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Alektiar JM, Shan M, Radyk MD, Zhang L, Halbrook CJ, Lin L, Espinoza C, Mier IF, Lavoie BL, Salvatore L, Pasca di Magliano M, Cantley LC, Mueller JL, Lyssiotis CA. Malic enzyme 1 knockout has no deleterious phenotype and is favored in the male germline under standard laboratory conditions. PLoS One 2024; 19:e0303577. [PMID: 38843233 PMCID: PMC11156412 DOI: 10.1371/journal.pone.0303577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 04/26/2024] [Indexed: 06/09/2024] Open
Abstract
Malic Enzyme 1 (ME1) plays an integral role in fatty acid synthesis and cellular energetics through its production of NADPH and pyruvate. As such, it has been identified as a gene of interest in obesity, type 2 diabetes, and an array of epithelial cancers, with most work being performed in vitro. The current standard model for ME1 loss in vivo is the spontaneous Mod-1 null allele, which produces a canonically inactive form of ME1. Herein, we describe two new genetically engineered mouse models exhibiting ME1 loss at dynamic timepoints. Using murine embryonic stem cells and Flp/FRT and Cre/loxP class switch recombination, we established a germline Me1 knockout model (Me1 KO) and an inducible conditional knockout model (Me1 cKO), activated upon tamoxifen treatment in adulthood. Collectively, neither the Me1 KO nor Me1 cKO models exhibited deleterious phenotype under standard laboratory conditions. Knockout of ME1 was validated by immunohistochemistry and genotype confirmed by PCR. Transmission patterns favor Me1 loss in Me1 KO mice when maternally transmitted to male progeny. Hematological examination of these models through complete blood count and serum chemistry panels revealed no discrepancy with their wild-type counterparts. Orthotopic pancreatic tumors in Me1 cKO mice grow similarly to Me1 expressing mice. Similarly, no behavioral phenotype was observed in Me1 cKO mice when aged for 52 weeks. Histological analysis of several tissues revealed no pathological phenotype. These models provide a more modern approach to ME1 knockout in vivo while opening the door for further study into the role of ME1 loss under more biologically relevant, stressful conditions.
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Affiliation(s)
- Jonathan M. Alektiar
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mengrou Shan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Megan D. Radyk
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher J. Halbrook
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lin Lin
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carlos Espinoza
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ivan F. Mier
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Brooke L. Lavoie
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucie Salvatore
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lewis C. Cantley
- Department of Cancer Biology, Dana Farber Cancer Center, Boston, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jacob L. Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Costas A. Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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Rendulić T, Perpelea A, Ortiz JPR, Casal M, Nevoigt E. Mitochondrial membrane transporters as attractive targets for the fermentative production of succinic acid from glycerol in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae009. [PMID: 38587863 PMCID: PMC11014245 DOI: 10.1093/femsyr/foae009] [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: 12/21/2023] [Revised: 02/08/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Previously, we reported an engineered Saccharomyces cerevisiae CEN.PK113-1A derivative able to produce succinic acid (SA) from glycerol with net CO2 fixation. Apart from an engineered glycerol utilization pathway that generates NADH, the strain was equipped with the NADH-dependent reductive branch of the TCA cycle (rTCA) and a heterologous SA exporter. However, the results indicated that a significant amount of carbon still entered the CO2-releasing oxidative TCA cycle. The current study aimed to tune down the flux through the oxidative TCA cycle by targeting the mitochondrial uptake of pyruvate and cytosolic intermediates of the rTCA pathway, as well as the succinate dehydrogenase complex. Thus, we tested the effects of deletions of MPC1, MPC3, OAC1, DIC1, SFC1, and SDH1 on SA production. The highest improvement was achieved by the combined deletion of MPC3 and SDH1. The respective strain produced up to 45.5 g/L of SA, reached a maximum SA yield of 0.66 gSA/gglycerol, and accumulated the lowest amounts of byproducts when cultivated in shake-flasks. Based on the obtained data, we consider a further reduction of mitochondrial import of pyruvate and rTCA intermediates highly attractive. Moreover, the approaches presented in the current study might also be valuable for improving SA production when sugars (instead of glycerol) are the source of carbon.
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Affiliation(s)
- Toni Rendulić
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Andreea Perpelea
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | | | - Margarida Casal
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Elke Nevoigt
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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Rußmayer H, Buchetics M, Mattanovich M, Neubauer S, Steiger M, Graf AB, Koellensperger G, Hann S, Sauer M, Gasser B, Mattanovich D. Customizing amino acid metabolism of Pichia pastoris for recombinant protein production. Biotechnol J 2023; 18:e2300033. [PMID: 37668396 DOI: 10.1002/biot.202300033] [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: 01/19/2023] [Revised: 07/31/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Amino acids are the building blocks of proteins. In this respect, a reciprocal effect of recombinant protein production on amino acid biosynthesis as well as the impact of the availability of free amino acids on protein production can be anticipated. In this study, the impact of engineering the amino acid metabolism on the production of recombinant proteins was investigated in the yeast Pichia pastoris (syn Komagataella phaffii). Based on comprehensive systems-level analyses of the metabolomes and transcriptomes of different P. pastoris strains secreting antibody fragments, cell engineering targets were selected. Our working hypothesis that increasing intracellular amino acid levels could help unburden cellular metabolism and improve recombinant protein production was examined by constitutive overexpression of genes related to amino acid metabolism. In addition to 12 genes involved in specific amino acid biosynthetic pathways, the transcription factor GCN4 responsible for regulation of amino acid biosynthetic genes was overexpressed. The production of the used model protein, a secreted carboxylesterase (CES) from Sphingopyxis macrogoltabida, was increased by overexpression of pathway genes for alanine and for aromatic amino acids, and most pronounced, when overexpressing the regulator GCN4. The analysis of intracellular amino acid levels of selected clones indicated a direct linkage of improved recombinant protein production to the increased availability of intracellular amino acids. Finally, fed batch cultures showed that overexpression of GCN4 increased CES titers 2.6-fold, while the positive effect of other amino acid synthesis genes could not be transferred from screening to bioreactor cultures.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Matthias Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Copenhagen University, Copenhagen, Denmark
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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Szatkowska R, Furmanek E, Kierzek AM, Ludwig C, Adamczyk M. Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis. Int J Mol Sci 2023; 24:14763. [PMID: 37834211 PMCID: PMC10572830 DOI: 10.3390/ijms241914763] [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: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.
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Affiliation(s)
- Roza Szatkowska
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Emil Furmanek
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Andrzej M. Kierzek
- Certara UK Limited, Sheffield S1 2BJ, UK;
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
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Luo Y, Yan X, Xia Y, Cao Y. Tetracarboxylic acid transporter regulates growth, conidiation, and carbon utilization in Metarhizium acridum. Appl Microbiol Biotechnol 2023; 107:2969-2982. [PMID: 36941435 DOI: 10.1007/s00253-023-12471-x] [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: 12/10/2022] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/23/2023]
Abstract
Carbon sources and their utilization are vital for fungal growth and development. C4-dicarboxylic acids are important carbon and energy sources that function as intermediate products of the tricarboxylic acid cycle. Transport and regulation of C4-dicarboxylic acid uptake are mainly dependent on tetracarboxylic acid transporters (Dcts) in many microbes, although the roles of Dct genes in fungi have only been partially characterized. Here, we report on the functions of two Dct genes (Dct1 and Dct2) in the entomopathogenic fungus Metarhizium acridum. Our data showed that loss of the MaDct1 gene affected utilization of tetracarboxylic acids and other carbon sources. ΔMaDct1 mutants showed larger colony sizes with extensive mycelial growth but were delayed in conidiation with decreased conidia yield as compared to the wild-type parental strain. On the nutrient-deficient medium, SYA, the wild-type strain produced microcycle conidia, whereas the ΔMaDct1 mutant produced (normal) aerial conidia. In addition, ΔMaDct1 had decreased tolerance to cell wall perturbing agents, but increased tolerances to UV-B radiation and osmotic stress. Insect bioassays indicated that loss of MaDct1 did not affect pathogenicity. In contrast, no distinct phenotypic change was observed for the MaDct2 mutant in terms of growth and biocontrol characteristics. Transcriptomic profiling between wild type and ΔMaDct1 showed that differentially expressed genes were enriched in carbohydrate and amino acid metabolism, transport and catabolism, and signal transduction. These results demonstrate that MaDct1 regulates the conidiation pattern shift and mycelial growth by affecting utilization of carbon sources. These findings are helpful for better understanding the effect of intermediates of carbon metabolism on fungal growth and conidiation. KEY POINTS: • MaDct1 influences fungal growth and conidiation by affecting carbon source utilization. • MaDct1 regulates conidiation pattern shift under nutrient deficiency condition. • MaDct1 is involved in stress tolerance and has no effect on virulence. • MaDct2 has no effect on growth and biocontrol characteristic.
