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Luangphai S, Thuptimdang P, Buddhiranon S, Chanawanno K. Aza-BODIPY-based logic gate chemosensors and their applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124806. [PMID: 39018674 DOI: 10.1016/j.saa.2024.124806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/06/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Dimethylaniline-substituted aza-BODIPY dyes (DA, DM, DP) were designed and synthesized aiming for ion detection. The Zn2+ recognition ability was found in all compounds and the binding mechanism was possibly via dimethylaniline sites linked to the aza-BODIPY core. Upon Zn2+ addition, the new absorption band and the color change occurred due to the altered charge transfer of the adducts. The custom-made colorimeter was successfully integrated into the dye's application, demonstrating a good linear relationship between resistance values and Zn2+ concentration. The chromophore test strips were fabricated and exhibited distinct color changes upon aqueous Zn2+ exposure. The compound DA also exhibits logical behavior with DA-Zn2+-Cu2+ system. In terms of environmental hazards, the compounds exhibited no adverse effect on Pseudomonas putida at the concentration level of 0.2 mg/mL. These findings indicated that all synthesized aza-BODIPYs might be suitable for chemosensor probes for Zn2+ detection with possibly low environmental risk.
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Affiliation(s)
- Sasipan Luangphai
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pumis Thuptimdang
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sasiwimon Buddhiranon
- Department of Materials Engineering, Faculty of Engineering, Kasetsart University, Bangkok 10900, Thailand
| | - Kullapa Chanawanno
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
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2
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Cabrera MÁ, Márquez SL, Pérez-Donoso JM. New insights into xenobiotic tolerance of Antarctic bacteria: transcriptomic analysis of Pseudomonas sp. TNT3 during 2,4,6-trinitrotoluene biotransformation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:17256-17274. [PMID: 38337121 DOI: 10.1007/s11356-024-32298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
The xenobiotic 2,4,6-trinitrotoluene (TNT) is a highly persistent environmental contaminant, whose biotransformation by microorganisms has attracted renewed attention. In previous research, we reported the discovery of Pseudomonas sp. TNT3, the first described Antarctic bacterium with the ability to biotransform TNT. Furthermore, through genomic analysis, we identified distinctive features in this isolate associated with the biotransformation of TNT and other xenobiotics. However, the metabolic pathways and genes active during TNT exposure in this bacterium remained unexplored. In the present transcriptomic study, we used RNA-sequencing to investigate gene expression changes in Pseudomonas sp. TNT3 exposed to 100 mg/L of TNT. The results showed differential expression of 194 genes (54 upregulated and 140 downregulated), mostly encoding hypothetical proteins. The most highly upregulated gene (> 1000-fold) encoded an azoreductase enzyme not previously described. Other significantly upregulated genes were associated with (nitro)aromatics detoxification, oxidative, thiol-specific, and nitrosative stress responses, and (nitro)aromatic xenobiotic tolerance via efflux pumps. Most of the downregulated genes were involved in the electron transport chain, pyrroloquinoline quinone (PQQ)-related alcohol oxidation, and motility. These findings highlight a complex cellular response to TNT exposure, with the azoreductase enzyme likely playing a crucial role in TNT biotransformation. Our study provides new insights into the molecular mechanisms of TNT biotransformation and aids in developing effective TNT bioremediation strategies. To the best of our knowledge, this report is the first transcriptomic response analysis of an Antarctic bacterium during TNT biotransformation.
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Affiliation(s)
- Ma Ángeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Sebastián L Márquez
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de La Vida, Universidad Andrés Bello, Av. República 330, Santiago, Chile.
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3
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Wang Z, Ma R, Chen B, Yu X, Wang X, Zuo X, Liang B, Yang J. A transcription factor-based bacterial biosensor system and its application for on-site detection of explosives. Biosens Bioelectron 2024; 244:115805. [PMID: 37948915 DOI: 10.1016/j.bios.2023.115805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/01/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Detecting unexploded landmines is critical due to the environmental pollution and potential humanitarian risks caused by buried landmines. Therefore, this study focused on developing a biosensor system capable of detecting explosives safely and efficiently. A novel transcription factor-based Escherichia coli biosensor was designed to detect 1,3-dinitrobenzene (1,3-DNB). The MexT transcription factor from Pseudomonas putida (P. putida) was identified as the fundamental sensing element in this biosensor. The study found that MexT positively regulated the transcription of PP_2827 by binding to the bidirectional promoter region between them, and significantly enhanced the expression of downstream genes under the condition of 1,3-DNB. The MexT-based biosensor for 1,3-DNB was developed by adopting different combinations of the mexT gene and promoters. The optimized biosensor demonstrated adequate sensitivity for detecting 0.1 μg/mL of 1,3-DNB in a liquid solution with satisfactory specificity and long-term stability. Subsequently, the MexT-based biosensor was integrated into a detection device to simulate the in-field exploration of explosives. The system exhibited a detection sensitivity of 0.5 mg/kg for 1,3-DNB in the sand, and realized the detection of on-site and large-scale area and the location of buried 1,3-DNB under the soil. The study provided a novel transcription factor-based bacterial biosensor and a complete system (China Earth Eye, CEE) for sensitive detection of 1,3-DNB. The good performance of this biosensor system can facilitate the development of accurate, on-site, and high-efficient exploration of explosives in real extensive minefields. Moreover, this 1,3-DNB biosensor can be complementary to the 2,4-DNT biosensor reported before, demonstrating its potential applications in military situations.
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Affiliation(s)
- Zhaobao Wang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Ran Ma
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Bingjing Chen
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Xiaotong Yu
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Xue Wang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Xinyun Zuo
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China
| | - Bo Liang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China.
| | - Jianming Yang
- Energy-rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, PR China.
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4
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Zhang H, Song J, Zheng Z, Li T, Shi N, Han Y, Zhang L, Yu Y, Fang H. Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation. WATER RESEARCH 2023; 233:119789. [PMID: 36863279 DOI: 10.1016/j.watres.2023.119789] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic resistant plasmid RP4 were established to examine conjugative transfer frequency under stress from four widely used fungicides: triadimefon, chlorothalonil, azoxystrobin, and carbendazim. The mechanisms were elucidated at the cellular and molecular levels using transmission electron microscopy, flow cytometry, RT-qPCR, and RNA-seq techniques. The conjugative transfer frequency of plasmid RP4 between Escherichia coli strains increased with the rising exposure concentrations of chlorothalonil, azoxystrobin, and carbendazim, but was suppressed between E. coli and Pseudomonas putida by a high fungicide concentration (10 µg/mL). Triadimefon did not significantly affect conjugative transfer frequency. Exploration of the underlying mechanisms revealed that: (i) chlorothalonil exposure mainly promoted generation of intracellular reactive oxygen species, stimulated the SOS response, and increased cell membrane permeability, while (ii) azoxystrobin and carbendazim primarily enhanced expression of conjugation-related genes on the plasmid. These findings reveal the fungicide-triggered mechanisms associated with plasmid conjugation and highlight the potential role of non-bactericidal pesticides on the dissemination of ARGs.
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Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR. China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Zhiruo Zheng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Tongxin Li
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China
| | - Nan Shi
- Department of Developmental and Cell Biology, University of California, Irvine CA 92697, United States
| | - Yuling Han
- Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR. China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture and Rural Affairs, PR. China.
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5
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Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microb Biotechnol 2023; 16:645-661. [PMID: 36691869 PMCID: PMC9948227 DOI: 10.1111/1751-7915.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas putida has emerged as a promising host for the conversion of biomass-derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non-native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass-derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non-native genes was achieved by using chassis-independent recombinase-assisted genome engineering (CRAGE) for single-step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.
