1
|
Sumranwanich T, Amosu E, Chankhamhaengdecha S, Phetruen T, Loktumraks W, Ounjai P, Harnvoravongchai P. Evaluating lignin degradation under limited oxygen conditions by bacterial isolates from forest soil. Sci Rep 2024; 14:13350. [PMID: 38858437 PMCID: PMC11164938 DOI: 10.1038/s41598-024-64237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
Lignin, a heterogeneous aromatic polymer present in plant biomass, is intertwined with cellulose and hemicellulose fibrils, posing challenges to its effective utilization due to its phenolic nature and recalcitrance to degradation. In this study, three lignin utilizing bacteria, Klebsiella sp. LEA1, Pseudomonas sp. LEA2, and Burkholderia sp. LEA3, were isolated from deciduous forest soil samples in Nan province, Thailand. These isolates were capable of growing on alkali lignin and various lignin-associated monomers at 40 °C under microaerobic conditions. The presence of Cu2+ significantly enhanced guaiacol oxidation in Klebsiella sp. LEA1 and Pseudomonas sp. LEA2. Lignin-related monomers and intermediates such as 2,6-dimethoxyphenol, 4-vinyl guaiacol, 4-hydroxybenzoic acid, benzoic acid, catechol, and succinic acid were detected mostly during the late stage of incubation of Klebsiella sp. LEA1 and Pseudomonas sp. LEA2 in lignin minimal salt media via GC-MS analysis. The intermediates identified from Klebsiella sp. LEA1 degradation suggested that conversion and utilization occurred through the β-ketoadipate (ortho-cleavage) pathway under limited oxygen conditions. The ability of these bacteria to thrive on alkaline lignin and produce various lignin-related intermediates under limited oxygen conditions suggests their potential utility in oxygen-limited processes and the production of renewable chemicals from plant biomass.
Collapse
Affiliation(s)
- Thitinun Sumranwanich
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Esther Amosu
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Wethaka Loktumraks
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand.
| |
Collapse
|
2
|
Lu C, Wijffels RH, Martins Dos Santos VAP, Weusthuis RA. Pseudomonas putida as a platform for medium-chain length α,ω-diol production: Opportunities and challenges. Microb Biotechnol 2024; 17:e14423. [PMID: 38528784 DOI: 10.1111/1751-7915.14423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 03/27/2024] Open
Abstract
Medium-chain-length α,ω-diols (mcl-diols) play an important role in polymer production, traditionally depending on energy-intensive chemical processes. Microbial cell factories offer an alternative, but conventional strains like Escherichia coli and Saccharomyces cerevisiae face challenges in mcl-diol production due to the toxicity of intermediates such as alcohols and acids. Metabolic engineering and synthetic biology enable the engineering of non-model strains for such purposes with P. putida emerging as a promising microbial platform. This study reviews the advancement in diol production using P. putida and proposes a four-module approach for the sustainable production of diols. Despite progress, challenges persist, and this study discusses current obstacles and future opportunities for leveraging P. putida as a microbial cell factory for mcl-diol production. Furthermore, this study highlights the potential of using P. putida as an efficient chassis for diol synthesis.
Collapse
Affiliation(s)
- Chunzhe Lu
- Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Vitor A P Martins Dos Santos
- Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
- Lifeglimmer GmbH, Berlin, Germany
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
3
|
Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
Collapse
Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
| |
Collapse
|
4
|
Aksu D, Diallo MM, Şahar U, Uyaniker TA, Ozdemir G. High expression of ring-hydroxylating dioxygenase genes ensure efficient degradation of p-toluate, phthalate, and terephthalate by Comamonas testosteroni strain 3a2. Arch Microbiol 2021; 203:4101-4112. [PMID: 34057546 DOI: 10.1007/s00203-021-02395-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Para-toluic acid, a major pollutant in industrial wastewater, is hazardous to human health. It has been demonstrated that Gram-negative bacteria are among the most effective degraders of para-toluic acid. In this study, the ability of Comamonas testosteroni strain 3a2, isolated from a petrochemical industry wastewater, to degrade para-toluic acid was investigated. The effect of different carbon (glucose and ethylene glycol) and nitrogen sources (urea, yeast extract, peptone, NaNO3, NH4NO3) on the biodegradation of para-toluic acid by the isolate 3a2 was evaluated. Furthermore, ring hydroxylating dioxygenase genes were amplified by PCR and their expression was evaluated during the biodegradation of para-toluic acid. The results indicated that strain 3a2 was able to degrade up to 1000 mg/L of para-toluic acid after 14 h. The highest degradation yield was recorded in the presence of yeast extract as nitrogen source. However, the formation of terephthalic acid and phthalic acid was noted during para-toluic acid degradation by the isolate 3a2. Toluate 1,2-dioxygenase, terephthalate 1,2 dioxygenase, and phthalate 4,5 dioxygenase genes were detected in the genomic DNA of 3a2. The induction of ring hydroxylating dioxygenase genes was proportional to the concentration of each hydrocarbon. This study showed that the isolate 3a2 can produce terephthalate and phthalate during the para-toluic acid biodegradation, which were also degraded after 24 h.
Collapse
Affiliation(s)
- Didem Aksu
- Application and Research Center for Testing and Analysis, Ege University, Izmir, Turkey.
| | | | - Umut Şahar
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
| | | | - Guven Ozdemir
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
| |
Collapse
|
5
|
Lee GLY, Zakaria NN, Convey P, Futamata H, Zulkharnain A, Suzuki K, Abdul Khalil K, Shaharuddin NA, Alias SA, González-Rocha G, Ahmad SA. Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07. Int J Mol Sci 2020; 21:ijms21249363. [PMID: 33316871 PMCID: PMC7764105 DOI: 10.3390/ijms21249363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.
Collapse
Affiliation(s)
- Gillian Li Yin Lee
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang UPM 43400, Selangor, Malaysia; (G.L.Y.L.); (N.N.Z.); (N.A.S.)
| | - Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang UPM 43400, Selangor, Malaysia; (G.L.Y.L.); (N.N.Z.); (N.A.S.)
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8561, Japan;
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Kenshi Suzuki
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Khalilah Abdul Khalil
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam 40450, Selangor, Malaysia;
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang UPM 43400, Selangor, Malaysia; (G.L.Y.L.); (N.N.Z.); (N.A.S.)
| | - Siti Aisyah Alias
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Institute of Ocean and Earth Sciences, B303 Level 3, Block B, Universiti Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Gerardo González-Rocha
- Laboratorio de Investigacion en Agentes Antibacterianos, Facultad de Ciencias Biologicas, Universidad de Concepcion, Concepcion 4070386, Chile;
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang UPM 43400, Selangor, Malaysia; (G.L.Y.L.); (N.N.Z.); (N.A.S.)
