1
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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2
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Edwards S, León-Zayas R, Ditter R, Laster H, Sheehan G, Anderson O, Beattie T, Mellies JL. Microbial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria. Int J Mol Sci 2022; 23:5612. [PMID: 35628419 PMCID: PMC9146961 DOI: 10.3390/ijms23105612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches, we identified the key genes implicated in PET degradation within the consortium's pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, which has been observed to hydrolyze the oligomer BHET and the polymer PET. Besides the genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degradation-related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based assay, which, paired with an abundant number of plastic- and plasticizer-degrading enzymes, indicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation, including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer metabolism was also observed, including the generation of polyhydroxyalkanoate (PHA)/polyhydroxybutyrate (PHB) biopolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential.
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Affiliation(s)
- Sabrina Edwards
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Rosa León-Zayas
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Riyaz Ditter
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Helen Laster
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Grace Sheehan
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Oliver Anderson
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Toby Beattie
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Jay L. Mellies
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
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3
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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4
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Gómez-Álvarez H, Iturbe P, Rivero-Buceta V, Mines P, Bugg TDH, Nogales J, Díaz E. Bioconversion of lignin-derived aromatics into the building block pyridine 2,4-dicarboxylic acid by engineering recombinant Pseudomonas putida strains. BIORESOURCE TECHNOLOGY 2022; 346:126638. [PMID: 34971782 DOI: 10.1016/j.biortech.2021.126638] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
2,4 pyridine dicarboxylic acid (2,4 PDCA) is an analogue of terephthalate, and hence a target chemical in the field of bio-based plastics. Here, Pseudomonas putida KT2440 strains were engineered to efficiently drive the metabolism of lignin-derived monoaromatics towards 2,4 PDCA in a resting cells-based bioprocess that alleviates growth-coupled limitations and allows biocatalysts recycling. Native β-ketoadipate pathway was blocked by replacing protocatechuate 3,4-dioxygenase by the exogenous LigAB extradiol dioxygenase. Overexpression of pcaK encoding a transporter increased 8-fold 2,4 PDCA productivity from protocatechuate, reaching the highest value reported so far (0.58 g L-1h-1). Overexpression of the 4-hydroxybenzoate monooxygenase (pobA) speed up drastically the production of 2,4 PDCA from 4-hydroxybenzoate (0.056 g L-1h-1) or p-coumarate (0.012 g L-1h-1) achieving values 15-fold higher than those reported with Rhodococcus jostii biocatalysts. 2,4 PDCA was also bioproduced by using soda lignin as feedstock, paving the way for future polymeric lignin valorization approaches.
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Affiliation(s)
- Helena Gómez-Álvarez
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Iturbe
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain; Navarrabiomed, University of Navarra, Irunlarrea 3, 31008 Pamplona, Spain
| | - Virginia Rivero-Buceta
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Paul Mines
- Biome Bioplastics Ltd, North Road, Marchwood, Southampton SO40 4BL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Juan Nogales
- National Centre for Biotechnology, Spanish National Research Council, Darwin 3, 28049 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Eduardo Díaz
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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5
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Dong X, Li Y, Zhu R, Wang C, Ge S. Biotreatment of Cr(VI) and pyrene combined water pollution by loofa-immobilized bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:45619-45628. [PMID: 33871775 DOI: 10.1007/s11356-021-13893-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Hexavalent chromium (Cr(VI)) and pyrene are toxic pollutants that are difficult to remediate from soils and wastewater. Serratia sp. strains have been previously demonstrated to remove either Cr(VI) or pyrene and here a new isolate, called the Z6 strain, was demonstrated to remove both simultaneously. The removal occurs primarily by Cr(VI) reduction and pyrene biodegradation, and genome analysis suggests the removal mechanisms are the putative chromate reductase and two assumable pathways of pyrene degradation. The Z6 strain effectively removed most Cr(VI) (up to approximately 86%) and pyrene (up to approximately 57%) in seven different types of wastewater after 7 days of biotreatment. Additionally, the carrier loofa used for bacteria immobilization did not change the kinetics of Cr(VI) reduction or pyrene degradation. The carrier loofa was also effective for multiple uses, with removal capacity not being significantly affected over the first seven cycles with the same carrier loofa. These results provide data for developing practical biotreatment applications of Cr(VI) and pyrene contaminated sites.
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Affiliation(s)
- Xinjiao Dong
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang Province, China
| | - Yaru Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang Province, China
| | - Rui Zhu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang Province, China
| | - Chuanhua Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang Province, China
| | - Shimei Ge
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang Province, China.
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6
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Wang W, Li Q, Zhang L, Cui J, Yu H, Wang X, Ouyang X, Tao F, Xu P, Tang H. Genetic mapping of highly versatile and solvent-tolerant Pseudomonas putida B6-2 (ATCC BAA-2545) as a 'superstar' for mineralization of PAHs and dioxin-like compounds. Environ Microbiol 2021; 23:4309-4325. [PMID: 34056829 DOI: 10.1111/1462-2920.15613] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and dioxin-like compounds, including sulfur, nitrogen and oxygen heterocycles, are widespread and toxic environmental pollutants. A wide variety of microorganisms capable of growing with aromatic polycyclic compounds are essential for bioremediation of the contaminated sites and the Earth's carbon cycle. Here, cells of Pseudomonas putida B6-2 (ATCC BAA-2545) grown in the presence of biphenyl (BP) are able to simultaneously degrade PAHs and their derivatives, even when they are present as mixtures, and tolerate high concentrations of extremely toxic solvents. Genetic analysis of the 6.37 Mb genome of strain B6-2 reveals coexistence of gene clusters responsible for central catabolic systems of aromatic compounds and for solvent tolerance. We used functional transcriptomics and proteomics to identify the candidate genes associated with catabolism of BP and a mixture of BP, dibenzofuran, dibenzothiophene and carbazole. Moreover, we observed dynamic changes in transcriptional levels with BP, including in metabolic pathways of aromatic compounds, chemotaxis, efflux pumps and transporters potentially involved in adaptation to PAHs. This study on the highly versatile activities of strain B6-2 suggests it to be a potentially useful model for bioremediation of polluted sites and for investigation of biochemical, genetic and evolutionary aspects of Pseudomonas.
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Affiliation(s)
- Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qinggang Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Cui
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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7
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Moriuchi R, Dohra H, Kanesaki Y, Ogawa N. Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate. Biosci Biotechnol Biochem 2021; 85:1546-1561. [PMID: 33720310 DOI: 10.1093/bbb/zbab044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 01/05/2023]
Abstract
RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.
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Affiliation(s)
- Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan.,Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
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8
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Wada A, Prates ÉT, Hirano R, Werner AZ, Kamimura N, Jacobson DA, Beckham GT, Masai E. Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics. Metab Eng 2021; 64:167-179. [PMID: 33549838 DOI: 10.1016/j.ymben.2021.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H+ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using 14C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.
