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Xie D, Zheng J, Sun Y, Li X, Ren S. Effects of Ca 2+ signal on the activities of key enzymes and expression of related genes in yeast ethanol metabolism and mitochondrial function during high sugar fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5077-5088. [PMID: 38284794 DOI: 10.1002/jsfa.13341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND During high sugar fermentation, yeast is mainly affected by high sugar stress in the early stage. It becomes jointly affected by high sugar and ethanol stress as ethanol accumulates during fermentation. Ca2+, as the second messenger of the cell, mediates various metabolic processes. In this study, the effects of the Ca2+ signal on the activities of key enzymes, expression of related genes of ethanol metabolism, and mitochondrial function were investigated. RESULTS The results showed a significant increase in the activities of enzymes related to ethanol metabolism in yeast cells under a high sugar environment. Ca2+ significantly promoted the activities of enzymes related to mitochondrial respiratory metabolism and regulated the carbon flow between ethanol metabolism and the tricarboxylic acid cycle. The high sugar environment affected the expression of genes related to carbon metabolism, while the addition of Ca2+ stabilized the expression of related genes. CONCLUSION Ca2+ signal participated in ethanol and mitochondrial metabolism and regulated the key enzymes and related gene expression to enhance the resistance of yeast to stress during high sugar fermentation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Xie
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Jiaxin Zheng
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yingqi Sun
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Xing Li
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Shuncheng Ren
- Food Engineering Technology Research Center/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
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2
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Theorell A, Jadebeck JF, Wiechert W, McFadden J, Nöh K. Rethinking 13C-metabolic flux analysis - The Bayesian way of flux inference. Metab Eng 2024; 83:137-149. [PMID: 38582144 DOI: 10.1016/j.ymben.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Metabolic reaction rates (fluxes) play a crucial role in comprehending cellular phenotypes and are essential in areas such as metabolic engineering, biotechnology, and biomedical research. The state-of-the-art technique for estimating fluxes is metabolic flux analysis using isotopic labelling (13C-MFA), which uses a dataset-model combination to determine the fluxes. Bayesian statistical methods are gaining popularity in the field of life sciences, but the use of 13C-MFA is still dominated by conventional best-fit approaches. The slow take-up of Bayesian approaches is, at least partly, due to the unfamiliarity of Bayesian methods to metabolic engineering researchers. To address this unfamiliarity, we here outline similarities and differences between the two approaches and highlight particular advantages of the Bayesian way of flux analysis. With a real-life example, re-analysing a moderately informative labelling dataset of E. coli, we identify situations in which Bayesian methods are advantageous and more informative, pointing to potential pitfalls of current 13C-MFA evaluation approaches. We propose the use of Bayesian model averaging (BMA) for flux inference as a means of overcoming the problem of model uncertainty through its tendency to assign low probabilities to both, models that are unsupported by data, and models that are overly complex. In this capacity, BMA resembles a tempered Ockham's razor. With the tempered razor as a guide, BMA-based 13C-MFA alleviates the problem of model selection uncertainty and is thereby capable of becoming a game changer for metabolic engineering by uncovering new insights and inspiring novel approaches.
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Affiliation(s)
- Axel Theorell
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Johann F Jadebeck
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062 Aachen, Germany
| | - Johnjoe McFadden
- Department of Microbial and Cellular Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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Kim M, Oh JW, Jeong DW, Cho BH, Chang J, Shi X, Han SO. Biosynthesis of l-histidine from marine biomass-derived galactans in metabolically engineered Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2024; 391:129963. [PMID: 37925085 DOI: 10.1016/j.biortech.2023.129963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
l-Histidine plays significant roles in the food and pharmaceutical industries, and its demand has been steadily increasing recently. As demand for l-histidine continues, the development of eco-friendly processes is required. To pursue this goal, D-galactose, a primary component of red algae, was employed as a carbon source for synthesizing l-histidine. To harness this marine biomass, κ-carrageenan was preferentially hydrolyzed to obtain D-galactose using κ-carrageenase (CgkA) and iduronate-2-sulfatase (IdsA3). Subsequently, l-histidine production was enhanced by modifying precursor pathways in Corynebacterium glutamicum. The resulting strain, TDPH6 exhibited a remarkable 2.15-fold increase in l-histidine production compared to TDP. Furthermore, a galactose utilization system was introduced and named TDPH6G2. During fermentation, this strain efficiently consumed 100 % of the D-galactose and synthesized 0.395 g/L of l-histidine. In conclusion, this study presents a sustainable approach to L-histidine synthesis by introducing a galactose utilization system into C. glutamicum.
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Affiliation(s)
- Minhye Kim
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jun Won Oh
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Da Woon Jeong
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Amtixbio CO., LTD., Seoul 01411, Republic of Korea
| | - Byeong-Hyeon Cho
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Joonhee Chang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Xiaoyu Shi
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea.