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Correspondence:
| |
Collapse
|
6
|
Rybczyńska-Tkaczyk K, Korniłłowicz-Kowalska T, Szychowski KA, Gmiński J. Biotransformation and toxicity effect of monoanthraquinone dyes during Bjerkandera adusta CCBAS 930 cultures. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110203. [PMID: 31972453 DOI: 10.1016/j.ecoenv.2020.110203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/04/2020] [Accepted: 01/11/2020] [Indexed: 06/10/2023]
Abstract
The aim of this study was to evaluate of possibility of biotransformation and toxicity effect of monoanthraquinone dyes in cultures of Bjerkandera adusta CCBAS 930. Phenolic compounds, free radicals, phytotoxicity (Lepidium sativum L.), ecotoxicity (Vibrio fischeri) and cytotoxicity effect were evaluated to determine the toxicity of anthraquinone dyes before and after the treatment with B. adusta CCBAS 930. More than 80% of ABBB and AB129 was removed by biodegradation (decolorization) and biosorption, but biodegradation using oxidoreductases was the main dye removing mechanism. Secondary products toxic to plants and bacteria were formed in B. adusta strain CCBAS 930 cultures, despite efficient decolorization. ABBB and AB129 metabolites increased reactive oxygen species (ROS) production in human fibroblasts, but did not increase LDH release, did not affect the resazurine reduction assay and did not change caspase-9 or caspase-3 activity.
Collapse
Affiliation(s)
- K Rybczyńska-Tkaczyk
- Department of Environmental Microbiology, The University of Life Sciences, Leszczyńskiego Street 7, Lublin, 20-069, Poland.
| | - T Korniłłowicz-Kowalska
- Department of Environmental Microbiology, The University of Life Sciences, Leszczyńskiego Street 7, Lublin, 20-069, Poland
| | - K A Szychowski
- Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - J Gmiński
- Department of Clinical Biochemistry and Laboratory Diagnostics, Institute of Medical Sciences, University of Opole, Oleska 48, Opole, 45-052, Poland
| |
Collapse
|
7
|
Xiao M, Ma H, Sun M, Yin X, Feng Q, Song H, Gai H. Characterization of cometabolic degradation of p-cresol with phenol as growth substrate by Chlorella vulgaris. BIORESOURCE TECHNOLOGY 2019; 281:296-302. [PMID: 30826515 DOI: 10.1016/j.biortech.2019.02.079] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
To investigate the potential application of Chlorella vulgaris in the treatment of coal gasification wastewater, the characteristics of phenol and p-cresol cometabolism by Chlorella vulgaris were studied, including phenol degradation, ammonia nitrogen removal, antioxidant enzyme activities, and phenol hydroxylase activity. The results showed that the highest tolerable concentrations of phenol and p-cresol for Chlorella vulgaris were 800 and 400 mg/L, respectively. During cometabolism, phenol at low concentrations (100 mg/L) significantly promoted the degradation of p-cresol. Meanwhile, the removal efficiency of ammonia nitrogen was approximately 60% and was not affected by variations in phenol concentration. Furthermore, the cometabolism of phenol and p-cresol was enhanced by improvement of phenol hydroxylase activity of Chlorella vulgaris after the addition of NaHCO3 as an exogenous nutrient. Therefore, Chlorella vulgaris has a great potential for the biochemical treatment of coal gasification wastewater.
Collapse
Affiliation(s)
- Meng Xiao
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Honglei Ma
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Meng Sun
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xiangyang Yin
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qingmin Feng
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Hongbing Song
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Hengjun Gai
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
| |
Collapse
|
8
|
Kottara A, Hall JPJ, Harrison E, Brockhurst MA. Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol Ecol 2019; 94:4689093. [PMID: 29228229 PMCID: PMC5812508 DOI: 10.1093/femsec/fix172] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/30/2017] [Indexed: 11/28/2022] Open
Abstract
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently, we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid. Whereas Pseudomonas fluorescens and Pseudomonas savastanoi stably maintained the plasmid in both environments, the plasmid was highly unstable in Pseudomonas aeruginosa and Pseudomonas putida, where plasmid-free genotypes with Tn5042 captured to the chromosome invaded to higher frequency under mercury selection. These data confirm that plasmid stability is dependent upon the specific genetic interaction of the plasmid and host chromosome rather than being a property of plasmids alone, and moreover imply that MGE dynamics in diverse natural communities are likely to be complex and driven by a subset of species capable of stably maintaining plasmids that would then act as hubs of HGT.
Collapse
Affiliation(s)
- Anastasia Kottara
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Corresponding author: Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. Tel: +44 (0)1142220051; E-mail:
| |
Collapse
|
9
|
Williams A, Pétriacq P, Beerling DJ, Cotton TEA, Ton J. Impacts of Atmospheric CO 2 and Soil Nutritional Value on Plant Responses to Rhizosphere Colonization by Soil Bacteria. FRONTIERS IN PLANT SCIENCE 2018; 9:1493. [PMID: 30405655 PMCID: PMC6204664 DOI: 10.3389/fpls.2018.01493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/25/2018] [Indexed: 05/24/2023]
Abstract
Concerns over rising atmospheric CO2 concentrations have led to growing interest in the effects of global change on plant-microbe interactions. As a primary substrate of plant metabolism, atmospheric CO2 influences below-ground carbon allocation and root exudation chemistry, potentially affecting rhizosphere interactions with beneficial soil microbes. In this study, we have examined the effects of different atmospheric CO2 concentrations on Arabidopsis rhizosphere colonization by the rhizobacterial strain Pseudomonas simiae WCS417 and the saprophytic strain Pseudomonas putida KT2440. Rhizosphere colonization by saprophytic KT2440 was not influenced by sub-ambient (200 ppm) and elevated (1,200 ppm) concentrations of CO2, irrespective of the carbon (C) and nitrogen (N) content of the soil. Conversely, rhizosphere colonization by WCS417 in soil with relatively low C and N content increased from sub-ambient to elevated CO2. Examination of plant responses to WCS417 revealed that plant growth and systemic resistance varied according to atmospheric CO2 concentration and soil-type, ranging from growth promotion with induced susceptibility at sub-ambient CO2, to growth repression with induced resistance at elevated CO2. Collectively, our results demonstrate that the interaction between atmospheric CO2 and soil nutritional status has a profound impact on plant responses to rhizobacteria. We conclude that predictions about plant performance under past and future climate scenarios depend on interactive plant responses to soil nutritional status and rhizobacteria.
