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Ribeiro S, Alves K, Nourikyan J, Lavergne JP, de Bernard S, Buffat L. Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis. Front Microbiol 2025; 16:1494490. [PMID: 40376455 PMCID: PMC12078273 DOI: 10.3389/fmicb.2025.1494490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/14/2025] [Indexed: 05/18/2025] Open
Abstract
Introduction The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health. Novel approaches to uncover potential novel diagnostic and therapeutic targets for these pathogens are needed. Methods In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains across 734 strains from 514 species and 91 families. Results Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by both statistical testing and complementary protein domain analysis. Discussion By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a novel resource for bacterial pathogenicity research.
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Affiliation(s)
- Sara Ribeiro
- AltraBio SAS, Lyon, France
- Molecular Microbiology and Structural Biochemistry, Université de Lyon, CNRS, Lyon, France
| | | | | | - Jean-Pierre Lavergne
- Molecular Microbiology and Structural Biochemistry, Université de Lyon, CNRS, Lyon, France
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2
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Su J, Tian X, Cheng H, Liu D, Wang Z, Sun S, Wang HW, Sui SF. Structural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase. Nat Struct Mol Biol 2025; 32:73-85. [PMID: 39223421 DOI: 10.1038/s41594-024-01379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The enzymes 3-methylcrotonyl-coenzyme A (CoA) carboxylase (MCC), pyruvate carboxylase and propionyl-CoA carboxylase belong to the biotin-dependent carboxylase family located in mitochondria. They participate in various metabolic pathways in human such as amino acid metabolism and tricarboxylic acid cycle. Many human diseases are caused by mutations in those enzymes but their structures have not been fully resolved so far. Here we report an optimized purification strategy to obtain high-resolution structures of intact human endogenous MCC, propionyl-CoA carboxylase and pyruvate carboxylase in different conformational states. We also determine the structures of MCC bound to different substrates. Analysis of MCC structures in different states reveals the mechanism of the substrate-induced, multi-element synergistic activation of MCC. These results provide important insights into the catalytic mechanism of the biotin-dependent carboxylase family and are of great value for the development of new drugs for the treatment of related diseases.
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Affiliation(s)
- Jiayue Su
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuyang Tian
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hang Cheng
- The California Institute for Quantitative Biosciences (QB3), University of California campuses at Berkeley, Berkeley, CA, USA
| | - Desheng Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ziyi Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
- School of Life Sciences, Cryo-EM Center, Southern University of Science and Technology, Shenzhen, China.
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3
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Raveendran A, Gupta A, Lewis LE, Prabhu K, Moorkoth S. A comprehensive approach for detection of biotin deficiency from dried blood spot samples using liquid chromatography-mass spectrometry. Future Sci OA 2024; 10:2355038. [PMID: 38963009 PMCID: PMC11229587 DOI: 10.1080/20565623.2024.2355038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 07/05/2024] Open
Abstract
Aim: The aim of the present study is to develop a liquid chromatography-mass spectrometry method to measure two important biomarkers of biotin deficiency from dried blood spot samples for effective management of the disorder. Materials & methods: The method was developed on a liquid chromatography-mass spectrometry system using pentafluorophenyl column employing a mobile phase composition of methanol and water in the isocratic mode. A full validation of the method was performed as per relevant guidelines. Results & conclusion: Correlation between the results of dried blood spot and plasma method was evaluated to determine the interconvertibility of the method. The developed method was successfully applied for establishing the reference ranges for these biomarkers in the population of Udupi, a coastal district of South India.
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Affiliation(s)
- Arya Raveendran
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ashutosh Gupta
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Leslie E Lewis
- Department of Pediatrics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Krishnananda Prabhu
- Department of Biochemistry, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Sudheer Moorkoth
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
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4
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Bookout T, Shideler S, Cooper E, Goff K, Headley JV, Gieg LM, Lewenza S. Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water. ACS Synth Biol 2024; 13:3197-3211. [PMID: 39312753 PMCID: PMC11495318 DOI: 10.1021/acssynbio.4c00260] [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: 04/11/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024]
Abstract
After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids (NA) in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were the atuAR promoters from a naphthenic acid degradation operon and upstream TetR regulator, the marR operon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptional lux reporter plasmids that were introduced into a tailings pond-derived Pseudomonas species. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner to simple, acyclic, and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 and 15 mg/L. The atuA and marR promoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.
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Affiliation(s)
- Tyson Bookout
- Department
of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Steve Shideler
- Department
of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Evan Cooper
- Faculty
of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department
of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Kira Goff
- Faculty
of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department
of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - John V. Headley
- Environment
and Climate Change Canada, National Hydrology Research Centre, Saskatoon, Saskatchewan, Canada S7N 3H5
| | - Lisa M. Gieg
- Biological
Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Shawn Lewenza
- Faculty
of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department
of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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5
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Kanno M, Shiota T, Ueno S, Takahara M, Haneda K, Tahara YO, Shintani M, Nakao R, Miyata M, Kimbara K, Futamata H, Tashiro Y. Identification of genes involved in enhanced membrane vesicle formation in Pseudomonas aeruginosa biofilms: surface sensing facilitates vesiculation. Front Microbiol 2023; 14:1252155. [PMID: 38107868 PMCID: PMC10722149 DOI: 10.3389/fmicb.2023.1252155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Membrane vesicles (MVs) are small spherical structures (20-400 nm) produced by most bacteria and have important biological functions including toxin delivery, signal transfer, biofilm formation, and immunomodulation of the host. Although MV formation is enhanced in biofilms of a wide range of bacterial species, the underlying mechanisms are not fully understood. An opportunistic pathogen, Pseudomonas aeruginosa, causes chronic infections that can be difficult to treat due to biofilm formation. Since MVs are abundant in biofilms, can transport virulence factors to the host, and have inflammation-inducing functions, the mechanisms of enhanced MV formation in biofilms needs to be elucidated to effectively treat infections. In this study, we evaluated the characteristics of MVs in P. aeruginosa PAO1 biofilms, and identified factors that contribute to enhanced MV formation. Vesiculation was significantly enhanced in the static culture; MVs were connected to filamentous substances in the biofilm, and separation between the outer and inner membranes and curvature of the membrane were observed in biofilm cells. By screening a transposon mutant library (8,023 mutants) for alterations in MV formation in biofilms, 66 mutants were identified as low-vesiculation strains (2/3 decrease relative to wild type), whereas no mutant was obtained that produced more MVs (twofold increase). Some transposons were inserted into genes related to biofilm formation, including flagellar motility (flg, fli, and mot) and extracellular polysaccharide synthesis (psl). ΔpelAΔpslA, which does not synthesize the extracellular polysaccharides Pel and Psl, showed reduced MV production in biofilms but not in planktonic conditions, suggesting that enhanced vesiculation is closely related to the synthesis of biofilm matrices in P. aeruginosa. Additionally, we found that blebbing occurred during bacterial attachment. Our findings indicate that biofilm-related factors are closely involved in enhanced MV formation in biofilms and that surface sensing facilitates vesiculation. Furthermore, this work expands the understanding of the infection strategy in P. aeruginosa biofilms.
