1
|
Sun Y, Zhou Y, Long Q, Xing J, Guo P, Liu Y, Zhang C, Zhang Y, Fernie AR, Shi Y, Luo Y, Luo J, Jin C. OsBCAT2, a gene responsible for the degradation of branched-chain amino acids, positively regulates salt tolerance by promoting the synthesis of vitamin B5. THE NEW PHYTOLOGIST 2024; 241:2558-2574. [PMID: 38258425 DOI: 10.1111/nph.19551] [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: 07/08/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Salt stress negatively affects rice growth, development and yield. Metabolic adjustments contribute to the adaptation of rice under salt stress. Branched-chain amino acids (BCAA) are three essential amino acids that cannot be synthesized by humans or animals. However, little is known about the role of BCAA in response to salt stress in plants. Here, we showed that BCAAs may function as scavengers of reactive oxygen species (ROS) to provide protection against damage caused by salinity. We determined that branched-chain aminotransferase 2 (OsBCAT2), a protein responsible for the degradation of BCAA, positively regulates salt tolerance. Salt significantly induces the expression of OsBCAT2 rather than BCAA synthesis genes, which indicated that salt mainly promotes BCAA degradation and not de novo synthesis. Metabolomics analysis revealed that vitamin B5 (VB5) biosynthesis pathway intermediates were higher in the OsBCAT2-overexpressing plants but lower in osbcat2 mutants under salt stress. The salt stress-sensitive phenotypes of the osbcat2 mutants are rescued by exogenous VB5, indicating that OsBCAT2 affects rice salt tolerance by regulating VB5 synthesis. Our work provides new insights into the enzymes involved in BCAAs degradation and VB5 biosynthesis and sheds light on the molecular mechanism of BCAAs in response to salt stress.
Collapse
Affiliation(s)
- Yangyang Sun
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
- Sanya Research Institute of Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Yutong Zhou
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Qiyuan Long
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Junwei Xing
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Peizhen Guo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yanchen Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Changjian Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Yuanyuan Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Yuheng Shi
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Yuehua Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| | - Jie Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Cheng Jin
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 570288, China
| |
Collapse
|
2
|
Tomonaga K, Tanaka J, Kiyoshi K, Akao T, Watanabe K, Kadokura T, Nakayama S. Physiological role of the EHL gene in sake yeast and its effects on quality of sake. J Biosci Bioeng 2024; 137:195-203. [PMID: 38242756 DOI: 10.1016/j.jbiosc.2023.12.001] [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: 09/19/2023] [Revised: 11/09/2023] [Accepted: 12/02/2023] [Indexed: 01/21/2024]
Abstract
The EHL1/2/3 genes were identified by whole-genome sequencing of Kyokai No. 7 (K7), which is a well-known representative Japanese sake yeast Saccharomyces cerevisiae. The genes are present in K7, but not in laboratory strain S288C. Although the genes were presumed to encode epoxide hydrolase based on homology analysis, their effect on cellular metabolism in sake yeast has not yet been clarified. We constructed ehl1/2/3 mutants harboring a stop codon in each gene using the haploid yeast strain H3 as the parental strain, which was derived from K701, and investigated the physiological role and effects of the EHL1/2/3 genes on sake quality. Metabolome analysis and vitamin requirement testing revealed that the EHL1/2/3 genes are partly responsible for the synthesis of pantothenate. For fermentation profiles, ethanol production by the ehl1/2/3 mutant was comparable with that of strain H3, but succinate production was decreased in the ehl1/2/3 mutant compared to strain H3 when cultured in yeast malt (YM) medium containing 10% glucose and during sake brewing. Ethyl hexanoate and isoamyl acetate levels in the ehl1/2/3 mutant strain were decreased compared to those of strain H3 during sake brewing. Thus, the EHL1/2/3 genes did not affect ethanol production but did affect the production of organic acids and aromatic components during sake brewing.
Collapse
Affiliation(s)
- Kazuko Tomonaga
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Jumpei Tanaka
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Keiji Kiyoshi
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Kota Watanabe
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Toshimori Kadokura
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunichi Nakayama
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
| |
Collapse
|
3
|
Chen C, Naveed H, Chen K. Research progress on branched-chain amino acid aminotransferases. Front Genet 2023; 14:1233669. [PMID: 38028625 PMCID: PMC10658711 DOI: 10.3389/fgene.2023.1233669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.
Collapse
Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| |
Collapse
|
4
|
Yoshimoto H, Bogaki T. Mechanisms of production and control of acetate esters in yeasts. J Biosci Bioeng 2023; 136:261-269. [PMID: 37607842 DOI: 10.1016/j.jbiosc.2023.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 08/24/2023]
Abstract
Acetate esters, such as isoamyl acetate and ethyl acetate, are major aroma components of alcoholic beverages. They are produced through synthesis from acetyl CoA and the corresponding alcohol by alcohol acetyltransferase (AATase) with specific control of reaction factors, including unsaturated fatty acids and precursors, the percentage of nitrogen, and oxygen. However, the mechanisms by which these specific reaction factors affect acetate ester production remain largely unknown. The cellular mechanisms underlying the effects of these factors on acetate ester production were examined by purifying AATase from yeast, characterizing it, and cloning the ATF gene encoding AATase from sake yeast and bottom-fermenting yeast. Genetic and biochemical studies suggested that the decrease in acetate production with the addition of oxygen and unsaturated fatty acids was due to a decrease in enzyme synthesis resulting from transcriptional repression of the ATF1 gene, which is responsible for most of the AATase activity. Furthermore, these results suggest that expression of the ATF1 gene is intricately regulated by a number of transcriptional regulatory genes such as ROX1 and RAP1. Based on these results, the mechanism of ester regulation by oxygen, unsaturated fatty acids and precursors, and ratio of nitrogen source are becoming clearer from a molecular biological point of view. The physiological significance of ester production by yeast is then discussed. In this review, we summarize the studies on AATase, ATF gene, regulation of ester production, and physiological significance of acetate ester.
Collapse
Affiliation(s)
- Hiroyuki Yoshimoto
- Institute for Future Beverages, Research & Development Division, Kirin Holdings Company Limited, Technovilleage Center 3F, 1-17-1 Namamugi, Tsurumi-ku, Yokohama, Kanagawa 236-8628, Japan.
| | - Takayuki Bogaki
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan
| |
Collapse
|
5
|
Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
Collapse
Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| |
Collapse
|
6
|
Lin CL, Petersen MA, Gottlieb A. Increasing Higher Alcohols and Acetates in Low-Alcohol Beer by Proteases. Molecules 2023; 28:molecules28114419. [PMID: 37298894 DOI: 10.3390/molecules28114419] [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: 04/05/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
The market of non-alcoholic and low-alcohol beer has grown continuously thanks to the advocacy for healthy and responsible drinking. Non-alcoholic and low-alcohol products usually possess less higher alcohols and acetates and more aldehyde off-flavors due to the manufacturing processes. The employment of non-conventional yeasts partially mitigates this problem. In this study, we used proteases to optimize the wort amino acid profile for better aroma production during yeast fermentation. The design of experiments was applied to increase the leucine molar fraction, aiming to boost 3-methylbutan-1-ol and 3-methylbutyl acetate (banana-like aromas). This led to an increase from 7% to 11% leucine in wort after protease treatment. The aroma output in the subsequent fermentation, however, was yeast-dependent. An 87% increase of 3-methylbutan-1-ol and a 64% increase of 3-methylbutyl acetate were observed when Saccharomycodes ludwigii was used. When Pichia kluyveri was employed, higher alcohols and esters from valine and isoleucine were increased: 58% more of 2-methylpropyl acetate, 67% more of 2-methylbutan-1-ol, and 24% more of 2-methylbutyl acetate were observed. Conversely, 3-methylbutan-1-ol decreased by 58% and 3-methylbutyl acetate largely remained the same. Apart from these, the amounts of aldehyde intermediates were increased to a varying extent. The impact of such increases in aromas and off-flavors on the perception of low-alcohol beer remains to be evaluated by sensory analysis in future studies.