Collapse
Affiliation(s)
- Alex Williams
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- P Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Pierre Pétriacq
- P Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- UMR 1332 Fruit Biology and Pathology, INRA-Bordeaux & University of Bordeaux, Villenave d’Ornon, France
- Plateforme Métabolome du Centre de Génomique Fonctionnelle de Bordeaux, INRA – Bordeaux, Villenave d’Ornon, France
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - T. E. Anne Cotton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- P Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
10
|
A Novel Nonantibiotic, lgt-Based Selection System for Stable Maintenance of Expression Vectors in Escherichia coli and Vibrio cholerae. Appl Environ Microbiol 2018; 84:AEM.02143-17. [PMID: 29222103 PMCID: PMC5795084 DOI: 10.1128/aem.02143-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 12/02/2022] Open
Abstract
Antibiotic selection for the maintenance of expression plasmids is discouraged in the production of recombinant proteins for pharmaceutical or other human uses due to the risks of antibiotic residue contamination of the final products and the release of DNA encoding antibiotic resistance into the environment. We describe the construction of expression plasmids that are instead maintained by complementation of the lgt gene encoding a (pro)lipoprotein glyceryl transferase essential for the biosynthesis of bacterial lipoprotein. Mutations in lgt are lethal in Escherichia coli and other Gram-negative organisms. The lgt gene was deleted from E. coli and complemented by the Vibrio cholerae-derived gene provided in trans on a temperature-sensitive plasmid, allowing cells to grow at 30°C but not at 37°C. A temperature-insensitive expression vector carrying the V. cholerae-derived lgt gene was constructed, whereby transformants were selected by growth at 39°C. The vector was successfully used to express two recombinant proteins, one soluble and one forming insoluble inclusion bodies. Reciprocal construction was done by deleting the lgt gene from V. cholerae and complementing the lesion with the corresponding gene from E. coli. The resulting strain was used to produce the secreted recombinant cholera toxin B subunit (CTB) protein, a component of licensed as well as newly developed oral cholera vaccines. Overall, the lgt system described here confers extreme stability on expression plasmids, and this strategy can be easily transferred to other Gram-negative species using the E. coli-derived lgt gene for complementation. IMPORTANCE Many recombinant proteins are produced in bacteria from genes carried on autonomously replicating DNA elements called plasmids. These plasmids are usually inherently unstable and rapidly lost. This can be prevented by using genes encoding antibiotic resistance. Plasmids are thus maintained by allowing only plasmid-containing cells to survive when the bacteria are grown in medium supplemented with antibiotics. In the described antibiotic-free system for the production of recombinant proteins, an essential gene is deleted from the bacterial chromosome and instead provided on a plasmid. The loss of the plasmid becomes lethal for the bacteria. Such plasmids can be used for the expression of recombinant proteins. This broadly applicable system removes the need for antibiotics in recombinant protein production, thereby contributing to reducing the spread of genes encoding antibiotic resistance, reducing the release of antibiotics into the environment, and freeing the final products (often used in pharmaceuticals) from contamination with potentially harmful antibiotic residues.
Collapse
|
11
|
Choudhary A, Purohit H, Phale PS. Benzoate transport in Pseudomonas putida CSV86. FEMS Microbiol Lett 2018; 364:3861963. [PMID: 28591829 DOI: 10.1093/femsle/fnx118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas putida strain CSV86 metabolizes variety of aromatic compounds as the sole carbon source. Genome analysis revealed the presence of genes encoding putative transporters for benzoate, p-hydroxybenzoate, phenylacetate, p-hydroxyphenylacetate and vanillate. Bioinformatic analysis revealed that benzoate transport and metabolism genes are clustered at the ben locus as benK-catA-benE-benF. Protein topology prediction suggests that BenK (aromatic acid-H+ symporter of major facilitator superfamily) has 12 transmembrane α-helices with the conserved motif LADRXGRKX in loop 2, while BenE (benzoate-H+ symporter protein) has 11 predicted transmembrane α-helices. benF and catA encode benzoate specific porin, OprD and catechol 1,2-dioxygenase, respectively. Biochemical studies suggest that benzoate was transported by an inducible and active process. Inhibition (90%-100%) in the presence of dinitrophenol suggests that the energy for the transport process is derived from the proton motive force. The maximum rate of benzoate transport was 484 pmole min-1 mg-1 cells with an affinity constant, Kmof 4.5 μM. Transcriptional analysis of the benzoate and glucose-grown cells showed inducible expression of benF, benK and benE, suggesting that besides outer membrane porin, both inner membrane transporters probably contribute for the benzoate transport in P. putida strain CSV86.
Collapse
Affiliation(s)
- Alpa Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
| | - Hemant Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur 440020; India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
12
|
Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol 2017; 122:940-952. [PMID: 28092137 DOI: 10.1111/jam.13401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.
Collapse
Affiliation(s)
- C A Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M Prabhakaran
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - K D Ramachandriya
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, Stillwater, OK, USA
| | - P Canaan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - B Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
13
|
Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A, Kasai D, Yamazoe A, Fujita N, Ezaki T, Fukuda M. Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group. J GEN APPL MICROBIOL 2017; 63:1-10. [DOI: 10.2323/jgam.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kenta Yonezuka
- Department of Bioengineering, Nagaoka University of Technology
| | - Jun Shimodaira
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Michiro Tabata
- Department of Bioengineering, Nagaoka University of Technology
| | - Shoko Ohji
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Nobuyuki Fujita
- Biological Resource Center, National Institute of Technology and Evaluation
| | - Takayuki Ezaki
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology
| |
Collapse
|
14
|
Puntus IF, Ryazanova LP, Zvonarev AN, Funtikova TV, Kulakovskaya TV. The role of mineral phosphorus compounds in naphthalene biodegradation by Pseudomonas putida. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Lieder S, Jahn M, Seifert J, von Bergen M, Müller S, Takors R. Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440. AMB Express 2014; 4:71. [PMID: 25401072 PMCID: PMC4230896 DOI: 10.1186/s13568-014-0071-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 12/14/2022] Open
Abstract
Population heterogeneity occurring in industrial microbial bioprocesses is regarded as a putative effector causing performance loss in large scale. While the existence of subpopulations is a commonly accepted fact, their appearance and impact on process performance still remains rather unclear. During cell cycling, distinct subpopulations differing in cell division state and DNA content appear which contribute individually to the efficiency of the bioprocess. To identify stressed or impaired subpopulations, we analyzed the interplay of growth rate, cell cycle and phenotypic profile of subpopulations by using flow cytometry and cell sorting in conjunction with mass spectrometry based global proteomics. Adjusting distinct growth rates in chemostats with the model strain Pseudomonas putida KT2440, cells were differentiated by DNA content reflecting different cell cycle stages. The proteome of separated subpopulations at given growth rates was found to be highly similar, while different growth rates caused major changes of the protein inventory with respect to e.g. carbon storage, motility, lipid metabolism and the translational machinery. In conclusion, cells in various cell cycle stages at the same growth rate were found to have similar to identical proteome profiles showing no significant population heterogeneity on the proteome level. In contrast, the growth rate clearly determines the protein composition and therefore the metabolic strategy of the cells.
Collapse
Affiliation(s)
- Sarah Lieder
- Institute for Biochemical Engineering, University of Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Michael Jahn
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
| | - Jana Seifert
- Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Institute of Animal Nutrition, University of Hohenheim, Emil-Wolff-Straße 8 and 10, Stuttgart, 70599, Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Department of Metabolomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Sohngaardsholmsvej 49, Aalborg, 9000, Denmark
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, Leipzig, 04318, Germany
| | - Ralf Takors
- Institute for Biochemical Engineering, University of Stuttgart, Allmandring 31, Stuttgart, Germany
| |
Collapse
|
16
|
Modeling the differences in biochemical capabilities of pseudomonas species by flux balance analysis: how good are genome-scale metabolic networks at predicting the differences? ScientificWorldJournal 2014; 2014:416289. [PMID: 24707203 PMCID: PMC3953581 DOI: 10.1155/2014/416289] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/24/2013] [Indexed: 12/02/2022] Open
Abstract
To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. Such models have provided us with a framework for systematic analysis of metabolism. However, little effort has been put towards comparing biochemical capabilities of closely related species using their metabolic models. The accuracy of a model is highly dependent on the reconstruction process, as some errors may be included in the model during reconstruction. In this study, we investigated the ability of three Pseudomonas metabolic models to predict the biochemical differences, namely, iMO1086, iJP962, and iSB1139, which are related to P. aeruginosa PAO1, P. putida KT2440, and P. fluorescens SBW25, respectively. We did a comprehensive literature search for previous works containing biochemically distinguishable traits over these species. Amongst more than 1700 articles, we chose a subset of them which included experimental results suitable for in silico simulation. By simulating the conditions provided in the actual biological experiment, we performed case-dependent tests to compare the in silico results to the biological ones. We found out that iMO1086 and iJP962 were able to predict the experimental data and were much more accurate than iSB1139.