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Affiliation(s)
- Yunxiao Luo
- School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticides, Chongqing, 401331, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing, China
| | - Xi Yan
- School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticides, Chongqing, 401331, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing, China
| | - Yuxian Xia
- School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China.
- Chongqing Engineering Research Center for Fungal Insecticides, Chongqing, 401331, People's Republic of China.
- Key Laboratory of Gene Function and Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing, China.
| | - Yueqing Cao
- School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China.
- Chongqing Engineering Research Center for Fungal Insecticides, Chongqing, 401331, People's Republic of China.
- Key Laboratory of Gene Function and Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing, China.
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Grigaitis P, van den Bogaard SL, Teusink B. Elevated energy costs of biomass production in mitochondrial respiration-deficient Saccharomyces cerevisia. FEMS Yeast Res 2023; 23:7000830. [PMID: 36694952 PMCID: PMC9949590 DOI: 10.1093/femsyr/foad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Microbial growth requires energy for maintaining the existing cells and producing components for the new ones. Microbes therefore invest a considerable amount of their resources into proteins needed for energy harvesting. Growth in different environments is associated with different energy demands for growth of yeast Saccharomyces cerevisiae, although the cross-condition differences remain poorly characterized. Furthermore, a direct comparison of the energy costs for the biosynthesis of the new biomass across conditions is not feasible experimentally; computational models, on the contrary, allow comparing the optimal metabolic strategies and quantify the respective costs of energy and nutrients. Thus in this study, we used a resource allocation model of S. cerevisiae to compare the optimal metabolic strategies between different conditions. We found that S. cerevisiae with respiratory-impaired mitochondria required additional energetic investments for growth, while growth on amino acid-rich media was not affected. Amino acid supplementation in anaerobic conditions also was predicted to rescue the growth reduction in mitochondrial respiratory shuttle-deficient mutants of S. cerevisiae. Collectively, these results point to elevated costs of resolving the redox imbalance caused by de novo biosynthesis of amino acids in mitochondria. To sum up, our study provides an example of how resource allocation modeling can be used to address and suggest explanations to open questions in microbial physiology.
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Affiliation(s)
- Pranas Grigaitis
- Corresponding author. Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands; E-mail:
| | - Samira L van den Bogaard
- Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, A-Life/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
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Fonseca GG. Metabolic engineering of Kluyveromyces marxianus for biomass-based applications. 3 Biotech 2022; 12:259. [PMID: 36068842 PMCID: PMC9440961 DOI: 10.1007/s13205-022-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/22/2022] [Indexed: 11/01/2022] Open
Abstract
Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03324-x.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Business and Science, University of Akureyri, Borgir v. Nordurslod, 600 Akureyri, Iceland
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8
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Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
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Shuib S, Nazir MYM, Ibrahim I, Song Y, Ratledge C, Hamid AA. Co-existence of type I fatty acid synthase and polyketide synthase metabolons in Aurantiochytrium SW1 and their implications for lipid biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159224. [PMID: 36007759 DOI: 10.1016/j.bbalip.2022.159224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The key enzymes of lipid biosynthesis in oleaginous filamentous fungi exist as metabolons. However, the existence of a similar organization in other groups of oleaginous microorganisms is still unknown. In this study, we confirmed the occurrence of two separate and distinct lipogenic metabolons in a thraustochytrid, Aurantiochytrium SW1. These involve the Type I Fatty Acid Synthase (FAS) pathway, consisting of six enzymes: fatty acid synthase, malic enzyme (ME), ATP: citrate lyase (ACL), acetyl-CoA carboxylase (ACC), malate dehydrogenase (MD) and pyruvate carboxylase (PC), and the Polyketide Synthase-like (PKS) pathway, consisting of PKS subunits a, b, c, glucose-6-phosphate dehydrogenase (G6PDH) 6-phosphogluconate dehydrogenase (6PGDH), ACL and ACC. This suggests that the NADPH requirement for the FAS pathway is primarily generated and channelled by ME whereas G6PDH and 6PGDH fulfil this role for the PKS pathway. Diminished biosynthesis of palmitic acid (16:0), docosahexaenoic acid (22:6 n-3, DHA) and docosapentaenoic acid (22:5 n-6, DPA) correlated with the dissociation of their respective metabolons thereby suggesting that regulation of the pathways is achieved through the formation and dissociation of the metabolons.
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Affiliation(s)
- Shuwahida Shuib
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Autoimmune Unit, Allergy and Immunology Research Centre, Institute for Medical Research (IMR), National Institute of Health (NIH) Malaysia, No. 1, Jalan Setia Murni U13/52, Bandar Setia Alam, 40170 Shah Alam, Selangor, Malaysia
| | - Mohamed Yusuf Mohamed Nazir
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; Innovation Centre for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Izyanti Ibrahim
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, 266 Xincun Rd., Zibo, Shandong, PR China
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Kingston upon Hull HU6 7RX, United Kingdom
| | - Aidil Abdul Hamid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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Burgos A, Miranda E, Vilaprinyo E, Meza-Canales ID, Alves R. CAM Models: Lessons and Implications for CAM Evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:893095. [PMID: 35812979 PMCID: PMC9260309 DOI: 10.3389/fpls.2022.893095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The evolution of Crassulacean acid metabolism (CAM) by plants has been one of the most successful strategies in response to aridity. On the onset of climate change, expanding the use of water efficient crops and engineering higher water use efficiency into C3 and C4 crops constitute a plausible solution for the problems of agriculture in hotter and drier environments. A firm understanding of CAM is thus crucial for the development of agricultural responses to climate change. Computational models on CAM can contribute significantly to this understanding. Two types of models have been used so far. Early CAM models based on ordinary differential equations (ODE) reproduced the typical diel CAM features with a minimal set of components and investigated endogenous day/night rhythmicity. This line of research brought to light the preponderant role of vacuolar malate accumulation in diel rhythms. A second wave of CAM models used flux balance analysis (FBA) to better understand the role of CO2 uptake in flux distribution. They showed that flux distributions resembling CAM metabolism emerge upon constraining CO2 uptake by the system. We discuss the evolutionary implications of this and also how CAM components from unrelated pathways could have integrated along evolution.
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Affiliation(s)
- Asdrubal Burgos
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Enoc Miranda
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ester Vilaprinyo
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Iván David Meza-Canales
- Departamento de Ecología Aplicada, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Biología Molecular, Genómica y Proteómica, ITRANS-CUCEI, Universidad de Guadalajara, Guadalajara, Mexico
| | - Rui Alves
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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Peltier E, Vion C, Abou Saada O, Friedrich A, Schacherer J, Marullo P. Flor Yeasts Rewire the Central Carbon Metabolism During Wine Alcoholic Fermentation. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:733513. [PMID: 37744152 PMCID: PMC10512321 DOI: 10.3389/ffunb.2021.733513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/31/2021] [Indexed: 09/26/2023]
Abstract
The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from human-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism of Saccharomyces cerevisiae were investigated in the context of the enological fermentation. The genetic determinism of this trait was found out by a quantitative trait loci (QTL) mapping approach using the offspring of two strains belonging to the wine genetic group of the species. A total of 14 QTL were identified from which 8 were validated down to the gene level by genetic engineering. The allelic frequencies of the validated genes within 403 enological strains showed that most of the validated QTL had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that contains introgressions from the flor yeast genetic group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These results also reveal that introgressions originated from intraspecific hybridization events promoted phenotypic variability of carbon metabolism observed in wine strains.
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Affiliation(s)
- Emilien Peltier
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Charlotte Vion
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Philippe Marullo
- Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, ISVV, Université de Bordeaux, Bordeaux, France
- Biolaffort, Bordeaux, France
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12
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Peltier E, Bibi-Triki S, Dutreux F, Caradec C, Friedrich A, Llorente B, Schacherer J. Dissection of quantitative trait loci in the Lachancea waltii yeast species highlights major hotspots. G3 (BETHESDA, MD.) 2021; 11:jkab242. [PMID: 34544138 PMCID: PMC8496267 DOI: 10.1093/g3journal/jkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Dissecting the genetic basis of complex trait remains a real challenge. The budding yeast Saccharomyces cerevisiae has become a model organism for studying quantitative traits, successfully increasing our knowledge in many aspects. However, the exploration of the genotype-phenotype relationship in non-model yeast species could provide a deeper insight into the genetic basis of complex traits. Here, we have studied this relationship in the Lachancea waltii species which diverged from the S. cerevisiae lineage prior to the whole-genome duplication. By performing linkage mapping analyses in this species, we identified 86 quantitative trait loci (QTL) impacting the growth in a large number of conditions. The distribution of these loci across the genome has revealed two major QTL hotspots. A first hotspot corresponds to a general growth QTL, impacting a wide range of conditions. By contrast, the second hotspot highlighted a trade-off with a disadvantageous allele for drug-free conditions which proved to be advantageous in the presence of several drugs. Finally, a comparison of the detected QTL in L. waltii with those which had been previously identified for the same trait in a closely related species, Lachancea kluyveri was performed. This analysis clearly showed the absence of shared QTL across these species. Altogether, our results represent a first step toward the exploration of the genetic architecture of quantitative trait across different yeast species.