Collapse
Affiliation(s)
- Claire Lin Lin
- Brewing AR 345, Novozymes A/S, Biologiensvej 2, 2800 Kongens Lyngby, Denmark
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Mikael Agerlin Petersen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Andrea Gottlieb
- Brewing AR 345, Novozymes A/S, Biologiensvej 2, 2800 Kongens Lyngby, Denmark
| |
Collapse
|
7
|
Yeast Protein Kinase A Isoforms: A Means of Encoding Specificity in the Response to Diverse Stress Conditions? Biomolecules 2022; 12:biom12070958. [PMID: 35883514 PMCID: PMC9313097 DOI: 10.3390/biom12070958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic cells have developed a complex circuitry of signalling molecules which monitor changes in their intra- and extracellular environments. One of the most widely studied signalling pathways is the highly conserved cyclic AMP (cAMP)/protein kinase A (PKA) pathway, which is a major glucose sensing circuit in the yeast Saccharomyces cerevisiae. PKA activity regulates diverse targets in yeast, positively activating the processes that are associated with rapid cell growth (e.g., fermentative metabolism, ribosome biogenesis and cell division) and negatively regulating the processes that are associated with slow growth, such as respiratory growth, carbohydrate storage and entry into stationary phase. As in higher eukaryotes, yeast has evolved complexity at the level of the PKA catalytic subunit, and Saccharomyces cerevisiae expresses three isoforms, denoted Tpk1-3. Despite evidence for isoform differences in multiple biological processes, the molecular basis of PKA signalling specificity remains poorly defined, and many studies continue to assume redundancy with regards to PKA-mediated regulation. PKA has canonically been shown to play a key role in fine-tuning the cellular response to diverse stressors; however, recent studies have now begun to interrogate the requirement for individual PKA catalytic isoforms in coordinating distinct steps in stress response pathways. In this review, we discuss the known non-redundant functions of the Tpk catalytic subunits and the evolving picture of how these isoforms establish specificity in the response to different stress conditions.
Collapse
|
8
|
The Effects of Catabolism Relationships of Leucine and Isoleucine with BAT2 Gene of Saccharomyces cerevisiae on High Alcohols and Esters. Genes (Basel) 2022; 13:genes13071178. [PMID: 35885961 PMCID: PMC9321263 DOI: 10.3390/genes13071178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/18/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
This study sought to provide a theoretical basis for effectively controlling the content of higher alcohols and esters in fermented foods. In this work, isoleucine (Ile) or leucine (Leu) at high levels was used as the sole nitrogen source for a BAT2 mutant and its parental Saccharomyces. cerevisiae 38 to investigate the effects of the addition of amounts of Ile or Leu and BAT2 on the aroma components in the flavor profile using gas chromatography mass spectrometer (GC-MS). The results showed that 2-methyl-butyraldehyde, 2-methyl-1-butanol, and 2-methylbutyl-acetate were the products positively correlated with the Ile addition amount. In addition, 3-methyl-butyraldehyde, 3-methyl-1-butanol, and 3-methylbutyl-acetate were the products positively correlated with Leu addition amount. BAT2 deletion resulted in a significant decline in the yields of 2-methyl-butyraldehyde, 3-methyl-butyraldehyde,2-methyl-1-butanol, and 3-methyl-1-butanol, but also an increase in the yields of 2-methylbutyl-acetate and 3-methylbutyl-acetate. We speculated that BAT2 regulated the front and end of this metabolite chain in a feedback manner. Improved metabolic chain analyses, including the simulated energy metabolism of Ile or Leu, indicated that reducing the added amount of branched-chain amino acids, BAT mutation, and eliminating the role of energy cofactors such as NADH/NAD+ were three important ways to control the content of high alcohols and esters in fermented foods.
Collapse
|
9
|
Improvement of Fusel Alcohol Production by Engineering of the Yeast Branched-Chain Amino Acid Aminotransaminase. Appl Environ Microbiol 2022; 88:e0055722. [PMID: 35699439 PMCID: PMC9275217 DOI: 10.1128/aem.00557-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Branched-chain higher alcohols (BCHAs), or fusel alcohols, including isobutanol, isoamyl alcohol, and active amyl alcohol, are useful compounds in several industries. The yeast Saccharomyces cerevisiae can synthesize these compounds via the metabolic pathways of branched-chain amino acids (BCAAs). Branched-chain amino acid aminotransaminases (BCATs) are the key enzymes for BCHA production via the Ehrlich pathway of BCAAs. BCATs catalyze a bidirectional transamination reaction between branched-chain α-keto acids (BCKAs) and BCAAs. In S. cerevisiae, there are two BCAT isoforms, Bat1 and Bat2, which are encoded by the genes BAT1 and BAT2. Although many studies have shown the effects of deletion or overexpression of BAT1 and BAT2 on BCHA production, there have been no reports on the enhancement of BCHA production by functional variants of BCATs. Here, to improve BCHA productivity, we designed variants of Bat1 and Bat2 with altered enzyme activity by using in silico computational analysis: the Gly333Ser and Gly333Trp Bat1 and corresponding Gly316Ser and Gly316Trp Bat2 variants, respectively. When expressed in S. cerevisiae cells, most of these variants caused a growth defect in minimal medium. Interestingly, the Gly333Trp Bat1 and Gly316Ser Bat2 variants achieved 18.7-fold and 17.4-fold increases in isobutanol above that for the wild-type enzyme, respectively. The enzyme assay revealed that the catalytic activities of all four BCAT variants were lower than that of the wild-type enzyme. Our results indicate that the decreased BCAT activity enhanced BCHA production by reducing BCAA biosynthesis, which occurs via a pathway that directly competes with BCHA production. IMPORTANCE Recently, several studies have attempted to increase the production of branched-chain higher alcohols (BCHAs) in the yeast Saccharomyces cerevisiae. The key enzymes for BCHA biosynthesis in S. cerevisiae are the branched-chain amino acid aminotransaminases (BCATs) Bat1 and Bat2. Deletion or overexpression of the genes encoding BCATs has an impact on the production of BCHAs; however, amino acid substitution variants of Bat1 and Bat2 that could affect enzymatic properties—and ultimately BCHA productivity—have not been fully studied. By using in silico analysis, we designed variants of Bat1 and Bat2 and expressed them in yeast cells. We found that the engineered BCATs decreased catalytic activities and increased BCHA production. Our approach provides new insight into the functions of BCATs and will be useful in the future construction of enzymes optimized for high-level production of BCHAs.
Collapse
|
10
|
Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans. mBio 2021; 12:e0076821. [PMID: 34154419 PMCID: PMC8262921 DOI: 10.1128/mbio.00768-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fungi, bacteria, and plants, but not animals, synthesize the branched-chain amino acids: leucine, isoleucine, and valine. While branched-chain amino acid (BCAA) biosynthesis has been well characterized in the yeast Saccharomyces cerevisiae, it is incompletely understood in filamentous fungi. The three BCAAs share several early biosynthesis steps before divergence into specific pathways. In Aspergillus nidulans, the genes for the first two dedicated steps in leucine biosynthesis have been characterized, but the final two have not. We used sequence searches of the A. nidulans genome to identify two genes encoding β-isopropylmalate dehydrogenase, which catalyzes the penultimate step of leucine biosynthesis, and six genes encoding BCAA aminotransferase, which catalyzes the final step in biosynthesis of all three BCAA. We have used combinations of gene knockouts to determine the relative contribution of each of these genes to BCAA biosynthesis. While both β-isopropylmalate dehydrogenase genes act in leucine biosynthesis, the two most highly expressed BCAA aminotransferases are responsible for BCAA biosynthesis. We have also characterized the expression of leucine biosynthesis genes using reverse transcriptase-quantitative PCR and found regulation in response to leucine availability is mediated through the Zn(II)2Cys6 transcription factor LeuB. IMPORTANCE Branched-chain amino acid (BCAA) biosynthesis is important for pathogenic fungi to successfully cause disease in human and plant hosts. The enzymes for their production are absent from humans and, therefore, provide potential antifungal targets. While BCAA biosynthesis is well characterized in yeasts, it is poorly understood in filamentous fungal pathogens. Developing a thorough understanding of both the genes encoding the metabolic enzymes for BCAA biosynthesis and how their expression is regulated will inform target selection for antifungal drug development.