Collapse
|
17
|
Jiménez JI, Pérez-Pantoja D, Chavarría M, Díaz E, de Lorenzo V. A second chromosomal copy of thecatAgene endowsPseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol 2014; 16:1767-78. [DOI: 10.1111/1462-2920.12361] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Jose I. Jiménez
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Danilo Pérez-Pantoja
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Max Chavarría
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Eduardo Díaz
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| |
Collapse
|
18
|
Rokade K, Mali G. Biodegradation of benzyl benzoate by Pseudomonas desmolyticum NCIM 2112. World J Microbiol Biotechnol 2013; 30:827-33. [PMID: 24146308 DOI: 10.1007/s11274-013-1484-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/04/2013] [Indexed: 11/25/2022]
Abstract
Commercial grade insecticides are supplemented with the chemical additives to enhance the insecticidal activity before the action of main insecticide commence. Benzyl benzoate is one of such additive used in the formulation of many insecticides. Due to deposition of such additive the soil and plant health get deteriorated. The present research work describes the biodegradation of benzyl benzoate by Pseudomonas desmolyticum NCIM 2112. The biodegradation was influenced by factors such as pH, temperature and other carbon and nitrogen sources. The optimum pH and temperature for biodegradation was found to be 7.0 and 30 °C respectively. It was more effective at 0.5 % glucose and lactose concentration and at 0.05 % NaNO₃ and peptone concentration. Pseudomonas desmolyticum NCIM 2112 degrades benzyl benzoate into compounds like benzaldehyde and benzoic acid which are nontoxic in nature. Phytotoxicity study shows no germination inhibition in presence of degraded metabolites.
Collapse
Affiliation(s)
- Kedar Rokade
- Department of Microbiology, JJT University, Vidyanagari, Jhunjhunu, 333001, Rajasthan, India,
| | | |
Collapse
|
19
|
Cadmium increases catechol 2,3-dioxygenase activity in Variovorax sp. 12S, a metal-tolerant and phenol-degrading strain. Antonie van Leeuwenhoek 2013; 104:845-53. [DOI: 10.1007/s10482-013-9997-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/05/2013] [Indexed: 11/26/2022]
|
20
|
Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 2012; 93:2279-90. [DOI: 10.1007/s00253-012-3928-0] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/29/2022]
|
21
|
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.
Collapse
|
22
|
A novel degradation pathway of chloroaniline in Diaphorobacter sp. PCA039 entails initial hydroxylation. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0221-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
23
|
Continuous cultures of Pseudomonas putida mt-2 overcome catabolic function loss under real case operating conditions. Appl Microbiol Biotechnol 2009; 83:189-98. [DOI: 10.1007/s00253-009-1928-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 02/20/2009] [Accepted: 02/20/2009] [Indexed: 10/21/2022]
|
24
|
Parales RE, Parales JV, Pelletier DA, Ditty JL. Diversity of microbial toluene degradation pathways. ADVANCES IN APPLIED MICROBIOLOGY 2008; 64:1-73, 2 p following 264. [PMID: 18485280 DOI: 10.1016/s0065-2164(08)00401-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- R E Parales
- Department of Microbiology, University of California, Davis, California 95616, USA
| | | | | | | |
Collapse
|
25
|
Zeinali M, Vossoughi M, Ardestani SK. Naphthalene metabolism in Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic microorganism. CHEMOSPHERE 2008; 72:905-909. [PMID: 18471862 DOI: 10.1016/j.chemosphere.2008.03.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 03/11/2008] [Accepted: 03/18/2008] [Indexed: 05/26/2023]
Abstract
The thermophilic bacterium Nocardia otitidiscaviarum strain TSH1, originally isolated in our laboratory from a petroindustrial wastewater contaminated soil in Iran, grows at 50 degrees C on a broad range of hydrocarbons. Transformation of naphthalene by strain TSH1 which is able to use this two ring-polycyclic aromatic hydrocarbon (PAH) as a sole source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that strain TSH1 initiates its attack on naphthalene by dioxygenation at its C-1 and C-2 positions to give 1,2-dihydro-1,2-dihydroxynaphthalene. The intermediate 2-hydroxycinnamic acid, characteristic of the meta-cleavage of the resulting diol was identified in the acidic extract. Apart from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as an intermediate for the naphthalene pathway of this Nocardia strain. Neither phthalic acid nor salicylic acid metabolites were detected in culture extracts. Enzymatic experiments with cell extract showed the catechol 1,2-dioxygenase activity while transformation of phthalic acid and protocatechuic acid was not observed. The results of enzyme activity assays and identification of benzoic acid in culture extract provide strong indications that further degradation goes through benzoate and beta-ketoadipate pathway. Our results indicate that naphthalene degradation by thermophilic N. otitidiscaviarum strain TSH1 differs from the known pathways found for the thermophilic Bacillus thermoleovorans Hamburg 2 and mesophilic bacteria.
Collapse
Affiliation(s)
- Majid Zeinali
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | | |
Collapse
|
26
|
Shintani M, Yano H, Habe H, Omori T, Yamane H, Tsuda M, Nojiri H. Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. Appl Environ Microbiol 2006; 72:3206-16. [PMID: 16672459 PMCID: PMC1472330 DOI: 10.1128/aem.72.5.3206-3216.2006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2005] [Accepted: 02/08/2006] [Indexed: 11/20/2022] Open
Abstract
Isolated from Pseudomonas resinovorans CA10, pCAR1 is a 199-kb plasmid that carries genes involved in the degradation of carbazole and dioxin. The nucleotide sequence of pCAR1 has been determined previously. In this study, we characterized pCAR1 in terms of its replication, maintenance, and conjugation. By constructing miniplasmids of pCAR1 and testing their establishment in Pseudomonas putida DS1, we show that pCAR1 replication is due to the repA gene and its upstream DNA region. The repA gene and putative oriV region could be separated in P. putida DS1, and the oriV region was determined to be located within the 345-bp region between the repA and parW genes. Incompatibility testing using the minireplicon of pCAR1 and IncP plasmids indicated that pCAR1 belongs to the IncP-7 group. Monitoring of the maintenance properties of serial miniplasmids in nonselective medium, and mutation and complementation analyses of the parWABC genes, showed that the stability of pCAR1 is attributable to the products of the parWAB genes. In mating assays, the transfer of pCAR1 from CA10 was detected in a CA10 derivative that was cured of pCAR1 (CA10dm4) and in P. putida KT2440 at frequencies of 3 x 10(-1) and 3 x 10(-3) per donor strain, respectively. This is the first report of the characterization of this completely sequenced IncP-7 plasmid.
