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Melnikov OI, Rozova ON, Reshetnikov AS, Khmelenina VN, Mustakhimov II. Mannitol as a Growth Substrate for Facultative Methylotroph Methylobrevis pamukkalensis PK2. Curr Microbiol 2024; 81:300. [PMID: 39110243 DOI: 10.1007/s00284-024-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024]
Abstract
Biochemistry of carbon assimilation in aerobic methylotrophs growing on reduced C1 compounds has been intensively studied due to the vital role of these microorganisms in nature. The biochemical pathways of carbon assimilation in methylotrophs growing on multi-carbon substrates are insufficiently explored. Here we elucidated the metabolic route of mannitol assimilation in the alphaproteobacterial facultative methylotroph Methylobrevis pamukkalensis PK2. Two key enzymes of mannitol metabolism, mannitol-2-dehydrogenase (MTD) and fructokinase (FruK), were obtained as His-tagged proteins by cloning and expression of mtd and fruK genes in Escherichia coli and characterized. Genomic analysis revealed that further transformation of fructose-6-phosphate proceeds via the Entner-Doudoroff pathway. During growth on mannitol + methanol mixture, the strain PK2 consumed both substrates simultaneously demonstrating independence of C1 and C6 metabolic pathways. Genome screening showed that genes for mannitol utilization enzymes are present in other alphaproteobacterial methylotrophs predominantly capable of living in association with plants. The capability to utilize a variety of carbohydrates (sorbitol, glucose, fructose, arabinose and xylose) suggests a broad adaptability of the strain PK2 to live in environments where availability of carbon substrate dynamically changes.
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Affiliation(s)
- Oleg I Melnikov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Olga N Rozova
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation.
| | - Alexander S Reshetnikov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Valentina N Khmelenina
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Ildar I Mustakhimov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
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2
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Mitic BM, Troyer C, Lutz L, Baumschabl M, Hann S, Mattanovich D. The oxygen-tolerant reductive glycine pathway assimilates methanol, formate and CO 2 in the yeast Komagataella phaffii. Nat Commun 2023; 14:7754. [PMID: 38012236 PMCID: PMC10682033 DOI: 10.1038/s41467-023-43610-7] [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: 08/09/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
The current climatic change is predominantly driven by excessive anthropogenic CO2 emissions. As industrial bioprocesses primarily depend on food-competing organic feedstocks or fossil raw materials, CO2 co-assimilation or the use of CO2-derived methanol or formate as carbon sources are considered pathbreaking contributions to solving this global problem. The number of industrially-relevant microorganisms that can use these two carbon sources is limited, and even fewer can concurrently co-assimilate CO2. Here, we search for alternative native methanol and formate assimilation pathways that co-assimilate CO2 in the industrially-relevant methylotrophic yeast Komagataella phaffii (Pichia pastoris). Using 13C-tracer-based metabolomic techniques and metabolic engineering approaches, we discover and confirm a growth supporting pathway based on native enzymes that can perform all three assimilations: namely, the oxygen-tolerant reductive glycine pathway. This finding paves the way towards metabolic engineering of formate and CO2 utilisation to produce proteins, biomass, or chemicals in yeast.
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Affiliation(s)
- Bernd M Mitic
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Christina Troyer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Lisa Lutz
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Michael Baumschabl
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Stephan Hann
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Diethard Mattanovich
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria.