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Affiliation(s)
- Ayumu Wada
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Érica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ryo Hirano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
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9
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Zhang L, Hang P, Zhou XY, Qiao WJ, Jiang JD. Enantioselective Catabolism of the Two Enantiomers of the Phenoxyalkanoic Acid Herbicide Dichlorprop by Sphingopyxis sp. DBS4. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6967-6976. [PMID: 32530641 DOI: 10.1021/acs.jafc.0c01066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dichlorprop [(RS)-2-(2,4-dichlorophenoxy)propanoic acid; DCPP], an important phenoxyalkanoic acid herbicide (PAAH), is extensively used in the form of racemic mixtures (Rac-DCPP), and the environmental fates of both DCPP enantiomers [(R)-DCPP and (S)-DCPP] mediated by microorganisms are of great concern. In this study, a bacterial strain Sphingopyxis sp. DBS4 was isolated from contaminated soil and was capable of utilizing both (R)-DCPP and (S)-DCPP as the sole carbon source for growth. Strain DBS4 preferentially catabolized (S)-DCPP as compared to (R)-DCPP. The optimal conditions for Rac-DCPP degradation by strain DBS4 were 30 °C and pH 7.0. In addition to Rac-DCPP, other PAAHs such as (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid, 2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid, and 2,4-dichlorophenoxyacetic acid butyl ester could also be catabolized by strain DBS4. Bioremediation of Rac-DCPP-contaminated soil by inoculation of strain DBS4 exhibited an effective removal of both (R)-DCPP and (S)-DCPP from the soil. Due to its broad substrate spectrum, strain DBS4 showed great potential in the bioremediation of PAAH-contaminated sites.
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Ping Hang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xi-Yi Zhou
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Wen-Jing Qiao
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, 210095 Nanjing, China
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10
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Tan Z, Clomburg JM, Cheong S, Qian S, Gonzalez R. A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 2020. [DOI: 10.1038/s41929-020-0471-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Quantifying secondary transport at single-molecule resolution. Nature 2019; 575:528-534. [PMID: 31723269 DOI: 10.1038/s41586-019-1747-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/07/2019] [Indexed: 01/07/2023]
Abstract
Secondary active transporters, which are vital for a multitude of physiological processes, use the energy of electrochemical ion gradients to power substrate transport across cell membranes1,2. Efforts to investigate their mechanisms of action have been hampered by their slow transport rates and the inherent limitations of ensemble methods. Here we quantify the activity of individual MhsT transporters, which are representative of the neurotransmitter:sodium symporter family of secondary transporters3, by imaging the transport of individual substrate molecules across lipid bilayers at both single- and multi-turnover resolution. We show that MhsT is active only when physiologically oriented and that the rate-limiting step of the transport cycle varies with the nature of the transported substrate. These findings are consistent with an extracellular allosteric substrate-binding site that modulates the rate-limiting aspects of the transport mechanism4,5, including the rate at which the transporter returns to an outward-facing state after the transported substrate is released.
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12
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Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol Adv 2019; 37:107396. [PMID: 31075306 DOI: 10.1016/j.biotechadv.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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13
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D'Arrigo I, Cardoso JGR, Rennig M, Sonnenschein N, Herrgård MJ, Long KS. Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:87-97. [PMID: 30298597 DOI: 10.1111/1758-2229.12704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modelling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.
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Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - João G R Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Maja Rennig
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
| | - Katherine S Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kongens Lyngby, Denmark
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14
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Lindemann D, Westerwalbesloh C, Kohlheyer D, Grünberger A, von Lieres E. Microbial single-cell growth response at defined carbon limiting conditions. RSC Adv 2019; 9:14040-14050. [PMID: 35519298 PMCID: PMC9064036 DOI: 10.1039/c9ra02454a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/16/2019] [Indexed: 12/22/2022] Open
Abstract
Using microfluidic single-cell cultivation technologies and modelling we examined how single-cell growth at defined carbon conditions, ranging from strongly limiting conditions to a carbon surplus, influenced cell-to-cell variability.
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Affiliation(s)
- Dorina Lindemann
- Institute of Bio- and Geosciences
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- Jülich 52425
- Germany
| | | | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- Jülich 52425
- Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- Jülich 52425
- Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- Jülich 52425
- Germany
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15
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Zhang R, Li C, Wang J, Yan Y. Microbial Ligninolysis: Toward a Bottom-Up Approach for Lignin Upgrading. Biochemistry 2018; 58:1501-1510. [DOI: 10.1021/acs.biochem.8b00920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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16
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Shin B, Park C, Imlay JA, Park W. 4-Hydroxybenzaldehyde sensitizes Acinetobacter baumannii to amphenicols. Appl Microbiol Biotechnol 2018; 102:2323-2335. [PMID: 29387955 DOI: 10.1007/s00253-018-8791-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/02/2018] [Accepted: 01/16/2018] [Indexed: 12/21/2022]
Abstract
Bacterial metabolism modulated by environmental chemicals could alter antibiotic susceptibility. 4-Hydroxybenzaldehyde (4-HBA), which cannot support the growth of Acinetobacter baumannii, exhibited synergism only with amphenicol antibiotics including chloramphenicol (CAM) and thiamphenicol. Interestingly, this synergistic effect was not observed with other growth-supporting, structurally similar compounds such as 4-hydroxybenzoate. Transcriptomic analysis demonstrated that genes involved in protocatechuate metabolism (pca genes) and osmotic stress (bet genes) were significantly upregulated by 4-HBA and CAM treatment. The 14C-labeled CAM influx was lower in a pcaK1 (encoding a transporter of protocatechuate) deletion mutant and was higher in the pcaK1 overexpressing cells relative to that in the wild type upon 4-HBA treatment. Our kinetic data using 14C-labeled CAM clearly showed that CAM uptake is possibly through facilitated diffusion. Deletion of pcaK1 did not result in the elimination of CAM influx, indicating that CAM does not enter only through PcaK1. The amount of 4-HBA in the culture supernatant was, however, unaffected during the test conditions, validating that it was not metabolized by the bacteria. CAM resistant A. baumannii cells derived by serial passages through CAM-amended media exhibited lower level of pcaK1 gene expression. These results led us to conclude that the activation of PcaK1 transporter is probably linked to cellular CAM susceptibility. This is the first report showing a relationship between CAM influx and aromatic compound metabolism in A. baumannii.