Collapse
Affiliation(s)
- Masaki Shintani
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | | | | | | | | | |
Collapse
|
27
|
Volkova OV, Anokhina TO, Puntus IF, Kochetkov VV, Filonov AE, Boronin AM. Effects of Naphthalene Degradative Plasmids on the Physiological Characteristics of Rhizosphere Bacteria of the Genus Pseudomonas. APPL BIOCHEM MICRO+ 2005. [DOI: 10.1007/s10438-005-0082-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Kesseru P, Kiss I, Bihari Z, Pál K, Portöro P, Polyák B. Nitrate-dependent salicylate degradation by Pseudomonas butanovora under anaerobic conditions. BIORESOURCE TECHNOLOGY 2005; 96:779-784. [PMID: 15607190 DOI: 10.1016/j.biortech.2004.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/05/2004] [Accepted: 08/04/2004] [Indexed: 05/24/2023]
Abstract
Nitrate-dependent salicylate degradation by the denitrifying Pseudomonas butanovora was investigated and the molar ratio of the cometabolism under anaerobic circumstances was determined. The bacterium was able to utilize salicylate as an electron donor for the reduction of nitrate. Salicylate was eliminated via catechol, which is degraded by means of catechol 2,3-oxygenases (meta-cleavage), forming 2-hydroxymuconic semialdehyde. The molar ratios of NO(3)(-)-N:salicylate existing during the experiment accorded well with the assumed 1:1 molar ratio. The tolerances of the growth, the salicylate degradation and the denitrification of P. butanovora to various heavy metal ions were also studied. Although the strain was tolerant to Pb(2+) and Cu(2+) up to 1 mM in complete medium, salicylate utilization took place only up to a concentration of 0.1 mM for both heavy metal ions. Of the heavy metal ions investigated, Cd(2+) (at a concentration of 0.05 mM) displayed the highest inhibitory effect on salicylate degradation by P. butanovora.
Collapse
Affiliation(s)
- Péter Kesseru
- Bay Zoltán Foundation for Applied Research, Institute for Biotechnology, Derkovits fasor 2., Szeged H-6726, Hungary.
| | | | | | | | | | | |
Collapse
|
29
|
Lambertsen LM, Molin S, Kroer N, Thomas CM. Transcriptional regulation of pWW0 transfer genes in Pseudomonas putida KT2440. Plasmid 2005; 52:169-81. [PMID: 15518874 DOI: 10.1016/j.plasmid.2004.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Revised: 06/01/2004] [Indexed: 11/26/2022]
Abstract
The conjugative IncP-9 plasmid pWW0 (TOL) carries transfer genes, many of whose functions can be predicted from sequence similarities to the well-studied IncW and IncP-1 plasmids, and that are clustered with the replication and maintenance genes of the plasmid core. In this study we show that the IncP-9 transfer genes are transcribed from at least three promoter regions. The promoters for traA and traD act divergently from the region found to encode the origin of transfer, oriT. These promoters regulate expression of traA, B, and perhaps traC in one direction and traD in the other, all of whose gene products are predicted to be involved in relaxasome formation and DNA processing during transfer, and they are repressed by TraA. The third promoter region, upstream of mpfR, is responsible for transcription of mpfR and mpfA to mpfJ, encoding proteins involved in mating pair formation. Transcription from this region is negatively autoregulated by MpfR. Thus the pWW0 transfer genes, like those of the IncP-1 plasmids, are expressed at all times, but kept in control by a negative feed back loop to limit the metabolic burden on the host. Although many of the related mating pair formation systems are, as in pWW0, transcribed divergently from an operon for replication and/or stable inheritance functions, MpfR is not related to the known regulatory proteins of these other transfer systems outside those of the IncP-9 family and indeed the regulators tend to be specific for each plasmid family. This suggests that the general pattern of genetic organisation exhibited by these systems has arisen a number of times independently and must therefore be highly favourable to plasmid survival and spread.
Collapse
Affiliation(s)
- Lotte M Lambertsen
- Molecular Microbial Ecology Group, Centre for Biomedical Microbiology, BioCentrum-DTU, Building 301, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | | | | |
Collapse
|
30
|
Kleinsteuber S, Hoffmann D, Müller RH, Babel W. Detection of chlorocatechol 1,2-dioxygenase genes in proteobacteria by PCR and gene probes. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/abio.370180306] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
31
|
Rapp P, Gabriel-Jürgens LHE. Degradation of alkanes and highly chlorinated benzenes, and production of biosurfactants, by a psychrophilic Rhodococcus sp. and genetic characterization of its chlorobenzene dioxygenase. Microbiology (Reading) 2003; 149:2879-2890. [PMID: 14523120 DOI: 10.1099/mic.0.26188-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus sp. strain MS11 was isolated from a mixed culture. It displays a diverse range of metabolic capabilities. During growth on 1,2,4-trichlorobenzene, 1,2,4,5-tetrachlorobenzene (1,2,4,5-TeCB) and 3-chlorobenzoate stoichiometric amounts of chloride were released. It also utilized all three isomeric dichlorobenzenes and 1,2,3-trichlorobenzene as the sole carbon and energy source. Furthermore, the bacterium grew well on a great number of n-alkanes ranging from n-heptane to n-triacontane and on the branched alkane 2,6,10,14-tetramethylpentadecane (pristane) and slowly on n-hexane and n-pentatriacontane. It was able to grow at temperatures from 5 to 30 °C, with optimal growth at 20 °C, and could tolerate 6 % NaCl in mineral salts medium. Genes encoding the initial chlorobenzene dioxygenase were detected by using a primer pair that was designed against the α-subunit (TecA1) of the chlorobenzene dioxygenase of Ralstonia (formerly Burkholderia) sp. strain PS12. The amino acid sequence of the amplified part of the α-subunit of the chlorobenzene dioxygenase of Rhodococcus sp. strain MS11 showed >99 % identity to the α-subunit of the chlorobenzene dioxygenase from Ralstonia sp. strain PS12 and the parts of both α-subunits responsible for substrate specificity were identical. The subsequent enzymes dihydrodiol dehydrogenase and chlorocatechol 1,2-dioxygenase were induced in cells grown on 1,2,4,5-TeCB. During cultivation on medium-chain-length n-alkanes ranging from n-decane to n-heptadecane, including 1-hexadecene, and on the branched alkane pristane, strain MS11 produced biosurfactants lowering the surface tension of the cultures from 72 to ⩽29 mN m−1. Glycolipids were extracted from the supernatant of a culture grown on n-hexadecane and characterized by 1H- and 13C-NMR-spectroscopy and mass spectrometry. The two major components consisted of α,α-trehalose esterified at C-2 or C-4 with a succinic acid and at C-2′ with a decanoic acid. They differed from one another in that one 2,3,4,2′-trehalosetetraester, found in higher concentration, was esterified at C-2, C-3 or C-4 with one octanoic and one decanoic acid and the other one, of lower concentration, with two octanoic acids. The results demonstrate that Rhodococcus sp. strain MS11 may be well suited for bioremediation of soils and sediments contaminated for a long time with di-, tri- and tetrachlorobenzenes as well as alkanes.