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Affiliation(s)
- Mizuki Kanno
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Takuya Shiota
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - So Ueno
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Minato Takahara
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Keisuke Haneda
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Masaki Shintani
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Ryoma Nakao
- Department of Bacteriology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Kazuhide Kimbara
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yosuke Tashiro
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Hamamatsu, Japan
- JST PRESTO, Kawaguchi, Japan
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6
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Zhang X, Wang X, Zhang Y, Wang F, Zhang C, Li X. Development of isopentenyl phosphate kinases and their application in terpenoid biosynthesis. Biotechnol Adv 2023; 64:108124. [PMID: 36863457 DOI: 10.1016/j.biotechadv.2023.108124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023]
Abstract
As the largest class of natural products, terpenoids (>90,000) have multiple biological activities and a wide range of applications (e.g., pharmaceutical, agricultural, personal care and food industries). Therefore, the sustainable production of terpenoids by microorganisms is of great interest. Microbial terpenoid production depends on two common building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In addition to the natural biosynthetic pathways, mevalonate and methyl-D-erythritol-4-phosphate pathways, IPP and DMAPP can be produced through the conversion of isopentenyl phosphate and dimethylallyl monophosphate by isopentenyl phosphate kinases (IPKs), offering an alternative route for terpenoid biosynthesis. This review summarizes the properties and functions of various IPKs, novel IPP/DMAPP synthesis pathways involving IPKs, and their applications in terpenoid biosynthesis. Furthermore, we have discussed strategies to exploit novel pathways and unleash their potential for terpenoid biosynthesis.
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Affiliation(s)
- Xinyi Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
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7
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Hu JJ, Lee JKJ, Liu YT, Yu C, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase. Structure 2023; 31:100-110.e4. [PMID: 36543169 PMCID: PMC9825669 DOI: 10.1016/j.str.2022.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. α6β6 LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking α6β6 LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
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Affiliation(s)
- Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA; Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
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8
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Agwunobi DO, Wang M, Wang Z, Bai R, Wang R, Hu Q, Yu Z, Liu J. The toxicity of the monoterpenes from lemongrass is mitigated by the detoxifying symbiosis of bacteria and fungi in the tick Haemaphysalis longicornis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114261. [PMID: 36332404 DOI: 10.1016/j.ecoenv.2022.114261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
The entry mode of terpenes into the atmosphere is via volatilization of hydrocarbons from foliage over heavily forested areas besides entering the environment through surface water runoff. Some monoterpenes in essential oils are phytotoxins, acting as plant chemical defenses against bacteria or fungi infections and plant-eating insects. For organisms to survive, their enzymatic systems are activated in response to an assault by potentially harmful compounds. Certain bacterial and fungal genera have developed special abilities to transform toxic terpenes into less toxic derivatives. Here, we investigated the response of the bacterial and fungal community in Haemaphysalis longicornis exposed to Cymbopogon citratus (lemongrass) essential oil (EO) and citronellal. Sequencing of bacterial 16S rRNA and fungal ITS1 regions on an Illumina NovaSeq PE250 sequencing platform was performed for H. longicornis tick samples treated with 15 and 20 mg/mL of lemongrass essential oil and citronellal. The diversity recorded in samples treated with C. citratus EO was higher in comparison to those treated with citronellal but significantly lower in the control samples as reflected by the Shannon diversity index. All major H. longicornis bacterial phyla, including Proteobacteria (93.81 %), Firmicutes (2.58 %), and Bacteroidota (0.99 %) were detected. A switch of dominance from Coxiella to Pseudomonas, which has high biotransformation capacity, was observed in the bacterial community, whereas the phylum Ascomycota (Genera: Aspergillus, Archaeorhizomyces, Alternaria, and Candida) dominated in the fungal community indicating detoxifying symbiosis. Other significantly abundant bacterial genera include Ralstonia, Acinetobacter, Vibrio, and Pseudoalteromonas, while Ganoderma and Trichosporon (yeasts) spp. represented the fungi Basidiomycota. This study expanded the understanding of enzymatic modification of phytotoxic substances by microorganisms, which could provide deeper insights into the mitigation of harmful phytotoxins and the synthesis of eco-friendly derivatives for the control of ticks.
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Affiliation(s)
- Desmond O Agwunobi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zihao Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Ruwei Bai
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Ruotong Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Qiuyu Hu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
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9
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Bär D, Konetschny B, Kulik A, Xu H, Paccagnella D, Beller P, Ziemert N, Dickschat JS, Gust B. Origin of the 3-methylglutaryl moiety in caprazamycin biosynthesis. Microb Cell Fact 2022; 21:232. [PMID: 36335365 PMCID: PMC9636800 DOI: 10.1186/s12934-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Caprazamycins are liponucleoside antibiotics showing bioactivity against Gram-positive bacteria including clinically relevant Mycobacterium tuberculosis by targeting the bacterial MraY-translocase. Their chemical structure contains a unique 3-methylglutaryl moiety which they only share with the closely related liposidomycins. Although the biosynthesis of caprazamycin is understood to some extent, the origin of 3-methylglutaryl-CoA for caprazamycin biosynthesis remains elusive. RESULTS In this work, we demonstrate two pathways of the heterologous producer Streptomyces coelicolor M1154 capable of supplying 3-methylglutaryl-CoA: One is encoded by the caprazamycin gene cluster itself including the 3-hydroxy-3-methylglutaryl-CoA synthase Cpz5. The second pathway is part of primary metabolism of the host cell and encodes for the leucine/isovalerate utilization pathway (Liu-pathway). We could identify the liu cluster in S. coelicolor M1154 and gene deletions showed that the intermediate 3-methylglutaconyl-CoA is used for 3-methylglutaryl-CoA biosynthesis. This is the first report of this intermediate being hijacked for secondary metabolite biosynthesis. Furthermore, Cpz20 and Cpz25 from the caprazamycin gene cluster were found to be part of a common route after both individual pathways are merged together. CONCLUSIONS The unique 3-methylglutaryl moiety in caprazamycin originates both from the caprazamycin gene cluster and the leucine/isovalerate utilization pathway of the heterologous host. Our study enhanced the knowledge on the caprazamycin biosynthesis and points out the importance of primary metabolism of the host cell for biosynthesis of natural products.
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Affiliation(s)
- Daniel Bär
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Benjamin Konetschny
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Davide Paccagnella
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Patrick Beller
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bertolt Gust
- Department of Pharmaceutical Biology, Eberhard-Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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Chen Y, Jia H, Liang Y, Zhang H, Che S, Liu R, Zhang Q, Bartlam M. Structural characterization of the Pseudomonas aeruginosa dehydrogenase AtuB involved in citronellol and geraniol catabolism. Biochem Biophys Res Commun 2020; 523:954-960. [PMID: 31964529 DOI: 10.1016/j.bbrc.2020.01.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
Pseudomonas aeruginosa can metabolize acyclic monoterpenoids (such as citronellol and geraniol) as the only carbon and energy sources. A total of seven proteins (AtuA, AtuB, AtuCF, AtuD, AtuE, AtuG, AtuH) have been identified in Pseudomonas aeruginosa as participating in the acyclic terpene utilization pathway. AtuB is a dehydrogenase enzyme responsible for citronellol and geraniol catabolism in the acyclic terpene utilization (Atu) pathway, although its structure and function have not been characterized to date. Here we report the crystal structure of AtuB from Pseudomonas aeruginosa PAO1 (PaAtuB) to 1.8 Å resolution. PaAtuB crystallizes in the space group F222 with a single monomer in the asymmetric unit. Analytical ultracentrifugation data shows that PaAtuB forms a stable tetramer in solution, which is consistent with the structure. Structural analysis confirms that AtuB belongs to the short-chain dehydrogenase/reductase (SDR) family. AtuB is predicted to bind NADP(H) from the crystal structure, which is confirmed by MicroScale Thermophoresis analysis that shows PaAtuB binds NADP(H) with a Kd value of 258 μM. This work provides a starting point to explore potential biotechnology and pharmaceutical applications of AtuB.