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3
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Gao X, Yin P, Ren Y, Yu L, Tian F, Zhao J, Chen W, Xue Y, Zhai Q. Predicting Personalized Diets Based on Microbial Characteristics between Patients with Superficial Gastritis and Atrophic Gastritis. Nutrients 2023; 15:4738. [PMID: 38004131 PMCID: PMC10675729 DOI: 10.3390/nu15224738] [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: 10/08/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND gastritis is a common stomach disease with a high global incidence and can potentially develop into gastric cancer. The treatment of gastritis focuses on medication or diets based on national guidelines. However, the specific diet that can alleviate gastritis remains largely unknown. METHODS we propose a microbiota-directed dietary strategy that investigates potential food factors using microbial exogenous metabolites. Given the current lack of understanding of the repeatable characteristics of gastric microbiota, we conducted a meta-analysis to identify the features of gastric bacteria. Local samples were collected as validation cohorts. Furthermore, RevEcoR was employed to identify bacteria's exogenous metabolites, and FooDB was used to retrieve foods that can target specific bacteria. RESULTS Bacteroides, Weissella, Actinomyces, Atopobium, Oribacterium, Peptostreptococcus, and Rothia were biomarkers between superficial gastritis (SG) and atrophic gastritis (AG) (AG_N) without H. pylori infection, whereas Bacillus, Actinomyces, Cutibacterium, Helicobacter, Novosphingobium, Pseudomonas, and Streptococcus were signatures between SG and AG (AG_P) with H. pylori infection. According to the exogenous metabolites, adenosyloobalamin, soybean, common wheat, dates, and barley were regarded as potential candidates for AG_N treatment, while gallate was regarded as a candidate for AG_P treatment. CONCLUSIONS this study firstly profiled the gastric microbiota of AG and SG with or without H. pylori and provided a recommended diet for global AG according to exogenous metabolites.
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Affiliation(s)
- Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Pingping Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yilin Ren
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Yuzheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (X.G.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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Peiro C, Vicente CM, Jallet D, Heux S. From a Hetero- to a Methylotrophic Lifestyle: Flash Back on the Engineering Strategies to Create Synthetic Methanol-User Strains. Front Bioeng Biotechnol 2022; 10:907861. [PMID: 35757790 PMCID: PMC9214030 DOI: 10.3389/fbioe.2022.907861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 12/31/2022] Open
Abstract
Engineering microorganisms to grow on alternative feedstocks is crucial not just because of the indisputable biotechnological applications but also to deepen our understanding of microbial metabolism. One-carbon (C1) substrate metabolism has been the focus of extensive research for the prominent role of C1 compounds in establishing a circular bioeconomy. Methanol in particular holds great promise as it can be produced directly from greenhouse gases methane and carbon dioxide using renewable resources. Synthetic methylotrophy, i.e. introducing a non-native methanol utilization pathway into a model host, has therefore been the focus of long-time efforts and is perhaps the pinnacle of metabolic engineering. It entails completely changing a microorganism's lifestyle, from breaking up multi-carbon nutrients for growth to building C-C bonds from a single-carbon molecule to obtain all metabolites necessary to biomass formation as well as energy. The frontiers of synthetic methylotrophy have been pushed further than ever before and in this review, we outline the advances that paved the way for the more recent accomplishments. These include optimizing the host's metabolism, "copy and pasting" naturally existing methylotrophic pathways, "mixing and matching" enzymes to build new pathways, and even creating novel enzymatic functions to obtain strains that are able to grow solely on methanol. Finally, new approaches are contemplated to further advance the field and succeed in obtaining a strain that efficiently grows on methanol and allows C1-based production of added-value compounds.
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Affiliation(s)
- Camille Peiro
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Denis Jallet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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5
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Irla M, Wendisch VF. Efficient cell factories for the production of N-methylated amino acids and for methanol-based amino acid production. Microb Biotechnol 2022; 15:2145-2159. [PMID: 35488805 PMCID: PMC9328739 DOI: 10.1111/1751-7915.14067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
The growing world needs commodity amino acids such as L‐glutamate and L‐lysine for use as food and feed, and specialty amino acids for dedicated applications. To meet the supply a paradigm shift regarding their production is required. On the one hand, the use of sustainable and cheap raw materials is necessary to sustain low production cost and decrease detrimental effects of sugar‐based feedstock on soil health and food security caused by competing uses of crops in the feed and food industries. On the other hand, the biotechnological methods to produce functionalized amino acids need to be developed further, and titres enhanced to become competitive with chemical synthesis methods. In the current review, we present successful strain mutagenesis and rational metabolic engineering examples leading to the construction of recombinant bacterial strains for the production of amino acids such as L‐glutamate, L‐lysine, L‐threonine and their derivatives from methanol as sole carbon source. In addition, the fermentative routes for bioproduction of N‐methylated amino acids are highlighted, with focus on three strategies: partial transfer of methylamine catabolism, S‐adenosyl‐L‐methionine dependent alkylation and reductive methylamination of 2‐oxoacids.