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4
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Liu J, Ou Y, Xu JZ, Rao ZM, Zhang WG. L-lysine production by systems metabolic engineering of an NADPH auto-regulated Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2023; 387:129701. [PMID: 37604260 DOI: 10.1016/j.biortech.2023.129701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Here, the systems metabolic engineering of L-lysine-overproducing Corynebacterium glutamicum is described to create a highly efficient microorganism producer. The key chromosomal mutations associated with L-lysine synthesis were identified based on whole-genome sequencing. The carbon flux was subsequently redirected into the L-lysine synthesis pathway and increased the availability of energy and product transport systems required for L-lysine synthesis. In addition, a promoter library sensitive to intracellular L-lysine concentration was constructed and applied to regulate the NADPH pool dynamically. In the fed-batch fermentation experiment, the L-lysine titer of the final engineered strain was 223.4 ± 6.5 g/L. This study is the first to improve L-lysine production by enhancing ATP supply and NADPH self-regulation to improve the intracellular environment.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Ying Ou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China.
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Chen SL, Liu TS, Zhang WG, Xu JZ. Cofactor Engineering for Efficient Production of α-Farnesene by Rational Modification of NADPH and ATP Regeneration Pathway in Pichia pastoris. Int J Mol Sci 2023; 24:ijms24021767. [PMID: 36675279 PMCID: PMC9860691 DOI: 10.3390/ijms24021767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 01/18/2023] Open
Abstract
α-Farnesene, an acyclic volatile sesquiterpene, plays important roles in aircraft fuel, food flavoring, agriculture, pharmaceutical and chemical industries. Here, by re-creating the NADPH and ATP biosynthetic pathways in Pichia pastoris, we increased the production of α-farnesene. First, the native oxiPPP was recreated by overexpressing its essential enzymes or by inactivating glucose-6-phosphate isomerase (PGI). This revealed that the combined over-expression of ZWF1 and SOL3 increases α-farnesene production by improving NADPH supply, whereas inactivating PGI did not do so because it caused a reduction in cell growth. The next step was to introduce heterologous cPOS5 at various expression levels into P. pastoris. It was discovered that a low intensity expression of cPOS5 aided in the production of α-farnesene. Finally, ATP was increased by the overexpression of APRT and inactivation of GPD1. The resultant strain P. pastoris X33-38 produced 3.09 ± 0.37 g/L of α-farnesene in shake flask fermentation, which was 41.7% higher than that of the parent strain. These findings open a new avenue for the development of an industrial-strength α-farnesene producer by rationally modifying the NADPH and ATP regeneration pathways in P. pastoris.
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Wang J, Yang J, Shi G, Li W, Ju Y, Wei L, Liu J, Xu N. Transcriptome profiles of high-lysine adaptation reveal insights into osmotic stress response in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 10:933325. [PMID: 36017356 PMCID: PMC9395588 DOI: 10.3389/fbioe.2022.933325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/06/2022] [Indexed: 12/05/2022] Open
Abstract
Corynebacterium glutamicum has been widely and effectively used for fermentative production of l-lysine on an industrial scale. However, high-level accumulation of end products inevitably leads to osmotic stress and hinders further increase of l-lysine production. At present, the underlying mechanism by which C. glutamicum cells adapt to high-lysine-induced osmotic stress is still unclear. In this study, we conducted a comparative transcriptomic analysis by RNA-seq to determine gene expression profiles under different high-lysine stress conditions. The results indicated that the increased expression of some metabolic pathways such as sulfur metabolism and specific amino acid biosynthesis might offer favorable benefits for high-lysine adaptation. Functional assays of 18 representative differentially expressed genes showed that the enhanced expression of multiple candidate genes, especially grpE chaperon, conferred high-lysine stress tolerance in C. glutamicum. Moreover, DNA repair component MutT and energy-transducing NADH dehydrogenase Ndh were also found to be important for protecting cells against high-lysine-induced osmotic stress. Taken together, these aforementioned findings provide broader views of transcriptome profiles and promising candidate targets of C. glutamicum for the adaptation of high-lysine stress during fermentation.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Jian Yang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Guoxin Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Weidong Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Yun Ju
- School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Ning Xu,
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Moe A, Kovalova T, Król S, Yanofsky DJ, Bott M, Sjöstrand D, Rubinstein JL, Högbom M, Brzezinski P. The respiratory supercomplex from C. glutamicum. Structure 2021; 30:338-349.e3. [PMID: 34910901 DOI: 10.1016/j.str.2021.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022]
Abstract
Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, respiratory complexes III and IV form a CIII2CIV2 supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 Å resolution. The structure shows a central CIII2 dimer flanked by a CIV on two sides. A menaquinone is bound in each of the QN and QP sites in each CIII and an additional menaquinone is positioned ∼14 Å from heme bL. A di-heme cyt. cc subunit electronically connects each CIII with an adjacent CIV, with the Rieske iron-sulfur protein positioned with the iron near heme bL. Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a path for proton transfer into CIV.
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Affiliation(s)
- Agnes Moe
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Sylwia Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - David J Yanofsky
- Molecular Medicine Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, The University of Toronto, 1 Kings College Circle, Toronto, ON M5S 1A8, Canada.
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden.
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden.
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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