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Transcriptome profiling of Paraburkholderia aromaticivorans AR20-38 during ferulic acid bioconversion. AMB Express 2022; 12:148. [DOI: 10.1186/s13568-022-01487-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/28/2022] Open
Abstract
AbstractThe importance and need of renewable-based, sustainable feedstocks increased in recent years. Lignin-derived monomers have high potential, energetic and economic value in the microbial bioconversion to valuable biomolecules. The bacterium Paraburkholderia aromaticivorans AR20-38 produces a remarkable yield of vanillic acid from ferulic acid at moderate and low temperatures and is therefore a good candidate for biotechnological applications. To understand this bioconversion process on a molecular level, a transcriptomic study during the bioconversion process was conducted to elucidate gene expression patterns. Differentially expressed genes, cellular transporters as well as transcriptional factors involved in the bioconversion process could be described. Additional enzymes known for xenobiotic degradation were differentially expressed and a potential membrane vesicle mechanism was detected. The bioconversion mechanism on a transcriptional level of P. aromaticivorans could be elucidated and results can be used for strain optimization. Additionally, the transcriptome study showed the high potential of the strain for other degradation applications.
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Park HS, Nah HJ, Kang SH, Choi SS, Kim ES. Screening and Isolation of a Novel Polyene-Producing Streptomyces Strain Inhibiting Phytopathogenic Fungi in the Soil Environment. Front Bioeng Biotechnol 2021; 9:692340. [PMID: 34322478 PMCID: PMC8312574 DOI: 10.3389/fbioe.2021.692340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial-based eco-friendly biological substances are needed to protect crops from phytopathogenic fungi and replace toxic chemical fungicides that cause serious environmental issues. This study screened for soil antifungal Streptomyces strains, which produce rich, diverse, and valuable bioactive metabolites in the soil environment. Bioassay-based antifungal screening of approximately 2,400 Streptomyces strains led to the isolation of 149 strains as tentative antifungal producers. One Streptomyces strain showing the most potent antifungal activities against Candida albicans and Fusarium oxysporum was identified as a putative anti-phytopathogenic soil isolate that is highly homologous to Streptomyces rubrisoli (named S. rubrisoli Inha 501). An in vitro antifungal assay, pot-test, and field-test against various phytopathogenic fungi confirmed that S. rubrisoli Inha 501 is a potential novel phytopathogenic fungicide producer to protect various crops in the soil environment. Whole-genome sequencing of S. rubrisoli Inha 501 and an anti-SMASH genome mining approach revealed an approximately 150-kb polyene biosynthetic gene cluster (BGC) in the chromosome. The target compound isolation and its BGC analysis confirmed that the giant linear polyene compound exhibiting the anti-phytopathogenic activity in S. rubrisoli Inha 501 was highly homologous to the previously reported compound, neotetrafibricin A. These results suggest that a bioassay-based screening of a novel antifungal Streptomyces strain followed by its genome mining for target compound BGC characterization would be an efficient approach to isolating a novel candidate phytopathogenic fungicide that can protect crops in the soil environment.
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Affiliation(s)
- Heung-Soon Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Hee-Ju Nah
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea.,Department of Biological Engineering, Inha University, Incheon, South Korea
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Fushinobu S. Molecular evolution and functional divergence of UDP-hexose 4-epimerases. Curr Opin Chem Biol 2020; 61:53-62. [PMID: 33171387 DOI: 10.1016/j.cbpa.2020.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023]
Abstract
UDP-glucose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) and/or the interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc) in sugar metabolism. GalEs belong to the short-chain dehydrogenase/reductase superfamily, use a conserved 'transient keto intermediate' mechanism and have variable substrate specificity. GalEs have been classified into three groups based on substrate specificity: group 1 prefers UDP-Glc/Gal, group 3 prefers UDP-GlcNAc/GalNAc, and group 2 has comparable activities for both types of the substrates. The phylogenetic relationship and structural basis for the specificities of GalEs revealed possible molecular evolution of UDP-hexose 4-epimerases in various organisms. Based on the recent advances in studies on GalEs and related enzymes, an updated view of their evolutional diversification is presented.
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Affiliation(s)
- Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
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Wagstaff BA, Rejzek M, Kuhaudomlarp S, Hill L, Mascia I, Nepogodiev SA, Dorfmueller HC, Field RA. Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae. J Biol Chem 2019; 294:9172-9185. [PMID: 31010825 PMCID: PMC6556577 DOI: 10.1074/jbc.ra118.006440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/19/2019] [Indexed: 11/06/2022] Open
Abstract
The 6-deoxy sugar l-rhamnose (l-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host-pathogen interactions often means that l-Rha plays an essential role in many organisms. l-Rha is most commonly biosynthesized as the activated sugar nucleotide uridine 5'-diphospho-β-l-rhamnose (UDP-β-l-Rha) or thymidine 5'-diphospho-β-l-rhamnose (TDP-β-l-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of l-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated l-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-β-l-Rha biosynthesis, from P. parvum Using this new sequence and also others, we explored l-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like l-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate β-l-Rha (NDP-β-l-Rha) pathways among algae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sakonwan Kuhaudomlarp
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Lionel Hill
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ilaria Mascia
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sergey A Nepogodiev
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom,
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Kenyon JJ, Shashkov AS, Senchenkova SN, Shneider MM, Liu B, Popova AV, Arbatsky NP, Miroshnikov KA, Wang L, Knirel YA, Hall RM. Acinetobacter baumannii K11 and K83 capsular polysaccharides have the same 6-deoxy-l-talose-containing pentasaccharide K units but different linkages between the K units. Int J Biol Macromol 2017; 103:648-655. [PMID: 28528003 DOI: 10.1016/j.ijbiomac.2017.05.082] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/18/2017] [Accepted: 05/15/2017] [Indexed: 12/18/2022]
Abstract
Acinetobacter baumannii produces a variety of capsular polysaccharides (CPS) via genes located at the chromosomal K locus and some KL gene clusters include genes for the synthesis of specific sugars. The structures of K11 and K83 CPS produced by isolates LUH5545 and LUH5538, which carry related KL11a and KL83 gene clusters, respectively, were established by sugar analysis and one- and two-dimensional 1H and 13C NMR spectroscopy. Both CPS contain l-rhamnose (l-Rha) and 6-deoxy-l-talose (l-6dTal), and both KL gene clusters include genes for dTDP-l-Rhap synthesis and a tle (talose epimerase) gene encoding an epimerase that converts dTDP-l-Rhap to dTDP-l-6dTalp. The K11 and K83 repeat units are the same pentasaccharide, consisting of d-glucose, l-Rha, l-6dTal, and N-acetyl-d-glucosamine, except that l-6dTal is 2-O-acetylated in K83. However, the K units are linked differently, with l-Rha in the main chain in K11, but as a side-branch in K83. KL11 and KL83 encode unrelated Wzy polymerases that link the K units together and different acetyltransferases, though only Atr8 from KL83 is active. The substrate specificity of each Wzy polymerase was assigned, and the functions of all glycosyltransferases were predicted. The CPS structures produced by three closely related K loci, KL29, KL105 and KL106, were also predicted.
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Affiliation(s)
- Johanna J Kenyon
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sof'ya N Senchenkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M Shneider
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, PR China
| | - Anastasiya V Popova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin A Miroshnikov
- M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, PR China
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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Sun Q, Li X, Sun J, Gong S, Liu G, Liu G. An improved P(V)-N activation strategy for the synthesis of nucleoside diphosphate 6-deoxy-l-sugars. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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