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Affiliation(s)
- Emilien Peltier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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13
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Valli M, Grillitsch K, Grünwald-Gruber C, Tatto NE, Hrobath B, Klug L, Ivashov V, Hauzmayer S, Koller M, Tir N, Leisch F, Gasser B, Graf AB, Altmann F, Daum G, Mattanovich D. A subcellular proteome atlas of the yeast Komagataella phaffii. FEMS Yeast Res 2021; 20:5700286. [PMID: 31922548 PMCID: PMC6981350 DOI: 10.1093/femsyr/foaa001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.
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Affiliation(s)
- Minoska Valli
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Nadine E Tatto
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Bernhard Hrobath
- Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Lisa Klug
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Vasyl Ivashov
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Sandra Hauzmayer
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Martina Koller
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Nora Tir
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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14
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Bifunctional Malic/Malolactic Enzyme Provides a Novel Mechanism for NADPH-Balancing in Bacillus subtilis. mBio 2021; 12:mBio.03438-20. [PMID: 33824210 PMCID: PMC8092299 DOI: 10.1128/mbio.03438-20] [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] [Indexed: 11/20/2022] Open
Abstract
A new mechanism for NADPH balancing was discovered in Bacillus subtilis. It pivots on the bifunctional enzyme YtsJ, which is known to catalyze NADP-dependent malate decarboxylation. We found that in the presence of excessive NADPH, the same enzyme switches to malolactic activity and creates a transhydrogenation cycle that ultimately converts NADPH to NADH. This provides a regulated mechanism to immediately adjust NADPH/NADP+ in response to instantaneous needs. The redox cofactor NADPH is required as a reducing equivalent in about 100 anabolic reactions throughout metabolism. To ensure fitness under all conditions, the demand is fulfilled by a few dehydrogenases in central carbon metabolism that reduce NADP+ with electrons derived from the catabolism of nutrients. In the case of Bacillus subtilis growing on glucose, quantitative flux analyses indicate that NADPH production largely exceeds biosynthetic needs, suggesting a hitherto unknown mechanism for NADPH balancing. We investigated the role of the four malic enzymes present in B. subtilis that could bring about a metabolic cycle for transhydrogenation of NADPH into NADH. Using quantitative 13C metabolic flux analysis, we found that isoform YtsJ alone contributes to NADPH balancing in vivo and demonstrated relevant NADPH-oxidizing activity by YtsJ in vitro. To our surprise, we discovered that depending on NADPH, YtsJ switches activity from a pyruvate-producing malic enzyme to a lactate-generating malolactic enzyme. This switch in activity allows YtsJ to adaptively compensate for cellular NADPH over- and underproduction upon demand. Finally, NADPH-dependent bifunctional activity was also detected in the YtsJ homolog in Escherichia coli MaeB. Overall, our study extends the known redox cofactor balancing mechanisms by providing first-time evidence that the type of catalyzed reaction by an enzyme depends on metabolite abundance.
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15
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Kuivanen J, Kannisto M, Mojzita D, Rischer H, Toivari M, Jäntti J. Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production. Microb Cell Fact 2021; 20:34. [PMID: 33536025 PMCID: PMC7860014 DOI: 10.1186/s12934-021-01532-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Anthranilate is a platform chemical used by the industry in the synthesis of a broad range of high-value products, such as dyes, perfumes and pharmaceutical compounds. Currently anthranilate is produced via chemical synthesis from non-renewable resources. Biological synthesis would allow the use of renewable carbon sources and avoid accumulation of toxic by-products. Microorganisms produce anthranilate as an intermediate in the tryptophan biosynthetic pathway. Several prokaryotic microorganisms have been engineered to overproduce anthranilate but attempts to engineer eukaryotic microorganisms for anthranilate production are scarce. Results We subjected Saccharomyces cerevisiae, a widely used eukaryotic production host organism, to metabolic engineering for anthranilate production. A single gene knockout was sufficient to trigger anthranilate accumulation both in minimal and SCD media and the titer could be further improved by subsequent genomic alterations. The effects of the modifications on anthranilate production depended heavily on the growth medium used. By growing an engineered strain in SCD medium an anthranilate titer of 567.9 mg l−1 was obtained, which is the highest reported with an eukaryotic microorganism. Furthermore, the anthranilate biosynthetic pathway was extended by expression of anthranilic acid methyltransferase 1 from Medicago truncatula. When cultivated in YPD medium, this pathway extension enabled production of the grape flavor compound methyl anthranilate in S. cerevisiae at 414 mg l−1. Conclusions In this study we have engineered metabolism of S. cerevisiae for improved anthranilate production. The resulting strains may serve as a basis for development of efficient production host organisms for anthranilate-derived compounds. In order to demonstrate suitability of the engineered S. cerevisiae strains for production of such compounds, we successfully extended the anthranilate biosynthesis pathway to synthesis of methyl anthranilate.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,eniferBio Oy, Espoo, Finland
| | - Matti Kannisto
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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16
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The Effect of Apple Juice Concentration on Cider Fermentation and Properties of the Final Product. Foods 2020; 9:foods9101401. [PMID: 33023161 PMCID: PMC7600676 DOI: 10.3390/foods9101401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
European legislation overall agrees that apple juice concentrate is allowed to be used to some extent in cider production. However, no comprehensive research is available to date on the differences in suitability for fermentation between fresh apple juice and that of reconstituted apple juice concentrate. This study aimed to apply freshly pressed juice and juice concentrate made from the same apple cultivar as a substrate for cider fermentation. Differences in yeast performance in terms of fermentation kinetics and consumption of nutrients have been assessed. Fermented ciders were compared according to volatile ester composition and off-flavor formation related to hydrogen sulfide. Based on the results, in the samples fermented with the concentrate, the yeasts consumed less fructose. The formation of long-chain fatty acid esters increased with the use of reconstituted juice concentrate while the differences in off-flavor formation could not be determined. Overall, the use of the concentrate can be considered efficient enough for the purpose of cider fermentation. However, some nutritional supplementation might be required to support the vitality of yeast.
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17
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Mendes Ferreira A, Mendes-Faia A. The Role of Yeasts and Lactic Acid Bacteria on the Metabolism of Organic Acids during Winemaking. Foods 2020; 9:E1231. [PMID: 32899297 PMCID: PMC7555314 DOI: 10.3390/foods9091231] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022] Open
Abstract
The main role of acidity and pH is to confer microbial stability to wines. No less relevant, they also preserve the color and sensory properties of wines. Tartaric and malic acids are generally the most prominent acids in wines, while others such as succinic, citric, lactic, and pyruvic can exist in minor concentrations. Multiple reactions occur during winemaking and processing, resulting in changes in the concentration of these acids in wines. Two major groups of microorganisms are involved in such modifications: the wine yeasts, particularly strains of Saccharomyces cerevisiae, which carry out alcoholic fermentation; and lactic acid bacteria, which commonly conduct malolactic fermentation. This review examines various such modifications that occur in the pre-existing acids of grape berries and in others that result from this microbial activity as a means to elucidate the link between microbial diversity and wine composition.