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Affiliation(s)
- Marta Irla
- Microbial Synthetic Biology, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, Bielefeld, 33615, Germany
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6
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Hoyt KO, Woolston BM. Adapting isotopic tracer and metabolic flux analysis approaches to study C1 metabolism. Curr Opin Biotechnol 2022; 75:102695. [PMID: 35182834 DOI: 10.1016/j.copbio.2022.102695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/20/2022]
Abstract
Single-carbon (C1, or one-carbon) substrates are promising feedstocks for sustainable biofuel and biochemical production. Crucial to the goal of engineering C1-utilizing strains for improved production is a quantitative understanding of the organization, regulation and rates of the reactions that underpin C1 metabolism. 13C Metabolic flux analysis (MFA) is a well-established platform for interrogating these questions with multi-carbon substrates, and uses the differential labeling of metabolites that results from feeding a substrate with position-specific incorporation of 13C in order to infer quantitative fluxes and pathway topology. Adapting isotopic tracer approaches to C1 metabolism, where position-specific substrate labeling is impossible, requires additional experimental considerations. Here we review recent studies that have developed isotopic tracer approaches to overcome the challenge of uniform metabolite labeling and provide quantitative insight into C1 metabolism.
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Affiliation(s)
- Kathryn O Hoyt
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, 201 Cullinane, Northeastern University, 360 Huntington Avenue, Boston, MA 02115-5000, USA.
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7
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Klein VJ, Irla M, Gil López M, Brautaset T, Fernandes Brito L. Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy. Microorganisms 2022; 10:microorganisms10020220. [PMID: 35208673 PMCID: PMC8879981 DOI: 10.3390/microorganisms10020220] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/26/2022] Open
Abstract
Formaldehyde metabolism is prevalent in all organisms, where the accumulation of formaldehyde can be prevented through the activity of dissimilation pathways. Furthermore, formaldehyde assimilatory pathways play a fundamental role in many methylotrophs, which are microorganisms able to build biomass and obtain energy from single- and multicarbon compounds with no carbon–carbon bonds. Here, we describe how formaldehyde is formed in the environment, the mechanisms of its toxicity to the cells, and the cell’s strategies to circumvent it. While their importance is unquestionable for cell survival in formaldehyde rich environments, we present examples of how the modification of native formaldehyde dissimilation pathways in nonmethylotrophic bacteria can be applied to redirect carbon flux toward heterologous, synthetic formaldehyde assimilation pathways introduced into their metabolism. Attempts to engineer methylotrophy into nonmethylotrophic hosts have gained interest in the past decade, with only limited successes leading to the creation of autonomous synthetic methylotrophy. Here, we discuss how native formaldehyde assimilation pathways can additionally be employed as a premise to achieving synthetic methylotrophy. Lastly, we discuss how emerging knowledge on regulation of formaldehyde metabolism can contribute to creating synthetic regulatory circuits applied in metabolic engineering strategies.