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Affiliation(s)
- Yujing Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haizhu Jia
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yakun Liang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hao Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shiyou Che
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China; Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China; Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- College of Life Sciences, Nankai University, Tianjin, 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin, 300071, China
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11
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Fléchard M, Duchesne R, Tahrioui A, Bouffartigues E, Depayras S, Hardouin J, Lagy C, Maillot O, Tortuel D, Azuama CO, Clamens T, Duclairoir-Poc C, Catel-Ferreira M, Gicquel G, Feuilloley MGJ, Lesouhaitier O, Heipieper HJ, Groleau MC, Déziel É, Cornelis P, Chevalier S. The absence of SigX results in impaired carbon metabolism and membrane fluidity in Pseudomonas aeruginosa. Sci Rep 2018; 8:17212. [PMID: 30464317 PMCID: PMC6249292 DOI: 10.1038/s41598-018-35503-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
In Pseudomonas aeruginosa, SigX is an extra-cytoplasmic function σ factor that belongs to the cell wall stress response network. In previous studies, we made the puzzling observation that sigX mutant growth was severely affected in rich lysogeny broth (LB) but not in minimal medium. Here, through comparative transcriptomic and proteomic analysis, we show that the absence of SigX results in dysregulation of genes, whose products are mainly involved in transport, carbon and energy metabolisms. Production of most of these genes is controlled by carbon catabolite repression (CCR), a key regulatory system than ensures preferential carbon source uptake and utilization, substrate prioritization and metabolism. The strong CCR response elicited in LB was lowered in a sigX mutant, suggesting altered nutrient uptake. Since the absence of SigX affects membrane composition and fluidity, we suspected membrane changes to cause such phenotype. The detergent polysorbate 80 (PS80) can moderately destabilize the envelope resulting in non-specific increased nutrient intake. Remarkably, growth, membrane fluidity and expression of dysregulated genes in the sigX mutant strain were restored in LB supplemented with PS80. Altogether, these data suggest that SigX is indirectly involved in CCR regulation, possibly via its effects on membrane integrity and fluidity.
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Affiliation(s)
- Maud Fléchard
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Rachel Duchesne
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ali Tahrioui
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Emeline Bouffartigues
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Ségolène Depayras
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Julie Hardouin
- Normandie Université, Université de Rouen Normandie, Laboratoire Polymères Biopolymères Surfaces, PBS, UMR, 6270 CNRS, Mont-Saint-Aignan, France
| | - Coralie Lagy
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Maillot
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Damien Tortuel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cecil Onyedikachi Azuama
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Thomas Clamens
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Cécile Duclairoir-Poc
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Manuella Catel-Ferreira
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Gwendoline Gicquel
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Marc G J Feuilloley
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Olivier Lesouhaitier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, UFZ Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Éric Déziel
- INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | - Pierre Cornelis
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France
| | - Sylvie Chevalier
- Normandie Université, Université de Rouen Normandie, Laboratoire de Microbiologie Signaux et Micro-environnement, LMSM EA 4312, Evreux, France.
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Tomassetti M, Garavaglia BS, Vranych CV, Gottig N, Ottado J, Gramajo H, Diacovich L. 3-methylcrotonyl Coenzyme A (CoA) carboxylase complex is involved in the Xanthomonas citri subsp. citri lifestyle during citrus infection. PLoS One 2018; 13:e0198414. [PMID: 29879157 PMCID: PMC5991677 DOI: 10.1371/journal.pone.0198414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/19/2018] [Indexed: 01/15/2023] Open
Abstract
Citrus canker is a disease caused by the phytopathogen Xanthomonas citri subsp. citri (Xcc), bacterium which is unable to survive out of the host for extended periods of time. Once established inside the plant, the pathogen must compete for resources and evade the defenses of the host cell. However, a number of aspects of Xcc metabolic and nutritional state, during the epiphytic stage and at different phases of infection, are poorly characterized. The 3-methylcrotonyl-CoA carboxylase complex (MCC) is an essential enzyme for the catabolism of the branched-chain amino acid leucine, which prevents the accumulation of toxic intermediaries, facilitates the generation of branched chain fatty acids and/or provides energy to the cell. The MCC complexes belong to a group of acyl-CoA carboxylases (ACCase) enzymes dependent of biotin. In this work, we have identified two ORFs (XAC0263 and XAC0264) encoding for the α and β subunits of an acyl-CoA carboxylase complex from Xanthomonas and demonstrated that this enzyme has MCC activity both in vitro and in vivo. We also found that this MCC complex is conserved in a group of pathogenic gram negative bacteria. The generation and analysis of an Xcc mutant strain deficient in MCC showed less canker lesions in the interaction with the host plant, suggesting that the expression of these proteins is necessary for Xcc fitness during infection.
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Affiliation(s)
- Mauro Tomassetti
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Betiana S. Garavaglia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Cecilia V. Vranych
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Natalia Gottig
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Ottado
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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PccD Regulates Branched-Chain Amino Acid Degradation and Exerts a Negative Effect on Erythromycin Production in Saccharopolyspora erythraea. Appl Environ Microbiol 2018; 84:AEM.00049-18. [PMID: 29439982 DOI: 10.1128/aem.00049-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
Branched-chain amino acid (BCAA) degradation is a major source of propionyl coenzyme A (propionyl-CoA), a key precursor of erythromycin biosynthesis in Saccharopolyspora erythraea In this study, we found that the bkd operon, responsible for BCAA degradation, was regulated directly by PccD, a transcriptional regulator of propionyl-CoA carboxylase genes. The transcriptional level of the bkd operon was upregulated 5-fold in a pccD gene deletion strain (ΔpccD strain) and decreased 3-fold in a pccD overexpression strain (WT/pIB-pccD), demonstrating that PccD was a negative transcriptional regulator of the operon. The deletion of pccD significantly improved the ΔpccD strain's growth rate, whereas pccD overexpression repressed WT/pIB-pccD growth rate, in basic Evans medium with 30 mM valine as the sole carbon and nitrogen source. The deletion of gdhA1 and the BcdhE1 gene (genes in the bkd operon) resulted in lower growth rates of ΔgdhA1 and ΔBcdhE1 strains, respectively, on 30 mM valine, further suggesting that the bkd operon is involved in BCAA degradation. Both bkd overexpression (WT/pIB-bkd) and pccD inactivation (ΔpccD strain) improve erythromycin production (38% and 64%, respectively), whereas the erythromycin production of strain WT/pIB-pccD was decreased by 48%. Lastly, we explored the applications of engineering pccD and bkd in an industrial high-erythromycin-producing strain. pccD deletion in industrial strain S. erythraea E3 (E3pccD) improved erythromycin production by 20%, and the overexpression of bkd in E3ΔpccD (E3ΔpccD/pIB-bkd) increased erythromycin production by 39% compared with S. erythraea E3 in an industrial fermentation medium. Addition of 30 mM valine to industrial fermentation medium further improved the erythromycin production by 23%, a 72% increase from the initial strain S. erythraea E3.IMPORTANCE We describe a bkd operon involved in BCAA degradation in S. erythraea The genes of the operon are repressed by a TetR regulator, PccD. The results demonstrated that PccD controlled the supply of precursors for biosynthesis of erythromycin via regulating the BCAA degradation and propionyl-CoA assimilation and exerted a negative effect on erythromycin production. The findings reveal a regulatory mechanism in feeder pathways and provide new strategies for designing metabolic engineering to increase erythromycin yield.