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Affiliation(s)
- Ana Mendes Ferreira
- University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- WM&B—Wine Microbiology & Biotechnology Laboratory, Department of Biology and Environment, UTAD, 5001-801 Vila Real, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Arlete Mendes-Faia
- University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- WM&B—Wine Microbiology & Biotechnology Laboratory, Department of Biology and Environment, UTAD, 5001-801 Vila Real, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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18
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Shen Q, Ray SC, Evans HM, Deepe GS, Rappleye CA. Metabolism of Gluconeogenic Substrates by an Intracellular Fungal Pathogen Circumvents Nutritional Limitations within Macrophages. mBio 2020; 11:e02712-19. [PMID: 32265333 PMCID: PMC7157778 DOI: 10.1128/mbio.02712-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/17/2020] [Indexed: 12/25/2022] Open
Abstract
Microbial pathogens exploit host nutrients to proliferate and cause disease. Intracellular pathogens, particularly those exclusively living in the phagosome such as Histoplasma capsulatum, must adapt and acquire nutrients within the nutrient-limited phagosomal environment. In this study, we investigated which host nutrients could be utilized by Histoplasma as carbon sources to proliferate within macrophages. Histoplasma yeasts can grow on hexoses and amino acids but not fatty acids as the carbon source in vitro Transcriptional analysis and metabolism profiling showed that Histoplasma yeasts downregulate glycolysis and fatty acid utilization but upregulate gluconeogenesis within macrophages. Depletion of glycolysis or fatty acid utilization pathways does not prevent Histoplasma growth within macrophages or impair virulence in vivo However, loss of function in Pck1, the enzyme catalyzing the first committed step of gluconeogenesis, impairs Histoplasma growth within macrophages and severely attenuates virulence in vivo, indicating that Histoplasma yeasts rely on catabolism of gluconeogenic substrates (e.g., amino acids) to proliferate within macrophages.IMPORTANCEHistoplasma is a primary human fungal pathogen that survives and proliferates within host immune cells, particularly within the macrophage phagosome compartment. The phagosome compartment is a nutrient-limited environment, requiring Histoplasma yeasts to be able to assimilate available carbon sources within the phagosome to meet their nutritional needs. In this study, we showed that Histoplasma yeasts do not utilize fatty acids or hexoses for growth within macrophages. Instead, Histoplasma yeasts consume gluconeogenic substrates to proliferate in macrophages. These findings reveal the phagosome composition from a nutrient standpoint and highlight essential metabolic pathways that are required for a phagosomal pathogen to proliferate in this intracellular environment.
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Affiliation(s)
- Qian Shen
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Stephanie C Ray
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Heather M Evans
- Division of Infectious Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - George S Deepe
- Division of Infectious Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Chad A Rappleye
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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19
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Sakihama Y, Hidese R, Hasunuma T, Kondo A. Increased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions. Sci Rep 2019; 9:5319. [PMID: 30926897 PMCID: PMC6440987 DOI: 10.1038/s41598-019-41863-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/14/2019] [Indexed: 11/10/2022] Open
Abstract
Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.
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Affiliation(s)
- Yuri Sakihama
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Ryota Hidese
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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20
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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21
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Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems 2019; 4:mSystems00170-18. [PMID: 30834327 PMCID: PMC6392091 DOI: 10.1128/msystems.00170-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/21/2019] [Indexed: 11/23/2022] Open
Abstract
Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism. Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.
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22
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Measures to improve wine malolactic fermentation. Appl Microbiol Biotechnol 2019; 103:2033-2051. [DOI: 10.1007/s00253-018-09608-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 01/06/2023]
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Schwechheimer SK, Becker J, Peyriga L, Portais JC, Wittmann C. Metabolic flux analysis in Ashbya gossypii using 13C-labeled yeast extract: industrial riboflavin production under complex nutrient conditions. Microb Cell Fact 2018; 17:162. [PMID: 30326916 PMCID: PMC6190667 DOI: 10.1186/s12934-018-1003-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/24/2018] [Indexed: 12/17/2022] Open
Abstract
Background The fungus Ashbya gossypii is an important industrial producer of the vitamin riboflavin. Using this microbe, riboflavin is manufactured in a two-stage process based on a rich medium with vegetable oil, yeast extract and different precursors: an initial growth and a subsequent riboflavin production phase. So far, our knowledge on the intracellular metabolic fluxes of the fungus in this complex process is limited, but appears highly relevant to better understand and rationally engineer the underlying metabolism. To quantify intracellular fluxes of growing and riboflavin producing A. gossypii, studies with different 13C tracers were embedded into a framework of experimental design, isotopic labeling analysis by MS and NMR techniques, and model-based data processing. The studies included the use 13C of yeast extract, a key component used in the process. Results During growth, the TCA cycle was found highly active, whereas the cells exhibited a low flux through gluconeogenesis as well as pentose phosphate pathway. Yeast extract was the main carbon donor for anabolism, while vegetable oil selectively contributed to the proteinogenic amino acids glutamate, aspartate, and alanine. During the subsequent riboflavin biosynthetic phase, the carbon flux through the TCA cycle remained high. Regarding riboflavin formation, most of the vitamin’s carbon originated from rapeseed oil (81 ± 1%), however extracellular glycine and yeast extract also contributed with 9 ± 0% and 8 ± 0%, respectively. In addition, advanced yeast extract-based building blocks such as guanine and GTP were directly incorporated into the vitamin. Conclusion Intracellular carbon fluxes for growth and riboflavin production on vegetable oil provide the first flux insight into a fungus on complex industrial medium. The knowledge gained therefrom is valuable for further strain and process improvement. Yeast extract, while being the main carbon source during growth, contributes valuable building blocks to the synthesis of vitamin B2. This highlights the importance of careful selection of the right yeast extract for a process based on its unique composition. Electronic supplementary material The online version of this article (10.1186/s12934-018-1003-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Lindsay Peyriga
- Université de Toulouse, INSA, UPS, INP, Toulouse, France.,INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse, INSA, UPS, INP, Toulouse, France.,INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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Metabolomics approach to reduce the Crabtree effect in continuous culture of Saccharomyces cerevisiae. J Biosci Bioeng 2018; 126:183-188. [DOI: 10.1016/j.jbiosc.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/24/2017] [Accepted: 02/12/2018] [Indexed: 11/21/2022]
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25
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Song P, Yuan K, Qin T, Zhang K, Ji XJ, Ren L, Guan R, Wen J, Huang H. Metabolomics profiling reveals the mechanism of increased pneumocandin B 0 production by comparing mutant and parent strains. J Ind Microbiol Biotechnol 2018; 45:767-780. [PMID: 29948195 DOI: 10.1007/s10295-018-2047-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/18/2018] [Indexed: 11/26/2022]
Abstract
Metabolic profiling was used to discover mechanisms of increased pneumocandin B0 production in a high-yield strain by comparing it with its parent strain. Initially, 79 intracellular metabolites were identified, and the levels of 15 metabolites involved in six pathways were found to be directly correlated with pneumocandin B0 biosynthesis. Then by combining the analysis of key enzymes, acetyl-CoA and NADPH were identified as the main factors limiting pneumocandin B0 biosynthesis. Other metabolites, such as pyruvate, α-ketoglutaric acid, lactate, unsaturated fatty acids and previously unreported metabolite γ-aminobutyric acid were shown to play important roles in pneumocandin B0 biosynthesis and cell growth. Finally, the overall metabolic mechanism hypothesis was formulated and a rational feeding strategy was implemented that increased the pneumocandin B0 yield from 1821 to 2768 mg/L. These results provide practical and theoretical guidance for strain selection, medium optimization, and genetic engineering for pneumocandin B0 production.
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Affiliation(s)
- Ping Song
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Kai Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Tingting Qin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ke Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lujing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Rongfeng Guan
- Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Jianping Wen
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
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26
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Miller D, Brandt N, Gresham D. Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen. PLoS Genet 2018; 14:e1007406. [PMID: 29782489 PMCID: PMC5983874 DOI: 10.1371/journal.pgen.1007406] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 01/20/2023] Open
Abstract
Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen the pooled deletion collection library for trans factors that mediate rapid GAP1 mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for GAP1 mRNA clearance. We also find that the decapping modulators EDC3 and SCD6, translation factor eIF4G2, and the 5' UTR of GAP1 are factors that mediate rapid repression of GAP1 mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.