Collapse
Affiliation(s)
- Peter Rapp
- GBF-National Research Centre for Biotechnology, Division of Microbiology, Mascheroderweg 1, D-38124 Braunschweig, Germany
| | - Lotte H E Gabriel-Jürgens
- GBF-National Research Centre for Biotechnology, Division of Microbiology, Mascheroderweg 1, D-38124 Braunschweig, Germany
| |
Collapse
|
32
|
|
33
|
Ge Y, Vaillancourt FH, Agar NYR, Eltis LD. Reactivity of toluate dioxygenase with substituted benzoates and dioxygen. J Bacteriol 2002; 184:4096-103. [PMID: 12107126 PMCID: PMC135208 DOI: 10.1128/jb.184.15.4096-4103.2002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toluate dioxygenase (TADO) of Pseudomonas putida mt-2 catalyzes the dihydroxylation of a broad range of substituted benzoates. The two components of this enzyme were hyperexpressed and anaerobically purified. Reconstituted TADO had a specific activity of 3.8 U/mg with m-toluate, and each component had a full complement of their respective Fe(2)S(2) centers. Steady-state kinetics data obtained by using an oxygraph assay and by varying the toluate and dioxygen concentrations were analyzed by a compulsory order ternary complex mechanism. TADO had greatest specificity for m-toluate, displaying apparent parameters of KmA = 9 +/- 1 microM, k(cat) = 3.9 +/- 0.2 s(-1), and K(m)O(2) = 16 +/- 2 microM (100 mM sodium phosphate, pH 7.0; 25 degrees C), where K(m)O(2) represents the K(m) for O(2) and KmA represents the K(m) for the aromatic substrate. The enzyme utilized benzoates in the following order of specificity: m-toluate > benzoate approximately 3-chlorobenzoate > p-toluate approximately 4-chlorobenzoate >> o-toluate approximately 2-chlorobenzoate. The transformation of each of the first five compounds was well coupled to O(2) utilization and yielded the corresponding 1,2-cis-dihydrodiol. In contrast, the transformation of ortho-substituted benzoates was poorly coupled to O(2) utilization, with >10 times more O(2) being consumed than benzoate. However, the apparent K(m) of TADO for these benzoates was >100 microM, indicating that they do not effectively inhibit the turnover of good substrates.
Collapse
Affiliation(s)
- Yong Ge
- Department of Microbiology and Immunology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | | | | | | |
Collapse
|
34
|
Loh KC, Chua SS. Ortho pathway of benzoate degradation in Pseudomonas putida: induction of meta pathway at high substrate concentrations. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(02)00016-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
35
|
Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marqués S. Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res 2002; 30:1826-33. [PMID: 11937637 PMCID: PMC113213 DOI: 10.1093/nar/30.8.1826] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas putida KT2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. Its genome has recently been sequenced. We describe that a 35 bp sequence with the structure of an imperfect palindrome, originally found repeated three times downstream of the rpoH gene terminator, is detected more than 800 times in the chromosome of this strain. The structure of this DNA segment is analogous to that of the so-called enterobacteriaceae repetitive extragenic palindromic (REP) sequences, although its sequence is different. Computer-assisted analysis of the presence and distribution of this repeated sequence in the P.putida chromosome revealed that in at least 80% of the cases the sequence is extragenic, and in 82% of the cases the distance of this extragenic element to the end of one of the neighbouring genes was <100 bp. This 35 bp element can be found either as a single element, as pairs of elements, or sometimes forming clusters of up to five elements in which they alternate orientation. PCR scanning of chromosomes from different isolates of Pseudomonas sp. strains using oligonucleotides complementary to the most conserved region of this sequence shows that it is only present in isolates of the species P.putida. For this reason we suggest that the P.putida 35 bp element is a distinctive REP sequence in P.putida. This is the first time that REP sequences have been described and characterised in a group of non-enterobacteriaceae.
Collapse
Affiliation(s)
- Isabel Aranda-Olmedo
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Departamento de Bioquímica y Biología Molecular y Celular de Plantas, Apdo. de correos 419, E-18080 Granada, Spain
| | | | | | | | | |
Collapse
|
36
|
Godfrin-Estevenon AM, Pasta F, Lane D. The parAB gene products of Pseudomonas putida exhibit partition activity in both P. putida and Escherichia coli. Mol Microbiol 2002; 43:39-49. [PMID: 11849535 DOI: 10.1046/j.1365-2958.2002.02735.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacteria for which there is evidence that proteins of the ParAB family act in chromosome segregation also undergo developmental transitions that involve the ParAB homologues, raising the question of whether the partition activity is equivalent to that of plasmid partition systems. We have investigated the role in partition of the parAB locus of a free-living bacterium, Pseudomonas putida, not known to pass through developmental phases. A parAB deletion mutant, compared with wild type, showed slightly higher frequencies of anucleate cells in exponentially growing cultures but much higher frequencies in deceleration phase. This increase was growth medium dependent. Oversupply of ParA and ParB proteins also raised anucleate cell levels, specifically in the deceleration phase, in wild-type and mutant strains and regardless of medium, as well as generating abnormal cell morphologies. Absence or oversupply of ParAB function had either slight or considerable effects on growth rate, depending on temperature and medium. The need for the Par proteins in chromosome partition thus appears to be subject to the cell's physiological state. Three sequences similar to cis-acting stabilization sites of Bacillus subtilis are present in the P. putida oriC-parAB region. One was inserted into an unstable mini-F and shown to stabilize it in E. coli in a ParAB-dependent manner.
Collapse
|
37
|
Haddad S, Eby DM, Neidle EL. Cloning and expression of the benzoate dioxygenase genes from Rhodococcus sp. strain 19070. Appl Environ Microbiol 2001; 67:2507-14. [PMID: 11375157 PMCID: PMC92901 DOI: 10.1128/aem.67.6.2507-2514.2001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bopXYZ genes from the gram-positive bacterium Rhodococcus sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled Escherichia coli to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic cis-diol or catechol, respectively. This expression system also rapidly transformed m-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in Rhodococcus sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both meta- and ortho-cleavage degradative pathways, which are associated in pseudomonads with the xyl and ben genes, respectively. Open reading frames downstream of bopXYZ, designated bopL and bopK, resembled genes encoding cis-diol dehydrogenases and benzoate transporters, respectively. The bop genes were in the same order as the chromosomal ben genes of P. putida PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in E. coli yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome c reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences.
Collapse
Affiliation(s)
- S Haddad
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA.
| | | | | |
Collapse
|
38
|
Briganti F, Pessione E, Giunta C, Mazzoli R, Scozzafava A. Purification and catalytic properties of two catechol 1,2-dioxygenase isozymes from benzoate-grown cells of Acinetobacter radioresistens. JOURNAL OF PROTEIN CHEMISTRY 2000; 19:709-16. [PMID: 11307956 DOI: 10.1023/a:1007116703991] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two catechol 1,2-dioxygenase (C1,2O) isozymes (IsoA and IsoB) have been purified to homogeneity from a strain of Acinetobacter radioresistens grown on benzoate as the sole carbon and energy source. IsoA and IsoB are both homodimers composed of a single type of subunit with molecular mass of 38,600 and 37,700, Da respectively. In conditions of low ionic strength, IsoA can aggregate as a trimer, in contrast to IsoB, which maintains the dimeric structure, as also supported by the kinetic parameters (Hill numbers). IsoA is identical to the enzyme previously purified from the same bacterium grown on phenol, whereas the IsoB is selectively expressed using benzoate as carbon source. This is the first evidence of the presence of differently expressed C1,2O isozymes in A. radioresistens or more generally of multiple C1,2O isozymes in benzoate-grown Acinetobacter cells. Purified IsoA and IsoB contain approximately 1 iron(III) ion per subunit and both show electronic absorbance and EPR features typical of Fe(III) intradiol dioxygenases. The kinetic properties of the two enzymes such as the specificities toward substituted catechols, the main catalytic parameters, and their behavior in the presence of different kind of inhibitors are, unexpectedly, very similar, in contrast to most of the previously known dioxygenase isozymes.