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Affiliation(s)
- Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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17
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Ravi K, García-Hidalgo J, Gorwa-Grauslund MF, Lidén G. Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost. Appl Microbiol Biotechnol 2017; 101:5059-5070. [PMID: 28299400 PMCID: PMC5486835 DOI: 10.1007/s00253-017-8211-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 11/29/2022]
Abstract
Starting from mature vegetable compost, four bacterial strains were selected using a lignin-rich medium. 16S ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. for three out of four isolates. Further characterization of growth on mixtures of six selected lignin model compounds (vanillin, vanillate, 4-hydroxybenzoate, p-coumarate, benzoate, and ferulate) was carried out with three of the Pseudomonas isolates and in addition with the strain Pseudomonas putida KT2440 from a culture collection. The specific growth rates on benzoate, p-coumarate, and 4-hydroxybenzoate were considerably higher (0.26–0.27 h−1) than those on ferulate and vanillate (0.21 and 0.22 h−1), as were the uptake rates. There was no direct growth of P. putida KT2440 on vanillin, but instead, vanillin was rapidly converted into vanillate at a rate of 4.87 mmol (gCDW h)−1 after which the accumulated vanillate was taken up. The growth curve reflected a diauxic growth when mixtures of the model compounds were used as carbon source. Vanillin, 4-hydroxybenzoate, and benzoate were preferentially consumed first, whereas ferulate was always the last substrate to be taken in. These results contribute to a better understanding of the aromatic metabolism of P. putida in terms of growth and uptake rates, which will be helpful for the utilization of these bacteria as cell factories for upgrading lignin-derived mixtures of aromatic molecules.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Marie F Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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18
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Wang H, Zhi XY, Qiu J, Shi L, Lu Z. Characterization of a Novel Nicotine Degradation Gene Cluster ndp in Sphingomonas melonis TY and Its Evolutionary Analysis. Front Microbiol 2017; 8:337. [PMID: 28337179 PMCID: PMC5343071 DOI: 10.3389/fmicb.2017.00337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Sphingomonas melonis TY utilizes nicotine as a sole source of carbon, nitrogen, and energy through a variant of the pyridine and pyrrolidine pathways (VPP). A 31-kb novel nicotine-degrading gene cluster, ndp, in strain TY exhibited a different genetic organization with the vpp cluster in strains Ochrobactrum rhizosphaerae SJY1 and Agrobacterium tumefaciens S33. Genes in vpp were separated by a 20-kb interval sequence, while genes in ndp were localized together. Half of the homolog genes were in different locus in ndp and vpp. Moreover, there was a gene encoding putative transporter of nicotine or other critical metabolite in ndp. Among the putative nicotine-degrading related genes, the nicotine hydroxylase, 6-hydroxy-L-nicotine oxidase, 6-hydroxypseudooxynicotine oxidase, and 6-hydroxy-3-succinyl-pyridine monooxygenase responsible for catalyzing the transformation of nicotine to 2, 5-dihydropyridine in the initial four steps of the VPP were characterized. Hydroxylation at C6 of the pyridine ring and dehydrogenation at the C2–C3 bond of the pyrrolidine ring were the key common reactions in the VPP, pyrrolidine and pyridine pathways. Besides, VPP and pyrrolidine pathway shared the same latter part of metabolic pathway. After analysis of metabolic genes in the pyridine, pyrrolidine, and VPP pathways, we found that both the evolutionary features and metabolic mechanisms of the VPP were more similar to the pyrrolidine pathway. The linked ndpHFEG genes shared by the VPP and pyrrolidine pathways indicated that these two pathways might share the same origin, but variants were observed in some bacteria. And we speculated that the pyridine pathway was distributed in Gram-positive bacteria and the VPP and pyrrolidine pathways were distributed in Gram-negative bacteria by using comprehensive homologs searching and phylogenetic tree construction.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University Kunming, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Longxiang Shi
- Institution of System Engineering, College of Computer Science and Technology, Zhejiang University Hangzhou, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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19
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Wang H, Xie C, Zhu P, Zhou NY, Lu Z. Two Novel Sets of Genes Essential for Nicotine Degradation by Sphingomonas melonis TY. Front Microbiol 2017; 7:2060. [PMID: 28144232 PMCID: PMC5239795 DOI: 10.3389/fmicb.2016.02060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
Nicotine is a type of environmental pollutant present in the tobacco waste that is generated during tobacco manufacturing. Sphingomonas melonis TY can utilize nicotine as a sole source of carbon, nitrogen and energy via a variant of the pyridine and pyrrolidine pathway (the VPP pathway). In this study, we report the identification of two novel sets of genes, ndrA1A2A3, and ndrB1B2B3B4, which are crucial for nicotine degradation by strain TY. ndrA1A2A3 and ndrB1B2B3B4 exhibit similarity with both nicotine dehydrogenase ndh from Arthrobacter nicotinovorans and nicotine hydroxylase vppA from Ochrobactrum sp. SJY1. The transcriptional levels of ndrA1A2A3 and ndrB1B2B3B4 in strain TY were significantly upregulated in the presence of nicotine. Furthermore, ndrA1 or ndrB2 knockout resulted in a loss of the ability to degrade nicotine, whereas gene complementation restored the capacity of each mutant to utilize nicotine for growth. Biodegradation assays indicated that the mutant strains retained the ability to degrade the first intermediate in the pathway, 6-hydroxynicotine (6 HN). However, heterologous expression of ndrA1A2A3 and ndrB1B2B3B4 did not confer nicotine dehydrogenase activity to E. coli DH5α, Pseudomonas putida KT2440 or Sphingomonas aquatilis. These results provide information on the VPP pathway of nicotine degradation in S. melonis TY, and we conclude that these two sets of genes have essential functions in the conversion of nicotine to 6 HN in strain TY.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Cuixiao Xie
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Panpan Zhu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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20
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Opportunities and challenges in biological lignin valorization. Curr Opin Biotechnol 2016; 42:40-53. [DOI: 10.1016/j.copbio.2016.02.030] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/24/2016] [Indexed: 02/08/2023]
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21
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Huang Z, Ni B, Jiang CY, Wu YF, He YZ, Parales RE, Liu SJ. Direct sensing and signal transduction during bacterial chemotaxis toward aromatic compounds inComamonas testosteroni. Mol Microbiol 2016; 101:224-37. [DOI: 10.1111/mmi.13385] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Zhou Huang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Bin Ni
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- IMCAS-RCEECAS Joint Laboratory for Environmental Microbial Technology; Beijing China
| | - Yu-Fan Wu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yun-Zhe He
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Rebecca E. Parales
- Department of Microbiology and Molecular Genetics; University of California; Davis CA 95616 USA
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
- IMCAS-RCEECAS Joint Laboratory for Environmental Microbial Technology; Beijing China
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22
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Fernández M, Morel B, Corral-Lugo A, Krell T. Identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives. Mol Microbiol 2015; 99:34-42. [PMID: 26355499 DOI: 10.1111/mmi.13215] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 11/30/2022]
Abstract
Chemotaxis is an essential mechanism that enables bacteria to move toward favorable ecological niches. Escherichia coli, the historical model organism for studying chemotaxis, has five well-studied chemoreceptors. However, many bacteria with different lifestyle have more chemoreceptors, most of unknown function. Using a high throughput screening approach, we identified a chemoreceptor from Pseudomonas putida KT2440, named McpH, which specifically recognizes purine and its derivatives, adenine, guanine, xanthine, hypoxanthine and uric acid. The latter five compounds form part of the purine degradation pathway, permitting their use as sole nitrogen sources. Isothermal titration calorimetry studies show that these six compounds bind McpH-Ligand Binding Domain (LBD) with very similar affinity. In contrast, non-metabolizable purine derivatives (caffeine, theophylline, theobromine), nucleotides, nucleosides or pyrimidines are unable to bind McpH-LBD. Mutation of mcpH abolished chemotaxis toward the McpH ligands identified - a phenotype that is restored by complementation. This is the first report on bacterial chemotaxis to purine derivatives and McpH the first chemoreceptor described that responds exclusively to intermediates of a catabolic pathway, illustrating a clear link between metabolism and chemotaxis. The evolution of McpH may reflect a saprophytic lifestyle, which would have exposed the studied bacterium to high concentrations of purines produced by nucleic acid degradation.