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Capture of endogenously biotinylated proteins from Pseudomonas aeruginosa displays unexpected downregulation of LiuD upon iron nutrition. Bioorg Med Chem 2016; 24:3330-5. [PMID: 27160053 DOI: 10.1016/j.bmc.2016.04.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/21/2016] [Accepted: 04/24/2016] [Indexed: 11/21/2022]
Abstract
The uptake and storage but also removal of excess iron are of utmost importance to microorganisms since surplus levels of iron may lead to the formation of reactive oxygen species. Therefore, iron homeostasis is generally tightly regulated by the ferric uptake regulator (Fur), a global iron regulator acting as a transcriptional repressor. While detecting biotinylated proteins in labelling experiments, we discovered that the endogenously biotinylated protein LiuD differentially accumulated upon iron treatment. LiuD represents the α-subunit of the methylcrotonyl-CoA-carboxylase (MCCase), an enzyme from the leucine/isovalerate utilization pathway. Real-time PCR transcription analysis revealed that the observed lower levels of LiuD biotinylation could be traced back to lower LiuD protein levels via a transcriptional repression of liuABCDE expression that however does not seem to be mediated by Fur. In accordance with LiuD's role for the leucine/isovalerate utilization pathway and its protein level regulation by nutritional iron levels, we found that wild-type Pseudomonas aeruginosa did not grow in the presence of iron if the medium contained only leucine as a carbon source. Conversely, iron stimulated the growth when glucose was used as a carbon source. Our study thus demonstrates the complexities of iron-regulated bacterial growth in Pseudomonas aeruginosa.
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The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family. Appl Environ Microbiol 2015; 81:6558-66. [PMID: 26162879 DOI: 10.1128/aem.01686-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/07/2015] [Indexed: 01/23/2023] Open
Abstract
Pseudomonas aeruginosa is one of only a few Pseudomonas species that are able to use acyclic monoterpenoids, such as citronellol and citronellate, as carbon and energy sources. This is achieved by the acyclic terpene utilization pathway (Atu), which includes at least six enzymes (AtuA, AtuB, AtuCF, AtuD, AtuE, AtuG) and is coupled to a functional leucine-isovalerate utilization (Liu) pathway. Here, quantitative proteome analysis was performed to elucidate the terpene metabolism of P. aeruginosa. The proteomics survey identified 187 proteins, including AtuA to AtuG and LiuA to LiuE, which were increased in abundance in the presence of citronellate. In particular, two hydratases, AtuE and the PA4330 gene product, out of more than a dozen predicted in the P. aeruginosa proteome showed an increased abundance in the presence of citronellate. AtuE (isohexenyl-glutaconyl coenzyme A [CoA] hydratase; EC 4.2.1.57) most likely catalyzes the hydration of the unsaturated distal double bond in the isohexenyl-glutaconyl-CoA thioester to yield 3-hydroxy-3-isohexenyl-glutaryl-CoA. Determination of the crystal structure of AtuE at a 2.13-Å resolution revealed a fold similar to that found in the hydratase (crotonase) superfamily and provided insights into the nature of the active site. The AtuE active-site architecture showed a significantly broader cavity than other crotonase superfamily members, in agreement with the need to accommodate the branched isoprenoid unit of terpenes. Glu139 was identified to be a potential catalytic residue, while the backbone NH groups of Gly116 and Gly68 likely form an oxyanion hole. The present work deepens the understanding of terpene metabolism in Pseudomonas and may serve as a basis to develop new strategies for the biotechnological production of terpenoids.
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Liu H, Yang CL, Ge MY, Ibrahim M, Li B, Zhao WJ, Chen GY, Zhu B, Xie GL. Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress. Front Microbiol 2014; 5:547. [PMID: 25374564 PMCID: PMC4204640 DOI: 10.3389/fmicb.2014.00547] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/01/2014] [Indexed: 01/14/2023] Open
Abstract
Acidovorax avenae subsp. avenae is the causal agent of bacterial brown stripe disease in rice. In this study, we characterized a novel horizontal transfer of a gene cluster, including tetR, on the chromosome of A. avenae subsp. avenae RS-1 by genome-wide analysis. TetR acted as a repressor in this gene cluster and the oxidative stress resistance was enhanced in tetR-deletion mutant strain. Electrophoretic mobility shift assay demonstrated that TetR regulator bound directly to the promoter of this gene cluster. Consistently, the results of quantitative real-time PCR also showed alterations in expression of associated genes. Moreover, the proteins affected by TetR under oxidative stress were revealed by comparing proteomic profiles of wild-type and mutant strains via 1D SDS-PAGE and LC-MS/MS analyses. Taken together, our results demonstrated that tetR gene in this novel gene cluster contributed to cell survival under oxidative stress, and TetR protein played an important regulatory role in growth kinetics, biofilm-forming capability, superoxide dismutase and catalase activity, and oxide detoxicating ability.
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Affiliation(s)
- He Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China ; Department of Plant Pathology, University of California Davis Davis, CA, USA
| | - Chun-Lan Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Meng-Yu Ge
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Muhammad Ibrahim
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China ; Department of Biosciences, COMSATS Institute of Information Technology Sahiwal, Pakistan
| | - Bin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Wen-Jun Zhao
- Chinese Academy of Inspection and Quarantine Beijing, China
| | - Gong-You Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Bo Zhu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Guan-Lin Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
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Marmulla R, Harder J. Microbial monoterpene transformations-a review. Front Microbiol 2014; 5:346. [PMID: 25076942 PMCID: PMC4097962 DOI: 10.3389/fmicb.2014.00346] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/21/2014] [Indexed: 11/17/2022] Open
Abstract
Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds can serve as carbon and energy source for aerobic and anaerobic microorganisms. Besides these catabolic reactions, transformations may occur as part of detoxification processes. Initial transformations of monoterpenes involve the introduction of functional groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge.
