cycloisomerases and muconate cycloisomerases. The corresponding genes, ccaA (C12O(ccaA)) and ccaB (MCI(ccaB)), were located in a 5.1-kb genomic region clustered with genes encoding trans-dienelactone hydrolase (ccaC) and maleylacetate reductase (ccaD) and a putative regulatory gene, ccaR, homologous to regulators of the IclR-type family. Thus, this region includes genes sufficient to enable MT1 to transform 4-chlorocatechol to 3-oxoadipate. Phylogenetic analysis showed that C12O(ccaA) and MCI(ccaB) are only distantly related to previously described catechol 1,2-dioxygenases and muconate cycloisomerases. Kinetic analysis indicated that MCI(ccaB) and the previously identified C12O(salD), rather than C12O(ccaA), are crucial for 5-chlorosalicylate degradation. Thus, MT1 uses enzymes encoded by a completely novel gene cluster for degradation of chlorosalicylates, which, together with a gene cluster encoding enzymes for channeling salicylates into the ortho-cleavage pathway, form an effective pathway for 4- and 5-chlorosalicylate mineralization.
Collapse
|
42
|
Martínková L, Uhnáková B, Pátek M, Nesvera J, Kren V. Biodegradation potential of the genus Rhodococcus. ENVIRONMENT INTERNATIONAL 2009; 35:162-77. [PMID: 18789530 DOI: 10.1016/j.envint.2008.07.018] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 07/02/2008] [Accepted: 07/22/2008] [Indexed: 05/24/2023]
Abstract
A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.
Collapse
Affiliation(s)
- Ludmila Martínková
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ-142 20 Prague 4, Czech Republic.
| | | | | | | | | |
Collapse
|
43
|
Nguyen TTH, Eiamphungporn W, Mäder U, Liebeke M, Lalk M, Hecker M, Helmann JD, Antelmann H. Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR). Mol Microbiol 2008; 71:876-94. [PMID: 19170879 DOI: 10.1111/j.1365-2958.2008.06568.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Quinones and alpha,beta-unsaturated carbonyls are naturally occurring electrophiles that target cysteine residues via thiol-(S)-alkylation. We analysed the global expression profile of Bacillus subtilis to the toxic carbonyls methylglyoxal (MG) and formaldehyde (FA). Both carbonyl compounds cause a stress response characteristic for thiol-reactive electrophiles as revealed by the induction of the Spx, CtsR, CymR, PerR, ArsR, CzrA, CsoR and SigmaD regulons. MG and FA triggered also a SOS response which indicates DNA damage. Protection against FA is mediated by both the hxlAB operon, encoding the ribulose monophosphate pathway for FA fixation, and a thiol-dependent formaldehyde dehydrogenase (AdhA) and DJ-1/PfpI-family cysteine proteinase (YraA). The adhA-yraA operon and the yraC gene, encoding a gamma-carboxymuconolactone decarboxylase, are positively regulated by the MerR-family regulator, YraB(AdhR). AdhR binds specifically to its target promoters which contain a 7-4-7 inverted repeat (CTTAAAG-N4-CTTTAAG) between the -35 and -10 elements. Activation of adhA-yraA transcription by AdhR requires the conserved Cys52 residue in vivo. We speculate that AdhR is redox-regulated via thiol-(S)-alkylation by aldehydes and that AdhA and YraA are specifically involved in reduction of aldehydes and degradation or repair of damaged thiol-containing proteins respectively.
Collapse
Affiliation(s)
- Thi Thu Huyen Nguyen
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487 Greifswald, Germany
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Pérez-Pantoja D, De la Iglesia R, Pieper DH, González B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134. FEMS Microbiol Rev 2008; 32:736-94. [DOI: 10.1111/j.1574-6976.2008.00122.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
45
|
Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LFW, Krogfelt KA, Struve C, Triplett EW, Methé BA. Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 2008; 4:e1000141. [PMID: 18654632 PMCID: PMC2453333 DOI: 10.1371/journal.pgen.1000141] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 06/24/2008] [Indexed: 12/25/2022] Open
Abstract
We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.
Collapse
|
46
|
Tomás-Gallardo L, Canosa I, Santero E, Camafeita E, Calvo E, López JA, Floriano B. Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB. Proteomics 2008; 6 Suppl 1:S119-32. [PMID: 16544280 DOI: 10.1002/pmic.200500422] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rhodococcus sp. strain TFB is a versatile gram-positive bacterium able to grow on a wide variety of aromatic compounds as carbon and energy sources. Since the strain is refractory to genetic analysis, a proteomic approach was used to study the metabolic pathways involved in the catabolism of such compounds by analyzing differentially induced proteins. The most marked difference was observed when the proteome profiles of phthalate-grown cells were compared with those cultured in the presence of tetralin- or naphthalene, suggesting that different metabolic pathways are involved in the degradation of mono- and polyaromatic compounds. Comparison with the proteome of glucose-grown cells indicated that each pathway was specifically induced by the corresponding aromatic compound. A combination of proteomics and molecular biology led to the identification of 14 proteins (65-80% identical to known Pht proteins) that describe a complete pathway for the catabolism of phthalate to central metabolites via intradiol cleavage of protochatechuic acid. Chaperonins were also induced in phthalate-grown cells, indicating that growth on this compound induces a stress response. Absence of catabolite repression by glucose was observed by both transcriptional and proteome analysis, suggesting that Rhodococcus sp. strain TFB may have advantages over other tightly regulated strains in bioremediation.