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Affiliation(s)
- Darach Miller
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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Eder M, Sanchez I, Brice C, Camarasa C, Legras JL, Dequin S. QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation. BMC Genomics 2018; 19:166. [PMID: 29490607 PMCID: PMC5831830 DOI: 10.1186/s12864-018-4562-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/20/2018] [Indexed: 01/07/2023] Open
Abstract
Background The volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermented beverages, such as wine. Although the metabolic pathways and genes behind yeast fermentative aroma formation are well described, little is known about the genetic mechanisms underlying variations between strains in the production of these aroma compounds. To increase our knowledge about the links between genetic variation and volatile production, we performed quantitative trait locus (QTL) mapping using 130 F2-meiotic segregants from two S. cerevisiae wine strains. The segregants were individually genotyped by next-generation sequencing and separately phenotyped during wine fermentation. Results Using different QTL mapping strategies, we were able to identify 65 QTLs in the genome, including 55 that influence the formation of 30 volatile secondary metabolites, 14 with an effect on sugar consumption and central carbon metabolite production, and 7 influencing fermentation parameters. For ethyl lactate, ethyl octanoate and propanol formation, we discovered 2 interacting QTLs each. Within 9 of the detected regions, we validated the contribution of 13 genes in the observed phenotypic variation by reciprocal hemizygosity analysis. These genes are involved in nitrogen uptake and metabolism (AGP1, ALP1, ILV6, LEU9), central carbon metabolism (HXT3, MAE1), fatty acid synthesis (FAS1) and regulation (AGP2, IXR1, NRG1, RGS2, RGT1, SIR2) and explain variations in the production of characteristic sensorial esters (e.g., 2-phenylethyl acetate, 2-metyhlpropyl acetate and ethyl hexanoate), higher alcohols and fatty acids. Conclusions The detection of QTLs and their interactions emphasizes the complexity of yeast fermentative aroma formation. The validation of underlying allelic variants increases knowledge about genetic variation impacting metabolic pathways that lead to the synthesis of sensorial important compounds. As a result, this work lays the foundation for tailoring S. cerevisiae strains with optimized volatile metabolite production for fermented beverages and other biotechnological applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4562-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Eder
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Isabelle Sanchez
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.,MISTEA, INRA, SupAgro, F-34060, Montpellier, France
| | - Claire Brice
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Carole Camarasa
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Jean-Luc Legras
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France
| | - Sylvie Dequin
- SPO, INRA, SupAgro, Université de Montpellier, F-34060, Montpellier, France.
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28
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You SK, Joo YC, Kang DH, Shin SK, Hyeon JE, Woo HM, Um Y, Park C, Han SO. Enhancing Fatty Acid Production of Saccharomyces cerevisiae as an Animal Feed Supplement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:11029-11035. [PMID: 29185736 DOI: 10.1021/acs.jafc.7b04485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Saccharomyces cerevisiae is used for edible purposes, such as human food or as an animal feed supplement. Fatty acids are also beneficial as feed supplements, but S. cerevisiae produces small amounts of fatty acids. In this study, we enhanced fatty acid production of S. cerevisiae by overexpressing acetyl-CoA carboxylase, thioesterase, and malic enzyme associated with fatty acid metabolism. The enhanced strain pAMT showed 2.4-fold higher fatty acids than the wild-type strain. To further increase the fatty acids, various nitrogen sources were analyzed and calcium nitrate was selected as an optimal nitrogen source for fatty acid production. By concentration optimization, 672 mg/L of fatty acids was produced, which was 4.7-fold higher than wild-type strain. These results complement the low level fatty acid production and make it possible to obtain the benefits of fatty acids as an animal feed supplement while, simultaneously, maintaining the advantages of S. cerevisiae.
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Affiliation(s)
- Seung Kyou You
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Young-Chul Joo
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Dae Hee Kang
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
- Institute of Life Science and Natural Resources, Korea University , Seoul 02841, Republic of Korea
| | - Sang Kyu Shin
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Institute of Life Science and Natural Resources, Korea University , Seoul 02841, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU) , 2066 Seobu-ro, Jangan-gu, Suwon 16419, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology , 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University , Seoul 139-701, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
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Badia MB, Mans R, Lis AV, Tronconi MA, Arias CL, Maurino VG, Andreo CS, Drincovich MF, van Maris AJA, Gerrard Wheeler MC. Specific Arabidopsis thaliana malic enzyme isoforms can provide anaplerotic pyruvate carboxylation function in Saccharomyces cerevisiae. FEBS J 2017; 284:654-665. [PMID: 28075062 DOI: 10.1111/febs.14013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 11/29/2022]
Abstract
NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO2 , and NAD(P)H and is present as a multigene family in Arabidopsis thaliana. The carboxylation reaction catalyzed by purified recombinant Arabidopsis NADP-ME proteins is faster than those reported for other animal or plant isoforms. In contrast, no carboxylation activity could be detected in vitro for the NAD-dependent counterparts. In order to further investigate their putative carboxylating role in vivo, Arabidopsis NAD(P)-ME isoforms, as well as the NADP-ME2del2 (with a decreased ability to carboxylate pyruvate) and NADP-ME2R115A (lacking fumarate activation) versions, were functionally expressed in the cytosol of pyruvate carboxylase-negative (Pyc- ) Saccharomyces cerevisiae strains. The heterologous expression of NADP-ME1, NADP-ME2 (and its mutant proteins), and NADP-ME3 restored the growth of Pyc- S. cerevisiae on glucose, and this capacity was dependent on the availability of CO2 . On the other hand, NADP-ME4, NAD-ME1, and NAD-ME2 could not rescue the Pyc- strains from C4 auxotrophy. NADP-ME carboxylation activity could be measured in leaf crude extracts of knockout and overexpressing Arabidopsis lines with modified levels of NADP-ME, where this activity was correlated with the amount of NADP-ME2 transcript. These results indicate that specific A. thaliana NADP-ME isoforms are able to play an anaplerotic role in vivo and provide a basis for the study on the carboxylating activity of NADP-ME, which may contribute to the synthesis of C4 compounds and redox shuttling in plant cells.
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Affiliation(s)
- Mariana Beatriz Badia
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Argentina
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, The Netherlands
| | - Alicia V Lis
- Department of Biotechnology, Delft University of Technology, The Netherlands.,Biochemical Engineering Institute, Saarland University, Saarbrücken, Germany
| | - Marcos Ariel Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Argentina
| | - Cintia Lucía Arias
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Argentina
| | - Verónica Graciela Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Carlos Santiago Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Argentina
| | - María Fabiana Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Argentina
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, The Netherlands.,Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
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30
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Yuan J, Mishra P, Ching CB. Metabolically engineered Saccharomyces cerevisiae for branched-chain ester productions. J Biotechnol 2016; 239:90-97. [DOI: 10.1016/j.jbiotec.2016.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/17/2022]
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31
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Irokawa H, Tachibana T, Watanabe T, Matsuyama Y, Motohashi H, Ogasawara A, Iwai K, Naganuma A, Kuge S. Redox-dependent Regulation of Gluconeogenesis by a Novel Mechanism Mediated by a Peroxidatic Cysteine of Peroxiredoxin. Sci Rep 2016; 6:33536. [PMID: 27634403 PMCID: PMC5025857 DOI: 10.1038/srep33536] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/30/2016] [Indexed: 11/09/2022] Open
Abstract
Peroxiredoxin is an abundant peroxidase, but its non-peroxidase function is also important. In this study, we discovered that Tsa1, a major peroxiredoxin of budding yeast cells, is required for the efficient flux of gluconeogenesis. We found that the suppression of pyruvate kinase (Pyk1) via the interaction with Tsa1 contributes in part to gluconeogenic enhancement. The physical interactions between Pyk1 and Tsa1 were augmented during the shift from glycolysis to gluconeogenesis. Intriguingly, a peroxidatic cysteine in the catalytic center of Tsa1 played an important role in the physical Tsa1-Pyk1 interactions. These interactions are enhanced by exogenous H2O2 and by endogenous reactive oxygen species, which is increased during gluconeogenesis. Only the peroxidatic cysteine, but no other catalytic cysteine of Tsa1, is required for efficient growth during the metabolic shift to obtain maximum yeast growth (biomass). This Tsa1 function is separable from the peroxidase function as an antioxidant. This is the first report to demonstrate that peroxiredoxin has a novel nonperoxidase function as a redox-dependent target modulator and that pyruvate kinase is modulated via an alternative mechanism.
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Affiliation(s)
- Hayato Irokawa
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
| | - Tsuyoshi Tachibana
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-0861, Japan
| | - Toshihiko Watanabe
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
| | - Yuka Matsuyama
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Ayako Ogasawara
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
| | - Kenta Iwai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
| | - Akira Naganuma
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-0861, Japan
| | - Shusuke Kuge
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi 981-8558, Japan
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Comparative genome analysis of the oleaginous yeast Trichosporon fermentans reveals its potential applications in lipid accumulation. Microbiol Res 2016; 192:203-210. [PMID: 27664738 DOI: 10.1016/j.micres.2016.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 11/22/2022]
Abstract
In this work, Trichosporon fermentans CICC 1368, which has been shown to accumulate cellular lipids efficiently using industry-agricultural wastes, was subjected to preliminary genome analysis, yielding a genome size of 31.3 million bases and 12,702 predicted protein-coding genes. Our analysis also showed a high degree of gene duplications and unique genes compared with those observed in other oleaginous yeasts, with 3-4-fold more genes related to fatty acid elongation and degradation compared with those in Rhodosporidium toruloides NP11 and Yarrowia lipolytica CLIB122. Phylogenetic analysis with other oleaginous microbes suggested that the lipogenic capacity of T. fermentans was obtained during evolution after the divergence of genera. Thus, our study provided the first draft genome and comparative analysis of T. fermentans, laying the foundation for its genetic improvement to facilitate cost-effective lipid production.
