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Wang J, Liu M, Mao C, Li S, Zhou J, Fan Y, Guo L, Yu H, Yang X. Comparative proteomics reveals the mechanism of cyclosporine production and mycelial growth in Tolypocladium inflatum affected by different carbon sources. Front Microbiol 2023; 14:1259101. [PMID: 38163081 PMCID: PMC10757567 DOI: 10.3389/fmicb.2023.1259101] [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: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Cyclosporine A (CsA) is a secondary cyclopeptide metabolite produced by Tolypocladium inflatum that is widely used clinically as an immunosuppressant. CsA production and mycelial growth differed when T. inflatum was cultured in different carbon source media. During early fermentation, CsA was preferred to be produced in fructose medium, while the mycelium preferred to accumulate in sucrose medium. On the sixth day, the difference was most pronounced. In this study, high-throughput comparative proteomics methods were applied to analyze differences in protein expression of mycelial samples on day 6, revealing the proteins and mechanisms that positively regulate CsA production related to carbon metabolism. The differences included small molecule acid metabolism, lipid metabolism, organic catabolism, exocrine secretion, CsA substrate Bmt synthesis, and transcriptional regulation processes. The proteins involved in the regulation of mycelial growth related to carbon metabolism were also revealed and were associated with waste reoxidation processes or coenzyme metabolism, small molecule synthesis or metabolism, the stress response, genetic information or epigenetic changes, cell component assembly, cell wall integrity, membrane metabolism, vesicle transport, intramembrane localization, and the regulation of filamentous growth. This study provides a reliable reference for CsA production from high-efficiency fermentation. This study provides key information for obtaining more CsA high-yielding strains through metabolic engineering strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuqing Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Zhao S, Pan C, Zhao J, Du H, Li M, Yu H, Chen X. Quantitative proteomic analysis of the microbial degradation of 3-aminobenzoic acid by Comamonas sp. QT12. Sci Rep 2022; 12:17609. [PMID: 36266292 PMCID: PMC9584955 DOI: 10.1038/s41598-022-17570-9] [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: 02/14/2022] [Accepted: 07/27/2022] [Indexed: 01/13/2023] Open
Abstract
A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to 3-aminobenzoic acid remains unclear. In this study, label-free quantitative proteome analysis based on LC-MS/MS was used to study the protein expression difference of strain QT12 under the condition of using 3AB (3AB) and citric acid/ammonium chloride as substrates (3ABCon). A total of 2068 proteins were identified, of which 239 were significantly up-regulated in 3AB group, 124 were significantly down-regulated in 3AB group, 624 were expressed only in 3AB group, and 216 were expressed only in 3ABCon group in 3AB group. KEGG pathway analysis found that 83 pathways were up-regulated and 49 pathways were down-regulated, In GO analysis, 315 paths were up-regulated and 156 paths were down-regulated. There were 6 genes in the mab cluster that were only detected in the 3AB group.The mab cluster was found to be related to degradation of 3AB. By knockout, it was found that the growth rate of the mutant △orf7 and △orf9 were slowed down. HPLC results showed that the mutant △orf7 and △orf9 could still degrade 3AB, it was found that orf7, orf9 were not key genes about 3AB degradation and they could be replaced by other genes in strain QT12. These findings improve our understanding of the molecular mechanisms underlying the cellular response of 3AB degradation in Comamonas bacterium.
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Affiliation(s)
- Shuxue Zhao
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China ,grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Chao Pan
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Junxing Zhao
- Qingdao Water Administration Bureau, Qingdao, 266071 China
| | - Haiyan Du
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Min Li
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Hao Yu
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Xi Chen
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
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Charlton SN, Hayes MA. Oxygenating Biocatalysts for Hydroxyl Functionalisation in Drug Discovery and Development. ChemMedChem 2022; 17:e202200115. [PMID: 35385205 PMCID: PMC9323455 DOI: 10.1002/cmdc.202200115] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Indexed: 11/12/2022]
Abstract
C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.