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Affiliation(s)
- Robert Marmulla
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
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Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zarzycki-Siek J, Norris MH, Kang Y, Sun Z, Bluhm AP, McMillan IA, Hoang TT. Elucidating the Pseudomonas aeruginosa fatty acid degradation pathway: identification of additional fatty acyl-CoA synthetase homologues. PLoS One 2013; 8:e64554. [PMID: 23737986 PMCID: PMC3667196 DOI: 10.1371/journal.pone.0064554] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/16/2013] [Indexed: 01/22/2023] Open
Abstract
The fatty acid (FA) degradation pathway of Pseudomonas aeruginosa, an opportunistic pathogen, was recently shown to be involved in nutrient acquisition during BALB/c mouse lung infection model. The source of FA in the lung is believed to be phosphatidylcholine, the major component of lung surfactant. Previous research indicated that P. aeruginosa has more than two fatty acyl-CoA synthetase genes (fadD; PA3299 and PA3300), which are responsible for activation of FAs using ATP and coenzyme A. Through a bioinformatics approach, 11 candidate genes were identified by their homology to the Escherichia coli FadD in the present study. Four new homologues of fadD (PA1617, PA2893, PA3860, and PA3924) were functionally confirmed by their ability to complement the E. coli fadD mutant on FA-containing media. Growth phenotypes of 17 combinatorial fadD mutants on different FAs, as sole carbon sources, indicated that the four new fadD homologues are involved in FA degradation, bringing the total number of P. aeruginosa fadD genes to six. Of the four new homologues, fadD4 (PA1617) contributed the most to the degradation of different chain length FAs. Growth patterns of various fadD mutants on plant-based perfumery substances, citronellic and geranic acids, as sole carbon and energy sources indicated that fadD4 is also involved in the degradation of these plant-derived compounds. A decrease in fitness of the sextuple fadD mutant, relative to the ΔfadD1D2 mutant, was only observed during BALB/c mouse lung infection at 24 h.
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Affiliation(s)
- Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Michael H. Norris
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Yun Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Zhenxin Sun
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Andrew P. Bluhm
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Ian A. McMillan
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Tung T. Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Molina G, Pimentel MR, Pastore GM. Pseudomonas: a promising biocatalyst for the bioconversion of terpenes. Appl Microbiol Biotechnol 2013; 97:1851-64. [DOI: 10.1007/s00253-013-4701-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/06/2013] [Accepted: 01/07/2013] [Indexed: 11/29/2022]
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Abstract
Adaptation of bacterial pathogens to a host can lead to the selection and accumulation of specific mutations in their genomes with profound effects on the overall physiology and virulence of the organisms. The opportunistic pathogen Pseudomonas aeruginosa is capable of colonizing the respiratory tract of individuals with cystic fibrosis (CF), where it undergoes evolution to optimize survival as a persistent chronic human colonizer. The transcriptome of a host-adapted, alginate-overproducing isolate from a CF patient was determined following growth of the bacteria in the presence of human respiratory mucus. This stable mucoid strain responded to a number of regulatory inputs from the mucus, resulting in an unexpected repression of alginate production. Mucus in the medium also induced the production of catalases and additional peroxide-detoxifying enzymes and caused reorganization of pathways of energy generation. A specific antibacterial type VI secretion system was also induced in mucus-grown cells. Finally, a group of small regulatory RNAs was identified and a fraction of these were mucus regulated. This report provides a snapshot of responses in a pathogen adapted to a human host through assimilation of regulatory signals from tissues, optimizing its long-term survival potential. The basis for chronic colonization of patients with cystic fibrosis (CF) by the opportunistic pathogen Pseudomonas aeruginosa continues to represent a challenging problem for basic scientists and clinicians. In this study, the host-adapted, alginate-overproducing Pseudomonas aeruginosa 2192 strain was used to assess the changes in its transcript levels following growth in respiratory CF mucus. Several significant and unexpected discoveries were made: (i) although the alginate overproduction in strain 2192 was caused by a stable mutation, a mucus-derived signal caused reduction in the transcript levels of alginate biosynthetic genes; (ii) mucus activated the expression of the type VI secretion system, a mechanism for killing of other bacteria in a mixed population; (iii) expression of a number of genes involved in respiration was altered; and (iv) several small regulatory RNAs were identified, some being mucus regulated. This work highlights the strong influence of the host environment in shaping bacterial survival strategies.
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Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012; 70:863-91. [PMID: 22869039 DOI: 10.1007/s00018-012-1096-0] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 12/14/2022]
Abstract
Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase, pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT), and biotin-carboxyl carrier protein components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC, or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC, and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.
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Co-expression of α and β subunits of the 3-methylcrotonyl-coenzyme A carboxylase from Pseudomonas aeruginosa. World J Microbiol Biotechnol 2011; 28:1185-91. [PMID: 22805839 DOI: 10.1007/s11274-011-0921-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/11/2011] [Indexed: 01/27/2023]
Abstract
Pseudomonas aeruginosa is a versatile bacterium that can grow using citronellol or leucine as sole carbon source. For both compounds the degradation pathways converge at the key enzyme 3-methylcrotonyl coenzyme-A carboxylase (MCCase). This enzyme is a complex formed by two subunits (α and β), encoded by the liuD and liuB genes, respectively; both are essential for enzyme function. Previously, both subunits had been separately expressed and then the complex re-constituted, however this methodology is laborious and produces low yield of active enzyme. In this work, the MCCase subunits were co-expressed in the same plasmid and purified in one step by affinity chromatography using the LiuD-His tag protein, interacting with the LiuB-S tag recombinant protein. The purified enzyme lost most of the activity within few hours of storage. The co-expressed subunits formed an (αβ)(4) complex that suffered a modification of its oligomerization state after storage, which probably contributed to the loss on activity observed. The recombinant MCCase enzyme presented optimum pH and temperature values of 9.0 and 30º C, respectively. Functionally, MCCase showed Michaelian kinetics behavior with a K(m) for its substrate and V(max) of 168 μM and 430 nmoles mg(-1)min(-1), respectively. The results suggest that the co-expression and co-purification of the subunits is a suitable procedure to obtain the active complex of the MCCase from Pseudomonas aeruginosa in a single step.
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Abstract
Carboxylases are among the most important enzymes in the biosphere, because they catalyze a key reaction in the global carbon cycle: the fixation of inorganic carbon (CO₂). This minireview discusses the physiological roles of carboxylases in different microbial pathways that range from autotrophy, carbon assimilation, and anaplerosis to biosynthetic and redox-balancing functions. In addition, the current and possible future uses of carboxylation reactions in synthetic biology are discussed. Such uses include the possible transformation of the greenhouse gas carbon dioxide into value-added compounds and the production of novel antibiotics.
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Chou CY, Tong L. Structural and biochemical studies on the regulation of biotin carboxylase by substrate inhibition and dimerization. J Biol Chem 2011; 286:24417-25. [PMID: 21592965 DOI: 10.1074/jbc.m111.220517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO(2) donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 Å resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca(2+) ions or two ADP molecules and one Mg(2+) ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADP molecule occupies the binding sites of bicarbonate and biotin. One Ca(2+) ion and the Mg(2+) ion are associated with the ADP molecule in the active site, and the other Ca(2+) ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.