Collapse
|
11
|
Porras-Agüera JA, Moreno-García J, García-Martínez T, Moreno J, Mauricio JC. Impact of CO 2 overpressure on yeast mitochondrial associated proteome during the "prise de mousse" of sparkling wine production. Int J Food Microbiol 2021; 348:109226. [PMID: 33964807 DOI: 10.1016/j.ijfoodmicro.2021.109226] [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: 12/16/2020] [Revised: 04/07/2021] [Accepted: 04/25/2021] [Indexed: 11/25/2022]
Abstract
The "prise de mousse" stage during sparkling wine elaboration by the traditional method (Champenoise) involves a second fermentation in a sealed bottle followed by a prolonged aging period, known to contribute significantly to the unique organoleptic properties of these wines. During this stage, CO2 overpressure, nutrient starvation and high ethanol concentrations are stress factors that affect yeast cells viability and metabolism. Since mitochondria are responsible for energy generation and are required for cell aging and response to numerous stresses, we hypothesized that these organelles may play an essential role during the prise de mousse. The objective of this study is to characterize the mitochondrial response of a Saccharomyces cerevisiae strain traditionally used in sparkling wine production along the "prise de mousse" and study the effect of CO2 overpressure through a proteomic analysis. We observed that pressure negatively affects the content of mitochondrion-related proteome, especially to those proteins involved in tricarboxylic acid cycle. However, proteins required for the branched-amino acid synthesis, implied in wine aromas, and respiratory chain, also previously reported by transcriptomic analyses, were found over-represented in the sealed bottles. Multivariate analysis of proteins required for tricarboxylic cycle, respiratory chain and amino acid metabolism revealed differences in concentrations, allowing the wine samples to group depending on the time and CO2 overpressure parameters. Ethanol content along the second fermentation could be the main reason for this changing behavior observed at proteomic level. Further research including genetic studies, determination of ROS, characterization of mitochondrial activity and targeted metabolomics analyses is required. The list of mitochondrial proteins provided in this work will lead to a better understanding of the yeast behavior under these conditions of special interest in the wine industry.
Collapse
Affiliation(s)
- Juan Antonio Porras-Agüera
- Department of Agricultural Chemistry, Edaphology and Microbiology, Severo Ochoa (C6) building, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Ctra. N-IV-A mm 396, 14014 Cordoba, Spain.
| | - Jaime Moreno-García
- Department of Agricultural Chemistry, Edaphology and Microbiology, Severo Ochoa (C6) building, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Ctra. N-IV-A mm 396, 14014 Cordoba, Spain.
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Severo Ochoa (C6) building, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Ctra. N-IV-A mm 396, 14014 Cordoba, Spain.
| | - Juan Moreno
- Department of Agricultural Chemistry, Edaphology and Microbiology, Severo Ochoa (C6) building, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Ctra. N-IV-A mm 396, 14014 Cordoba, Spain.
| | - Juan Carlos Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Severo Ochoa (C6) building, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Ctra. N-IV-A mm 396, 14014 Cordoba, Spain.
| |
Collapse
|
12
|
Autophagy sustains glutamate and aspartate synthesis in Saccharomyces cerevisiae during nitrogen starvation. Nat Commun 2021; 12:57. [PMID: 33397945 PMCID: PMC7782722 DOI: 10.1038/s41467-020-20253-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/20/2020] [Indexed: 01/29/2023] Open
Abstract
Autophagy catabolizes cellular constituents to promote survival during nutrient deprivation. Yet, a metabolic comprehension of this recycling operation, despite its crucial importance, remains incomplete. Here, we uncover a specific metabolic function of autophagy that exquisitely adjusts cellular metabolism according to nitrogen availability in the budding yeast Saccharomyces cerevisiae. Autophagy enables metabolic plasticity to promote glutamate and aspartate synthesis, which empowers nitrogen-starved cells to replenish their nitrogen currency and sustain macromolecule synthesis. Our findings provide critical insights into the metabolic basis by which autophagy recycles cellular components and may also have important implications in understanding the role of autophagy in diseases such as cancer.
Collapse
|
13
|
Li F, Yang G, Tachikawa H, Shao K, Yang Y, Gao XD, Nakanishi H. Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT. J GEN APPL MICROBIOL 2020; 67:33-41. [PMID: 33229814 DOI: 10.2323/jgam.2020.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
O-GlcNAc modification mediated by O-GlcNAc transferase (OGT) is a reversible protein modification in which O-GlcNAc moieties are attached to target proteins in the cytosol, nucleus, and mitochondria. O-GlcNAc moieties attached to proteins can be removed by O-GlcNAcase (OGA). The addition of an O-GlcNAc moiety can influence several aspects of protein function, and aberrant O-GlcNAc modification is linked to a number of diseases. While OGT and OGA are conserved across eukaryotic cells, yeasts lack these enzymes. Previously, we reported that protein O-GlcNAc modification occurred in the budding yeast Saccharomyces cerevisiae when OGT was ectopically expressed. Because yeast cells lack OGA, O-GlcNAc moieties are stably attached to target proteins. Thus, the yeast system may be useful for finding novel OST substrates. By proteomic analysis, we identified 468 O-GlcNAcylated proteins in yeast cells expressing human OGT. Among these proteins, 13 have human orthologues that show more than 30% identity to their corresponding yeast orthologue, and possible glycosylation residues are conserved in these human orthologues. In addition, the orthologues have not been reported as substrates of OGT. We verified that some of these human orthologues are O-GlcNAcylated in cultured human cells. These proteins include an ubiquitin-conjugating enzyme, UBE2D1, and an eRF3-similar protein, HBS1L. Thus, the yeast system would be useful to find previously unknown O-GlcNAcylated proteins and regulatory mechanisms.
Collapse
Affiliation(s)
- Feng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Ganglong Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Hiroyuki Tachikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Kankai Shao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Yan Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| |
Collapse
|
14
|
Effect of the Deletion of Genes Related to Amino Acid Metabolism on the Production of Higher Alcohols by Saccharomyces cerevisiae. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6802512. [PMID: 33204707 PMCID: PMC7665916 DOI: 10.1155/2020/6802512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/27/2020] [Accepted: 10/24/2020] [Indexed: 11/17/2022]
Abstract
The higher alcohols produced by Saccharomyces cerevisiae exert remarkable influence on the taste and flavour of Chinese Baijiu. In order to study the regulation mechanism of amino acid metabolism genes on higher alcohol production, eight recombinant strains with amino acid metabolism gene deletion were constructed. The growth, fermentation performance, higher alcohol production, and expression level of genes in recombinant and original α5 strains were determined. Results displayed that the total higher alcohol concentration in α5ΔGDH1 strain decreased by 27.31% to 348.68 mg/L compared with that of α5. The total content of higher alcohols in α5ΔCAN1 and α5ΔGAT1 strains increased by 211.44% and 28.36% to 1493.96 and 615.73 mg/L, respectively, compared with that of α5. This study is the first to report that the CAN1 and GAT1 genes have great influence on the generation of higher alcohols. The results demonstrated that amino acid metabolism plays a substantial role in the metabolism of higher alcohols by S. cerevisiae. Interestingly, we also found that gene knockout downregulated the expression levels of the knocked out gene and other genes in the recombinant strain and thus affected the formation of higher alcohols by S. cerevisiae. This study provides worthy insights for comprehending the metabolic mechanism of higher alcohols in S. cerevisiae for Baijiu fermentation.
Collapse
|
15
|
Medici V, Sarode GV, Napoli E, Song GY, Shibata NM, Guimarães AO, Mordaunt CE, Kieffer DA, Mazi TA, Czlonkowska A, Litwin T, LaSalle JM, Giulivi C. mtDNA depletion-like syndrome in Wilson disease. Liver Int 2020; 40:2776-2787. [PMID: 32996699 PMCID: PMC8079140 DOI: 10.1111/liv.14646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Wilson disease (WD) is caused by mutations in the copper transporter ATP7B, with its main pathology attributed to copper-mediated oxidative damage. The limited therapeutic effect of copper chelators and the early occurrence of mitochondrial deficits, however, undermine the prevalence of this mechanism. METHODS We characterized mitochondrial DNA copy number and mutations as well as bioenergetic deficits in blood from patients with WD and in livers of tx-j mice, a mouse model of hepatic copper accumulation. In vitro experiments with hepatocytes treated with CuSO4 were conducted to validate in vivo studies. RESULTS Here, for the first time, we characterized the bioenergetic deficits in WD as consistent with a mitochondrial DNA depletion-like syndrome. This is evidenced by enriched DNA synthesis/replication pathways in serum metabolomics and decreased mitochondrial DNA copy number in blood of WD patients as well as decreased mitochondrial DNA copy number, increased citrate synthase activity, and selective Complex IV deficit in livers of the tx-j mouse model of WD. Tx-j mice treated with the copper chelator penicillamine, methyl donor choline or both ameliorated mitochondrial DNA damage but further decreased mitochondrial DNA copy number. Experiments with copper-loaded HepG2 cells validated the concept of a direct copper-mitochondrial DNA interaction. CONCLUSIONS This study underlines the relevance of targeting the copper-mitochondrial DNA pool in the treatment of WD separate from the established copper-induced oxidative stress-mediated damage.