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8
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Wendisch VF, Kosec G, Heux S, Brautaset T. Aerobic Utilization of Methanol for Microbial Growth and Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:169-212. [PMID: 34761324 DOI: 10.1007/10_2021_177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Methanol is a reduced one-carbon (C1) compound. It supports growth of aerobic methylotrophs that gain ATP from reduced redox equivalents by respiratory phosphorylation in their electron transport chains. Notably, linear oxidation of methanol to carbon dioxide may yield three reduced redox equivalents if methanol oxidation is NAD-dependent as, e.g., in Bacillus methanolicus. Methanol has a higher degree of reduction per carbon than glucose (6 vs. 4), and thus, lends itself as an ideal carbon source for microbial production of reduced target compounds. However, C-C bond formation in the RuMP or serine cycle, a prerequisite for production of larger molecules, requires ATP and/or reduced redox equivalents. Moreover, heat dissipation and a high demand for oxygen during catabolic oxidation of methanol may pose challenges for fermentation processes. In this chapter, we summarize metabolic pathways for aerobic methanol utilization, aerobic methylotrophs as industrial production hosts, strain engineering, and methanol bioreactor processes. In addition, we provide technological and market outlooks.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.
| | | | - Stéphanie Heux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Trygve Brautaset
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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9
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Blombach B, Grünberger A, Centler F, Wierckx N, Schmid J. Exploiting unconventional prokaryotic hosts for industrial biotechnology. Trends Biotechnol 2021; 40:385-397. [PMID: 34482995 DOI: 10.1016/j.tibtech.2021.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Developing cost-efficient biotechnological processes is a major challenge in replacing fossil-based industrial production processes. The remarkable progress in genetic engineering ensures efficient and fast tailoring of microbial metabolism for a wide range of bioconversions. However, improving intrinsic properties such as tolerance, handling, growth, and substrate consumption rates is still challenging. At the same time, synthetic biology tools are becoming easier applicable and transferable to nonmodel organisms. These trends have resulted in the exploitation of new and unconventional microbial systems with sophisticated properties, which render them promising hosts for the bio-based industry. Here, we highlight the metabolic and cellular capabilities of representative prokaryotic newcomers and discuss the potential and drawbacks of these hosts for industrial application.
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Affiliation(s)
- Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany; SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | | | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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10
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Haupka C, Brito LF, Busche T, Wibberg D, Wendisch VF. Genomic and Transcriptomic Investigation of the Physiological Response of the Methylotroph Bacillus methanolicus to 5-Aminovalerate. Front Microbiol 2021; 12:664598. [PMID: 33995329 PMCID: PMC8119775 DOI: 10.3389/fmicb.2021.664598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
The methylotrophic thermophile Bacillus methanolicus can utilize the non-food substrate methanol as its sole carbon and energy source. Metabolism of L-lysine, in particular its biosynthesis, has been studied to some detail, and methanol-based L-lysine production has been achieved. However, little is known about L-lysine degradation, which may proceed via 5-aminovalerate (5AVA), a non-proteinogenic ω-amino acid with applications in bioplastics. The physiological role of 5AVA and related compounds in the native methylotroph was unknown. Here, we showed that B. methanolicus exhibits low tolerance to 5AVA, but not to related short-chain (C4–C6) amino acids, diamines, and dicarboxylic acids. In order to gain insight into the physiological response of B. methanolicus to 5AVA, transcriptomic analyses by differential RNA-Seq in the presence and absence of 5AVA were performed. Besides genes of the general stress response, RNA levels of genes of histidine biosynthesis, and iron acquisition were increased in the presence of 5AVA, while an Rrf2 family transcriptional regulator gene showed reduced RNA levels. In order to test if mutations can overcome growth inhibition by 5AVA, adaptive laboratory evolution (ALE) was performed and two mutants—AVA6 and AVA10—with higher tolerance to 5AVA were selected. Genome sequencing revealed mutations in genes related to iron homeostasis, including the gene for an iron siderophore-binding protein. Overexpression of this mutant gene in the wild-type (WT) strain MGA3 improved 5AVA tolerance significantly at high Fe2+ supplementation. The combined ALE, omics, and genetics approach helped elucidate the physiological response of thermophilic B. methanolicus to 5AVA and will guide future strain development for 5AVA production from methanol.