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Affiliation(s)
- Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
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Chattopadhyay A, Förster-Fromme K, Jendrossek D. PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes. J Basic Microbiol 2010; 50:119-24. [PMID: 20082374 DOI: 10.1002/jobm.200900178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Growth of Pseudomonas aeruginosa on acyclic terpene alcohols such as geraniol depends on the presence of the atuRABCDEFGH gene cluster and a functional acyclic terpene utilisation (Atu) pathway. The proteins encoded by the atu gene cluster are necessary but not sufficient for growth on acyclic terpenes. Comparative 2-dimensional polyacrylamide gel electrophoresis of soluble P. aeruginosa proteins revealed the presence of an additional spot (besides Atu proteins) that is specifically expressed in geraniol cells but is absent in isovalerate-grown cells. The spot was identified as PA1982 gene product a pyrroloquinoline quinone (PQQ) dependent ethanol oxidoreductase (QEDH). Inactivation of PA1982 by insertion mutagenesis resulted in inability of the mutant to utilise ethanol and in reduced growth on geraniol. Growth on ethanol was restored by transferring an intact copy of the PA1982 gene into the mutant. The PA1982 gene product was purified from recombinant Escherichia coli and revealed PQQ-dependent oxidoreductase activity with a variety of substrates including acyclic terpene derivates at comparable V(max)-values. Our results show that QEDH participates in oxidation of acyclic terpene derivates in addition to the well-known function in ethanol metabolism.
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Catabolism of citronellol and related acyclic terpenoids in pseudomonads. Appl Microbiol Biotechnol 2010; 87:859-69. [DOI: 10.1007/s00253-010-2644-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/23/2010] [Accepted: 04/23/2010] [Indexed: 10/19/2022]
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Gounaris Y. Biotechnology for the production of essential oils, flavours and volatile isolates. A review. FLAVOUR FRAG J 2010. [DOI: 10.1002/ffj.1996] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Förster-Fromme K, Jendrossek D. AtuR is a repressor of acyclic terpene utilization (Atu) gene cluster expression and specifically binds to two 13 bp inverted repeat sequences of the atuA-atuR intergenic region. FEMS Microbiol Lett 2010; 308:166-74. [PMID: 20487029 DOI: 10.1111/j.1574-6968.2010.02005.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The atuR-atuABCDEFGH gene cluster is essential for acyclic terpene utilization (Atu) in Pseudomonas aeruginosa and Pseudomonas citronellolis. The cluster encodes most proteins of the Atu pathway including the key enzyme, geranyl-CoA carboxylase. AtuR was identified as a repressor of the atu gene cluster expression by (1) amino acid similarity to TetR repressor family members, (2) constitutive expression of Atu proteins in the atuR insertion mutant and (3) specific binding of purified AtuR homodimers to the atuR-atuA intergenic region in electrophoretic mobility shift assay (EMSA). Two 13 bp inverted repeat sequences separated by 40 bp in the atuA operator/promoter region were identified to represent two sites of AtuR binding by EMSA. Changing of two or more bases within the inverted repeat sequences abolished the ability of AtuR to bind to its target. All EMSA experiments were sufficiently sensitive with ethidium bromide-stained DNA fragments after polyacrylamide gel electrophoresis.
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Chávez-Avilés M, Díaz-Pérez AL, Reyes-de la Cruz H, Campos-García J. The Pseudomonas aeruginosa liuE gene encodes the 3-hydroxy-3-methylglutaryl coenzyme A lyase, involved in leucine and acyclic terpene catabolism. FEMS Microbiol Lett 2009; 296:117-23. [PMID: 19459965 DOI: 10.1111/j.1574-6968.2009.01624.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The enzymes involved in the catabolism of leucine are encoded by the liu gene cluster in Pseudomonas aeruginosa PAO1. A mutant in the liuE gene (ORF PA2011) of P. aeruginosa was unable to utilize both leucine/isovalerate and acyclic terpenes as the carbon source. The liuE mutant grown in culture medium with citronellol accumulated metabolites of the acyclic terpene pathway, suggesting an involvement of liuE in both leucine/isovalerate and acyclic terpene catabolic pathways. The LiuE protein was expressed as a His-tagged recombinant polypeptide purified by affinity chromatography in Escherichia coli. LiuE showed a mass of 33 kDa under denaturing and 79 kDa under nondenaturing conditions. Protein sequence alignment and fingerprint sequencing suggested that liuE encodes 3-hydroxy-3-methylglutaryl-coenzyme A lyase (HMG-CoA lyase), which catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate. LiuE showed HMG-CoA lyase optimal activity at a pH of 7.0 and 37 degrees C, an apparent K(m) of 100 microM for HMG-CoA and a V(max) of 21 micromol min(-1) mg(-1). These results demonstrate that the liuE gene of P. aeruginosa encodes for the HMG-CoA lyase, an essential enzyme for growth in both leucine and acyclic terpenes.
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Affiliation(s)
- Mauricio Chávez-Avilés
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Bode HB, Ring MW, Schwär G, Altmeyer MO, Kegler C, Jose IR, Singer M, Müller R. Identification of additional players in the alternative biosynthesis pathway to isovaleryl-CoA in the myxobacterium Myxococcus xanthus. Chembiochem 2009; 10:128-40. [PMID: 18846531 DOI: 10.1002/cbic.200800219] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Isovaleryl-CoA (IV-CoA) is usually derived from the degradation of leucine by using the Bkd (branched-chain keto acid dehydrogenase) complex. We have previously identified an alternative pathway for IV-CoA formation in myxobacteria that branches from the well-known mevalonate-dependent isoprenoid biosynthesis pathway. We identified 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (MvaS) to be involved in this pathway in Myxococcus xanthus, which is induced in mutants with impaired leucine degradation (e.g., bkd(-)) or during myxobacterial fruiting-body formation. Here, we show that the proteins required for leucine degradation are also involved in the alternative IV-CoA biosynthesis pathway through the efficient catalysis of the reverse reactions. Moreover, we conducted a global gene-expression experiment and compared vegetative wild-type cells with bkd mutants, and identified a five-gene operon that is highly up-regulated in bkd mutants and contains mvaS and other genes that are directly involved in the alternative pathway. Based on our experiments, we assigned roles to the genes required for the formation of IV-CoA from HMG-CoA. Additionally, several genes involved in outer-membrane biosynthesis and a plethora of genes encoding regulatory proteins were decreased in expression levels in the bkd(-) mutant; this explains the complex phenotype of bkd mutants including a lack of adhesion in developmental submerse culture.