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Cardenas J, Da Silva NA. Engineering cofactor and transport mechanisms in Saccharomyces cerevisiae for enhanced acetyl-CoA and polyketide biosynthesis. Metab Eng 2016; 36:80-89. [PMID: 26969250 DOI: 10.1016/j.ymben.2016.02.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/04/2016] [Accepted: 02/23/2016] [Indexed: 01/01/2023]
Abstract
Synthesis of polyketides at high titer and yield is important for producing pharmaceuticals and biorenewable chemical precursors. In this work, we engineered cofactor and transport pathways in Saccharomyces cerevisiae to increase acetyl-CoA, an important polyketide building block. The highly regulated yeast pyruvate dehydrogenase bypass pathway was supplemented by overexpressing a modified Escherichia coli pyruvate dehydrogenase complex (PDHm) that accepts NADP(+) for acetyl-CoA production. After 24h of cultivation, a 3.7-fold increase in NADPH/NADP(+) ratio was observed relative to the base strain, and a 2.2-fold increase relative to introduction of the native E. coli PDH. Both E. coli pathways increased acetyl-CoA levels approximately 2-fold relative to the yeast base strain. Combining PDHm with a ZWF1 deletion to block the major yeast NADPH biosynthesis pathway resulted in a 12-fold NADPH boost and a 2.2-fold increase in acetyl-CoA. At 48h, only this coupled approach showed increased acetyl-CoA levels, 3.0-fold higher than that of the base strain. The impact on polyketide synthesis was evaluated in a S. cerevisiae strain expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for the production of the polyketide triacetic acid lactone (TAL). Titers of TAL relative to the base strain improved only 30% with the native E. coli PDH, but 3.0-fold with PDHm and 4.4-fold with PDHm in the Δzwf1 strain. Carbon was further routed toward TAL production by reducing mitochondrial transport of pyruvate and acetyl-CoA; deletions in genes POR2, MPC2, PDA1, or YAT2 each increased titer 2-3-fold over the base strain (up to 0.8g/L), and in combination to 1.4g/L. Combining the two approaches (NADPH-generating acetyl-CoA pathway plus reduced metabolite flux into the mitochondria) resulted in a final TAL titer of 1.6g/L, a 6.4-fold increase over the non-engineered yeast strain, and 35% of theoretical yield (0.16g/g glucose), the highest reported to date. These biological driving forces present new avenues for improving high-yield production of acetyl-CoA derived compounds.
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Affiliation(s)
- Javier Cardenas
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
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Kesten D, Kummer U, Sahle S, Hübner K. A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse. Biophys Chem 2015; 206:40-57. [DOI: 10.1016/j.bpc.2015.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/08/2023]
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35
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Ida K, Ishii J, Matsuda F, Kondo T, Kondo A. Eliminating the isoleucine biosynthetic pathway to reduce competitive carbon outflow during isobutanol production by Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:62. [PMID: 25925006 PMCID: PMC4417518 DOI: 10.1186/s12934-015-0240-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 04/02/2015] [Indexed: 11/10/2022] Open
Abstract
Background Isobutanol is an important biorefinery target alcohol that can be used as a fuel, fuel additive, or commodity chemical. Baker’s yeast, Saccharomyces cerevisiae, is a promising organism for the industrial manufacture of isobutanol because of its tolerance for low pH and resistance to autolysis. It has been reported that gene deletion of the pyruvate dehydrogenase complex, which is directly involved in pyruvate metabolism, improved isobutanol production by S. cerevisiae. However, the engineering strategies available for S. cerevisiae are immature compared to those available for bacterial hosts such as Escherichia coli, and several pathways in addition to pyruvate metabolism compete with isobutanol production. Results The isobutyrate, pantothenate or isoleucine biosynthetic pathways were deleted to reduce the outflow of carbon competing with isobutanol biosynthesis in S. cerevisiae. The judicious elimination of these competing pathways increased isobutanol production. ILV1 encodes threonine ammonia-lyase, the enzyme that converts threonine to 2-ketobutanoate, a precursor for isoleucine biosynthesis. S. cerevisiae mutants in which ILV1 had been deleted displayed 3.5-fold increased isobutanol productivity. The ΔILV1 strategy was further combined with two previously established engineering strategies (activation of two steps of the Ehrlich pathway and the transhydrogenase-like shunt), providing 11-fold higher isobutanol productivity as compared to the parent strain. The titer and yield of this engineered strain was 224 ± 5 mg/L and 12.04 ± 0.23 mg/g glucose, respectively. Conclusions The deletion of competitive pathways to reduce the outflow of carbon, including ILV1 deletion, is an important strategy for increasing isobutanol production by S. cerevisiae.
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Affiliation(s)
- Kengo Ida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Jun Ishii
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Fumio Matsuda
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 565-0871, Japan. .,RIKEN Biomass Engineering Program, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Takashi Kondo
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Present address: Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,RIKEN Biomass Engineering Program, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
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Hayakawa K, Kajihata S, Matsuda F, Shimizu H. (13)C-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:532-8. [PMID: 25912448 DOI: 10.1016/j.jbiosc.2015.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/16/2015] [Accepted: 03/16/2015] [Indexed: 11/28/2022]
Abstract
S-Adenosyl-L-methionine (SAM) is a major biological methyl group donor, and is used as a nutritional supplement and prescription drug. Yeast is used for the industrial production of SAM owing to its high intracellular SAM concentrations. To determine the regulation mechanisms responsible for such high SAM production, (13)C-metabolic flux analysis ((13)C-MFA) was conducted to compare the flux distributions in the central metabolism between Kyokai no. 6 (high SAM-producing) and S288C (control) strains. (13)C-MFA showed that the levels of tricarboxylic acid (TCA) cycle flux in SAM-overproducing strain were considerably increased compared to those in the S228C strain. Analysis of ATP balance also showed that a larger amount of excess ATP was produced in the Kyokai 6 strain because of increased oxidative phosphorylation. These results suggest that high SAM production in Kyokai 6 strains could be attributed to enhanced ATP regeneration with high TCA cycle fluxes and respiration activity. Thus, maintaining high respiration efficiency during cultivation is important for improving SAM production.
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Affiliation(s)
- Kenshi Hayakawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; KANEKA Fundamental Technology Research Alliance Laboratories, Graduate School of Engineering, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Shuichi Kajihata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Reassessment of the transhydrogenase/malate shunt pathway in Clostridium thermocellum ATCC 27405 through kinetic characterization of malic enzyme and malate dehydrogenase. Appl Environ Microbiol 2015; 81:2423-32. [PMID: 25616802 DOI: 10.1128/aem.03360-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Clostridium thermocellum produces ethanol as one of its major end products from direct fermentation of cellulosic biomass. Therefore, it is viewed as an attractive model for the production of biofuels via consolidated bioprocessing. However, a better understanding of the metabolic pathways, along with their putative regulation, could lead to improved strategies for increasing the production of ethanol. In the absence of an annotated pyruvate kinase in the genome, alternate means of generating pyruvate have been sought. Previous proteomic and transcriptomic work detected high levels of a malate dehydrogenase and malic enzyme, which may be used as part of a malate shunt for the generation of pyruvate from phosphoenolpyruvate. The purification and characterization of the malate dehydrogenase and malic enzyme are described in order to elucidate their putative roles in malate shunt and their potential role in C. thermocellum metabolism. The malate dehydrogenase catalyzed the reduction of oxaloacetate to malate utilizing NADH or NADPH with a kcat of 45.8 s(-1) or 14.9 s(-1), respectively, resulting in a 12-fold increase in catalytic efficiency when using NADH over NADPH. The malic enzyme displayed reversible malate decarboxylation activity with a kcat of 520.8 s(-1). The malic enzyme used NADP(+) as a cofactor along with NH4 (+) and Mn(2+) as activators. Pyrophosphate was found to be a potent inhibitor of malic enzyme activity, with a Ki of 0.036 mM. We propose a putative regulatory mechanism of the malate shunt by pyrophosphate and NH4 (+) based on the characterization of the malate dehydrogenase and malic enzyme.
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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Orlandi I, Coppola DP, Vai M. Rewiring yeast acetate metabolism through MPC1 loss of function leads to mitochondrial damage and decreases chronological lifespan. ACTA ACUST UNITED AC 2014; 1:393-405. [PMID: 28357219 PMCID: PMC5349135 DOI: 10.15698/mic2014.12.178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During growth on fermentable substrates, such as glucose, pyruvate, which is the
end-product of glycolysis, can be used to generate acetyl-CoA in the cytosol via
acetaldehyde and acetate, or in mitochondria by direct oxidative
decarboxylation. In the latter case, the mitochondrial pyruvate carrier (MPC) is
responsible for pyruvate transport into mitochondrial matrix space. During
chronological aging, yeast cells which lack the major structural subunit Mpc1
display a reduced lifespan accompanied by an age-dependent loss of autophagy.