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Affiliation(s)
- Rahul Gauttam
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas Eng
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhiying Zhao
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qurrat Ul Ain Rana
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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6
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Genomic Features of Pseudomonas putida PCL1760: A Biocontrol Agent Acting via Competition for Nutrient and Niche. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Pseudomonasputida strain PCL1760 is a biocontrol agent protecting plants from pathogens via the mechanism of competition for nutrients and niches (CNN). To confirm this mechanism as well as to adapt the strain for biotechnological applications, full genome analysis was compared with the known biotechnological model, P. putida S12, and other related species, which were analyzed on different genomic databases. Moreover, the antibacterial activity of PCL1760 was tested against Staphylococcus aureus, Pseudomonas aeruginosa, and Pseudomonas syringae. No genetic systems involved in antibiosis were revealed among the secondary metabolite clusters of the strain of PCL1760. The only antagonistic effect was observed against P. syringae, which might be because of siderophore (yellow-greenish fluorescence), although less than 19% pyoverdin biosynthesis clusters were predicted using the AntiSMASH server. P. putida PCL1760 in comparison with the Pseudomonas simiae strain PCL1751, another biocontrol agent acting solely via CNN, which lost its ‘luxury’ genes necessary for antibiosis or parasitism/predation mechanisms, but carries genetic systems providing motility. Interestingly, immunity genes (CRISPR/Cas and prophages) showed PCL1760 to be robust in comparison with S12, while annotation on OrthoVenn2 showed PCL1760 to be amenable for genetic manipulations. It is tempting to state that rhizobacteria using the mechanism of CNN are distinguishable from biocontrol agents acting via antibiosis or parasitism/predation at the genomic level. This confirms the CNN of PCL1760 as the sole mechanism for biocontrol and we suggest the strain as a new model for genetic engineering.
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7
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Sakai SA, Aoshima M, Sawada K, Horasawa S, Yoshikawa A, Fujisawa T, Kadowaki S, Denda T, Matsuhashi N, Yasui H, Goto M, Yamazaki K, Komatsu Y, Nakanishi R, Nakamura Y, Bando H, Hamaya Y, Kageyama SI, Yoshino T, Tsuchihara K, Yamashita R. Fecal microbiota in patients with a stoma decreases anaerobic bacteria and alters taxonomic and functional diversities. Front Cell Infect Microbiol 2022; 12:925444. [PMID: 36189350 PMCID: PMC9515963 DOI: 10.3389/fcimb.2022.925444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant diseases. Generally, stoma construction is performed following surgery for the resection of the primary tumor in patients with CRC. The association of CRC with the gut microbiota has been widely reported, and the gut microbiota is known to play an important role in the carcinogenesis, progression, and treatment of CRC. In this study, we compared the microbiota of patients with CRC between with and without a stoma using fecal metagenomic sequencing data from SCRUM-Japan MONSTAR-SCREEN, a joint industry-academia cancer research project in Japan. We found that the composition of anaerobes was reduced in patients with a stoma. In particular, the abundance of Alistipes, Akkermansia, Intestinimonas, and methane-producing archaea decreased. We also compared gene function (e.g., KEGG Orthology and KEGG pathway) and found that gene function for methane and short-chain fatty acids (SCFAs) production was underrepresented in patients with a stoma. Furthermore, a stoma decreased Shannon diversity based on taxonomic composition but increased that of the KEGG pathway. These results suggest that the feces of patients with a stoma have a reduced abundance of favorable microbes for cancer immunotherapy. In conclusion, we showed that a stoma alters the taxonomic and functional profiles in feces and may be a confounding factor in fecal microbiota analysis.
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Affiliation(s)
- Shunsuke A. Sakai
- Graduate School of Frontier Science, Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Masato Aoshima
- Graduate School of Frontier Science, Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Kentaro Sawada
- Department of Medical Oncology, Kushiro Rosai Hospital, Kushiro, Japan
| | - Satoshi Horasawa
- Translational Research Support Section, National Cancer Center Hospital East, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ayumu Yoshikawa
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takao Fujisawa
- Department Head and Neck Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Shigenori Kadowaki
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Tadamichi Denda
- Divisioin of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Nobuhisa Matsuhashi
- Department of Gastroenterological surgery Pediatric surgery, Gifu University Hospital, Gifu, Japan
| | - Hisateru Yasui
- Department of Medical Oncology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Masahiro Goto
- Cancer Chemotherapy Center, Osaka Medical and Pharmaceutical University Hospital, Takatsuki, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yoshito Komatsu
- Department of Cancer Center, Hokkaido University Hospital, Hokkaido, Japan
| | - Ryota Nakanishi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Section, National Cancer Center Hospital East, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Section, National Cancer Center Hospital East, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yamato Hamaya
- Graduate School of Frontier Science, Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Shun-Ichiro Kageyama
- Department of Radiation Oncology and Particle Therapy, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Katsuya Tsuchihara
- Graduate School of Frontier Science, Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Japan
- *Correspondence: Riu Yamashita,
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8
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Asin-Garcia E, Batianis C, Li Y, Fawcett JD, de Jong I, Dos Santos VAPM. Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida. Microb Cell Fact 2022; 21:156. [PMID: 35934698 PMCID: PMC9358898 DOI: 10.1186/s12934-022-01883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/26/2022] [Indexed: 11/12/2022] Open
Abstract
The inclusion of biosafety strategies into strain engineering pipelines is crucial for safe-by-design biobased processes. This in turn might enable a more rapid regulatory acceptance of bioengineered organisms in both industrial and environmental applications. For this reason, we equipped the industrially relevant microbial chassis Pseudomonas putida KT2440 with an effective biocontainment strategy based on a synthetic dependency on phosphite, which is generally not readily available in the environment. The produced PSAG-9 strain was first engineered to assimilate phosphite through the genome-integration of a phosphite dehydrogenase and a phosphite-specific transport complex. Subsequently, to deter the strain from growing on naturally assimilated phosphate, all native genes related to its transport were identified and deleted generating a strain unable to grow on media containing any phosphorous source other than phosphite. PSAG-9 exhibited fitness levels with phosphite similar to those of the wild type with phosphate, and low levels of escape frequency. Beyond biosafety, this strategy endowed P. putida with the capacity to be cultured under non-sterile conditions using phosphite as the sole phosphorous source with a reduced risk of contamination by other microbes, while displaying enhanced NADH regenerative capacity. These industrially beneficial features complement the metabolic advantages for which this species is known for, thereby strengthening it as a synthetic biology chassis with potential uses in industry, with suitability towards environmental release.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Yunsong Li
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - James D Fawcett
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.,Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW72BX, UK
| | - Ivar de Jong
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands. .,LifeGlimmer GmbH, 12163, Berlin, Germany. .,Bioprocess Engineering Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands.
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9
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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10
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Brehl C, Brass HUC, Lüchtrath C, Böckmann L, Ihling N, Classen T, Pietruszka J, Büchs J. Optimized prodigiosin production with Pseudomonas putida KT2440 using parallelized non-invasive online monitoring. Biotechnol Prog 2022; 38:e3245. [PMID: 35170260 DOI: 10.1002/btpr.3245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2022]
Abstract
The red pigment prodigiosin is of high pharmaceutical interest, due to its potential applications as an antitumor drug and antibiotic agent. As previously demonstrated, Pseudomonas putida KT2440 is a suitable host for prodigiosin production, as it exhibits high tolerance towards the antimicrobial properties of prodigiosin. So far, prodigiosin concentrations of up to 94 mg/L have been achieved in shake flask cultivations. For the characterization and optimization of the prodigiosin production process, the scattered light of P. putida and fluorescence of prodigiosin was measured. The excitation and emission wavelengths for prodigiosin measurement were analyzed by recording 2D fluorescence spectra. The strongest prodigiosin fluorescence was obtained at a wavelength combination of 535/560 nm. By reducing the temperature to 18 °C and using 16 g/L glucose, the prodigiosin concentration was more than doubled compared to the initial cultivation conditions. The obtained results demonstrate the capabilities of parallelized microscale cultivations combined with non-invasive online monitoring of fluorescence for rapid bioprocess development, using prodigiosin as a molecule of current biotechnological interest.