Collapse
Affiliation(s)
- Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616,Correspondence: Authors share co-senior authorship, Valentina Medici, M.D., Professor, University of California Davis, Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, Sacramento, California 95817, ; Cecilia Giulivi, Ph.D., Professor, University of California Davis, Department of Molecular Biosciences, School of Veterinary Medicine, Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 1089 Veterinary Dr., 3017 Vet Med 3B, Davis, California 95616,
| | - Gaurav Vilas Sarode
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616
| | - Gyu-Young Song
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616
| | - Noreene M. Shibata
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Andre Oliveira Guimarães
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616,Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ, Brazil
| | - Charles E. Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817
| | - Dorothy A. Kieffer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, University of California Davis, Sacramento, CA 95616
| | - Tagreed A. Mazi
- Department of Nutrition, University of California Davis, Davis, CA 95616,Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anna Czlonkowska
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Tomasz Litwin
- Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, 1089 Veterinary Medicine Drive, University of California Davis, Davis, CA 95616,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 2825 50 St, University of California Davis, Davis, CA 95817,Correspondence: Authors share co-senior authorship, Valentina Medici, M.D., Professor, University of California Davis, Department of Internal Medicine, Division of Gastroenterology and Hepatology, 4150 V Street, PSSB Suite 3500, Sacramento, California 95817, ; Cecilia Giulivi, Ph.D., Professor, University of California Davis, Department of Molecular Biosciences, School of Veterinary Medicine, Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, 1089 Veterinary Dr., 3017 Vet Med 3B, Davis, California 95616,
| |
Collapse
|
16
|
Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Appl Microbiol Biotechnol 2020; 104:7915-7925. [PMID: 32776205 DOI: 10.1007/s00253-020-10800-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.
Collapse
|
17
|
Understanding and Eliminating the Detrimental Effect of Thiamine Deficiency on the Oleaginous Yeast Yarrowia lipolytica. Appl Environ Microbiol 2020; 86:AEM.02299-19. [PMID: 31704686 DOI: 10.1128/aem.02299-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Thiamine is a vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism in all living cells. While most plants, fungi, and bacteria can synthesize thiamine de novo, the oleaginous yeast Yarrowia lipolytica cannot. In this study, we used proteomics together with physiological characterization to elucidate key metabolic processes influenced and regulated by thiamine availability and to identify the genetic basis of thiamine auxotrophy in Y. lipolytica Specifically, we found that thiamine depletion results in decreased protein abundance for the lipid biosynthesis pathway and energy metabolism (i.e., ATP synthase), leading to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (THI13) gene for the de novo thiamine biosynthesis in Y. lipolytica and discovered an exceptional promoter, P3, that exhibits strong activation and tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene from Saccharomyces cerevisiae (scTHI13), we engineered a thiamine-prototrophic Y. lipolytica strain. By comparing this engineered strain to the wild-type strain, we revealed the tight relationship between thiamine availability and lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophic Y. lipolytica strain.IMPORTANCE Thiamine plays a crucial role as an essential cofactor for enzymes involved in carbon and energy metabolism in all living cells. Thiamine deficiency has detrimental consequences for cellular health. Yarrowia lipolytica, a nonconventional oleaginous yeast with broad biotechnological applications, is a native thiamine auxotroph whose affected cellular metabolism is not well understood. Therefore, Y. lipolytica is an ideal eukaryotic host for the study of thiamine metabolism, especially because mammalian cells are also thiamine auxotrophic and thiamine deficiency is implicated in several human diseases. This study elucidates the fundamental effects of thiamine deficiency on cellular metabolism in Y. lipolytica and identifies genes and novel thiamine-regulated elements that eliminate thiamine auxotrophy in Y. lipolytica Furthermore, the discovery of thiamine-regulated elements enables the development of thiamine biosensors with useful applications in synthetic biology and metabolic engineering.
Collapse
|
18
|
Tokpohozin SE, Fischer S, Becker T. Selection of a new Saccharomyces yeast to enhance relevant sorghum beer aroma components, higher alcohols and esters. Food Microbiol 2019; 83:181-186. [DOI: 10.1016/j.fm.2019.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/14/2022]
|
19
|
Que Y, Yue X, Yang N, Xu Z, Tang S, Wang C, Lv W, Xu L, Talbot NJ, Wang Z. Leucine biosynthesis is required for infection-related morphogenesis and pathogenicity in the rice blast fungus Magnaporthe oryzae. Curr Genet 2019; 66:155-171. [PMID: 31263943 DOI: 10.1007/s00294-019-01009-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
The rice blast fungus Magnaporthe oryzae causes one of the most devastating crop diseases world-wide and new control strategies for blast disease are urgently required. We have used insertional mutagenesis in M. oryzae to define biological processes that are critical for blast disease. Here, we report the identification of LEU2A by T-DNA mutagenesis, which putatively encodes 3-isopropylmalate dehydrogenase (3-IPMDH) required for leucine biosynthesis, implicating that synthesis of this amino acid is required for fungal pathogenesis. M. oryzae contains a further predicted 3-IPMDH gene (LEU2B), two 2-isopropylmalate synthase (2-IPMS) genes (LEU4 and LEU9) and an isopropylmalate isomerase (IPMI) gene (LEU1). Targeted gene deletion mutants of LEU1, LEU2A or LEU4 are leucine auxotrophs, and severely defective in pathogenicity. All phenotypes associated with mutants lacking LEU1, LEU2A or LEU4 could be overcome by adding exogenous leucine. The expression levels of LEU1, LEU2A or LEU4 genes were significantly down-regulated by deletion of the transcription factor gene LEU3, an ortholog of Saccharomyces cerevisiae LEU3. We also functionally characterized leucine biosynthesis genes in the wheat pathogen Fusarium graminearum and found that FgLEU1, FgLEU3 and FgLEU4 are essential for wheat head blight disease, suggesting that leucine biosynthesis in filamentous fungal pathogens may be a conserved factor for fungal pathogenicity and, therefore, a potential target for disease control.
Collapse
Affiliation(s)
- Yawei Que
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaofeng Yue
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Nan Yang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhe Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Shuai Tang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Chunyan Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Wuyun Lv
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Lin Xu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Nicholas J Talbot
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| |
Collapse
|
20
|
Daghino S, Di Vietro L, Petiti L, Martino E, Dallabona C, Lodi T, Perotto S. Yeast expression of mammalian Onzin and fungal FCR1 suggests ancestral functions of PLAC8 proteins in mitochondrial metabolism and DNA repair. Sci Rep 2019; 9:6629. [PMID: 31036870 PMCID: PMC6488628 DOI: 10.1038/s41598-019-43136-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/11/2019] [Indexed: 01/07/2023] Open
Abstract
The cysteine-rich PLAC8 domain of unknown function occurs in proteins found in most Eukaryotes. PLAC8-proteins play important yet diverse roles in different organisms, such as control of cell proliferation in animals and plants or heavy metal resistance in plants and fungi. Mammalian Onzin can be either pro-proliferative or pro-apoptotic, depending on the cell type, whereas fungal FCR1 confers cadmium tolerance. Despite their different role in different organisms, we hypothesized common ancestral functions linked to the PLAC8 domain. To address this hypothesis, and to investigate the molecular function of the PLAC8 domain, murine Onzin and fungal FCR1 were expressed in the PLAC8-free yeast Saccharomyces cerevisiae. The two PLAC8-proteins localized in the nucleus and induced almost identical phenotypes and transcriptional changes when exposed to cadmium stress. Like FCR1, Onzin also reduced DNA damage and increased cadmium tolerance by a DUN1-dependent pathway. Both proteins activated transcription of ancient mitochondrial pathways such as leucine and Fe-S cluster biosynthesis, known to regulate cell proliferation and DNA repair in yeast. These results strongly suggest a common ancestral function of PLAC8 proteins and open new perspectives to understand the role of the PLAC8 domain in the cellular biology of Eukaryotes.