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Affiliation(s)
- Carsten Haupka
- Genetics of Prokaryotes, Faculty of Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Luciana F Brito
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
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11
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Schultenkämper K, Gütle DD, López MG, Keller LB, Zhang L, Einsle O, Jacquot JP, Wendisch VF. Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference. Front Microbiol 2021; 12:669220. [PMID: 33995334 PMCID: PMC8119897 DOI: 10.3389/fmicb.2021.669220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
The Gram-positive Bacillus methanolicus shows plasmid-dependent methylotrophy. This facultative ribulose monophosphate (RuMP) cycle methylotroph possesses two fructose bisphosphate aldolases (FBA) with distinct kinetic properties. The chromosomally encoded FBAC is the major glycolytic aldolase. The gene for the major gluconeogenic aldolase FBAP is found on the natural plasmid pBM19 and is induced during methylotrophic growth. The crystal structures of both enzymes were solved at 2.2 Å and 2.0 Å, respectively, and they suggested amino acid residue 51 to be crucial for binding fructose-1,6-bisphosphate (FBP) as substrate and amino acid residue 140 for active site zinc atom coordination. As FBAC and FBAP differed at these positions, site-directed mutagenesis (SDM) was performed to exchange one or both amino acid residues of the respective proteins. The aldol cleavage reaction was negatively affected by the amino acid exchanges that led to a complete loss of glycolytic activity of FBAP. However, both FBAC and FBAP maintained gluconeogenic aldol condensation activity, and the amino acid exchanges improved the catalytic efficiency of the major glycolytic aldolase FBAC in gluconeogenic direction at least 3-fold. These results confirmed the importance of the structural differences between FBAC and FBAP concerning their distinct enzymatic properties. In order to investigate the physiological roles of both aldolases, the expression of their genes was repressed individually by CRISPR interference (CRISPRi). The fba C RNA levels were reduced by CRISPRi, but concomitantly the fba P RNA levels were increased. Vice versa, a similar compensatory increase of the fba C RNA levels was observed when fba P was repressed by CRISPRi. In addition, targeting fba P decreased tkt P RNA levels since both genes are cotranscribed in a bicistronic operon. However, reduced tkt P RNA levels were not compensated for by increased RNA levels of the chromosomal transketolase gene tkt C.
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Affiliation(s)
- Kerstin Schultenkämper
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Laura B Keller
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Lin Zhang
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | | | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
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12
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Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus methanolicus. Int J Mol Sci 2021; 22:ijms22094686. [PMID: 33925231 PMCID: PMC8124236 DOI: 10.3390/ijms22094686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 12/05/2022] Open
Abstract
Genome-wide transcriptomic data obtained in RNA-seq experiments can serve as a reliable source for identification of novel regulatory elements such as riboswitches and promoters. Riboswitches are parts of the 5′ untranslated region of mRNA molecules that can specifically bind various metabolites and control gene expression. For that reason, they have become an attractive tool for engineering biological systems, especially for the regulation of metabolic fluxes in industrial microorganisms. Promoters in the genomes of prokaryotes are located upstream of transcription start sites and their sequences are easily identifiable based on the primary transcriptome data. Bacillus methanolicus MGA3 is a candidate for use as an industrial workhorse in methanol-based bioprocesses and its metabolism has been studied in systems biology approaches in recent years, including transcriptome characterization through RNA-seq. Here, we identify a putative lysine riboswitch in B. methanolicus, and test and characterize it. We also select and experimentally verify 10 putative B. methanolicus-derived promoters differing in their predicted strength and present their functionality in combination with the lysine riboswitch. We further explore the potential of a B. subtilis-derived purine riboswitch for regulation of gene expression in the thermophilic B. methanolicus, establishing a novel tool for inducible gene expression in this bacterium.
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