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Affiliation(s)
- Carl Brehl
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Hannah U C Brass
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Jülich, Germany
| | - Clara Lüchtrath
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Lukas Böckmann
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Nina Ihling
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Classen
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute for Bio- and Geosciences 1: Bioorganic Chemistry (IBG-1), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jörg Pietruszka
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Jülich, Germany.,Institute for Bio- and Geosciences 1: Bioorganic Chemistry (IBG-1), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
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11
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Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP. Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 2022; 204:144. [PMID: 35044532 DOI: 10.1007/s00203-022-02757-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023]
Abstract
Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nahid Akhtar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
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12
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Bilal M, Bagheri AR, Bhatt P, Chen S. Environmental occurrence, toxicity concerns, and remediation of recalcitrant nitroaromatic compounds. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 291:112685. [PMID: 33930637 DOI: 10.1016/j.jenvman.2021.112685] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
Nitroaromatic compounds (NACs) are considered important groups of chemicals mainly produced by human and industrial activities. The large-scale application of these xenobiotics creates contamination of the water and soil environment. Despite applicability, NACs have been caused severe hazardous side effects in animals and human systems like different cancers, anemia, skin irritation, liver damage and mutagenic effects. The effective remediation of the NACs from the environment is a significant concern. Researchers have implemented physicochemical and biological methods for the remediation of NACs from the environment. Most of the applied methods are based on adsorption and degradation approaches. Among these methods, degradation is considered a versatile method for the subsequent removal of NACs due to its exceptional properties like simplicity, easy operation, cost-effectiveness, and availability. Most importantly, the degradation process does not generate hazardous side products and wastes compared to other methods. Hence, the importance of NACs, their remediation, and supreme attributes of the degradation method have encouraged us to review the recent progress and development for the removal of these perilous materials using degradation as a versatile method. Therefore, in this review, (i) NACs, physicochemical properties, and their hazardous side effects on humans and animals are discussed; (ii) Physicochemical methods, microbial, anaerobic bioremediation, mycoremediation, and aerobic degradation approaches for the degradation of NACs were thoroughly vetted; (iii) The possible mechanisms for degradation of NACs were investigated and discussed. (iv) The applied kinetic models for evaluation of the rate of degradation were also assessed and discussed. Finally, (vi) current challenges and future prospects of proposed methods for degradation and removal of NACs were also directed.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | | | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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13
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Molina-Santiago C, de Vicente A, Romero D. Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials. Comput Struct Biotechnol J 2021; 19:2796-2805. [PMID: 34093994 PMCID: PMC8138678 DOI: 10.1016/j.csbj.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
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14
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Elmore JR, Dexter GN, Salvachúa D, Martinez-Baird J, Hatmaker EA, Huenemann JD, Klingeman DM, Peabody GL, Peterson DJ, Singer C, Beckham GT, Guss AM. Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion. Nat Commun 2021; 12:2261. [PMID: 33859194 PMCID: PMC8050072 DOI: 10.1038/s41467-021-22556-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
Expanding the portfolio of products that can be made from lignin will be critical to enabling a viable bio-based economy. Here, we engineer Pseudomonas putida for high-yield production of the tricarboxylic acid cycle-derived building block chemical, itaconic acid, from model aromatic compounds and aromatics derived from lignin. We develop a nitrogen starvation-detecting biosensor for dynamic two-stage bioproduction in which itaconic acid is produced during a non-growth associated production phase. Through the use of two distinct itaconic acid production pathways, the tuning of TCA cycle gene expression, deletion of competing pathways, and dynamic regulation, we achieve an overall maximum yield of 56% (mol/mol) and titer of 1.3 g/L from p-coumarate, and 1.4 g/L titer from monomeric aromatic compounds produced from alkali-treated lignin. This work illustrates a proof-of-principle that using dynamic metabolic control to reroute carbon after it enters central metabolism enables production of valuable chemicals from lignin at high yields by relieving the burden of constitutively expressing toxic heterologous pathways.
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Affiliation(s)
- Joshua R. Elmore
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Gara N. Dexter
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Davinia Salvachúa
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Jessica Martinez-Baird
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - E. Anne Hatmaker
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jay D. Huenemann
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.411461.70000 0001 2315 1184Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN USA
| | - Dawn M. Klingeman
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - George L. Peabody
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Darren J. Peterson
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Christine Singer
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Gregg T. Beckham
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Adam M. Guss
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.411461.70000 0001 2315 1184Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN USA
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15
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Shropshire H, Jones RA, Aguilo-Ferretjans MM, Scanlan DJ, Chen Y. Proteomics insights into the Burkholderia cenocepacia phosphorus stress response. Environ Microbiol 2021; 23:5069-5086. [PMID: 33684254 DOI: 10.1111/1462-2920.15451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.
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Affiliation(s)
- Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Rebekah A Jones
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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16
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Mishra S, Lin Z, Pang S, Zhang W, Bhatt P, Chen S. Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities. Front Bioeng Biotechnol 2021; 9:632059. [PMID: 33644024 PMCID: PMC7902726 DOI: 10.3389/fbioe.2021.632059] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.
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Affiliation(s)
- Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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17
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Avellaneda H, Arbeli Z, Teran W, Roldan F. Transformation of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109 and exploration of the associated enzymes. World J Microbiol Biotechnol 2020; 36:190. [PMID: 33247357 DOI: 10.1007/s11274-020-02962-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
The nitrated compounds 2,4-dinitrotoluene (2,4-DNT), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN) are toxic xenobiotics widely used in various industries. They often coexist as environmental contaminants. The aims of this study were to evaluate the transformation of 100 mg L-1 of TNT, 2,4-DNT, and PETN by Raoultella planticola M30b and Rhizobium radiobacter M109c and identify enzymes that may participate in the transformation. These strains were selected from 34 TNT transforming bacteria. Cupriavidus metallidurans DNT was used as a reference strain for comparison purposes. Strains DNT, M30b and M109c transformed 2,4-DNT (100%), TNT (100, 94.7 and 63.6%, respectively), and PETN (72.7, 69.3 and 90.7%, respectively). However, the presence of TNT negatively affects 2,4-DNT and PETN transformation (inhibition > 40%) in strains DNT and M109c and fully inhibited (100% inhibition) 2,4-DNT transformation in R. planticola M30b.Genomes of R. planticola M30b and R. radiobacter M109c were sequenced to identify genes related with 2,4-DNT, TNT or PETN transformation. None of the tested strains presented DNT oxygenase, which has been previously reported in the transformation of 2,4-DNT. Thus, unidentified novel enzymes in these strains are involved in 2,4-DNT transformation. Genes encoding enzymes homologous to the previously reported TNT and PETN-transforming enzymes were identified in both genomes. R. planticola M30b have homologous genes of PETN reductase and xenobiotic reductase B, while R. radiobacter M109c have homologous genes to GTN reductase and PnrA nitroreductase. The ability of these strains to transform explosive mixtures has a potentially biotechnological application in the bioremediation of contaminated environments.
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Affiliation(s)
- Hernán Avellaneda
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Ziv Arbeli
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia
| | - Wilson Teran
- Facultad de Ciencias, Departamento de Biología, Biología de Plantas y Sistemas Productivos, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fabio Roldan
- Facultad de Ciencias, Departamento de Biología, Unidad de Saneamiento y Biotecnología Ambiental (USBA), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, DC, Colombia.