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Affiliation(s)
- Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008, Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008, Granada, Spain
| | - Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008, Granada, Spain
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23
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Parales RE, Luu RA, Hughes JG, Ditty JL. Bacterial chemotaxis to xenobiotic chemicals and naturally-occurring analogs. Curr Opin Biotechnol 2015; 33:318-26. [DOI: 10.1016/j.copbio.2015.03.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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24
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Luu RA, Kootstra JD, Nesteryuk V, Brunton CN, Parales JV, Ditty JL, Parales RE. Integration of chemotaxis, transport and catabolism inPseudomonas putidaand identification of the aromatic acid chemoreceptor PcaY. Mol Microbiol 2015; 96:134-47. [DOI: 10.1111/mmi.12929] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Rita A. Luu
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Joshua D. Kootstra
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Vasyl Nesteryuk
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Ceanne N. Brunton
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Juanito V. Parales
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Jayna L. Ditty
- Department of Biology; University of St. Thomas; St. Paul MN USA
| | - Rebecca E. Parales
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
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25
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Seralathan MV, Sivanesan S, Nargunanathan S, Bafana A, Kannan K, Chakrabarti T. Chemotaxis-based endosulfan biotransformation: enrichment and isolation of endosulfan-degrading bacteria. ENVIRONMENTAL TECHNOLOGY 2015; 36:60-67. [PMID: 25409584 DOI: 10.1080/09593330.2014.937464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The study was conducted to isolate endosulfan biotransforming or biodegrading microbes based on chemotaxis. Pseudomonas aeruginosa strain KKc3, Ochrobactrum sp. strain KKc4, Achromobacter xylosoxidans strain KKc6 and Bacillus megaterium KKc7 were isolated based on their migration towards endosulfan in a soil column. Out of the four bacteria, B. megaterium converted endosulfan into toxic metabolite endosulfan sulphate, while the other three bacteria followed the non-toxic endosulfan diol pathway. The mixed culture system consisting of P. aeruginosa, Ochrobactrum sp and A. xylosoxidans could remove 94% of total endosulfan by using endosulfan as the sole source of sulphur.
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Affiliation(s)
- Muhil Vannan Seralathan
- a Environmental Health Division , National Environmental Engineering Research Institute , Nagpur 440022 , India
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26
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Parales RE, Nesteryuk V, Hughes JG, Luu RA, Ditty JL. Cytosine chemoreceptor McpC in Pseudomonas putida F1 also detects nicotinic acid. MICROBIOLOGY-SGM 2014; 160:2661-2669. [PMID: 25294107 DOI: 10.1099/mic.0.081968-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Soil bacteria are generally capable of growth on a wide range of organic chemicals, and pseudomonads are particularly adept at utilizing aromatic compounds. Pseudomonads are motile bacteria that are capable of sensing a wide range of chemicals, using both energy taxis and chemotaxis. Whilst the identification of specific chemicals detected by the ≥26 chemoreceptors encoded in Pseudomonas genomes is ongoing, the functions of only a limited number of Pseudomonas chemoreceptors have been revealed to date. We report here that McpC, a methyl-accepting chemotaxis protein in Pseudomonas putida F1 that was previously shown to function as a receptor for cytosine, was also responsible for the chemotactic response to the carboxylated pyridine nicotinic acid.
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Affiliation(s)
- Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Vasyl Nesteryuk
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Jonathan G Hughes
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Rita A Luu
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Jayna L Ditty
- Department of Biology, University of St Thomas, St Paul, MN, USA
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27
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Pernstich C, Senior L, MacInnes KA, Forsaith M, Curnow P. Expression, purification and reconstitution of the 4-hydroxybenzoate transporter PcaK from Acinetobacter sp. ADP1. Protein Expr Purif 2014; 101:68-75. [PMID: 24907408 PMCID: PMC4148202 DOI: 10.1016/j.pep.2014.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 11/19/2022]
Abstract
The aromatic acid transporter PcaK was recombinantly expressed and purified. PcaK is a stable homotrimer in n-dodecyl-β-d-maltoside. A reconstituted assay shows asymmetric transport. The electrical component of the proton gradient drives transport. Unexpectedly, PcaK is active in transporting 2-hydroxybenzoates.
The aromatic acid:H+ symporter family of integral membrane proteins play an important role in the microbial metabolism of aromatic compounds. Here, we show that the 4-hydroxybenzoate transporter from Acinetobacter sp. ADP1, PcaK, can be successfully overexpressed in Escherichia coli and purified by affinity chromatography. Affinity-purified PcaK is a stable, monodisperse homotrimer in the detergent n-dodecyl-β-d-maltopyranoside supplemented with cholesteryl hemisuccinate. The purified protein has α-helical secondary structure and can be reconstituted to a functional state in synthetic proteoliposomes. Asymmetric substrate transport was observed when proteoliposomes were energized by applying an electrochemical proton gradient (Δμ‾H+) or a membrane potential (ΔΨ) but not by ΔpH alone. PcaK was selective in transporting 4-hydroxybenzoate and 3,4-dihydroxybenzoate over closely related compounds, confirming previous reports on substrate specificity. However, PcaK also showed an unexpected preference for transporting 2-hydroxybenzoates. These results provide the basis for further detailed studies of the structure and function of this family of transporters.
