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Hengardi MT, Liang C, Madivannan K, Yang LK, Koduru L, Kanagasundaram Y, Arumugam P. Reversing the directionality of reactions between non-oxidative pentose phosphate pathway and glycolytic pathway boosts mycosporine-like amino acid production in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:121. [PMID: 38725068 PMCID: PMC11080194 DOI: 10.1186/s12934-024-02365-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Mycosporine-like amino acids (MAAs) are a class of strongly UV-absorbing compounds produced by cyanobacteria, algae and corals and are promising candidates for natural sunscreen components. Low MAA yields from natural sources, coupled with difficulties in culturing its native producers, have catalyzed synthetic biology-guided approaches to produce MAAs in tractable microbial hosts like Escherichia coli, Saccharomyces cerevisiae and Corynebacterium glutamicum. However, the MAA titres obtained in these hosts are still low, necessitating a thorough understanding of cellular factors regulating MAA production. RESULTS To delineate factors that regulate MAA production, we constructed a shinorine (mycosporine-glycine-serine) producing yeast strain by expressing the four MAA biosynthetic enzymes from Nostoc punctiforme in Saccharomyces cerevisiae. We show that shinorine is produced from the pentose phosphate pathway intermediate sedoheptulose 7-phosphate (S7P), and not from the shikimate pathway intermediate 3-dehydroquinate (3DHQ) as previously suggested. Deletions of transaldolase (TAL1) and phosphofructokinase (PFK1/PFK2) genes boosted S7P/shinorine production via independent mechanisms. Unexpectedly, the enhanced S7P/shinorine production in the PFK mutants was not entirely due to increased flux towards the pentose phosphate pathway. We provide multiple lines of evidence in support of a reversed pathway between glycolysis and the non-oxidative pentose phosphate pathway (NOPPP) that boosts S7P/shinorine production in the phosphofructokinase mutant cells. CONCLUSION Reversing the direction of flux between glycolysis and the NOPPP offers a novel metabolic engineering strategy in Saccharomyces cerevisiae.
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Affiliation(s)
- Miselle Tiana Hengardi
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
| | - Cui Liang
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Keshiniy Madivannan
- Innovation & Enterprise, Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Lay Kien Yang
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Yoganathan Kanagasundaram
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Prakash Arumugam
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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Hirayama H, Takaki Y, Abe M, Miyazaki M, Uematsu K, Matsui Y, Takai K. Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field. Int J Syst Evol Microbiol 2024; 74:006288. [PMID: 38478579 PMCID: PMC10950024 DOI: 10.1099/ijsem.0.006288] [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: 07/27/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.
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Affiliation(s)
- Hisako Hirayama
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mariko Abe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Yohei Matsui
- Research Institute for Global Change (RIGC), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
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Koendjbiharie JG, Hon S, Pabst M, Hooftman R, Stevenson DM, Cui J, Amador-Noguez D, Lynd LR, Olson DG, van Kranenburg R. The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase. J Biol Chem 2020; 295:1867-1878. [PMID: 31871051 PMCID: PMC7029132 DOI: 10.1074/jbc.ra119.011239] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Indexed: 01/24/2023] Open
Abstract
The genomes of most cellulolytic clostridia do not contain genes annotated as transaldolase. Therefore, for assimilating pentose sugars or for generating C5 precursors (such as ribose) during growth on other (non-C5) substrates, they must possess a pathway that connects pentose metabolism with the rest of metabolism. Here we provide evidence that for this connection cellulolytic clostridia rely on the sedoheptulose 1,7-bisphosphate (SBP) pathway, using pyrophosphate-dependent phosphofructokinase (PPi-PFK) instead of transaldolase. In this reversible pathway, PFK converts sedoheptulose 7-phosphate (S7P) to SBP, after which fructose-bisphosphate aldolase cleaves SBP into dihydroxyacetone phosphate and erythrose 4-phosphate. We show that PPi-PFKs of Clostridium thermosuccinogenes and Clostridium thermocellum indeed can convert S7P to SBP, and have similar affinities for S7P and the canonical substrate fructose 6-phosphate (F6P). By contrast, (ATP-dependent) PfkA of Escherichia coli, which does rely on transaldolase, had a very poor affinity for S7P. This indicates that the PPi-PFK of cellulolytic clostridia has evolved the use of S7P. We further show that C. thermosuccinogenes contains a significant SBP pool, an unusual metabolite that is elevated during growth on xylose, demonstrating its relevance for pentose assimilation. Last, we demonstrate that a second PFK of C. thermosuccinogenes that operates with ATP and GTP exhibits unusual kinetics toward F6P, as it appears to have an extremely high degree of cooperative binding, resulting in a virtual on/off switch for substrate concentrations near its K½ value. In summary, our results confirm the existence of an SBP pathway for pentose assimilation in cellulolytic clostridia.
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Affiliation(s)
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Martin Pabst
- Cell Systems Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Robert Hooftman
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jingxuan Cui
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel Amador-Noguez
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Richard van Kranenburg
- Corbion, 4206 AC Gorinchem, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
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Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants. Nat Commun 2018; 9:1765. [PMID: 29720581 PMCID: PMC5931981 DOI: 10.1038/s41467-018-04201-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes. While most kinases are ATP-dependent some utilize pyrophosphate (PPi) instead. Here the authors structurally characterize a PPi-dependent kinase, identify its key recognition residues and find further PPi-dependent ribokinase family members with this signature pattern.
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Khmelenina VN, Rozova ON, But SY, Mustakhimov II, Reshetnikov AS, Beschastnyi AP, Trotsenko YA. Biosynthesis of secondary metabolites in methanotrophs: Biochemical and genetic aspects (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020088] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Matsen JB, Yang S, Stein LY, Beck D, Kalyuzhnaya MG. Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic Study. Front Microbiol 2013; 4:40. [PMID: 23565111 PMCID: PMC3615186 DOI: 10.3389/fmicb.2013.00040] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 02/17/2013] [Indexed: 11/20/2022] Open
Abstract
Methane utilizing bacteria (methanotrophs) are important in both environmental and biotechnological applications, due to their ability to convert methane to multicarbon compounds. However, systems-level studies of methane metabolism have not been carried out in methanotrophs. In this work we have integrated genomic and transcriptomic information to provide an overview of central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotroph. Particulate methane monooxygenase, PQQ-dependent methanol dehydrogenase, the H4MPT-pathway, and NAD-dependent formate dehydrogenase are involved in methane oxidation to CO2. All genes essential for operation of the serine cycle, the ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle were expressed. PEP-pyruvate-oxaloacetate interconversions may have a function in regulation and balancing carbon between the serine cycle and the EMC pathway. A set of transaminases may contribute to carbon partitioning between the pathways. Metabolic pathways for acquisition and/or assimilation of nitrogen and iron are discussed.
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Affiliation(s)
- Janet B Matsen
- Department of Chemical Engineering, University of Washington Seattle, WA, USA
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