Collapse
Affiliation(s)
- Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Luigi Di Vietro
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy.,Department of Biochemistry and Biotechnology, Bayer SAS, centre de recherche "la Dargoire" 14, impasse Pierre Baizet CS 99163, 69263, Lyon, CEDEX 09, France
| | - Luca Petiti
- Italian Institute for Genomic Medicine, via Nizza 52, 10126, Torino, Italy
| | - Elena Martino
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A, 43124, Parma, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A, 43124, Parma, Italy
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125, Torino, Italy.
| |
Collapse
|
21
|
Malina C, Larsson C, Nielsen J. Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res 2019; 18:4969682. [PMID: 29788060 DOI: 10.1093/femsyr/foy040] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
Collapse
Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| |
Collapse
|
22
|
Overexpression of branched-chain amino acid aminotransferases rescues the growth defects of cells lacking the Barth syndrome-related gene TAZ1. J Mol Med (Berl) 2019; 97:269-279. [PMID: 30604168 DOI: 10.1007/s00109-018-1728-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/23/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
Abstract
The yeast protein Taz1 is the orthologue of human Tafazzin, a phospholipid acyltransferase involved in cardiolipin (CL) remodeling via a monolyso CL (MLCL) intermediate. Mutations in Tafazzin lead to Barth syndrome (BTHS), a metabolic and neuromuscular disorder that primarily affects the heart, muscles, and immune system. Similar to observations in fibroblasts and platelets from patients with BTHS or from animal models, abolishing yeast Taz1 results in decreased total CL amounts, increased levels of MLCL, and mitochondrial dysfunction. However, the biochemical mechanisms underlying the mitochondrial dysfunction in BTHS remain unclear. To better understand the pathomechanism of BTHS, we searched for multi-copy suppressors of the taz1Δ growth defect in yeast cells. We identified the branched-chain amino acid transaminases (BCATs) Bat1 and Bat2 as such suppressors. Similarly, overexpression of the mitochondrial isoform BCAT2 in mammalian cells lacking TAZ improves their growth. Elevated levels of Bat1 or Bat2 did not restore the reduced membrane potential, altered stability of respiratory complexes, or the defective accumulation of MLCL species in yeast taz1Δ cells. Importantly, supplying yeast or mammalian cells lacking TAZ1 with certain amino acids restored their growth behavior. Hence, our findings suggest that the metabolism of amino acids has an important and disease-relevant role in cells lacking Taz1 function. KEY MESSAGES: Bat1 and Bat2 are multi-copy suppressors of retarded growth of taz1Δ yeast cells. Overexpression of Bat1/2 in taz1Δ cells does not rescue known mitochondrial defects. Supplementation of amino acids enhances growth of cells lacking Taz1 or Tafazzin. Altered metabolism of amino acids might be involved in the pathomechanism of BTSH.
Collapse
|
23
|
Wess J, Brinek M, Boles E. Improving isobutanol production with the yeast Saccharomyces cerevisiae by successively blocking competing metabolic pathways as well as ethanol and glycerol formation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:173. [PMID: 31303893 PMCID: PMC6604370 DOI: 10.1186/s13068-019-1486-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/07/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Isobutanol is a promising candidate as second-generation biofuel and has several advantages compared to bioethanol. Another benefit of isobutanol is that it is already formed as a by-product in fermentations with the yeast Saccharomyces cerevisiae, although only in very small amounts. Isobutanol formation results from valine degradation in the cytosol via the Ehrlich pathway. In contrast, valine is synthesized from pyruvate in mitochondria. This spatial separation into two different cell compartments is one of the limiting factors for higher isobutanol production in yeast. Furthermore, some intermediate metabolites are also substrates for various isobutanol competing pathways, reducing the metabolic flux toward isobutanol production. We hypothesized that a relocation of all enzymes involved in anabolic and catabolic reactions of valine metabolism in only one cell compartment, the cytosol, in combination with blocking non-essential isobutanol competing pathways will increase isobutanol production in yeast. RESULTS Here, we overexpressed the three endogenous enzymes acetolactate synthase (Ilv2), acetohydroxyacid reductoisomerase (Ilv5) and dihydroxy-acid dehydratase (Ilv3) of the valine synthesis pathway in the cytosol and blocked the first step of mitochondrial valine synthesis by disrupting endogenous ILV2, leading to a 22-fold increase of isobutanol production up to 0.22 g/L (5.28 mg/g glucose) with aerobic shake flask cultures. Then, we successively deleted essential genes of competing pathways for synthesis of 2,3-butanediol (BDH1 and BDH2), leucine (LEU4 and LEU9), pantothenate (ECM31) and isoleucine (ILV1) resulting in an optimized metabolic flux toward isobutanol and titers of up to 0.56 g/L (13.54 mg/g glucose). Reducing ethanol formation by deletion of the ADH1 gene encoding the major alcohol dehydrogenase did not result in further increased isobutanol production, but in strongly enhanced glycerol formation. Nevertheless, deletion of glycerol-3-phosphate dehydrogenase genes GPD1 and GPD2 prevented formation of glycerol and increased isobutanol production up to 1.32 g/L. Finally, additional deletion of aldehyde dehydrogenase gene ALD6 reduced the synthesis of the by-product isobutyrate, thereby further increasing isobutanol production up to 2.09 g/L with a yield of 59.55 mg/g glucose, corresponding to a more than 200-fold increase compared to the wild type. CONCLUSIONS By overexpressing a cytosolic isobutanol synthesis pathway and by blocking non-essential isobutanol competing pathways, we could achieve isobutanol production with a yield of 59.55 mg/g glucose, which is the highest yield ever obtained with S. cerevisiae in shake flask cultures. Nevertheless, our results indicate a still limiting capacity of the isobutanol synthesis pathway itself.
Collapse
Affiliation(s)
- Johannes Wess
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Martin Brinek
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| |
Collapse
|
24
|
Optimization of malting conditions for two landraces of West African sorghum and influence of mash bio-acidification on saccharification improvement. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
25
|
Martins TS, Costa V, Pereira C. Signaling pathways governing iron homeostasis in budding yeast. Mol Microbiol 2018; 109:422-432. [DOI: 10.1111/mmi.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Telma S. Martins
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
| | - Vítor Costa
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
| | - Clara Pereira
- I3S-Instituto de Investigação e Inovação em Saúde; Universidade do Porto; Porto Portugal
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto; Porto Portugal
| |
Collapse
|
26
|
Querol A, Pérez-Torrado R, Alonso-Del-Real J, Minebois R, Stribny J, Oliveira BM, Barrio E. New Trends in the Uses of Yeasts in Oenology. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 85:177-210. [PMID: 29860974 DOI: 10.1016/bs.afnr.2018.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The most important factor in winemaking is the quality of the final product and the new trends in oenology are dictated by wine consumers and producers. Traditionally the red wine is the most consumed and more popular; however, in the last times, the wine companies try to attract other groups of populations, especially young people and women that prefer sweet, whites or rosé wines, very fruity and with low alcohol content. Besides the new trends in consumer preferences, there are also increased concerns on the effects of alcohol consumption on health and the effects of global climate change on grape ripening and wine composition producing wines with high alcohol content. Although S. cerevisiae is the most frequent species in wines, and the subject of most studies, S. uvarum and hybrids between Saccharomyces species such as S. cerevisiae×S. kudriavzevii and S. cerevisiae×S. uvarum are also involved in wine fermentations and can be preponderant in certain wine regions. New yeast starters of non-cerevisiae strains (S. uvarum) or hybrids (S. cerevisiae×S. uvarum and S. cerevisiae×S. kudriavzevii) can contribute to solve some problems of the wineries. They exhibit good fermentative capabilities at low temperatures, producing wines with lower alcohol and higher glycerol amounts, while fulfilling the requirements of the commercial yeasts, such as a good fermentative performance and aromatic profiles that are of great interest for the wine industry. In this review, we will analyze different applications of nonconventional yeasts to solve the current winemaking demands.
Collapse
Affiliation(s)
- Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Jiri Stribny
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Bruno M Oliveira
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain; Departament de Genètica, Universitat de València, Valencia, Spain
| |
Collapse
|
27
|
Petersen EE, Margaritis A, Stewart RJ, Pilkington PH, Mensour NA. The Effects of Wort Valine Concentration on the Total Diacetyl Profile and Levels Late in Batch Fermentations with Brewing YeastSaccharomyces Carlsbergensis. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-62-0131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Erin E. Petersen
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London N6A 5B9, Ontario, Canada
| | - Argyrios Margaritis
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London N6A 5B9, Ontario, Canada
| | - Robert J. Stewart
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
| | - P. Heather Pilkington
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
| | - Normand A. Mensour
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
| |
Collapse
|
28
|
Kodama Y, Omura F, Miyajima K, Ashikari T. Control of Higher Alcohol Production by Manipulation of theBAP2Gene in Brewing Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-59-0157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yukiko Kodama
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Fumihiko Omura
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Keiji Miyajima
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Toshihiko Ashikari
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| |
Collapse
|
29
|
Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng 2017; 44:302-312. [DOI: 10.1016/j.ymben.2017.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022]
|
30
|
Efficient protein production by yeast requires global tuning of metabolism. Nat Commun 2017; 8:1131. [PMID: 29070809 PMCID: PMC5656615 DOI: 10.1038/s41467-017-00999-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/09/2017] [Indexed: 01/20/2023] Open
Abstract
The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion. The contribution of metabolic pathways to protein secretion is largely unknown. Here, the authors find conserved metabolic patterns in yeast by examining genome-wide transcriptional responses in high protein secretion mutants and reveal critical factors that can be tuned for efficient protein secretion.