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Affiliation(s)
| | - Laura Senior
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1TD, UK
| | | | - Marc Forsaith
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
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28
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mhpT encodes an active transporter involved in 3-(3-hydroxyphenyl)propionate catabolism by Escherichia coli K-12. Appl Environ Microbiol 2013; 79:6362-8. [PMID: 23934492 DOI: 10.1128/aem.02110-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli K-12 utilizes 3-(3-hydroxyphenyl)propionate (3HPP) as a sole carbon and energy source. Among the genes in its catabolic cluster in the genome, mhpT was proposed to encode a hypothetical transporter. Since no transporter for 3HPP uptake has been identified, we investigated whether MhpT is responsible for 3HPP uptake. MhpT fused with green fluorescent protein was found to be located at the periphery of cells by confocal microscopy, consistent with localization to the cytoplasmic membrane. Gene knockout and complementation studies clearly indicated that mhpT is essential for 3HPP catabolism in E. coli K-12 W3110 at pH 8.2. Uptake assays with (14)C-labeled substrates demonstrated that strain W3110 and strain W3110ΔmhpT containing recombinant MhpT specifically transported 3HPP but not benzoate, 3-hydroxybenzoate, or gentisate into cells. Energy dependence assays suggested that MhpT-mediated 3HPP transport was driven by the proton motive force. The change of Ala-272 of MhpT to a histidine, surprisingly, resulted in enhanced transport activity, and strain W3110ΔmhpT containing the MhpT A272H mutation had a slightly higher growth rate than the wild-type strain at pH 8.2. Hence, we demonstrated that MhpT is a specific 3HPP transporter and vital for E. coli K-12 W3110 growth on this substrate under basic conditions.
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29
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Functional characterization of the bacterial iac genes for degradation of the plant hormone indole-3-acetic acid. J Chem Ecol 2013; 39:942-51. [PMID: 23881445 DOI: 10.1007/s10886-013-0324-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 06/29/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
Abstract
Pseudomonas putida 1290 is a model organism for the study of bacterial degradation of the plant hormone indole-3-acetic acid (IAA). This property is encoded by the iac gene cluster. Insertional inactivation and/or deletion of individual iac genes and heterologous expression of the gene cluster in Escherichia coli were combined with mass spectrometry to demonstrate that iac-based degradation of IAA is likely to involve 2-hydroxy-IAA, 3-hydroxy-2-oxo-IAA, and catechol as intermediates. The first gene of the cluster, iacA encodes for the first step in the pathway, and also can convert indole to indoxyl to produce the blue pigment indigo. Transcriptional profiling of iac genes in P. putida 1290 revealed that they were induced in the presence of IAA. Based on results with an iacR knockout, we propose that this gene codes for a repressor of iacA expression and that exposure to IAA relieves this repression. Transformation of P. putida KT2440 (which cannot degrade IAA) with the iac gene cluster conferred the ability to grow on IAA as a sole source of carbon and energy, but not the ability to chemotaxi towards IAA. We could show such tactic response for P. putida 1290, thus representing the first demonstration of bacterial chemotaxis towards IAA. We discuss the ecological significance of our findings, and specifically the following question: under what circumstances do bacteria with the ability to degrade, recognize, and move towards IAA have a selective advantage?
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Shen X, Hu H, Peng H, Wang W, Zhang X. Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics 2013; 14:271. [PMID: 23607266 PMCID: PMC3644233 DOI: 10.1186/1471-2164-14-271] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 04/16/2013] [Indexed: 12/21/2022] Open
Abstract
Background Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity. Results The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained the cus operon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability. Conclusions Comparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.
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Affiliation(s)
- Xuemei Shen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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Simultaneous catabolism of plant-derived aromatic compounds results in enhanced growth for members of the Roseobacter lineage. Appl Environ Microbiol 2013; 79:3716-23. [PMID: 23563956 DOI: 10.1128/aem.00405-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, including Sagittula stellata E-37, utilize aromatic compounds as primary growth substrates. The genome sequence of S. stellata contains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists in S. stellata when the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them, p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated that S. stellata simultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed when S. stellata was provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member, Ruegeria pomeroyi DSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.
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Romero-Silva MJ, Méndez V, Agulló L, Seeger M. Genomic and functional analyses of the gentisate and protocatechuate ring-cleavage pathways and related 3-hydroxybenzoate and 4-hydroxybenzoate peripheral pathways in Burkholderia xenovorans LB400. PLoS One 2013; 8:e56038. [PMID: 23418504 PMCID: PMC3572157 DOI: 10.1371/journal.pone.0056038] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/04/2013] [Indexed: 11/24/2022] Open
Abstract
In this study, the gentisate and protocatechuate pathways in Burkholderia xenovorans LB400 were analyzed by genomic and functional approaches, and their role in 3-hydroxybenzoate (3-HBA) and 4-hydroxybenzoate (4-HBA) degradation was proposed. The LB400 genome possesses two identical mhbRTDHI gene clusters encoding the gentisate pathway and one mhbM gene encoding a 3-HBA 6-hydroxylase that converts 3-HBA into gentisate. The pca genes encoding the protocatechuate pathway and the pobA gene encoding the 4-HBA 3-monooxygenase that oxidizes 4-HBA into protocatechuate are arranged in gene clusters and single genes mainly at the minor chromosome, but also at the major chromosome and the megaplasmid. Strain LB400 was able to grow on gentisate, protocatechuate, 3-HBA and 4-HBA. Transcriptional analyses showed that the mhbD gene encoding the gentisate 1,2-dioxygenase was expressed during growth on 3-HBA, 4-HBA and gentisate, whereas the pcaG gene encoding the protocatechuate 3,4-dioxygenase was expressed only during growth on 4-HBA and protocatechuate. The mhbM gene encoding the 3-HBA 6-hydroxylase was transcribed in strain LB400 during growth on HBAs, gentisate, protocatechuate and glucose. The pobA gene encoding the 4-HBA 3-monooxygenase was expressed during growth on HBAs and glucose. 3-HBA- and 4-HBA-grown LB400 cells showed gentisate 1,2-dioxygenase activity, whereas protocatechuate 3,4-dioxygenase activity was observed only in 4-HBA-grown cells. The mhbR gene encoding a MarR-type transcriptional regulator that probably regulates the expression of the MhbT transporter, and the pcaQ and pcaR genes encoding LysR-type transcriptional regulators that regulate pcaHG and pcaIJBDC genes, respectively, were transcribed during growth on both HBAs, gentisate, protocatechuate and glucose, suggesting a basal constitutive expression. The results indicate active gentisate, protocatechuate, 3-HBA and 4-HBA catabolic pathways in B. xenovorans LB400 and suggest that 3-HBA is channeled exclusively through the gentisate route, whereas 4-HBA is funneled into the protocatechuate central pathway and potentially into the gentisate pathway.