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18
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Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid. Metab Eng 2020; 62:62-71. [DOI: 10.1016/j.ymben.2020.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 11/21/2022]
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19
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Cabrera MÁ, Márquez SL, Quezada CP, Osorio MI, Castro-Nallar E, González-Nilo FD, Pérez-Donoso JM. Biotransformation of 2,4,6-Trinitrotoluene by Pseudomonas sp. TNT3 isolated from Deception Island, Antarctica. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:113922. [PMID: 32443190 DOI: 10.1016/j.envpol.2020.113922] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 12/11/2019] [Accepted: 01/05/2020] [Indexed: 06/11/2023]
Abstract
2,4,6-Trinitrotoluene (TNT) is a nitroaromatic explosive, highly toxic and mutagenic for organisms. In this study, we report for the first time the screening and isolation of TNT-degrading bacteria from Antarctic environmental samples with potential use as bioremediation agents. Ten TNT-degrading bacterial strains were isolated from Deception Island. Among them, Pseudomonas sp. TNT3 was selected as the best candidate since it showed the highest tolerance, growth, and TNT biotransformation capabilities. Our results showed that TNT biotransformation involves the reduction of the nitro groups. Additionally, Pseudomonas sp. TNT3 was capable of transforming 100 mg/L TNT within 48 h at 28 °C, showing higher biotransformation capability than Pseudomonas putida KT2440, a known TNT-degrading bacterium. Functional annotation of Pseudomonas sp. TNT3 genome revealed a versatile set of molecular functions involved in xenobiotic degradation pathways. Two putative xenobiotic reductases (XenA_TNT3 and XenB_TNT3) were identified by means of homology searches and phylogenetic relationships. These enzymes were also characterized at molecular level using homology modelling and molecular dynamics simulations. Both enzymes share different levels of sequence similarity with other previously described TNT-degrading enzymes and with their closest potential homologues in databases.
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Affiliation(s)
- Ma Ángeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Sebastián L Márquez
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Carolina P Quezada
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Manuel I Osorio
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - Fernando D González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Life Sciences, Universidad Andrés Bello, Av. República 330, Santiago, Chile.
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20
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Xia J, Sun H, Zhang XX, Zhang T, Ren H, Ye L. Aromatic compounds lead to increased abundance of antibiotic resistance genes in wastewater treatment bioreactors. WATER RESEARCH 2019; 166:115073. [PMID: 31542545 DOI: 10.1016/j.watres.2019.115073] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/29/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Various aromatic compounds in wastewater, especially industrial wastewater, are treated by biological processes in bioreactors which are regarded as hotspots and reservoirs of antibiotic resistance genes (ARGs). Yet, little is known about the relationship between the aromatic compound degradation process and antibiotic resistance. Here, we report on the co-occurrence of ARGs and aromatic degradation genes (ADGs) in bacteria in bioreactors. We confirmed this by bioreactor experiments and bioinformatics analysis of over 10,000 publicly available bacterial genomes. We observed a significant enrichment of ARGs in bioreactors treating wastewater that contained p-aminophenol and p-nitrophenol. The potential hosts harboring ARGs and ADGs were mainly Pseudomonas, Leucobacter, Xanthobacter, Acinetobacter, and Burkholderiaceae. Genome analysis revealed that 67.6% of the publicly available bacterial genomes harboring ADGs also harbor ARGs. Over 80% of Burkholderiales, Xanthomonales, Enterobacteriaceae, Acinetobacter, Pseudomonas, and Nocardiaceae genomes harbor both ARGs and ADGs, which strongly suggests the co-occurrence of these genes. Furthermore, bacteria carrying ADGs harbored more than twice the number of ARGs than bacteria only carrying ARGs. Network analysis suggested that multidrug, beta-lactam, aminoglycoside, macrolide-lincosamide-streptogramin, and polymyxin resistance genes are the major ARGs associated with ADGs. Taken together, the presented findings improve the understanding of ARG prevalence in biological wastewater treatment plants, and highlight the potential risk of the effect of regular aromatic compounds on the selection and spread of ARGs.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China; School of Public Health, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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21
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Wang R, Lin CY, Chen SH, Lo KJ, Liu CT, Chou TH, Shih YH. Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:249-258. [PMID: 31349166 DOI: 10.1016/j.scitotenv.2019.07.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
We discovered one purple photosynthetic bacterium, Rhodopseudomonas palustris YSC3, which has a specific ability to degrade 1, 2, 5, 6, 9, 10-hexabromocyclododecane (HBCD). The whole transcriptome of R. palustris YSC3 was analyzed using the RNA-based sequencing technology in illumina and was compared as well as discussed through Multi-Omics onLine Analysis System (MOLAS, http://molas.iis.sinica.edu.tw/NTUIOBYSC3/) platform we built. By using genome based mapping approach, we can align the trimmed reads on the genome of R. palustris and estimate the expression profiling for each transcript. A total of 341 differentially expressed genes (DEGs) in HBCD-treated R. palustris (RPH) versus control R. palustris (RPC) was identified by 2-fold changes, among which 305 genes were up-regulated and 36 genes were down-regulated. The regulated genes were mapped to the database of Gene Ontology (GO) and Genes and Genomes Encyclopedia of Kyoto (KEGG), resulting in 78 pathways being identified. Among those DEGs which annotated to important functions in several metabolic pathways, including those involved in two-component system (13.6%), ribosome assembly (10.7%), glyoxylate and dicarboxylate metabolism (5.3%), fatty acid degradation (4.7%), drug metabolism-cytochrome P450 (2.3%), and chlorocyclohexane and chlorobenzene degradation (3.0%) were differentially expressed in RPH and RPC samples. We also identified one transcript annotated as dehalogenase and other genes involved in the HBCD biotransformation in R. palustris. Furthermore, the putative HBCD biotransformation mechanism in R. palustris was proposed.
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Affiliation(s)
- Reuben Wang
- Department of Food Science, Tunghai University, Taiwan, No.1727, Sec.4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan
| | - Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan
| | - Kai-Jiun Lo
- Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan
| | - Tzu-Ho Chou
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Yang-Hsin Shih
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.
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22
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Osorio MI, Cabrera MA, González-Nilo F, Pérez-Donoso JM. Odd Loop Regions of XenA and XenB Enzymes Modulate Their Interaction with Nitro-explosives Compounds and Provide Structural Support for Their Regioselectivity. J Chem Inf Model 2019; 59:3860-3870. [PMID: 31454238 DOI: 10.1021/acs.jcim.9b00357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nitro-explosive compounds 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, and 1,2,3-trinitroglycerol are persistent environmental contaminants. The presence of different functional groups in these molecules represents a great challenge to enzymatic catalysis. The chemical variety of these three substrates is such that they do not bind and interact with catalytic residues within an enzyme with the same affinity. In this context, two Xenobiotic Reductase enzymes produced by the bacteria Pseudomonas putida can catalyze the reduction of these compounds with different affinities and regioselectivity. The structural bases that support this substrate promiscuity and catalytic preferences are unknown. Therefore, through molecular dynamics simulations and free energy calculations, we explored the structural properties driving the specific interactions of these enzymes with their substrates and cofactor. Models of Xenobiotic Reductase A and B enzymes in complex with 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, or 1,2,3-trinitroglycerol were built, and the ligand enzyme interaction was simulated by molecular dynamics. The structural analysis of the molecular dynamics simulations shows that loops 3, 5, 7, 9, 11, and 13 of Xenobiotic Reductase B, and loops 4, 5, 7, 11, 13, and 15 Xenobiotic Reductase A, are in contact with the ligands during the first stages of the molecular recognition. These loops are the most flexible regions for both enzymes; however, Xenobiotic Reductase B presents a greater range of movement and a higher number of residues interacting with the ligands. Finally, the distance between the cofactor and the different reactive groups in the substrate reflects the regioselectivity of the enzymes, and the free energy calculations are consistent with the substrate specificity of both enzymes studied. The simulation shows a stable interaction between the aromatic ring of the substrates and Xenobiotic Reductase B. In contrast, a less stable interaction with the different nitro groups of the aromatic ligands was observed. In the case of 1,2,3-trinitroglycerol, Xenobiotic Reductase B interacts more closely with the nitro groups of carbon 1 or 3, while Xenobiotic Reductase A is more selective by nitro groups of carbon 2. The obtained results suggest that the flexibility of the loops in Xenobiotic Reductase B and the presence of polar and aromatic residues present in loops 5 and 7 are fundamental to determine the affinity of the enzyme with the different substrates, and they also contribute to the proper orientation of the ligands that directs the catalytic reaction.