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Affiliation(s)
- Helge B Bode
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
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Arenskötter Q, Heller J, Dietz D, Arenskötter M, Steinbüchel A. Cloning and characterization of alpha-methylacyl coenzyme A racemase from Gordonia polyisoprenivorans VH2. Appl Environ Microbiol 2008; 74:7085-9. [PMID: 18820059 PMCID: PMC2583472 DOI: 10.1128/aem.01491-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 09/18/2008] [Indexed: 11/20/2022] Open
Abstract
The mcr gene of Gordonia polyisoprenivorans VH2 is not clustered with genes required for rubber degradation. Its disruption by insertion of a kanamycin resistance cassette impaired growth on methyl-branched isoprenoids but not on linear hydrocarbons. Intact mcr from this bacterium or from Nocardia farcinica IFM 10152 complemented the mutant. Reverse transcription analysis showed similar mcr(VH2) expression results during cultivation with poly(cis-1,4-isoprene) and propionate. Additional genes coding for a putative cytochrome P450 monooxygenase and a short-chain dehydrogenase/reductase involved in beta-oxidation and poly(cis-1,4-isoprene) degradation were also characterized.
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Affiliation(s)
- Quyen Arenskötter
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Correnstrasse 3, D-48149 Münster, Germany
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Puchałka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VAP. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 2008; 4:e1000210. [PMID: 18974823 PMCID: PMC2563689 DOI: 10.1371/journal.pcbi.1000210] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 09/19/2008] [Indexed: 11/28/2022] Open
Abstract
A cornerstone of biotechnology is the use of microorganisms for the efficient
production of chemicals and the elimination of harmful waste.
Pseudomonas putida is an archetype of such microbes due to
its metabolic versatility, stress resistance, amenability to genetic
modifications, and vast potential for environmental and industrial applications.
To address both the elucidation of the metabolic wiring in P.
putida and its uses in biocatalysis, in particular for the production
of non-growth-related biochemicals, we developed and present here a genome-scale
constraint-based model of the metabolism of P. putida KT2440.
Network reconstruction and flux balance analysis (FBA) enabled definition of the
structure of the metabolic network, identification of knowledge gaps, and
pin-pointing of essential metabolic functions, facilitating thereby the
refinement of gene annotations. FBA and flux variability analysis were used to
analyze the properties, potential, and limits of the model. These analyses
allowed identification, under various conditions, of key features of metabolism
such as growth yield, resource distribution, network robustness, and gene
essentiality. The model was validated with data from continuous cell cultures,
high-throughput phenotyping data, 13C-measurement of internal flux
distributions, and specifically generated knock-out mutants. Auxotrophy was
correctly predicted in 75% of the cases. These systematic analyses
revealed that the metabolic network structure is the main factor determining the
accuracy of predictions, whereas biomass composition has negligible influence.
Finally, we drew on the model to devise metabolic engineering strategies to
improve production of polyhydroxyalkanoates, a class of biotechnologically
useful compounds whose synthesis is not coupled to cell survival. The solidly
validated model yields valuable insights into genotype–phenotype
relationships and provides a sound framework to explore this versatile bacterium
and to capitalize on its vast biotechnological potential. The pseudomonads include a diverse set of bacteria whose metabolic versatility
and genetic plasticity have enabled their survival in a broad range of
environments. Many members of this family are able to either degrade toxic
compounds or to efficiently produce high value compounds and are therefore of
interest for both bioremediation and bulk chemical production. To better
understand the growth and metabolism of these bacteria, we developed a
large-scale mathematical model of the metabolism of Pseudomonas
putida, a representative of the industrially relevant pseudomonads. The
model was initially expanded and validated with substrate utilization data and
carbon-tracking data. Next, the model was used to identify key features of
metabolism such as growth yield, internal distribution of resources, and network
robustness. We then used the model to predict novel strategies for the
production of precursors for bioplastics of medical and industrial relevance.
Such an integrated computational and experimental approach can be used to study
its metabolism and to explore the potential of other industrially and
environmentally important microorganisms.
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Affiliation(s)
- Jacek Puchałka
- Synthetic and Systems Biology Group, Helmholtz Center for Infection
Research (HZI), Braunschweig, Germany
| | - Matthew A. Oberhardt
- Department of Biomedical Engineering, University of Virginia, Health
System, Charlottesville, Virginia, United States of America
| | - Miguel Godinho
- Synthetic and Systems Biology Group, Helmholtz Center for Infection
Research (HZI), Braunschweig, Germany
| | - Agata Bielecka
- Synthetic and Systems Biology Group, Helmholtz Center for Infection
Research (HZI), Braunschweig, Germany
| | - Daniela Regenhardt
- Environmental Microbiology Group, Helmholtz Center for Infection Research
(HZI), Braunschweig, Germany
| | - Kenneth N. Timmis
- Environmental Microbiology Group, Helmholtz Center for Infection Research
(HZI), Braunschweig, Germany
| | - Jason A. Papin
- Department of Biomedical Engineering, University of Virginia, Health
System, Charlottesville, Virginia, United States of America
- * E-mail: (JAP); (VAPMdS)
| | - Vítor A. P. Martins dos Santos
- Synthetic and Systems Biology Group, Helmholtz Center for Infection
Research (HZI), Braunschweig, Germany
- * E-mail: (JAP); (VAPMdS)
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Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol 2008; 191:52-64. [PMID: 18820024 DOI: 10.1128/jb.01175-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA), propanoyl-CoA, and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR, and GntR families binding to 11 distinct DNA motifs. The ILV degradation genes in gamma- and betaproteobacteria are regulated mainly by a novel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species); in addition, the TetR-type regulator LiuQ was identified in some betaproteobacteria (eight species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gammaproteobacteria (34 species), PsrA in gamma- and betaproteobacteria (45 species), FadP in betaproteobacteria (14 species), and LiuR orthologs in alphaproteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from functional and evolutionary points of view.
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Substrate specificity of the 3-methylcrotonyl coenzyme A (CoA) and geranyl-CoA carboxylases from Pseudomonas aeruginosa. J Bacteriol 2008; 190:4888-93. [PMID: 18469096 DOI: 10.1128/jb.00454-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotin-containing 3-methylcrotonyl coenzyme A (MC-CoA) carboxylase (MCCase) and geranyl-CoA (G-CoA) carboxylase (GCCase) from Pseudomonas aeruginosa were expressed as His-tagged recombinant proteins in Escherichia coli. Both native and recombinant MCCase and GCCase showed pH and temperature optima of 8.5 and 37 degrees C. The apparent K(0.5) (affinity constant for non-Michaelis-Menten kinetics behavior) values of MCCase for MC-CoA, ATP, and bicarbonate were 9.8 microM, 13 microM, and 0.8 microM, respectively. MCCase activity showed sigmoidal kinetics for all the substrates and did not carboxylate G-CoA. In contrast, GCCase catalyzed the carboxylation of both G-CoA and MC-CoA. GCCase also showed sigmoidal kinetic behavior for G-CoA and bicarbonate but showed Michaelis-Menten kinetics for MC-CoA and the cosubstrate ATP. The apparent K(0.5) values of GCCase were 8.8 microM and 1.2 microM for G-CoA and bicarbonate, respectively, and the apparent K(m) values of GCCase were 10 microM for ATP and 14 microM for MC-CoA. The catalytic efficiencies of GCCase for G-CoA and MC-CoA were 56 and 22, respectively, indicating that G-CoA is preferred over MC-CoA as a substrate. The enzymatic properties of GCCase suggest that it may substitute for MCCase in leucine catabolism and that both the MCCase and GCCase enzymes play important roles in the leucine and acyclic terpene catabolic pathways.