Collapse
|
31
|
Diversification of Transcriptional Regulation Determines Subfunctionalization of Paralogous Branched Chain Aminotransferases in the Yeast Saccharomyces cerevisiae. Genetics 2017; 207:975-991. [PMID: 28912343 DOI: 10.1534/genetics.117.300290] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae harbors BAT1 and BAT2 paralogous genes that encode branched chain aminotransferases and have opposed expression profiles and physiological roles . Accordingly, in primary nitrogen sources such as glutamine, BAT1 expression is induced, supporting Bat1-dependent valine-isoleucine-leucine (VIL) biosynthesis, while BAT2 expression is repressed. Conversely, in the presence of VIL as the sole nitrogen source, BAT1 expression is hindered while that of BAT2 is activated, resulting in Bat2-dependent VIL catabolism. The presented results confirm that BAT1 expression is determined by transcriptional activation through the action of the Leu3-α-isopropylmalate (α-IPM) active isoform, and uncovers the existence of a novel α-IPM biosynthetic pathway operating in a put3Δ mutant grown on VIL, through Bat2-Leu2-Leu1 consecutive action. The classic α-IPM biosynthetic route operates in glutamine through the action of the leucine-sensitive α-IPM synthases. The presented results also show that BAT2 repression in glutamine can be alleviated in a ure2Δ mutant or through Gcn4-dependent transcriptional activation. Thus, when S. cerevisiae is grown on glutamine, VIL biosynthesis is predominant and is preferentially achieved through BAT1; while on VIL as the sole nitrogen source, catabolism prevails and is mainly afforded by BAT2.
Collapse
|
32
|
Li J, Feng R, Wen Z, Zhang A. Overexpression of ARO10 in pdc5Δmutant resulted in higher isobutanol titers in Saccharomyces cerevisiae. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0028-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Bereketoglu C, Arga KY, Eraslan S, Mertoglu B. Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure. Physiol Genomics 2017; 49:549-566. [PMID: 28887370 DOI: 10.1152/physiolgenomics.00034.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/17/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023] Open
Abstract
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a nonionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/l; <15% cell number reduction) and high (5 mg/l; >65% cell number reduction) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/l NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed. Similarly, 678 (168 repressed, 510 induced) and 688 genes (215 repressed, 473 induced) were differentially expressed in cells exposed to 5 mg/l NP for 120 and 180 min, respectively. Only 15 downregulated and 63 upregulated genes were common between low and high NP inhibitory concentration exposure for 120 min, whereas 16 downregulated and 31 upregulated genes were common after the 180-min exposure. Several processes/pathways were prominently affected by either low or high inhibitory concentration exposure, while certain processes were affected by both inhibitory concentrations, including ion transport, response to chemicals, transmembrane transport, cellular amino acids, and carbohydrate metabolism. While minimal expression changes were observed with low inhibitory concentration exposure, 5 mg/l NP treatment induced substantial expression changes in genes involved in oxidative phosphorylation, cell wall biogenesis, ribosomal biogenesis, and RNA processing, and encoding heat shock proteins and ubiquitin-conjugating enzymes. Collectively, these results provide considerable information on effects of NP at the molecular level.
Collapse
Affiliation(s)
- Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey; .,Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University; Baglarbasi, Gumushane, Turkey; and
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| | - Serpil Eraslan
- Department of Chemical Engineering, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| |
Collapse
|
34
|
Dzialo MC, Park R, Steensels J, Lievens B, Verstrepen KJ. Physiology, ecology and industrial applications of aroma formation in yeast. FEMS Microbiol Rev 2017; 41:S95-S128. [PMID: 28830094 PMCID: PMC5916228 DOI: 10.1093/femsre/fux031] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023] Open
Abstract
Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.
Collapse
Affiliation(s)
- Maria C Dzialo
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Rahel Park
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A B-2860 Sint-Katelijne Waver, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| |
Collapse
|
35
|
Regulation of Saccharomyces cerevisiae genetic engineering on the production of acetate esters and higher alcohols during Chinese Baijiu fermentation. J Ind Microbiol Biotechnol 2017; 44:949-960. [PMID: 28176138 DOI: 10.1007/s10295-017-1907-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Acetate esters and higher alcohols greatly influence the quality and flavor profiles of Chinese Baijiu (Chinese liquor). Various mutants have been constructed to investigate the interactions of ATF1 overexpression, IAH1 deletion, and BAT2 deletion on the production of acetate esters and higher alcohols. The results showed that the overexpression of ATF1 under the control of the PGK1 promoter with BAT2 and IAH1 double-gene deletion led to a higher production of acetate esters and a lower production of higher alcohols than the overexpression of ATF1 with IAH1 deletion or overexpression of ATF1 with BAT2 deletion. Moreover, deletion of IAH1 in ATF1 overexpression strains effectively increased the production of isobutyl acetate and isoamyl acetate by reducing the hydrolysis of acetate esters. The decline in the production of higher alcohol by the ATF1 overexpression strains with BAT2 deletion is due to the interaction of ATF1 overexpression and BAT2 deletion. Mutants with varying abilities of producing acetate esters and higher alcohols were developed by genetic engineering. These strains have great potential for industrial application.
Collapse
|
36
|
Ghosh A, Stuehr DJ. Regulation of sGC via hsp90, Cellular Heme, sGC Agonists, and NO: New Pathways and Clinical Perspectives. Antioxid Redox Signal 2017; 26:182-190. [PMID: 26983679 PMCID: PMC5278824 DOI: 10.1089/ars.2016.6690] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Soluble guanylate cyclase (sGC) is an intracellular enzyme that plays a primary role in sensing nitric oxide (NO) and transducing its multiple signaling effects in mammals. Recent Advances: The chaperone heat shock protein 90 (hsp90) associates with signaling proteins in cells, including sGC, where it helps to drive heme insertion into the sGC-β1 subunit. This allows sGC-β1 to associate with a partner sGC-α1 subunit and mature into an NO-responsive active form. CRITICAL ISSUES In this article, we review evidence to date regarding the mechanisms that modulate sGC activity by a pathway where binding of hsp90 or sGC agonist to heme-free sGC dictates the assembly and fate of an active sGC heterodimer, both by NO and heme-dependent or heme-independent pathways. FUTURE DIRECTIONS We discuss some therapeutic implications of the NO-sGC-hsp90 nexus and its potential as a marker of inflammatory disease. Antioxid. Redox Signal. 26, 182-190.