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Affiliation(s)
- Manuel I Osorio
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - Ma Angeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
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23
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Hsu DW, Wang TI, Huang DJ, Pao YJ, Lin YA, Cheng TW, Liang SH, Chen CY, Kao CM, Sheu YT, Chen CC. Copper promotes E. coli laccase-mediated TNT biotransformation and alters the toxicity of TNT metabolites toward Tigriopus japonicus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 173:452-460. [PMID: 30798189 DOI: 10.1016/j.ecoenv.2019.02.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
Although laccase is involved in the biotransformation of 2,4,6-trinitrotoluene (TNT), little is known regarding the effect of E. coli laccase on TNT biotransformation. In this study, E. coli K12 served as the parental strain to construct a laccase deletion strain and two laccase-overexpressing strains. These E. coli strains were used to investigate the effect of laccase together with copper ions on the efficiency of TNT biotransformation, the variety of TNT biotransformation products generated and the toxicity of the TNT metabolites. The results showed that the laccase level was not relevant to TNT biotransformation in the soluble fraction of the culture medium. Conversely, TNT metabolites varied in the insoluble fraction analyzed by thin-layer chromatography (TLC). The insoluble fraction from the laccase-null strain showed fewer and relatively fainter spots than those detected in the wild-type and laccase-overexpressing strains, indicating that laccase expression levels were interrelated determinants of the varieties and amounts of TNT metabolites produced. In addition, the aquatic invertebrate Tigriopus japonicus was used to assess the toxicity of the TNT metabolites. The toxicity of the TNT metabolite mixture increased when the intracellular laccase level in strains increased or when purified E. coli recombinant Laccase (rLaccase) was added to the culture medium. Thus, our results suggest that laccase activity must be considered when performing microbial TNT remediation.
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Affiliation(s)
- Duen-Wei Hsu
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Tzu-I Wang
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Da-Ji Huang
- Department of Environmental Resources Management, Chia Nan University of Pharmacy & Science, Tainan, Taiwan
| | - Yu-Jie Pao
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Yuya A Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ting-Wen Cheng
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Shih-Hsiung Liang
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yih-Terng Sheu
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan.
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24
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Giglio KM, Keohane CE, Stodghill PV, Steele AD, Fetzer C, Sieber SA, Filiatrault MJ, Wuest WM. Transcriptomic Profiling Suggests That Promysalin Alters the Metabolic Flux, Motility, and Iron Regulation in Pseudomonas putida KT2440. ACS Infect Dis 2018; 4:1179-1187. [PMID: 29801413 DOI: 10.1021/acsinfecdis.8b00041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Promysalin, a secondary metabolite produced by P. putida RW10S1, is a narrow-spectrum antibiotic that targets P. aeruginosa over other Pseudomonas spp. P. putida KT2440, a nonproducing strain, displays increased swarming motility and decreased pyoverdine production in the presence of exogenous promysalin. Herein, proteomic and transcriptomic experiments were used to provide insight about how promysalin elicits responses in PPKT2440 and rationalize its species selectivity. RNA-sequencing results suggest that promysalin affects PPKT2440 by (1) increasing swarming in a flagella-independent manner; (2) causing cells to behave as if they were experiencing an iron-deficient environment, and (3) shifting metabolism away from glucose conversion to pyruvate via the Entner-Doudoroff pathway. These findings highlight nature's ability to develop small molecules with specific targets, resulting in exquisite selectivity.
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Affiliation(s)
- Krista M. Giglio
- Emerging Pests and Pathogens
Research, United States Department of Agriculture, Agricultural Research
Service, 538 Tower Road, Ithaca, New York 14853, United States
| | - Colleen E. Keohane
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Paul V. Stodghill
- Emerging Pests and Pathogens
Research, United States Department of Agriculture, Agricultural Research
Service, 538 Tower Road, Ithaca, New York 14853, United States
| | - Andrew D. Steele
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Christian Fetzer
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Melanie J. Filiatrault
- Emerging Pests and Pathogens
Research, United States Department of Agriculture, Agricultural Research
Service, 538 Tower Road, Ithaca, New York 14853, United States
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, 236 Tower Road, Ithaca, New York 14853, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- Emory Antibiotic Resistance Center, Emory University, 201 Dowman Drive, Atlanta, Georgia 30322, United States
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25
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Thijs S, Sillen W, Truyens S, Beckers B, van Hamme J, van Dillewijn P, Samyn P, Carleer R, Weyens N, Vangronsveld J. The Sycamore Maple Bacterial Culture Collection From a TNT Polluted Site Shows Novel Plant-Growth Promoting and Explosives Degrading Bacteria. FRONTIERS IN PLANT SCIENCE 2018; 9:1134. [PMID: 30123233 PMCID: PMC6085565 DOI: 10.3389/fpls.2018.01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/13/2018] [Indexed: 05/23/2023]
Abstract
Military activities have worldwide introduced toxic explosives into the environment with considerable effects on soil and plant-associated microbiota. Fortunately, these microorganisms, and their collective metabolic activities, can be harnessed for site restoration via in situ phytoremediation. We characterized the bacterial communities inhabiting the bulk soil and rhizosphere of sycamore maple (Acer pseudoplatanus) in two chronically 2,4,6-trinitrotoluene (TNT) polluted soils. Three hundred strains were isolated, purified and characterized, a majority of which showed multiple plant growth promoting (PGP) traits. Several isolates showed high nitroreductase enzyme activity and concurrent TNT-transformation. A 12-member bacterial consortium, comprising selected TNT-detoxifying and rhizobacterial strains, significantly enhanced TNT removal from soil compared to non-inoculated plants, increased root and shoot weight, and the plants were less stressed than the un-inoculated plants as estimated by the responses of antioxidative enzymes. The sycamore maple tree (SYCAM) culture collection is a significant resource of plant-associated strains with multiple PGP and catalytic properties, available for further genetic and phenotypic discovery and use in field applications.
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Affiliation(s)
- Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sascha Truyens
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Bram Beckers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jonathan van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Pieter van Dillewijn
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Pieter Samyn
- Applied and Analytical Chemistry, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Robert Carleer
- Applied and Analytical Chemistry, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Nele Weyens
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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26
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Liao HY, Chien CC, Tang P, Chen CC, Chen CY, Chen SC. The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. JOURNAL OF HAZARDOUS MATERIALS 2018; 349:79-90. [PMID: 29414755 DOI: 10.1016/j.jhazmat.2018.01.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
Citrobacter sp. has been shown to degrade 2,4,6-trinitrotoluene (TNT). However, the mechanism of its TNT biodegradation is poorly understood. An integrated proteome and transcriptome analysis was performed for investigating the differential genes and differential proteins in bacterial growth at the onset of experiments and after 12 h treatment with TNT. With the RNA sequencing, we found a total of 3792 transcripts and 569 differentially expressed genes (≥2 fold, P < 0.05) by. Genes for amino acid transport, cellular metabolism and stress-shock proteins were up-regulated, while carbohydrate transport and metabolism were down-regulated. A total of 42 protein spots (≥1.5 fold, P < 0.05) showed differential expression on two-dimensional gel electrophoresis and these proteins were identified by mass spectrometry. The most prominent proteins up-regulated were involved in energy production and conversion, amino acid transport and metabolism, posttranslational modification, protein turnover and chaperones. Proteins involved in carbohydrate transport and metabolism were down-regulated. Most notably, we observed that nemA encoding N-ethylmaleimide reductase was the most up-regulated gene involved in TNT degradation, and further proved that it can transform TNT to 4-amino-2,6-dinitrotoluene (4-ADNT) and 2-amino-4,6-dinitrotoluene (2-ADNT). This study highlights the molecular mechanisms of Citrobacter sp. for TNT removal.