Collapse
Affiliation(s)
- F Briganti
- Dipartimento di Chimica, Università degli Studi di Firenze, Florence, Italy.
| | | | | | | | | |
Collapse
|
39
|
Ramos-Díaz MA, Ramos JL. Combined physical and genetic map of the Pseudomonas putida KT2440 chromosome. J Bacteriol 1998; 180:6352-63. [PMID: 9829947 PMCID: PMC107723 DOI: 10.1128/jb.180.23.6352-6363.1998] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/1998] [Accepted: 09/23/1998] [Indexed: 11/20/2022] Open
Abstract
A combined physical and genetic map of the Pseudomonas putida KT2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (PFGE) and Southern hybridization. Circular genome size was estimated at 6.0 Mb by adding the sizes of 19 SwaI, 9 PmeI, 6 PacI, and 6 I-CeuI fragments. A complete physical map was achieved by combining the results of (i) analysis of PFGE of the DNA fragments resulting from digestion of the whole genome with PmeI, SwaI, I-CeuI, and PacI as well as double digestion with combinations of these enzymes and (ii) Southern hybridization analysis of the whole wild-type genome digested with different enzymes and hybridized against a series of probes obtained as cloned genes from different pseudomonads of rRNA group I and Escherichia coli, as P. putida DNA obtained by PCR amplification based on sequences deposited at the GenBank database, and by labeling of macrorestriction fragments of the P. putida genome eluted from agarose gels. As an alternative, 10 random mini-Tn5-Km mutants of P. putida KT2440 were used as a source of DNA, and the band carrying the mini-Tn5 in each mutant was identified after PFGE of a series of complete chromosomal digestions and hybridization with the kanamycin resistance gene of the mini-Tn5 as a probe. We established a circular genome map with an average resolution of 160 kb. Among the 63 genes located on the genetic map were key markers such as oriC, 6 rrn loci (rnnA to -F), recA, ftsZ, rpoS, rpoD, rpoN, and gyrB; auxotrophic markers; and catabolic genes for the metabolism of aromatic compounds. The genetic map of P. putida KT2440 was compared to those of Pseudomonas aeruginosa PAO1 and Pseudomonas fluorescens SBW25. The chromosomal backbone revealed some similarity in gene clustering among the three pseudomonads but differences in physical organization, probably as a result of intraspecific rearrangements.
Collapse
Affiliation(s)
- M A Ramos-Díaz
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | | |
Collapse
|
40
|
Abstract
Pseudomonas chlororaphis RW71 mineralized 1,2,3,4-tetrachlorobenzene, a highly recalcitrant pollutant hitherto not known to be degraded by pure cultures, as a sole source of carbon and energy, thereby releasing stoichiometric amounts of chloride. The transient excretion of tetrachlorocatechol in the early growth phase suggests an initial attack by a dioxygenase to form the corresponding dihydrodiol which rearomatizes to the catechol. The activity of chlorocatechol 1,2-dioxygenase in crude cell extracts was found to be extraordinarily high towards 3-chlorocatechol (ratio of 2.6 compared to catechol) and other chlorocatechols, including tetrachlorocatechol, which was transformed at a low but significant rate. Further identification of tetrachloromuconic acid, 2,3, 5-trichlorodienelactone, 2,3,5-trichloromaleyl acetic acid, and 2, 4-dichloro-3-oxoadipic acid as their methyl esters, together with high specific enzyme activities for chlorinated substrates, implicated a functioning chlorocatechol pathway to be induced during growth.
Collapse
|
41
|
Ramos JL, Marqués S, Timmis KN. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 1997; 51:341-73. [PMID: 9343354 DOI: 10.1146/annurev.micro.51.1.341] [Citation(s) in RCA: 278] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The xyl genes of Pseudomonas putida TOL plasmid that specify catabolism of toluene and xylenes are organized in four transcriptional units: the upper-operon xylUWCAMBN for conversion of toluene/xylenes into benzoate/alkylbenzoates; the meta-operon xylXYZLTEGFJQKIH, which encodes the enzymes for further conversion of these compounds into Krebs cycle intermediates; and xylS and xylR, which are involved in transcriptional control. The XylS and XylR proteins are members of the XylS/AraC and NtrC families, respectively, of transcriptional regulators. The xylS gene is constitutively expressed at a low level from the Ps2 promoter. The XylS protein is activated by interaction with alkylbenzoates, and this active form stimulates transcription from Pm by sigma70- or sigmaS-containing RNA polymerase (the meta loop). The xylR gene is also expressed constitutively. The XylR protein, which in the absence of effectors binds in a nonactive form to target DNA sequences, is activated by aromatic hydrocarbons and ATP; it subsequently undergoes multimerization and structural changes that result in stimulation of transcription from Pu of the upper operon. This latter process is assisted by the IHF protein and mediated by sigma54-containing RNA polymerase. Once activated, the XylR protein also stimulates transcription from the Ps1 promoter of xylS without interfering with expression from Ps2. This process is assisted by the HU protein and is mediated by sigma54-containing RNA polymerase. As a consequence of hyperexpression of the xylS gene, the XylS protein is hyperproduced and stimulates transcription from Pm even in the absence of effectors (the cascade loop). The two sigma54-dependent promoters are additionally subject to global (catabolite repression) control.
Collapse
Affiliation(s)
- J L Ramos
- Consejo Superior de Investigaciones Científicas, Department of Biochemistry and Molecular and Cellular Biology of Plants, Granada, Spain.
| | | | | |
Collapse
|
42
|
Mars AE, Kasberg T, Kaschabek SR, van Agteren MH, Janssen DB, Reineke W. Microbial degradation of chloroaromatics: use of the meta-cleavage pathway for mineralization of chlorobenzene. J Bacteriol 1997; 179:4530-7. [PMID: 9226262 PMCID: PMC179288 DOI: 10.1128/jb.179.14.4530-4537.1997] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas putida GJ31 is able to simultaneously grow on toluene and chlorobenzene. When cultures of this strain were inhibited with 3-fluorocatechol while growing on toluene or chlorobenzene, 3-methylcatechol or 3-chlorocatechol, respectively, accumulated in the medium. To establish the catabolic routes for these catechols, activities of enzymes of the (modified) ortho- and meta-cleavage pathways were measured in crude extracts of cells of P. putida GJ31 grown on various aromatic substrates, including chlorobenzene. The enzymes of the modified ortho-cleavage pathway were never present, while the enzymes of the meta-cleavage pathway were detected in all cultures. This indicated that chloroaromatics and methylaromatics are both converted via the meta-cleavage pathway. Meta cleavage of 3-chlorocatechol usually leads to the formation of a reactive acylchloride, which inactivates the catechol 2,3-dioxygenase and blocks further degradation of catechols. However, partially purified catechol 2,3-dioxygenase of P. putida GJ31 converted 3-chlorocatechol to 2-hydroxy-cis,cis-muconic acid. Apparently, P. putida GJ31 has a meta-cleavage enzyme which is resistant to inactivation by the acylchloride, providing this strain with the exceptional ability to degrade both toluene and chlorobenzene via the meta-cleavage pathway.