Collapse
Affiliation(s)
- Arnab Ghosh
- Department of Pathobiology, Lerner Research Institute , Cleveland Clinic, Cleveland, Ohio
| | - Dennis J Stuehr
- Department of Pathobiology, Lerner Research Institute , Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
37
|
Khatami M. Is cancer a severe delayed hypersensitivity reaction and histamine a blueprint? Clin Transl Med 2016; 5:35. [PMID: 27558401 PMCID: PMC4996813 DOI: 10.1186/s40169-016-0108-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/04/2016] [Indexed: 02/08/2023] Open
Abstract
Longevity and accumulation of multiple context-dependent signaling pathways of long-standing inflammation (antigen-load or oxidative stress) are the results of decreased/altered regulation of immunity and loss of control switch mechanisms that we defined as Yin and Yang of acute inflammation or immune surveillance. Chronic inflammation is initiated by immune disruptors-induced progressive changes in physiology and function of susceptible host tissues that lead to increased immune suppression and multistep disease processes including carcinogenesis. The interrelated multiple hypotheses that are presented for the first time in this article are extension of author's earlier series of 'accidental' discoveries on the role of inflammation in developmental stages of immune dysfunction toward tumorigenesis and angiogenesis. Detailed analyses of data on chronic diseases suggest that nearly all age-associated illnesses, generally categorized as 'mild' (e.g., increased allergies), 'moderate' (e.g., hypertension, colitis, gastritis, pancreatitis, emphysema) or 'severe' (e.g., accelerated neurodegenerative and autoimmune diseases or site-specific cancers and metastasis) are variations of hypersensitivity responses of tissues that are manifested as different diseases in immune-responsive or immune-privileged tissues. Continuous release/presence of low level histamine (subclinical) in circulation could contribute to sustained oxidative stress and induction of 'mild' or 'moderate' or 'severe' (immune tsunami) immune disorders in susceptible tissues. Site-specific cancers are proposed to be 'severe' (irreversible) forms of cumulative delayed hypersensitivity responses that would induce immunological chaos in favor of tissue growth in target tissues. Shared or special features of growth from fetus development into adulthood and aging processes and carcinogenesis are briefly compared with regard to energy requirements of highly complex function of Yin and Yang. Features of Yang (growth-promoting) arm of acute inflammation during fetus and cancer growth will be compared for consuming low energy from glycolysis (Warburg effect). Growth of fetus and cancer cells under hypoxic conditions and impaired mitochondrial energy requirements of tissues including metabolism of essential branched amino acids (e.g., val, leu, isoleu) will be compared for proposing a working model for future systematic research on cancer biology, prevention and therapy. Presentation of a working model provides insightful clues into bioenergetics that are required for fetus growth (absence of external threat and lack of high energy-demands of Yin events and parasite-like survival in host), normal growth in adulthood (balance in Yin and Yang processes) or disease processes and carcinogenesis (loss of balance in Yin-Yang). Future studies require focusing on dynamics and promotion of natural/inherent balance between Yin (tumoricidal) and Yang (tumorigenic) of effective immunity that develop after birth. Lawless growth of cancerous cells and loss of cell contact inhibition could partially be due to impaired mitochondria (mitophagy) that influence metabolism of branched chain amino acids for biosynthesis of structural proteins. The author invites interested scientists with diverse expertise to provide comments, confirm, dispute and question and/or expand and collaborate on many components of the proposed working model with the goal to better understand cancer biology for future designs of cost-effective research and clinical trials and prevention of cancer. Initial events during oxidative stress-induced damages to DNA/RNA repair mechanisms and inappropriate expression of inflammatory mediators are potentially correctable, preventable or druggable, if future studies were to focus on systematic understanding of early altered immune response dynamics toward multistep chronic diseases and carcinogenesis.
Collapse
Affiliation(s)
- Mahin Khatami
- National Cancer Institute (NCI), the National Institutes of Health (NIH), Bethesda, MD, USA.
| |
Collapse
|
38
|
Random sample consensus combined with partial least squares regression (RANSAC-PLS) for microbial metabolomics data mining and phenotype improvement. J Biosci Bioeng 2016; 122:168-75. [DOI: 10.1016/j.jbiosc.2016.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 11/18/2022]
|
39
|
Improvement of isobutanol production in Saccharomyces cerevisiae by increasing mitochondrial import of pyruvate through mitochondrial pyruvate carrier. Appl Microbiol Biotechnol 2016; 100:7591-8. [DOI: 10.1007/s00253-016-7636-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/17/2016] [Accepted: 05/14/2016] [Indexed: 12/31/2022]
|
40
|
Stribny J, Romagnoli G, Pérez-Torrado R, Daran JM, Querol A. Characterisation of the broad substrate specificity 2-keto acid decarboxylase Aro10p of Saccharomyces kudriavzevii and its implication in aroma development. Microb Cell Fact 2016; 15:51. [PMID: 26971319 PMCID: PMC4789280 DOI: 10.1186/s12934-016-0449-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/01/2016] [Indexed: 12/02/2022] Open
Abstract
Background The yeast amino acid catabolism plays an important role in flavour generation since higher alcohols and acetate esters, amino acid catabolism end products, are key components of overall flavour and aroma in fermented products. Comparative studies have shown that other Saccharomyces species, such as S. kudriavzevii, differ during the production of aroma-active higher alcohols and their esters compared to S. cerevisiae. Results In this study, we performed a comparative analysis of the enzymes involved in the amino acid catabolism of S. kudriavzevii with their potential to improve the flavour production capacity of S. cerevisiae. In silico screening, based on the severity of amino acid substitutions evaluated by Grantham matrix, revealed four candidates, of which S. kudriavzevii Aro10p (SkAro10p) had the highest score. The analysis of higher alcohols and esters produced by S. cerevisiae then revealed enhanced formation of isobutanol, isoamyl alcohol and their esters when endogenous ARO10 was replaced with ARO10 from S. kudriavzevii. Also, significant differences in the aroma profile were found in fermentations of synthetic wine must. Substrate specificities of SkAro10p were compared with those of S. cerevisiae Aro10p (ScAro10p) by their expression in a 2-keto acid decarboxylase-null S. cerevisiae strain. Unlike the cell extracts with expressed ScAro10p which showed greater activity for phenylpyruvate, which suggests this phenylalanine-derivative to be the preferred substrate, the decarboxylation activities measured in the cell extracts with SkAro10p ranged with all the tested substrates at the same level. The activities of SkAro10p towards substrates (except phenylpyruvate) were higher than of those for ScAro10p. Conclusions The results indicate that the amino acid variations observed between the orthologues decarboxylases encoded by SkARO10 and ScARO10 could be the reason for the distinct enzyme properties, which possibly lead to the enhanced production of several flavour compounds. The knowledge on the important enzyme involved in higher alcohols biosynthesis by S. kudriavzevii could be of scientific as well as of applied interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0449-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jiri Stribny
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, (IATA-CSIC) Avda, Agustín Escardino, 7, Paterna, 46980, Valencia, Spain
| | - Gabriele Romagnoli
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Roberto Pérez-Torrado
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, (IATA-CSIC) Avda, Agustín Escardino, 7, Paterna, 46980, Valencia, Spain
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.,Platform Green Synthetic Biology, Delft, The Netherlands
| | - Amparo Querol
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology, (IATA-CSIC) Avda, Agustín Escardino, 7, Paterna, 46980, Valencia, Spain.
| |
Collapse
|
41
|
Soto IC, Barrientos A. Mitochondrial Cytochrome c Oxidase Biogenesis Is Regulated by the Redox State of a Heme-Binding Translational Activator. Antioxid Redox Signal 2016; 24:281-98. [PMID: 26415097 PMCID: PMC4761835 DOI: 10.1089/ars.2015.6429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIM Mitochondrial cytochrome c oxidase (COX), the last enzyme of the respiratory chain, catalyzes the reduction of oxygen to water and therefore is essential for cell function and viability. COX is a multimeric complex, whose biogenesis is extensively regulated. One type of control targets cytochrome c oxidase subunit 1 (Cox1), a key COX enzymatic core subunit translated on mitochondrial ribosomes. In Saccharomyces cerevisiae, Cox1 synthesis and COX assembly are coordinated through a negative feedback regulatory loop. This coordination is mediated by Mss51, a heme-sensing COX1 mRNA-specific processing factor and translational activator that is also a Cox1 chaperone. In this study, we investigated whether Mss51 hemylation and Mss51-mediated Cox1 synthesis are both modulated by the reduction-oxidation (redox) environment. RESULTS We report that Cox1 synthesis is attenuated under oxidative stress conditions and have identified one of the underlying mechanisms. We show that in vitro and in vivo exposure to hydrogen peroxide induces the formation of a disulfide bond in Mss51 involving CPX motif heme-coordinating cysteines. Mss51 oxidation results in a heme ligand switch, thereby lowering heme-binding affinity and promoting its release. We demonstrate that in addition to affecting Mss51-dependent heme sensing, oxidative stress compromises Mss51 roles in COX1 mRNA processing and translation. INNOVATION H2O2-induced downregulation of mitochondrial translation has so far not been reported. We show that high H2O2 concentrations induce a global attenuation effect, but milder concentrations specifically affect COX1 mRNA processing and translation in an Mss51-dependent manner. CONCLUSION The redox environment modulates Mss51 functions, which are essential for regulation of COX biogenesis and aerobic energy production.