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Affiliation(s)
- Sacha N. Charlton
- School of ChemistryUniversity of Bristol, Cantock's CloseBristolBS8 1TSUK
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery SciencesBiopharmaceuticals R&DAstraZenecaGothenburgSweden
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Zhao S, Chen X, Sun Q, Wang F, Hu C, Guo L, Bai J, Yu H. Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1. Front Microbiol 2021; 12:694874. [PMID: 34447357 PMCID: PMC8383072 DOI: 10.3389/fmicb.2021.694874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.
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Affiliation(s)
- Shuxue Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xi Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qianshu Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fei Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Hu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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Zhao S, Hu C, Guo L, Li K, Yu H. Isolation of a 3-hydroxypyridine degrading bacterium, Agrobacterium sp. DW-1, and its proposed degradation pathway. AMB Express 2019; 9:65. [PMID: 31102032 PMCID: PMC6525221 DOI: 10.1186/s13568-019-0782-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 01/02/2023] Open
Abstract
A 3-hydroxypyridine degrading bacterium, designated strain DW-1, was isolated from petroleum contaminated soil in Liao River China. 16S rRNA-based phylogenetic analysis indicates that strain DW-1 belongs to genus Agrobacterium. The optimal cultivation temperature and pH for strain DW-1 with 3-hydroxypyridine were 30 °C and 8.0, respectively. Under optimal conditions, strain DW-1 could completely degrade up to 1500 mg/L of 3-hydroxypyridine in 66 h. The 3-hydroxypyridine degradation pathway of strain DW-1 was suggested by HPLC and LC-MS analysis. The first reaction of 3-hydroxypyridine degradation in strain DW-1 was α-hydroxylation so that the major metabolite 2,5-dihydroxypyridine was produced, and then 2,5-dihydroxypyridine was transformed by a Fe2+-dependent dioxygenase to form N-formylmaleamic acid. N-Formylmaleamic acid will be transformed to maleic acid and fumaric acid through maleamic acid. This is the first report of the 3-hydroxypyridine degradation pathway and the utilization of 3-hydroxypyridine by a Agrobacterium sp. It may be potentially used for the bioremediation of environments polluted with 3-hydroxypyridine.
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Affiliation(s)
- Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
- Key Laboratory of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, 238 Songling Road, Laoshan District, Qingdao, 266100 Shandong Province People’s Republic of China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Kuiran Li
- Key Laboratory of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, 238 Songling Road, Laoshan District, Qingdao, 266100 Shandong Province People’s Republic of China
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
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Microbial Degradation of Nicotinamide by a Strain Alcaligenes sp. P156. Sci Rep 2019; 9:3647. [PMID: 30842479 PMCID: PMC6403243 DOI: 10.1038/s41598-019-40199-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/04/2019] [Indexed: 12/11/2022] Open
Abstract
A novel Alcaligenes sp. strain P156, which can utilize nicotinamide as its sole source of carbon, nitrogen and energy, was enriched and isolated from soil in a solid waste treatment plant. Aerobic growth and degradation with nicotinamide were characterized. Seven nicotinamide degradation-related genes were obtained by sequence alignment from the genome sequence of strain P156. Four genes, designated naaA, naaD, naaE and naaF, were cloned and heterologously expressed. Nicotinamide degradation is initiated by deamination to form nicotinic acid catalyzed by the nicotinamidase NaaA, which shares highest amino acid sequence identity (27.2%) with nicotinamidase from Arabidopsis thaliana. Nicotinic acid is converted to 6-hydroxynicotinic acid, which is further oxidized to 2,5-dihydroxypyridine (2,5-DHP). 2,5-DHP is then transformed to a ring-cleavage product, N-formylmaleamic acid, by an Fe2+ dependent dioxygenase NaaD. N-formylmaleamic acid is transformed to fumaric acid through maleamic acid and maleic acid by NaaE and NaaF, respectively. To our knowledge, this is the first report of the complete microbial degradation of nicotinamide in bacteria. Nicotinamide is considered as a model compound for the study of microbial degradation of pyridinic compounds, and the nicotinamide degrading related genes in strain P156 were distributed differently from the reported similar gene clusters. Therefore, this study contribute to the knowledge on the degradation of pyridinic compounds.
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