Collapse
Affiliation(s)
- A E Mars
- Department of Biochemistry, University of Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
43
|
Mathematical modelling and simulation of catechol production from benzoate using resting cells of Pseudomonas putida. Process Biochem 1997. [DOI: 10.1016/s0032-9592(96)00100-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
44
|
Choi WJ, Lee EY, Cho MH, Choi CY. Enhanced production of cis,cis-muconate in a cell-recycle bioreactor. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)82789-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
45
|
Production ofcis,cis-muconic acid from benzoic acidvia microbial transformation. BIOTECHNOL BIOPROC E 1996. [DOI: 10.1007/bf02949142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
46
|
Abstract
The eukaryotic alga Ochromonas danica, a nutritionally versatile, mixotrophic chrysophyte, grew on phenol as the sole carbon source in axenic culture and removed the phenol carbon from the growth medium. Respirometric studies confirmed that the enzymes involved in phenol catabolism were inducible and that the alga oxidized phenol; the amount of oxygen consumed per mole of oxidized substrate was approximately 65% of the theoretical value. [U-14C]phenol was completely mineralized, with 65% of the 14C label appearing as 14CO2, approximately 15% remaining in the aqueous medium, and the rest accounted for in the biomass. Analysis of the biomass showed that 14C label had been incorporated into the protein, nucleic acid, and lipid fractions; phenol carbon is thus unequivocally assimilated by the alga. Phenol-grown cultures of O. danica converted phenols to the corresponding catechols, which were further metabolized by the meta-cleavage pathway. This surprising result was rigorously confirmed by taking the working stock culture through a variety of procedures to check that it was axenic and repeating the experiments with algal extracts. This is, as far as is known, the first definitive identification of the meta-cleavage pathway for aromatic ring degradation in a eukaryotic alga, though its incidence in other eukaryotes has been (infrequently) suggested.
Collapse
Affiliation(s)
- K T Semple
- Department of Biological and Nutritional Sciences, The University, Newcastle upon Tyne, United Kingdom
| | | |
Collapse
|
47
|
Commandeur LC, May RJ, Mokross H, Bedard DL, Reineke W, Govers HA, Parsons JR. Aerobic degradation of polychlorinated biphenyls by Alcaligenes sp. JB1: metabolites and enzymes. Biodegradation 1996; 7:435-43. [PMID: 9188193 DOI: 10.1007/bf00115290] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In contrast to the degradation of penta- and hexachlorobiphenyls in chemostat cultures, the metabolism of PCBs by Alcaligenes sp. JB1 was shown to be restricted to PCBs with up to four chlorine substituents in resting-cell assays. Among these, the PCB congeners containing ortho chlorine substituents on both phenyl rings were found to be least degraded. Monochloro-benzoates and dichlorobenzoates were detected as metabolites. Resting cell assays with chlorobenzoates showed that JB1 could metabolize all three monochlorobenzoates and dichlorobenzoates containing only meta and para chlorine substituents, but not dichlorobenzoates possessing an ortho chlorine substituent. In enzyme activity assays, meta cleaving 2,3-dihydroxybiphenyl 1,2-dioxygenase and catechol 2,3-dioxygenase activities were constitutive, whereas benzoate dioxygenase and ortho cleaving catechol 1,2-dioxygenase activities were induced by their substrates. No activity was found for pyrocatechase II, the enzyme that is specific for chlorocatechols. The data suggest that complete mineralization of PCBs with three or more chlorine substituents by Alcaligenes sp. JB1 is unlikely.
Collapse
Affiliation(s)
- L C Commandeur
- Department of Environmental and Toxicological Chemistry, Amsterdam Research Institute for Substances in Ecosystems, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
48
|
Mineralization of phenol and its derivatives by Pseudomonas sp. strain CP4. World J Microbiol Biotechnol 1995; 11:661-4. [DOI: 10.1007/bf00361012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/1995] [Accepted: 07/11/1995] [Indexed: 11/25/2022]
|
49
|
Leddy MB, Phipps DW, Ridgway HF. Catabolite-mediated mutations in alternate toluene degradative pathways in Pseudomonas putida. J Bacteriol 1995; 177:4713-20. [PMID: 7642499 PMCID: PMC177237 DOI: 10.1128/jb.177.16.4713-4720.1995] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas putida 54g grew on mineral salts with toluene and exhibited catechol-2,3-dioxygenase (C23O) activity, indicating a meta pathway. After 10 to 15 days on toluene, nondegrading (Tol-) variants approached nearly 10% of total CFU. Auxotrophs were not detected among variants, suggesting selective loss of catabolic function(s). Variant formation was substrate dependent, since Tol- cells were observed on neither ethylbenzene, glucose, nor peptone-based media nor when toluene catabolism was suppressed by glucose. Unlike wild-type cells, variants did not grow on gasoline, toluene, benzene, ethylbenzene, benzoate, or catechol, suggesting loss of meta pathway function. Catabolic and C23O activities were restored to variants via transfer of a 78-mDa TOL-like plasmid from a wild-type Tol+ donor. Tests for reversion of variants to Tol+ were uniformly negative, suggesting possible delection or excision of catabolic genes. Deletions were confirmed in some variants by failure to hybridize with a DNA probe specific for the xylE gene encoding C23O. Cells grown on benzoate remained Tol+ but were C23O- and contained a plasmid of reduced size or were plasmid free, suggesting an alternate chromosomal catabolic pathway, also defective in variants. Cells exposed to benzyl alcohol, the initial oxidation product of toluene, accumulated > 13% variants in 5 days, even when cell division was repressed by nitrogen deprivation to abrogate selection processes. No variants formed in identical ethylbenzene-exposed controls. The results suggest that benzyl alcohol mediates irreversible defects in both a plasmid-associated meta pathway and an alternate chromosomal pathway.
Collapse
Affiliation(s)
- M B Leddy
- Biotechnology Research Department, Orange County Water District, Fountain Valley, California 92728-8300, USA
| | | | | |
Collapse
|
50
|
Pieper DH, Stadler-Fritzsche K, Knackmuss H, Timmis KN. Formation of Dimethylmuconolactones from Dimethylphenols by Alcaligenes eutrophus JMP 134. Appl Environ Microbiol 1995; 61:2159-65. [PMID: 16535041 PMCID: PMC1388459 DOI: 10.1128/aem.61.6.2159-2165.1995] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,3-, 2,4-, 2,5-, 3,4-, and 3,5-dimethylphenols were cometabolized by 2,4-dichlorophenoxyacetate-grown Alcaligenes eutrophus JMP 134 or the constitutive derivative JMP 134-1 via the ortho pathway into dimethylmuconolactones as dead-end products. Formation of two distinct lactones from 3,4-dimethylphenol is indicative of 2- as well as 6-hydroxylation. Induction of the meta-cleavage pathway by 2,3- and 3,4-dimethylphenols resulted in growth and no accumulation of products. In contrast, 3,5-dimethylphenol is not metabolized by the meta-cleavage pathway.
Collapse
|