Here, we show that the impairment of pyruvate import into mitochondria linked to
Mpc1 loss is compensated by a flux redirection of TCA cycle intermediates
through the malic enzyme-dependent alternative route. In such a way, the TCA
cycle operates in a “branched” fashion to generate pyruvate and is depleted of
intermediates. Mutant cells cope with this depletion by increasing the activity
of glyoxylate cycle and of the pathway which provides the nucleocytosolic
acetyl-CoA. Moreover, cellular respiration decreases and ROS accumulate in the
mitochondria which, in turn, undergo severe damage. These acquired traits in
concert with the reduced autophagy restrict cell survival of the mpc1∆ mutant
during chronological aging. Conversely, the activation of the carnitine shuttle
by supplying acetyl-CoA to the mitochondria is sufficient to abrogate the
short-lived phenotype of the mutant.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Damiano Pellegrino Coppola
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marina Vai
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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Averesch NJH, Krömer JO. Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. Metab Eng Commun 2014; 1:19-28. [PMID: 34150501 PMCID: PMC8193250 DOI: 10.1016/j.meteno.2014.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/18/2014] [Accepted: 09/27/2014] [Indexed: 02/02/2023] Open
Abstract
There is currently a strong interest to derive the biological precursor cis,cis-muconic acid from shikimate pathway-branches to develop a biological replacement for adipic acid. Pioneered by the Frost laboratory this concept has regained interest: Recent approaches (Boles, Alper, Yan) however suffer from low product titres. Here an in silico comparison of all strain construction strategies was conducted to highlight stoichiometric optimizations. Using elementary mode analysis new knock-out strategies were determined in Saccharomyces cerevisiae and Escherichia coli. The strain construction strategies are unique to each pathway-branch and organism, allowing significantly different maximum and minimum yields. The maximum theoretical product carbon yields on glucose ranged from 86% (dehydroshikimate-branch) to 69% (anthranilate-branch). In most cases a coupling of product formation to growth was possible. Especially in S. cerevisiae chorismate-routes a minimum yield constraint of 46.9% could be reached. The knock-out targets are non-obvious, and not-transferable, highlighting the importance of tailored strain construction strategies. Maximum theoretical product carbon yields for biological production of cis,cis-muconic acid from glucose were calculated. Existing strain construction strategies were compared in silico and weaknesses were identified. New strain construction strategies were determined to allow coupling of product formation to growth for E. coli and S. cerevisiae. In particular abolishing one target reaction introduces a minimum yield constraint of 28% in S. cerevisiae. Determined knock-out targets are unique to each pathway and organism, highlighting the importance of tailored strain construction strategies.
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Key Words
- ADH, acetaldehyde dehydrogenase
- ANTH, anthranilate
- Adipic
- Carbon yield
- DAHP, 3-deoxy-arabinoheptulosonate 7-phosphate
- DHBA, 2,3-dihydroxybenzoate
- DHS, 3-dehydroshikimate
- E4P, erythrose 4-phosphate
- EDA, 2-dehydro-3-deoxy-phosphogluconate aldolase
- EDP, Entner–Doudoroff pathway
- EFM, elementary flux modes
- EMA, elementary mode analysis
- EPSP, 5-enolpyruvylshikimate-3-phosphate
- Elementary mode analysis
- F6P, fructose-6-phosphate
- FRD, fumarate reductase
- G6PD, glucose-6-phosphate dehydrogenase
- GPDH, glycerol-3-phosphate dehydrogenase
- Knock-out strategies
- LDH, lactate dehydrogenase
- MAE, malic enzyme
- Muconic
- PCA, protocatechuate
- PCK, phosphoenolpyruvate carboxykinase
- PEP, phosphoenolpyruvate
- PPP, pentose phosphate pathway
- PPS, phosphoenolpyruvate synthase
- PTS, phosphotransferase system
- PYK, pyruvate kinase
- SA, salicylate
- WT, wild type
- Ymax, maximum theoretical carbon yield
- Ymin, minimum theoretical carbon yield
- cMCs, constrained minimal cut sets
- ccMA, cis,cis-muconic acid
- pHBA, para-hydroxybenzoate
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Affiliation(s)
- Nils J H Averesch
- Centre for Microbial Electrosynthesis (CEMES), University of Queensland, Brisbane, Australia.,Advanced Water Management Centre (AWMC), University of Queensland, Brisbane, Australia
| | - Jens O Krömer
- Centre for Microbial Electrosynthesis (CEMES), University of Queensland, Brisbane, Australia.,Advanced Water Management Centre (AWMC), University of Queensland, Brisbane, Australia
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Park SH, Kim S, Hahn JS. Metabolic engineering of Saccharomyces cerevisiae for the production of isobutanol and 3-methyl-1-butanol. Appl Microbiol Biotechnol 2014; 98:9139-47. [DOI: 10.1007/s00253-014-6081-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
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Oba T, Kusumoto K, Kichise Y, Izumoto E, Nakayama S, Tashiro K, Kuhara S, Kitagaki H. Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates ofSaccharomyces cerevisiaesake strains. FEMS Yeast Res 2014; 14:789-96. [DOI: 10.1111/1567-1364.12170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/01/2014] [Accepted: 05/21/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Takahiro Oba
- Biotechnology and Food Research Institute; Fukuoka Industrial Technology Center; Kurume Fukuoka Japan
| | - Kenichi Kusumoto
- Biotechnology and Food Research Institute; Fukuoka Industrial Technology Center; Kurume Fukuoka Japan
| | - Yuki Kichise
- Department of Biochemistry and Applied Chemistry; Kurume National College of Technology; Kurume Fukuoka Japan
| | - Eiji Izumoto
- Department of Biochemistry and Applied Chemistry; Kurume National College of Technology; Kurume Fukuoka Japan
| | - Shunichi Nakayama
- Department of Fermentation Science and Technology; Faculty of Applied Bio-science; Tokyo University of Agriculture; Setagaya-ku Tokyo Japan
| | - Kosuke Tashiro
- Graduate School of Genetic Resources Technology; Kyushu University; Higashi-ku Fukuoka Japan
| | - Satoru Kuhara
- Graduate School of Genetic Resources Technology; Kyushu University; Higashi-ku Fukuoka Japan
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Del Mónaco SM, Barda NB, Rubio NC, Caballero AC. Selection and characterization of a Patagonian Pichia kudriavzevii for wine deacidification. J Appl Microbiol 2014; 117:451-64. [PMID: 24844932 DOI: 10.1111/jam.12547] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 05/07/2014] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
Abstract
AIMS The purpose of this study was to select autochthonous yeasts with metabolic ability to degrade L-malic acid for its potential use in young wine deacidification. METHODS AND RESULTS Fifty seven Patagonian nonSaccharomyces yeast of oenological origin were identified by conventional molecular methods and tested in their capability to grow at the expense of L-malic acid. Only four isolates belonging to Pichia kudriavzevii species showed this property, and one of them was selected to continue with the study. This isolate, named as P. kudriavzevii ÑNI15, was able to degrade L-malic acid in microvinifications, increasing the pH 0·2-0·3 units with a minimal effect on the acid structure of wine. Additionally, this isolate produced low levels of ethanol, important levels of glycerol (10·41 ± 0·48 g l(-1) ) and acceptable amounts of acetic acid (0·86 ± 0·13 g l(-1) ). In addition, it improved the sensorial attributes of wine increasing its fruity aroma. CONCLUSIONS The selection of yeasts for oenological use among nonSaccharomyces species led to the finding of a yeast strain with novel and interesting oenological characteristics which could have significant implications in the production of well-balanced and more physicochemical and microbiological stable young wines. SIGNIFICANCE AND IMPACT OF THE STUDY The use of P. kudriavzevii ÑNI15 as mixed starter with S. cerevisiae would eliminate the cultural and cellar operations undertaken to adjust the musts acidity, therefore improving wine quality and reducing production costs.