Collapse
Affiliation(s)
- Laura Tomás-Gallardo
- Centro Andaluz de Biología del Desarrollo, Departamento de Ciencias Ambientales, Universidad Pablo de Olavide, Seville, Spain
| | | | | | | | | | | | | |
Collapse
|
47
|
Brown S, Babbitt P. Using the Structure-function Linkage Database to characterize functional domains in enzymes. ACTA ACUST UNITED AC 2008; Chapter 2:Unit 2.10. [PMID: 18428763 DOI: 10.1002/0471250953.bi0210s13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of newly sequenced enzymes and to correct misannotated functional assignments for enzymes currently in public databases. It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases.
Collapse
Affiliation(s)
- Shoshana Brown
- University of California, San Francisco, San Francisco, California, USA
| | | |
Collapse
|
48
|
Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 2008; 19:859-81. [PMID: 18421421 DOI: 10.1007/s10532-008-9189-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/28/2008] [Indexed: 11/29/2022]
Abstract
Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 approximately 643 kb (region A), with an additional 31 kb region at positions 4,711 approximately 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the beta-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.
Collapse
Affiliation(s)
- Seong-Jae Kim
- Division of Microbiology, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
| | | | | | | | | |
Collapse
|
49
|
Kwon SY, Kang BS, Kim GH, Kim KJ. Expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from Corynebacterium glutamicum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:944-6. [PMID: 18007046 DOI: 10.1107/s1744309107046386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 09/21/2007] [Indexed: 11/10/2022]
Abstract
p-Hydroxybenzoate hydroxylase (PHBH) is an FAD-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pOHB) to 3,4-dihydroxybenzoate in an NADPH-dependent reaction and plays an important role in the biodegradation of aromatic compounds. PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH(2)PO(4) and K(2)HPO(4) as precipitants. X-ray diffraction data were collected to a maximum resolution of 2.5 A on a synchrotron beamline. The crystal belongs to the hexagonal space group P6(3)22, with unit-cell parameters a = b = 94.72, c = 359.68 A, gamma = 120 degrees . The asymmetric unit contains two molecules, corresponding to a packing density of 2.65 A(3) Da(-1). The structure was solved by molecular replacement. Structure refinement is in progress.
Collapse
Affiliation(s)
- Soo Young Kwon
- Beamline Division, Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, South Korea
| | | | | | | |
Collapse
|
50
|
Lee SE, Seo JS, Keum YS, Lee KJ, Li QX. Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14. Proteomics 2007; 7:2059-69. [PMID: 17514677 DOI: 10.1002/pmic.200600489] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluoranthene is a polycyclic aromatic hydrocarbon (PAH) commonly present in PAH-contaminated soils. We studied fluoranthene catabolism and associated proteins in Mycobacterium sp. JS14, a bacterium isolated from a PAH-contaminated soil in Hilo (HI, USA). Fluoranthene degrades in at least three separated pathways via 1-indanone, 2',3'-dihydroxybiphenyl-2,3,-dicarboxylic acid, and naphthalene-1,8-dicarboxylic acid. Part of the diverse catabolism is converged into phthalate catabolism. An increased expression of 25 proteins related to fluoranthene catabolism is found with 1-D PAGE or 2-DE and nano-LC-MS/MS. Detection of fluoranthene catabolism associated proteins coincides well with its multiple degradation pathways that are mapped via metabolites identified. Among the up-regulated proteins, PAH ring-hydroxylating dioxygenase alpha-subunit and beta-subunit and 2,3-dihydroxybiphenyl 1,2-dioxygenase are notably induced. The up-regulation of trans-2-carboxybenzalpyruvate hydratase suggests that some of fluoranthene metabolites may be further degraded through aromatic dicarboxylic acid pathways. Catalase and superoxide dismutase were up-regulated to control unexpected oxidative stress during the fluoranthene catabolism. The up-regulation of chorismate synthase and nicotine-nucleotide phosphorylase may be necessary for sustaining shikimate pathway and pyrimidine biosynthesis, respectively. A fluoranthene degradation pathway for Mycobacterium sp. JS14 was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of fluoranthene degradation.
Collapse
Affiliation(s)
- Sung-Eun Lee
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 9682, USA
| | | | | | | | | |
Collapse
|