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Affiliation(s)
- Hung-Yu Liao
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135, Yuantung Rd., Jhongli City, Taoyuan, 32003, Taiwan
| | - Petrus Tang
- Department of Parasitology, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dis., Taoyuan City, 33302, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, No.116, Heping 1st Rd., Lingya District, Kaohsiung City, 80201, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan.
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27
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Iman M, Sobati T, Panahi Y, Mobasheri M. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. Molecules 2017; 22:E1242. [PMID: 28805729 PMCID: PMC6152126 DOI: 10.3390/molecules22081242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023] Open
Abstract
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA) methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research.
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Affiliation(s)
- Maryam Iman
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Tabassom Sobati
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
| | - Yunes Panahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Meysam Mobasheri
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
- Department of Biotechnology, Faculty of Advanced Sciences & Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), 194193311 Tehran, Iran.
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28
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Avila-Arias H, Avellaneda H, Garzón V, Rodríguez G, Arbeli Z, Garcia-Bonilla E, Villegas-Plazas M, Roldan F. Screening for biosurfactant production by 2,4,6-trinitrotoluene-transforming bacteria. J Appl Microbiol 2017; 123:401-413. [DOI: 10.1111/jam.13504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 05/18/2017] [Accepted: 05/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- H. Avila-Arias
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - H. Avellaneda
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - V. Garzón
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - G. Rodríguez
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - Z. Arbeli
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - E. Garcia-Bonilla
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - M. Villegas-Plazas
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
| | - F. Roldan
- Unidad de Saneamiento y Biotecnología Ambiental (USBA); Departamento de Biología; Facultad de Ciencias; Pontificia Universidad Javeriana; Bogotá Colombia
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29
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Katzke N, Knapp A, Loeschcke A, Drepper T, Jaeger KE. Novel Tools for the Functional Expression of Metagenomic DNA. Methods Mol Biol 2017; 1539:159-196. [PMID: 27900689 DOI: 10.1007/978-1-4939-6691-2_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus. Different broad-host-range shuttle vectors are described that allow activity-based screening of metagenomic DNA in these bacteria. Furthermore, we describe the newly developed transfer-and-expression system TREX which comprises genetic elements essential to allow for expression of large clusters of functionally coupled genes in different microbial species.
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Affiliation(s)
- Nadine Katzke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany.
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30
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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31
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Mi J, Schewe H, Buchhaupt M, Holtmann D, Schrader J. Efficient hydroxylation of 1,8-cineole with monoterpenoid-resistant recombinant Pseudomonas putida GS1. World J Microbiol Biotechnol 2016; 32:112. [PMID: 27263007 DOI: 10.1007/s11274-016-2071-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/23/2016] [Indexed: 10/21/2022]
Abstract
In this work, monoterpenoid hydroxylation with Pseudomonas putida GS1 and KT2440 were investigated as host strains, and the cytochrome P450 monooxygenase CYP176A1 (P450cin) and its native redox partner cindoxin (CinC) from Citrobacter braakii were introduced in P. putida to catalyze the stereoselective hydroxylation of 1,8-cineole to (1R)-6β-hydroxy-1,8-cineole. Growth experiments in the presence of 1,8-cineole confirmed pseudomonads' superior resilience compared to E. coli. Whole-cell P. putida harboring P450cin with and without CinC were capable of hydroxylating 1,8-cineole, whereas coexpression of CinC has been shown to accelerate this bioconversion. Under the same conditions, P. putida GS1 produced more than twice the amount of heterologous P450cin and bioconversion product than P. putida KT2440. A concentration of 1.1 ± 0.1 g/L (1R)-6β-hydroxy-1,8-cineole was obtained within 55 h in shake flasks and 13.3 ± 1.9 g/L in 89 h in a bioreactor, the latter of which corresponds to a yield YP/S of 79 %. To the authors' knowledge, this is the highest product titer for a P450 based whole-cell monoterpene oxyfunctionalization reported so far. These results show that solvent-tolerant P. putida GS1 can be used as a highly efficient recombinant whole-cell biocatalyst for a P450 monooxygenase-based valorization of monoterpenoids.
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Affiliation(s)
- Jia Mi
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Hendrik Schewe
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Markus Buchhaupt
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Dirk Holtmann
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Jens Schrader
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany.
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Domröse A, Klein AS, Hage-Hülsmann J, Thies S, Svensson V, Classen T, Pietruszka J, Jaeger KE, Drepper T, Loeschcke A. Efficient recombinant production of prodigiosin in Pseudomonas putida. Front Microbiol 2015; 6:972. [PMID: 26441905 PMCID: PMC4569968 DOI: 10.3389/fmicb.2015.00972] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022] Open
Abstract
Serratia marcescens and several other bacteria produce the red-colored pigment prodigiosin which possesses bioactivities as an antimicrobial, anticancer, and immunosuppressive agent. Therefore, there is a great interest to produce this natural compound. Efforts aiming at its biotechnological production have so far largely focused on the original producer and opportunistic human pathogen S. marcescens. Here, we demonstrate efficient prodigiosin production in the heterologous host Pseudomonas putida. Random chromosomal integration of the 21 kb prodigiosin biosynthesis gene cluster of S. marcescens in P. putida KT2440 was employed to construct constitutive prodigiosin production strains. Standard cultivation parameters were optimized such that titers of 94 mg/L culture were obtained upon growth of P. putida at 20°C using rich medium under high aeration conditions. Subsequently, a novel, fast and effective protocol for prodigiosin extraction and purification was established enabling the straightforward isolation of prodigiosin from P. putida growth medium. In summary, we describe here a highly efficient method for the heterologous biosynthetic production of prodigiosin which may serve as a basis to produce large amounts of this bioactive natural compound and may provide a platform for further in-depth studies of prodiginine biosynthesis.
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Affiliation(s)
- Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Andreas S Klein
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Vera Svensson
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany ; Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany ; Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH Jülich, Germany
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Pseudomonas putida-a versatile host for the production of natural products. Appl Microbiol Biotechnol 2015; 99:6197-214. [PMID: 26099332 PMCID: PMC4495716 DOI: 10.1007/s00253-015-6745-4] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 10/30/2022]
Abstract
The biosynthesis of natural products by heterologous expression of biosynthetic pathways in amenable production strains enables biotechnological access to a variety of valuable compounds by conversion of renewable resources. Pseudomonas putida has emerged as a microbial laboratory work horse, with elaborated techniques for cultivation and genetic manipulation available. Beyond that, this bacterium offers several particular advantages with regard to natural product biosynthesis, notably a versatile intrinsic metabolism with diverse enzymatic capacities as well as an outstanding tolerance to xenobiotics. Therefore, it has been applied for recombinant biosynthesis of several valuable natural products. This review provides an overview of applications of P. putida as a host organism for the recombinant biosynthesis of such natural products, including rhamnolipids, terpenoids, polyketides and non-ribosomal peptides, and other amino acid-derived compounds. The focus is on de novo natural product synthesis from intrinsic building blocks by means of heterologous gene expression and strain engineering. Finally, the future potential of the bacterium as a chassis organism for synthetic microbiology is pointed out.