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Affiliation(s)
- María José Romero-Silva
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Loreine Agulló
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center for Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
- * E-mail:
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Taxis of Pseudomonas putida F1 toward phenylacetic acid is mediated by the energy taxis receptor Aer2. Appl Environ Microbiol 2013; 79:2416-23. [PMID: 23377939 DOI: 10.1128/aem.03895-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The phenylacetic acid (PAA) degradation pathway is a widely distributed funneling pathway for the catabolism of aromatic compounds, including the environmental pollutants styrene and ethylbenzene. However, bacterial chemotaxis to PAA has not been studied. The chemotactic strain Pseudomonas putida F1 has the ability to utilize PAA as a sole carbon and energy source. We identified a putative PAA degradation gene cluster (paa) in P. putida F1 and demonstrated that PAA serves as a chemoattractant. The chemotactic response was induced during growth with PAA and was dependent on PAA metabolism. A functional cheA gene was required for the response, indicating that PAA is sensed through the conserved chemotaxis signal transduction system. A P. putida F1 mutant lacking the energy taxis receptor Aer2 was deficient in PAA taxis, indicating that Aer2 is responsible for mediating the response to PAA. The requirement for metabolism and the role of Aer2 in the response indicate that P. putida F1 uses energy taxis to detect PAA. We also revealed that PAA is an attractant for Escherichia coli; however, a mutant lacking a functional Aer energy receptor had a wild-type response to PAA in swim plate assays, suggesting that PAA is detected through a different mechanism in E. coli. The role of Aer2 as an energy taxis receptor provides the potential to sense a broad range of aromatic growth substrates as chemoattractants. Since chemotaxis has been shown to enhance the biodegradation of toxic pollutants, the ability to sense PAA gradients may have implications for the bioremediation of aromatic hydrocarbons that are degraded via the PAA pathway.
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Ditty JL, Williams KM, Keller MM, Chen GY, Liu X, Parales RE. Integrating grant-funded research into the undergraduate biology curriculum using IMG-ACT. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:16-23. [PMID: 23382122 DOI: 10.1002/bmb.20662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 06/01/2023]
Abstract
It has become clear in current scientific pedagogy that the emersion of students in the scientific process in terms of designing, implementing, and analyzing experiments is imperative for their education; as such, it has been our goal to model this active learning process in the classroom and laboratory in the context of a genuine scientific question. Toward this objective, the National Science Foundation funded a collaborative research grant between a primarily undergraduate institution and a research-intensive institution to study the chemotactic responses of the bacterium Pseudomonas putida F1. As part of the project, a new Bioinformatics course was developed in which undergraduates annotate relevant regions of the P. putida F1 genome using Integrated Microbial Genomes Annotation Collaboration Toolkit, a bioinformatics interface specifically developed for undergraduate programs by the Department of Energy Joint Genome Institute. Based on annotations of putative chemotaxis genes in P. putida F1 and comparative genomics studies, undergraduate students from both institutions developed functional genomics research projects that evolved from the annotations. The purpose of this study is to describe the nature of the NSF grant, the development of the Bioinformatics lecture and wet laboratory course, and how undergraduate student involvement in the project that was initiated in the classroom has served as a springboard for independent undergraduate research projects.
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Affiliation(s)
- Jayna L Ditty
- Department of Biology, University of St. Thomas, St. Paul, MN, USA.
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Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, Rouy Z, Barbe V, Herrera AM, González V, Mavingui P. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation. Genes (Basel) 2012; 3:576-602. [PMID: 24705077 PMCID: PMC3899980 DOI: 10.3390/genes3040576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/24/2012] [Accepted: 09/13/2012] [Indexed: 11/29/2022] Open
Abstract
Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.
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Affiliation(s)
- Florence Wisniewski-Dyé
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Erika Acosta-Cruz
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Stéphanie Borland
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Benoît Drogue
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Claire Prigent-Combaret
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Zoé Rouy
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme CNRS UMR8030, France.
| | - Valérie Barbe
- Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - Alberto Mendoza Herrera
- Centro de Biotecnología Genómica, Instituto politécnico Nacional, 88710 Reynosa, Tamaulipas, México.
| | - Victor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Patrick Mavingui
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
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Ni B, Zhang Y, Chen DW, Wang BJ, Liu SJ. Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria. Appl Microbiol Biotechnol 2012; 97:6031-41. [DOI: 10.1007/s00253-012-4402-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/25/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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MhbT is a specific transporter for 3-hydroxybenzoate uptake by Gram-negative bacteria. Appl Environ Microbiol 2012; 78:6113-20. [PMID: 22729544 DOI: 10.1128/aem.01511-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae M5a1 is capable of utilizing 3-hydroxybenzoate via gentisate, and the 6.3-kb gene cluster mhbRTDHIM conferred the ability to grow on 3-hydroxybenzoate to Escherichia coli and Pseudomonas putida PaW340. Four of the six genes (mhbDHIM) encode enzymes converting 3-hydroxybenzoate to pyruvate and fumarate via gentisate. MhbR is a gene activator, and MhbT is a hypothetical protein belonging to the transporter of the aromatic acid/H(+) symporter family. Since a transporter for 3-hydrxybenzoate uptake has not been characterized to date, we investigated whether MhbT is responsible for the uptake of 3-hydroxybenzoate, its metabolic intermediate gentisate, or both. The MhbT-green fluorescent protein (GFP) fusion protein was located on the cytoplasmic membrane. P. putida PaW340 containing mhbRΔTDHIM could not grow on 3-hydroxybenzoate; however, supplying mhbT in trans allowed the bacterium to grow on the substrate. K. pneumoniae M5a1 and P. putida PaW340 containing recombinant MhbT transported (14)C-labeled 3-hydroxybenzoate but not (14)C-labeled gentisate and benzoate into the cells. Site-directed mutagenesis of two conserved amino acid residues (Asp-82 and Asp-314) and a less-conserved residue (Val-311) among the members of the symporter family in the hydrophilic cytoplasmic loops resulted in the loss of 3-hydroxybenzoate uptake by P. putida PaW340 carrying the mutant proteins. Hence, we demonstrated that MhbT is a specific 3-hydroxybenzoate transporter.
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Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS One 2012; 7:e35498. [PMID: 22545111 PMCID: PMC3335876 DOI: 10.1371/journal.pone.0035498] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Accepted: 03/19/2012] [Indexed: 01/26/2023] Open
Abstract
Benzoxazinoids, such as 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), are secondary metabolites in grasses. In addition to their function in plant defence against pests and diseases above-ground, benzoxazinoids (BXs) have also been implicated in defence below-ground, where they can exert allelochemical or antimicrobial activities. We have studied the impact of BXs on the interaction between maize and Pseudomonas putida KT2440, a competitive coloniser of the maize rhizosphere with plant-beneficial traits. Chromatographic analyses revealed that DIMBOA is the main BX compound in root exudates of maize. In vitro analysis of DIMBOA stability indicated that KT2440 tolerance of DIMBOA is based on metabolism-dependent breakdown of this BX compound. Transcriptome analysis of DIMBOA-exposed P. putida identified increased transcription of genes controlling benzoate catabolism and chemotaxis. Chemotaxis assays confirmed motility of P. putida towards DIMBOA. Moreover, colonisation essays in soil with Green Fluorescent Protein (GFP)-expressing P. putida showed that DIMBOA-producing roots of wild-type maize attract significantly higher numbers of P. putida cells than roots of the DIMBOA-deficient bx1 mutant. Our results demonstrate a central role for DIMBOA as a below-ground semiochemical for recruitment of plant-beneficial rhizobacteria during the relatively young and vulnerable growth stages of maize.