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Förster-Fromme K, Chattopadhyay A, Jendrossek D. Biochemical characterization of AtuD from Pseudomonas aeruginosa, the first member of a new subgroup of acyl-CoA dehydrogenases with specificity for citronellyl-CoA. MICROBIOLOGY-SGM 2008; 154:789-796. [PMID: 18310025 DOI: 10.1099/mic.0.2007/014530-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The atuRABCDEFGH gene cluster is essential for acyclic terpene utilization (Atu) in Pseudomonas aeruginosa. The biochemical functions of most Atu proteins have not been experimentally verified; exceptions are AtuC/AtuF, which constitute the two subunits of geranyl-CoA carboxylase, the key enzyme of the Atu pathway. In this study we investigated the biochemical function of AtuD and of the PA1535 gene product, a protein related to AtuD in amino acid sequence. 2D gel electrophoresis showed that AtuD and the PA1535 protein were specifically expressed in cells grown on acyclic terpenes but were absent in isovalerate- or succinate-grown cells. Mutant analysis indicated that AtuD but not the product of PA1535 is essential for acyclic terpene utilization. AtuD and PA1535 gene product were expressed in recombinant Escherichia coli and purified to homogeneity. Purified AtuD showed citronellyl-CoA dehydrogenase activity (V(max) 850 mU mg(-1)) and high affinity to citronellyl-CoA (K(m) 1.6 microM). AtuD was inactive with octanoyl-CoA, 5-methylhex-4-enoyl-CoA or isovaleryl-CoA. Purified PA1535 gene product revealed high citronellyl-CoA dehydrogenase activity (V(max) 2450 mU mg(-1)) but had significantly lower affinity than AtuD to citronellyl-CoA (K(m) 18 microM). Purified PA1535 protein additionally utilized octanoyl-CoA as substrate (V(max), 610 mU mg(-1); K(m) 130 microM). To our knowledge AtuD is the first acyl-CoA dehydrogenase with a documented substrate specificity for terpenoid molecule structure and is essential for a functional Atu pathway. Potential other terpenoid-CoA dehydrogenases were found in the genomes of Pseudomonas citronellolis, Marinobacter aquaeolei and Hahella chejuensis but were absent in non-acyclic terpene-utilizing bacteria.
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Affiliation(s)
- Karin Förster-Fromme
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
| | - Ava Chattopadhyay
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
| | - Dieter Jendrossek
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
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Identification and functional analysis of cyclooxygenase-1 as a molecular target of boswellic acids. Biochem Pharmacol 2008; 75:503-13. [DOI: 10.1016/j.bcp.2007.09.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 09/03/2007] [Accepted: 09/10/2007] [Indexed: 11/13/2022]
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Förster-Fromme K, Höschle B, Mack C, Bott M, Armbruster W, Jendrossek D. Identification of genes and proteins necessary for catabolism of acyclic terpenes and leucine/isovalerate in Pseudomonas aeruginosa. Appl Environ Microbiol 2006; 72:4819-28. [PMID: 16820476 PMCID: PMC1489323 DOI: 10.1128/aem.00853-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geranyl-coenzyme A (CoA)-carboxylase (GCase; AtuC/AtuF) and methylcrotonyl-CoA-carboxylase (MCase; LiuB/LiuD) are characteristic enzymes of the catabolic pathway of acyclic terpenes (citronellol and geraniol) and of saturated methyl-branched compounds, such as leucine or isovalerate, respectively. Proteins encoded by two gene clusters (atuABCDEFGH and liuRABCDE) of Pseudomonas aeruginosa PAO1 were essential for acyclic terpene utilization (Atu) and for leucine and isovalerate utilization (Liu), respectively, as revealed by phenotype analysis of 10 insertion mutants, two-dimensional gel electrophoresis, determination of GCase and MCase activities, and Western blot analysis of wild-type and mutant strains. Analysis of the genome sequences of other pseudomonads (P. putida KT2440 and P. fluorescens Pf-5) revealed candidate genes for Liu proteins for both species and candidate genes for Atu proteins in P. fluorescens. This result concurred with the finding that P. fluorescens, but not P. putida, could grow on acyclic terpenes (citronellol and citronellate), while both species were able to utilize leucine and isovalerate. A regulatory gene, atuR, was identified upstream of atuABCDEFGH and negatively regulated expression of the atu gene cluster.
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Affiliation(s)
- Karin Förster-Fromme
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70550 Stuttgart, Germany
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Aguilar JA, Zavala AN, Díaz-Pérez C, Cervantes C, Díaz-Pérez AL, Campos-García J. The atu and liu clusters are involved in the catabolic pathways for acyclic monoterpenes and leucine in Pseudomonas aeruginosa. Appl Environ Microbiol 2006; 72:2070-9. [PMID: 16517656 PMCID: PMC1393232 DOI: 10.1128/aem.72.3.2070-2079.2006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evidence suggests that the Pseudomonas aeruginosa PAO1 gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation (A. L. Díaz-Pérez, N. A. Zavala-Hernández, C. Cervantes, and J. Campos-García, Appl. Environ. Microbiol. 70:5102-5110, 2004), corresponds to the liuRABCDE cluster (B. Hoschle, V. Gnau, and D. Jendrossek, Microbiology 151:3649-3656, 2005). A liu (leucine and isovalerate utilization) homolog cluster was found in the PAO1 genome and is related to the catabolism of acyclic monoterpenes of the citronellol family (AMTC); it was named the atu cluster (acyclic terpene utilization), consisting of the atuCDEF genes and lacking the hydroxymethyl-glutaryl-coenzyme A (CoA) lyase (HMG-CoA lyase) homolog. Mutagenesis of the atu and liu clusters showed that both are involved in AMTC and leucine catabolism by encoding the enzymes related to the geranyl-CoA and the 3-methylcrotonyl-CoA pathways, respectively. Intermediary metabolites of the acyclic monoterpene pathway, citronellic and geranic acids, were accumulated, and leucine degradation rates were affected in both atuF and liuD mutants. The alpha subunit of geranyl-CoA carboxylase and the alpha subunit of 3-methylcrotonyl-CoA carboxylase (alpha-MCCase), encoded by the atuF and liuD genes, respectively, were both induced by citronellol, whereas only the alpha-MCCase subunit was induced by leucine. Both citronellol and leucine also induced a LacZ transcriptional fusion at the liuB gene. The liuE gene encodes a probable hydroxy-acyl-CoA lyase (probably HMG-CoA lyase), an enzyme with bifunctional activity that is essential for both AMTC and leucine degradation. P. aeruginosa PAO1 products encoded by the liuABCD cluster showed a higher sequence similarity (77.2 to 79.5%) with the probable products of liu clusters from several Pseudomonas species than with the atuCDEF cluster from PAO1 (41.5%). Phylogenetic studies suggest that the atu cluster from P. aeruginosa could be the result of horizontal transfer from Alphaproteobacteria. Our results suggest that the atu and liu clusters are bifunctional operons involved in both the AMTC and leucine catabolic pathways.
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Affiliation(s)
- J A Aguilar
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. B-3, Ciudad Universitaria, CP 58030, Morelia, Michoacán, Mexico
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