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Simon O, Klaiber I, Huber A, Pfannstiel J. Comprehensive proteome analysis of the response of Pseudomonas putida KT2440 to the flavor compound vanillin. J Proteomics 2014; 109:212-27. [PMID: 25026441 DOI: 10.1016/j.jprot.2014.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/25/2014] [Accepted: 07/06/2014] [Indexed: 12/15/2022]
Abstract
UNLABELLED Understanding of the molecular response of bacteria to precursors, products and environmental conditions applied in bioconversions is essential for optimizing whole-cell biocatalysis. To investigate the molecular response of the potential biocatalyst Pseudomonas putida KT2440 to the flavor compound vanillin we applied complementary gel- and LC-MS-based quantitative proteomics approaches. Our comprehensive proteomics survey included cytoplasmic and membrane proteins and led to the identification and quantification of 1614 proteins, corresponding to 30% of the total KT2440 proteome. 662 proteins were altered in abundance during growth on vanillin as sole carbon source as compared to growth on glucose. The proteome response entailed an increased abundance of enzymes involved in vanillin degradation, significant changes in central energy metabolism and an activation of solvent tolerance mechanisms. With respect to vanillin metabolism, particularly enzymes belonging to the β-ketoadipate pathway including a transcriptional regulator and porins specific for vanillin uptake increased in abundance. However, catabolism of vanillin was not dependent on vanillin dehydrogenase (Vdh), as shown by quantitative proteome analysis of a Vdh-deficient KT2440 mutant (GN235). Other aldehyde dehydrogenases that were significantly increased in abundance in response to vanillin may replace Vdh and thus may represent interesting targets for improving vanillin production in P. putida KT2440. BIOLOGICAL SIGNIFICANCE The high demand for the flavor compound vanillin by the food and fragrance industry makes natural vanillin from vanilla pods a scarce and expensive resource rendering its biotechnological production economically attractive. Pseudomonas bacteria are metabolically very versatile and accept a broad range of hydrocarbons as carbon source making them suitable candidates for bioconversion processes. This work describes the impact of vanillin on the metabolism of the reference strain P. putida KT2440 on a proteome wide scale. The high proteome coverage of our proteomics survey allowed us to analyze the regulation of whole protein networks instead of single proteins. We were able to reconstruct the complete degradation pathway of vanillin and to monitor the changes in the energy metabolism of KT2440 induced by vanillin as sole carbon source. Vanillin dehydrogenase (Vdh) was not mandatory for vanillin degradation in KT2440 and may be substituted by other aldehyde dehydrogenases that were up-regulated in a wild-type as well as in a Vdh-deficient strain in the presence of vanillin. Aldehyde dehydrogenases, vanillin specific porins and efflux pump systems identified in study will be interesting targets for optimization of vanillin production in Pseudomonas bacteria. Furthermore, several mechanisms of solvent tolerance were induced by vanillin in KT2440. These include increased abundance of several efflux pump systems, chaperones as well as enzymes involved in cyclopropane fatty acid synthesis and trehalose formation. The present work will deepen the understanding of metabolism of aromatic compounds in P. putida and may lead to a more comprehensive understanding of solvent tolerance mechanisms in Gram-negative bacteria in general. Moreover, it will serve as a basis for further strain developments for a biotechnological production of vanillin in P. putida KT2440 or other Pseudomonas strains, highlighting the role of proteomics surveys as a powerful screening technology.
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Affiliation(s)
- Oliver Simon
- Department of Biosensorics, Institute of Physiology, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Iris Klaiber
- Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Armin Huber
- Department of Biosensorics, Institute of Physiology, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany; Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Jens Pfannstiel
- Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany.
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Molina L, Udaondo Z, Duque E, Fernández M, Molina-Santiago C, Roca A, Porcel M, de la Torre J, Segura A, Plesiat P, Jeannot K, Ramos JL. Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS One 2014; 9:e81604. [PMID: 24465371 PMCID: PMC3894933 DOI: 10.1371/journal.pone.0081604] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 10/15/2013] [Indexed: 12/31/2022] Open
Abstract
Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from in-patients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, ß-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts.
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Affiliation(s)
- Lázaro Molina
- Laboratorio de Investigación y Control Agroalimentario, Universidad de Huelva, Huelva, Spain
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Centro de Investigación en Química Sostenible, Universidad de Huelva, Huelva, Spain
| | - Zulema Udaondo
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Carlos Molina-Santiago
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Bio-Iliberis Research and Development, Peligros-Granada, Spain
| | - Mario Porcel
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Jesús de la Torre
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Ana Segura
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patrick Plesiat
- Centre Hospitalier Régional Universitaire - Hôpital Jean Minjoz, Besançon, France
| | - Katy Jeannot
- Centre Hospitalier Régional Universitaire - Hôpital Jean Minjoz, Besançon, France
| | - Juan-Luis Ramos
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 2012; 78:5104-10. [PMID: 22582075 PMCID: PMC3416403 DOI: 10.1128/aem.00619-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/04/2012] [Indexed: 01/16/2023] Open
Abstract
In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.
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Affiliation(s)
| | | | - Susana Conde
- Bio-Iliberis Research and Development, Granada, Spain
| | - Juan Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Müller C, Fetzner S. A Pseudomonas putida bioreporter for the detection of enzymes active on 2-alkyl-4(1H)-quinolone signalling molecules. Appl Microbiol Biotechnol 2012; 97:751-60. [PMID: 22740050 DOI: 10.1007/s00253-012-4236-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
Abstract
The quorum sensing signalling molecules 2-heptyl-3-hydroxy-4(1H)-quinolone, termed the "Pseudomonas quinolone signal" (PQS), and 2-heptyl-4(1H)-quinolone (HHQ) play an important role in the control of virulence gene expression in Pseudomonas aeruginosa. To construct a bioreporter for the specific and sensitive detection of these compounds, a plasmid with the pqsR gene encoding the PQS- and HHQ-responsive transcriptional regulator PqsR, and with the PqsR-controlled pqsA promoter fused to the lacZ gene, was established in Pseudomonas putida KT2440. The bioreporter responds to HHQ and PQS at concentrations in the range of 0.1-10 and 0.01-5 μM, respectively, with EC(50) values of 1.50 ± 0.25 μM for HHQ and 0.15 ± 0.02 μM for PQS. 2,4-Dihydroxyquinoline, a metabolite produced abundantly by P. aeruginosa, did not elicit an increase in reporter enzyme activity. To test whether the bioreporter can be used for the detection of enzymes active on AQ signalling molecules, the hodC gene coding for 2-methyl-3-hydroxy-4(1H)-quinolone 2,4-dioxygenase was expressed in the reporter strain. This dioxygenase catalyses the cleavage of PQS, albeit with very low activity. The response of the bioreporter to PQS was significantly quenched by co-expression of the hodC gene, and HPLC analysis of culture extracts verified that the PQS levels decreased during cultivation. The bioreporter can be applied to screen for AQ-converting enzymes, which will be useful tools to interfere with quorum sensing and thus virulence in P. aeruginosa.