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Three types of taxis used in the response of Acidovorax sp. strain JS42 to 2-nitrotoluene. Appl Environ Microbiol 2012; 78:2306-15. [PMID: 22286989 DOI: 10.1128/aem.07183-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer.
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Pérez-Pantoja D, Donoso R, Agulló L, Córdova M, Seeger M, Pieper DH, González B. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. Environ Microbiol 2011; 14:1091-117. [PMID: 22026719 DOI: 10.1111/j.1462-2920.2011.02613.x] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The relevance of the β-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring-cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring-cleavage, catechol ortho ring-cleavage, homogentisate ring-cleavage and phenylacetyl-CoA ring-cleavage pathways found in at least 60% of genomes analysed. In general, a genus-specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus-specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Center for Advanced Studies in Ecology and Biodiversity, Millennium Nucleus in Plant Functional Genomics, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago, Chile
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MacLean AM, Haerty W, Golding GB, Finan TM. The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti. Microbiology (Reading) 2011; 157:2522-2533. [DOI: 10.1099/mic.0.050542-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The LysR protein PcaQ regulates the expression of genes encoding products relevant to the degradation of the aromatic acid protocatechuate (3,4-dihydroxybenzoate), and we have previously defined a PcaQ DNA-binding site located upstream of the target pcaDCHGB operon in Sinorhizobium meliloti. In this work, we show that PcaQ also regulates the expression of the S. meliloti smb20568-smb20787-smb20786-smb20785-smb20784 gene cluster, which is predicted to encode an ABC transport system. ABC transport systems have not been shown before to transport protocatechuate, and we have designated this gene cluster pcaMNVWX. The transcriptional start site of pcaM was mapped, and the predicted PcaQ DNA-binding site was located at −73 to −58 relative to this site. Results from electrophoretic mobility shift assays with purified PcaQ and from expression assays indicated that PcaQ activates expression of the transport system in the presence of protocatechuate. To investigate this transport system further, we generated a pcaM deletion mutant (predicted to encode the substrate-binding protein) and introduced a polar insertion mutation into pcaN, a gene that is predicted to encode a permease. These mutants grew poorly on protocatechuate, presumably because they fail to transport protocatechuate. Genome analyses revealed PcaQ-like DNA-binding sites encoded upstream of ABC transport systems in other members of the α-proteobacteria, and thus it appears likely that these systems are involved in the uptake of protocatechuate.
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Affiliation(s)
- Allyson M. MacLean
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - Wilfried Haerty
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - G. Brian Golding
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
| | - Turlough M. Finan
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada
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Zhang Y, Jiang Z, Cao B, Hu M, Wang Z, Dong X. Chemotaxis to atrazine and detection of a xenobiotic catabolic plasmid in Arthrobacter sp. DNS10. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2011; 19:2951-2958. [PMID: 22351258 DOI: 10.1007/s11356-012-0805-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
INTRODUCTION A plasmid named pDNS10 was detected from an atrazine-degrading strain Arthrobacter sp. DNS10 which has been isolated previously in our laboratory. MATERIALS AND METHODS In this paper, a special plasmid-detecting method and drop assays experiments were mainly used to achieve research goals. RESULTS AND DISCUSSION pDNS10 exhibited an excellent stability because it also could be detected even when the strain DNS10 has been subcultured under nonselective conditions for eight times. Over a 48-h incubation period, the OD(600) of samples inoculated with strain DNS10 and strain DNS10-ST (both of them contained pDNS10) were 0.31 ± 0.042 and 0.305 ± 0.034, respectively ,whereas the OD(600) of samples inoculated strain without pDNS10 (strain DNS10-PE) was only 0.138 ± 0.018. No atrazine was detected in the inoculated strain DNS10 and strain DNS10-ST samples at this period. Contrarily, the atrazine-degrading rate of strain DNS10-PE was only 5.23 ± 0.71%. Furthermore, both the two types of strains containing pDNS10 confirmed the presence of known degrading genes such as trzN, atzB, and atzC. It suggests that pDNS10 is an atrazine catabolic plasmid. In drop assays experiments, the wild-type strain DNS10 cells were chemotactically attracted to atrazine, whereas strain DNS10-PE showed no chemotaxis to atrazine and hydroxyatrazine. There was some relationship between atrazine degradation and the chemotactic response towards atrazine in strain DNS10. CONCLUSIONS The biochemical characteristics of pDNS10 and the chemotaxis characteristics of strain DNS10 could help us in better understanding of the mechanism of atrazine degradation by strain DNS10.
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Affiliation(s)
- Ying Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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2D motility tracking of Pseudomonas putida KT2440 in growth phases using video microscopy. J Biosci Bioeng 2011; 111:605-11. [PMID: 21334971 DOI: 10.1016/j.jbiosc.2011.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 01/07/2011] [Accepted: 01/10/2011] [Indexed: 11/20/2022]
Abstract
Pseudomonas putida KT2440 is a gram negative motile soil bacterium important in bioremediation and biotechnology. Thus, it is important to understand its motility characteristics as individuals and in populations. Population characteristics were determined using a modified Gompertz model. Video microscopy and imaging software were utilized to analyze two dimensional (2D) bacteria movement tracks to quantify individual bacteria behavior. It was determined that inoculum density increased the lag time as seeding densities decreased, and that the maximum specific growth rate decreased as seeding densities increased. Average bacterial velocity remained relatively similar throughout the exponential growth phase (~20.9 μm/s), while maximum velocities peak early in the exponential growth phase at a velocity of 51.2 μm/s. P. putida KT2440 also favors smaller turn angles indicating that they often continue in the same direction after a change in flagella rotation throughout the exponential growth phase.
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Mattozzi MDLP, Keasling JD. Rationally engineered biotransformation of p-nitrophenol. Biotechnol Prog 2010; 26:616-21. [DOI: 10.1002/btpr.382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Li D, Yan Y, Ping S, Chen M, Zhang W, Li L, Lin W, Geng L, Liu W, Lu W, Lin M. Genome-wide investigation and functional characterization of the beta-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC Microbiol 2010; 10:36. [PMID: 20137101 PMCID: PMC2907835 DOI: 10.1186/1471-2180-10-36] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs. Results In this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of Pseudomonas stutzeri A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The P. stutzeri A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the catR and pcaK genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the ben operon, while transcription from the catBC promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate. Conclusions The expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.
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Affiliation(s)
- Danhua Li
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
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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.