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Affiliation(s)
- S M Del Mónaco
- Grupo de Enología, Facultad de Ingeniería, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN - Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Facultad de Ingeniería, Universidad Nacional del Comahue (UNCo), Neuquén, Argentina
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Benisch F, Boles E. The bacterial Entner–Doudoroff pathway does not replace glycolysis in Saccharomyces cerevisiae due to the lack of activity of iron–sulfur cluster enzyme 6-phosphogluconate dehydratase. J Biotechnol 2014; 171:45-55. [DOI: 10.1016/j.jbiotec.2013.11.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/02/2013] [Accepted: 11/22/2013] [Indexed: 01/04/2023]
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Ask M, Bettiga M, Duraiswamy VR, Olsson L. Pulsed addition of HMF and furfural to batch-grown xylose-utilizing Saccharomyces cerevisiae results in different physiological responses in glucose and xylose consumption phase. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:181. [PMID: 24341320 PMCID: PMC3878631 DOI: 10.1186/1754-6834-6-181] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/29/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Pretreatment of lignocellulosic biomass generates a number of undesired degradation products that can inhibit microbial metabolism. Two of these compounds, the furan aldehydes 5-hydroxymethylfurfural (HMF) and 2-furaldehyde (furfural), have been shown to be an impediment for viable ethanol production. In the present study, HMF and furfural were pulse-added during either the glucose or the xylose consumption phase in order to dissect the effects of these inhibitors on energy state, redox metabolism, and gene expression of xylose-consuming Saccharomyces cerevisiae. RESULTS Pulsed addition of 3.9 g L-1 HMF and 1.2 g L-1 furfural during either the glucose or the xylose consumption phase resulted in distinct physiological responses. Addition of furan aldehydes in the glucose consumption phase was followed by a decrease in the specific growth rate and the glycerol yield, whereas the acetate yield increased 7.3-fold, suggesting that NAD(P)H for furan aldehyde conversion was generated by acetate synthesis. No change in the intracellular levels of NAD(P)H was observed 1 hour after pulsing, whereas the intracellular concentration of ATP increased by 58%. An investigation of the response at transcriptional level revealed changes known to be correlated with perturbations in the specific growth rate, such as protein and nucleotide biosynthesis. Addition of furan aldehydes during the xylose consumption phase brought about an increase in the glycerol and acetate yields, whereas the xylitol yield was severely reduced. The intracellular concentrations of NADH and NADPH decreased by 58 and 85%, respectively, hence suggesting that HMF and furfural drained the cells of reducing power. The intracellular concentration of ATP was reduced by 42% 1 hour after pulsing of inhibitors, suggesting that energy-requiring repair or maintenance processes were activated. Transcriptome profiling showed that NADPH-requiring processes such as amino acid biosynthesis and sulfate and nitrogen assimilation were induced 1 hour after pulsing. CONCLUSIONS The redox and energy metabolism were found to be more severely affected after pulsing of furan aldehydes during the xylose consumption phase than during glucose consumption. Conceivably, this discrepancy resulted from the low xylose utilization rate, hence suggesting that xylose metabolism is a feasible target for metabolic engineering of more robust xylose-utilizing yeast strains.
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Affiliation(s)
- Magnus Ask
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Maurizio Bettiga
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Varuni Raju Duraiswamy
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
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Matsuda F, Ishii J, Kondo T, Ida K, Tezuka H, Kondo A. Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance. Microb Cell Fact 2013; 12:119. [PMID: 24305546 PMCID: PMC3866936 DOI: 10.1186/1475-2859-12-119] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/05/2013] [Indexed: 11/10/2022] Open
Abstract
Background Isobutanol is an important target for biorefinery research as a next-generation biofuel and a building block for commodity chemical production. Metabolically engineered microbial strains to produce isobutanol have been successfully developed by introducing the Ehrlich pathway into bacterial hosts. Isobutanol-producing baker’s yeast (Saccharomyces cerevisiae) strains have been developed following the strategy with respect to its advantageous characteristics for cost-effective isobutanol production. However, the isobutanol yields and titers attained by the developed strains need to be further improved through engineering of S. cerevisiae metabolism. Results Two strategies including eliminating competing pathways and resolving the cofactor imbalance were applied to improve isobutanol production in S. cerevisiae. Isobutanol production levels were increased in strains lacking genes encoding members of the pyruvate dehydrogenase complex such as LPD1, indicating that the pyruvate supply for isobutanol biosynthesis is competing with acetyl-CoA biosynthesis in mitochondria. Isobutanol production was increased by overexpression of enzymes responsible for transhydrogenase-like shunts such as pyruvate carboxylase, malate dehydrogenase, and malic enzyme. The integration of a single gene deletion lpd1Δ and the activation of the transhydrogenase-like shunt further increased isobutanol levels. In a batch fermentation test at the 50-mL scale from 100 g/L glucose using the two integrated strains, the isobutanol titer reached 1.62 ± 0.11 g/L and 1.61 ± 0.03 g/L at 24 h after the start of fermentation, which corresponds to the yield at 0.016 ± 0.001 g/g glucose consumed and 0.016 ± 0.0003 g/g glucose consumed, respectively. Conclusions These results demonstrate that downregulation of competing pathways and metabolic functions for resolving the cofactor imbalance are promising strategies to construct S. cerevisiae strains that effectively produce isobutanol.
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Affiliation(s)
| | | | | | | | | | - Akihiko Kondo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Turumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Vorapreeda T, Thammarongtham C, Cheevadhanarak S, Laoteng K. Repertoire of malic enzymes in yeast and fungi: insight into their evolutionary functional and structural significance. Microbiology (Reading) 2013; 159:2548-2557. [DOI: 10.1099/mic.0.065342-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Tayvich Vorapreeda
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology. King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology. King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Supapon Cheevadhanarak
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Kobkul Laoteng
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
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48
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Ayer A, Gourlay CW, Dawes IW. Cellular redox homeostasis, reactive oxygen species and replicative ageing inSaccharomyces cerevisiae. FEMS Yeast Res 2013; 14:60-72. [DOI: 10.1111/1567-1364.12114] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/09/2013] [Accepted: 10/13/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Anita Ayer
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney NSW Australia
- Victor Chang Cardiac Research Institute; Darlinghurst NSW Australia
| | | | - Ian W. Dawes
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney NSW Australia
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Gruchattka E, Hädicke O, Klamt S, Schütz V, Kayser O. In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. Microb Cell Fact 2013; 12:84. [PMID: 24059635 PMCID: PMC3852115 DOI: 10.1186/1475-2859-12-84] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/15/2013] [Indexed: 11/23/2022] Open
Abstract
Background Heterologous microbial production of rare plant terpenoids of medicinal or industrial interest is attracting more and more attention but terpenoid yields are still low. Escherichia coli and Saccharomyces cerevisiae are the most widely used heterologous hosts; a direct comparison of both hosts based on experimental data is difficult though. Hence, the terpenoid pathways of E. coli (via 1-deoxy-D-xylulose 5-phosphate, DXP) and S. cerevisiae (via mevalonate, MVA), the impact of the respective hosts metabolism as well as the impact of different carbon sources were compared in silico by means of elementary mode analysis. The focus was set on the yield of isopentenyl diphosphate (IPP), the general terpenoid precursor, to identify new metabolic engineering strategies for an enhanced terpenoid yield. Results Starting from the respective precursor metabolites of the terpenoid pathways (pyruvate and glyceraldehyde-3-phosphate for the DXP pathway and acetyl-CoA for the MVA pathway) and considering only carbon stoichiometry, the two terpenoid pathways are identical with respect to carbon yield. However, with glucose as substrate, the MVA pathway has a lower potential to supply terpenoids in high yields than the DXP pathway if the formation of the required precursors is taken into account, due to the carbon loss in the formation of acetyl-CoA. This maximum yield is further reduced in both hosts when the required energy and reduction equivalents are considered. Moreover, the choice of carbon source (glucose, xylose, ethanol or glycerol) has an effect on terpenoid yield with non-fermentable carbon sources being more promising. Both hosts have deficiencies in energy and redox equivalents for high yield terpenoid production leading to new overexpression strategies (heterologous enzymes/pathways) for an enhanced terpenoid yield. Finally, several knockout strategies are identified using constrained minimal cut sets enforcing a coupling of growth to a terpenoid yield which is higher than any yield published in scientific literature so far. Conclusions This study provides for the first time a comprehensive and detailed in silico comparison of the most prominent heterologous hosts E. coli and S. cerevisiae as terpenoid factories giving an overview on several promising metabolic engineering strategies paving the way for an enhanced terpenoid yield.
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Affiliation(s)
- Evamaria Gruchattka
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str, 66, 44227 Dortmund, Germany.
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Tomar N, De RK. Comparing methods for metabolic network analysis and an application to metabolic engineering. Gene 2013; 521:1-14. [PMID: 23537990 DOI: 10.1016/j.gene.2013.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
Abstract
Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.
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Affiliation(s)
- Namrata Tomar
- Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
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