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Affiliation(s)
- Christine Müller
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany
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Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 2012; 76:1-18. [PMID: 22232235 DOI: 10.1271/bbb.110620] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbazole degradation by several bacterial strains, including Pseudomonas resinovorans CA10, has been investigated over the last two decades. As the initial reaction in degradation pathways, carbazole is commonly oxygenated at angular (C9a) and adjacent (C1) carbons as two hydroxyl groups in a cis configuration. This type of dioxygenation is termed "angular dioxygenation," and is catalyzed by carbazole 1,9a-dioxygenase (CARDO), consisting of terminal oxygenase, ferredoxin, and ferredoxin reductase components. The crystal structures of all components and the electron transfer complex between terminal oxygenase and ferredoxin indicate substrate recognition mechanisms suitable for angular dioxygenation and specific electron transfer among the three components. In contrast, the carbazole degradative car operon of CA10 is located on IncP-7 conjugative plasmid pCAR1. Together with conventional molecular genetic and biochemical investigations, recent genome sequencing and RNA mapping studies have clarified that transcriptional cross-regulation via nucleoid-associated proteins is established between pCAR1 and the host chromosome.
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Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440. Antimicrob Agents Chemother 2011; 56:1001-9. [PMID: 22143519 DOI: 10.1128/aac.05398-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440 is a chloramphenicol-resistant bacterium that is able to grow in the presence of this antibiotic at a concentration of up to 25 μg/ml. Transcriptomic analyses revealed that the expression profile of 102 genes changed in response to this concentration of chloramphenicol in the culture medium. The genes that showed altered expression include those involved in general metabolism, cellular stress response, gene regulation, efflux pump transporters, and protein biosynthesis. Analysis of a genome-wide collection of mutants showed that survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol. The analysis also revealed that an ABC extrusion system (PP2669/PP2668/PP2667) and the AgmR regulator (PP2665) were needed for full resistance toward chloramphenicol. Transcriptional arrays revealed that AgmR controls the expression of the pqq genes and the operon encoding the ABC extrusion pump from the promoter upstream of open reading frame (ORF) PP2669.
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Affiliation(s)
- Pieter Van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E‐18008 Granada, Spain
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1‐1‐1 Yayoi, Bunkyo‐ku, Tokyo, Japan
| | - Jan Roelof Van Der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL‐Sorge, 1015 Lausanne, Switzerland
| | - Thomas K. Wood
- Artie McFerrin Department of Chemical Engineering
- Department of Biology, and
- Zachry Department of Civil Engineering, Texas A & M University, College Station, TX 77843‐3122, USA
- *E‐mail ; Tel. (979) 862‐1588; Fax (979) 845‐6446
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Godoy P, Molina‐Henares AJ, De La Torre J, Duque E, Ramos JL. Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups. Microb Biotechnol 2010; 3:691-700. [PMID: 21255364 PMCID: PMC3815342 DOI: 10.1111/j.1751-7915.2010.00189.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 05/04/2010] [Indexed: 11/12/2022] Open
Abstract
We have developed a generalized profile that identifies members of the root-nodulation-cell-division (RND) family of efflux pumps and classifies them into four functional subfamilies. According to Z-score values, efflux pumps can be grouped by their metabolic function, thus making it possible to distinguish pumps involved in antibiotic resistance (group 1) from those involved in metal resistance (group 3). In silico data regarding efflux pumps in group 1 were validated after identification of RND efflux pumps in a number of environmental microbes that were isolated as resistant to ethidium bromide. Analysis of the Pseudomonas putida KT2440 genome identified efflux pumps in all groups. A collection of mutants in efflux pumps and a screening platform consisting of 50 drugs were created to assign a function to the efflux pumps. We validated in silico data regarding efflux pumps in groups 1 and 3 using 9 different mutants. Four mutants belonging to group 2 were found to be more sensitive than the wild-type to oxidative stress-inducing agents such as bipyridyl and methyl viologen. The two remaining mutants belonging to group 4 were found to be more sensitive than the parental to tetracycline and one of them was particularly sensitive to rubidium and chromate. By effectively combining in vivo data with generalized profiles and gene annotation data, this approach allowed the assignment, according to metabolic function, of both known and uncharacterized RND efflux pumps into subgroups, thereby providing important new insight into the functions of proteins within this family.
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Affiliation(s)
| | | | | | | | - Juan L. Ramos
- Consejo Superior de Investigaciones Científicas, Department of Environmental Protection, E‐18008 Granada, Spain
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Expression of the Streptomyces coelicolor SoxR regulon is intimately linked with actinorhodin production. J Bacteriol 2010; 192:6428-38. [PMID: 20952574 DOI: 10.1128/jb.00916-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The [2Fe-2S]-containing transcription factor SoxR is conserved in diverse bacteria. SoxR is traditionally known as the regulator of a global oxidative stress response in Escherichia coli, but recent studies suggest that this function may be restricted to enteric bacteria. In the vast majority of nonenterics, SoxR is predicted to mediate a response to endogenously produced redox-active metabolites. We have examined the regulation and function of the SoxR regulon in the model antibiotic-producing filamentous bacterium Streptomyces coelicolor. Unlike the E. coli soxR deletion mutant, the S. coelicolor equivalent is not hypersensitive to oxidants, indicating that SoxR does not potentiate antioxidant defense in the latter. SoxR regulates five genes in S. coelicolor, including those encoding a putative ABC transporter, two oxidoreductases, a monooxygenase, and a possible NAD-dependent epimerase/dehydratase. Expression of these genes depends on the production of the benzochromanequinone antibiotic actinorhodin and requires intact [2Fe-2S] clusters in SoxR. These data indicate that actinorhodin, or a redox-active precursor, modulates SoxR activity in S. coelicolor to stimulate the production of a membrane transporter and proteins with homology to actinorhodin-tailoring enzymes. While the role of SoxR in S. coelicolor remains under investigation, these studies support the notion that SoxR has been adapted to perform distinct physiological functions to serve the needs of organisms that occupy different ecological niches and face different environmental challenges.
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Stenuit BA, Agathos SN. Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa? Appl Microbiol Biotechnol 2010; 88:1043-64. [DOI: 10.1007/s00253-010-2830-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 08/06/2010] [Accepted: 08/08/2010] [Indexed: 12/11/2022]
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Shintani M, Takahashi Y, Tokumaru H, Kadota K, Hara H, Miyakoshi M, Naito K, Yamane H, Nishida H, Nojiri H. Response of thePseudomonashost chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environ Microbiol 2009; 12:1413-26. [DOI: 10.1111/j.1462-2920.2009.02110.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription. J Mol Biol 2009; 394:576-86. [PMID: 19781550 DOI: 10.1016/j.jmb.2009.09.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 09/10/2009] [Accepted: 09/17/2009] [Indexed: 11/19/2022]
Abstract
The NtrC-family PhhR protein of Pseudomonas putida is involved in the control of the metabolism of aromatic amino acids, and it is a dual regulatory protein. When PhhR acts as an activator, it stimulates transcription from its cognate promoters with RNA polymerase/sigma(70) rather than with sigma(54), as is the case for most members of the family. The target binding sites in repressed and activated promoters are defined by the 5'-TGTAAAN(6)TTTACA-3' consensus sequence. PhhR binds to target sites as a dimer with affinity in the range of 0.03 to 6.6 microM, as shown by isothermal titration calorimetry. PhhR activates transcription from both the PP2827 and PP2078 promoters regardless of the absence or presence of aromatic amino acids, whereas PhhR stimulates transcription from certain positively regulated promoters (P(phhA), P(PP3122), P(PP3434), and P(hmg)) only in the presence of phenylalanine and tyrosine or their corresponding keto acids (i.e., phenylpyruvate and p-hydroxyphenylpyruvate). A surprising feature of PhhR-mediated transcriptional activation is that PhhR may bind to one or two upstream target sequences that are located at different distances from the RNA polymerase binding site. This allows PhhR to function as a class I regulator (target sites at -66/-83), a class II regulator (target sites around -40), as well as an enhancer protein (target sites >-128). When functioning as an enhancer protein, PhhR-mediated transcription is modulated by the integration host factor protein. PhhR represses transcription from its own promoter and the promoter of the paaY gene by steric hindrance.
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