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Liu X, Parales RE. Bacterial chemotaxis to atrazine and related s-triazines. Appl Environ Microbiol 2009; 75:5481-8. [PMID: 19581468 PMCID: PMC2737934 DOI: 10.1128/aem.01030-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 06/24/2009] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strain ADP utilizes the human-made s-triazine herbicide atrazine as the sole nitrogen source. The results reported here demonstrate that atrazine and the atrazine degradation intermediates N-isopropylammelide and cyanuric acid are chemoattractants for strain ADP. In addition, the nonmetabolized s-triazine ametryn was also an attractant. The chemotactic response to these s-triazines was not specifically induced during growth with atrazine, and atrazine metabolism was not required for the chemotactic response. A cured variant of strain ADP (ADP M13-2) was attracted to s-triazines, indicating that the atrazine catabolic plasmid pADP-1 is not necessary for the chemotactic response and that atrazine degradation and chemotaxis are not genetically linked. These results indicate that atrazine and related s-triazines are detected by one or more chromosomally encoded chemoreceptors in Pseudomonas sp. strain ADP. We demonstrated that Escherichia coli is attracted to the s-triazine compounds N-isopropylammelide and cyanuric acid, and an E. coli mutant lacking Tap (the pyrimidine chemoreceptor) was unable to respond to s-triazines. These data indicate that pyrimidines and triazines are detected by the same chemoreceptor (Tap) in E. coli. We showed that Pseudomonas sp. strain ADP is attracted to pyrimidines, which are the naturally occurring structures closest to triazines, and propose that chemotaxis toward s-triazines may be due to fortuitous recognition by a pyrimidine chemoreceptor in Pseudomonas sp. strain ADP. In competition assays, the presence of atrazine inhibited chemotaxis of Pseudomonas sp. strain ADP to cytosine, and cytosine inhibited chemotaxis to atrazine, suggesting that pyrimidines and s-triazines are detected by the same chemoreceptor.
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Affiliation(s)
- Xianxian Liu
- Department of Microbiology, College of Biological Sciences, University of California, Davis, California 95616, USA
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3-Chlorobenzoate is taken up by a chromosomally encoded transport system in Cupriavidus necator JMP134. Microbiology (Reading) 2009; 155:2757-2765. [DOI: 10.1099/mic.0.029207-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cupriavidus necator JMP134(pJP4) is able to grow on 3-chlorobenzoate (3-CB), a model chloroaromatic pollutant. Catabolism of 3-CB is achieved via the expression of the chromosomally encoded benABCD genes and the tfd genes from plasmid pJP4. Since passive diffusion of benzoic acid derivatives at physiological pH is negligible, the uptake of this compound should be facilitated by a transport system. However, no transporter has so far been described to perform this function, and identification of chloroaromatic compound transporters has been limited. In this work, uptake experiments using 3-[ring-UL-14C]CB showed an inducible transport system in strain JMP134, whose expression is activated by 3-CB and benzoate. A similar level of 3-CB uptake was found for a mutant strain of JMP134, defective in chlorobenzoate degradation, indicating that metabolic drag is not an important component of the measured uptake rate. Competitive inhibitor assays showed that uptake of 3-CB was inhibited by benzoate and, to a lesser degree, by 3-CB and 3,5-dichlorobenzoate, but not by any of 12 other substituted benzoates tested. The expression of several gene candidates for this transport function was analysed by RT-PCR, including both permease-type and ABC-type ATP-dependent transporters. Induction of a chromosomally encoded putative permease transporter (benP gene) was found specifically in the presence of 3-CB or benzoate. A benP knockout mutant of strain JMP134 displayed an almost complete loss of 3-CB transport activity. This is to our knowledge the first report of a 3-CB transporter.
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Buck U, Grossart HP, Amann R, Pernthaler J. Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environ Microbiol 2009; 11:1854-65. [PMID: 19320716 DOI: 10.1111/j.1462-2920.2009.01910.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (HBA) was investigated in an artificially divided humic lake (Grosse Fuchskuhle, Germany). Two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. High total and cell-specific incorporation rates were observed for glucose and HBA in stratified and mixed waters respectively, but only a small fraction of bacteria visibly incorporated HBA. The oxic layer of the more humic-rich basin featured a significantly lower fraction of glucose incorporating cells and substantially higher proportions of acetate assimilating bacteria. Niche differentiation was observed in two betaproteobacterial populations: cells affiliated with the Polynucleobacter C subcluster efficiently incorporated acetate but little glucose, whereas the opposite was found for members of the R-BT065 clade. By contrast, leucine incorporation was variable in both taxa. Considering the high concentrations and rapid photochemical generation of organic acids in humic waters our results may help to explain the success of the Polynucleobacter C lineage in such habitats. Specific substrate or habitat preferences were also present in three subgroups of the actinobacterial acI lineage: The numerically dominant clade in oxic waters (acI-840-1) was absent in the anoxic zone and did not incorporate acetate. A second group (acI-840-2) was found both in the epi- and hypolimnion, whereas the third one (acI-840-3) only occurred in anoxic waters. Altogether our results suggest a constitutive preference for some substrates versus an adaptive utilization of others in the studied microbial groups.
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Affiliation(s)
- Ulrike Buck
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Gábor K, Hailesellasse Sene K, Smidt H, de Vos WM, van der Oost J. Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression. MICROBIOLOGY-SGM 2009; 154:3686-3696. [PMID: 19047736 DOI: 10.1099/mic.0.2008/021584-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene duplication and horizontal gene transfer play an important role in the evolution of prokaryotic genomes. We have investigated the role of three CprK paralogues from the cAMP receptor protein-fumarate and nitrate reduction regulator (CRP-FNR) family of transcriptional regulators that are encoded in the genome of Desulfitobacterium hafniense DCB-2 and possibly regulate expression of genes involved in the energy-conserving terminal reduction of organohalides (halorespiration). The results from in vivo and in vitro promoter probe assays show that two regulators (CprK1 and CprK2) have an at least partially overlapping effector specificity, with preference for ortho-chlorophenols, while meta-chlorophenols proved to be effectors for CprK4. The presence of a potential transposase-encoding gene in the vicinity of the cprK genes indicates that their redundancy is probably caused by mobile genetic elements. The CprK paralogues activated transcription from promoters containing a 14 bp inverted repeat (dehalobox) that closely resembles the FNR-box. We found a strong negative correlation between the rate of transcriptional activation and the number of nucleotide changes from the optimal dehalobox sequence (TTAAT-N4-ATTAA). Transcription was initiated by CprK4 from a promoter that is situated upstream of a gene encoding a methyl-accepting chemotaxis protein. This might be the first indication of taxis of an anaerobic bacterium to halogenated aromatic compounds.
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Affiliation(s)
- Krisztina Gábor
- Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703-HB, The Netherlands
| | - Kagnew Hailesellasse Sene
- Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703-HB, The Netherlands
| | - Hauke Smidt
- Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703-HB, The Netherlands
| | - Willem M de Vos
- Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703-HB, The Netherlands
| | - John van der Oost
- Wageningen University and Research Centre, Laboratory of Microbiology, Dreijenplein 10, Wageningen 6703-HB, The Netherlands
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