Collapse
Affiliation(s)
- Iliana C Soto
- 1 Department of Neurology, University of Miami Miller School of Medicine , Miami, Florida
| | - Antoni Barrientos
- 1 Department of Neurology, University of Miami Miller School of Medicine , Miami, Florida.,2 Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine , Miami, Florida
| |
Collapse
|
42
|
Kingsbury JM, Sen ND, Cardenas ME. Branched-Chain Aminotransferases Control TORC1 Signaling in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1005714. [PMID: 26659116 PMCID: PMC4684349 DOI: 10.1371/journal.pgen.1005714] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
The conserved target of rapamycin complex 1 (TORC1) integrates nutrient signals to orchestrate cell growth and proliferation. Leucine availability is conveyed to control TORC1 activity via the leu-tRNA synthetase/EGOC-GTPase module in yeast and mammals, but the mechanisms sensing leucine remain only partially understood. We show here that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, effectively activate the yeast TORC1 kinase via both EGOC GTPase-dependent and -independent mechanisms. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT), which in yeast are represented by the mitochondrial and cytosolic enzymes Bat1 and Bat2, respectively. BCAT yeast mutants exhibit severely compromised TORC1 activity, which is partially restored by expression of Bat1 active site mutants, implicating both catalytic and structural roles of BCATs in TORC1 control. We find that Bat1 interacts with branched-chain amino acid metabolic enzymes and, in a leucine-dependent fashion, with the tricarboxylic acid (TCA)-cycle enzyme aconitase. BCAT mutation perturbed TCA-cycle intermediate levels, consistent with a TCA-cycle block, and resulted in low ATP levels, activation of AMPK, and TORC1 inhibition. We propose the biosynthetic capacity of BCAT and its role in forming multicomplex metabolons connecting branched-chain amino acids and TCA-cycle metabolism governs TCA-cycle flux to activate TORC1 signaling. Because mammalian mitochondrial BCAT is known to form a supramolecular branched-chain α-keto acid dehydrogenase enzyme complex that links leucine metabolism to the TCA-cycle, these findings establish a precedent for understanding TORC1 signaling in mammals. In all organisms from yeasts to mammals the target of rapamycin TORC1 pathway controls growth in response to nutrients such as leucine, but the leucine sensing mechanisms are only partially characterized. We show that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, are similarly capable of activating TORC1 kinase via EGOC GTPase-dependent and -independent mechanisms. Activation of TORC1 by leucine or α-ketoisocaproate is only partially mediated via EGOC-GTPase. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT). Disruption of BCAT caused reduced TORC1 activity, which was partially restored by expression of BCAT active site mutants, arguing for both structural and catalytic roles of BCAT in TORC1 control. We find BCAT interacts with several branched-chain amino acid metabolic enzymes, and in a leucine-dependent fashion with the tricarboxylic acid (TCA)-cycle enzyme aconitase. Both aconitase mutation or TCA-cycle inhibition impaired TORC1 activity. Mutation of BCAT resulted in a TCA-cycle intermediate profile consistent with a TCA-cycle block, low ATP levels, activation of AMPK, and TORC1 inhibition. Our results suggest a model whereby BCAT coordinates leucine and TCA cycle metabolism to control TORC1 signaling. Taken together, our findings forge key insights into how the TORC1 signaling cascade senses nutrients to control cell growth.
Collapse
Affiliation(s)
- Joanne M Kingsbury
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Neelam D Sen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Maria E Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
43
|
Whittaker JW. Intracellular trafficking of the pyridoxal cofactor. Implications for health and metabolic disease. Arch Biochem Biophys 2015; 592:20-6. [PMID: 26619753 DOI: 10.1016/j.abb.2015.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/09/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023]
Abstract
The importance of the vitamin B6-derived pyridoxal cofactor for human health has been established through more than 70 years of intensive biochemical research, revealing its fundamental roles in metabolism. B6 deficiency, resulting from nutritional limitation or impaired uptake from dietary sources, is associated with epilepsy, neuromuscular disease and neurodegeneration. Hereditary disorders of B6 processing are also known, and genetic defects in pathways involved in transport of B6 into the cell and its transformation to the pyridoxal-5'-phosphate enzyme cofactor can contribute to cardiovascular disease by interfering with homocysteine metabolism and the biosynthesis of vasomodulatory polyamines. Compared to the processes involved in cellular uptake and processing of the B6 vitamers, trafficking of the PLP cofactor across intracellular membranes is very poorly understood, even though the availability of PLP within subcellular compartments (particularly the mitochondrion) may have important health implications. The aim of this review is to concisely summarize the state of current knowledge of intracellular trafficking of PLP and to identify key directions for future research.
Collapse
Affiliation(s)
- James W Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA.
| |
Collapse
|
44
|
Montalvo-Arredondo J, Jiménez-Benítez Á, Colón-González M, González-Flores J, Flores-Villegas M, González A, Riego-Ruiz L. Functional roles of a predicted branched chain aminotransferase encoded by the LkBAT1 gene of the yeast Lachancea kluyveri. Fungal Genet Biol 2015; 85:71-82. [PMID: 26563416 DOI: 10.1016/j.fgb.2015.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 02/07/2023]
Abstract
Branched chain amino acid aminotransferases (BCATs) catalyze the last step of the biosynthesis and the first step of the catabolism of branched chain amino acids. In Saccharomyces cerevisiae, BCATs are encoded by the ScBAT1 and ScBAT2 paralogous genes. Analysis of Lachancea kluyveri genome sequence, allowed the identification of the LkBAT1 locus, which could presumably encode a BCAT. A second unlinked locus (LkBAT1bis), exhibiting sequence similarity to LkBAT1 was also identified. To determine the function of these putative BCATs, L. kluyveri mutant strains lacking LkBAT1, LkBAT1bis or both genes were generated and tested for VIL metabolism. LkBat1 displayed branched chain aminotransferase activity and is required for VIL biosynthesis and catabolism. However, Lkbat1Δ mutant is a valine and isoleucine auxotroph and a leucine bradytroph indicating that L. kluyveri harbors an alternative enzyme(s) involved in leucine biosynthesis. Additionally, heterologous reciprocal gene complementation between S. cerevisiae and L. kluyveri orthologous LkBAT1, ScBAT1 and ScBAT2 genes, confirmed that the mitochondrial LkBat1 functions as BCAT in S. cerevisiae, restoring wild type phenotype to the ScBAT1 null mutant. Conversely, LkBAT1bis did not display a role in BCAAs metabolism. However, when ethanol was used as carbon source, deletion of LkBAT1bis in an Lkbat1Δ null strain resulted in an extended 'lag' growth phase, pointing to a potential function of LkBAT1 and LkBAT1bis in the aerobic metabolism of L. kluyveri. These results confirm the BCAT function of LkBAT1 in L. kluyveri, and further support the proposition that the BCAT function in ancestral-type yeasts has been distributed in the two paralogous genes present in S. cerevisiae.
Collapse
Affiliation(s)
- Javier Montalvo-Arredondo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
| | - Ángel Jiménez-Benítez
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
| | - Maritrini Colón-González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - James González-Flores
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Mirelle Flores-Villegas
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, Mexico.
| | - Lina Riego-Ruiz
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4 Sección, San Luis Potosí, San Luis Potosí 78216, Mexico.
| |
Collapse
|
45
|
Longo V, Ždralević M, Guaragnella N, Giannattasio S, Zolla L, Timperio AM. Proteome and metabolome profiling of wild-type and YCA1-knock-out yeast cells during acetic acid-induced programmed cell death. J Proteomics 2015; 128:173-88. [PMID: 26269384 DOI: 10.1016/j.jprot.2015.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/03/2015] [Accepted: 08/05/2015] [Indexed: 01/13/2023]
Abstract
UNLABELLED Caspase proteases are responsible for the regulated disassembly of the cell into apoptotic bodies during mammalian apoptosis. Structural homologues of the caspase family (called metacaspases) are involved in programmed cell death in single-cell eukaryotes, yet the molecular mechanisms that contribute to death are currently undefined. Recent evidence revealed that a programmed cell death process is induced by acetic acid (AA-PCD) in Saccharomyces cerevisiae both in the presence and absence of metacaspase encoding gene YCA1. Here, we report an unexpected role for the yeast metacaspase in protein quality and metabolite control. By using an "omics" approach, we focused our attention on proteins and metabolites differentially modulated en route to AA-PCD either in wild type or YCA1-lacking cells. Quantitative proteomic and metabolomic analyses of wild type and Δyca1 cells identified significant alterations in carbohydrate catabolism, lipid metabolism, proteolysis and stress-response, highlighting the main roles of metacaspase in AA-PCD. Finally, deletion of YCA1 led to AA-PCD pathway through the activation of ceramides, whereas in the presence of the gene yeast cells underwent an AA-PCD pathway characterized by the shift of the main glycolytic pathway to the pentose phosphate pathway and a proteolytic mechanism to cope with oxidative stress. SIGNIFICANCE The yeast metacaspase regulates both proteolytic activities through the ubiquitin-proteasome system and ceramide metabolism as revealed by proteome and metabolome profiling of YCA1-knock-out cells during acetic-acid induced programmed cell death.
Collapse
Affiliation(s)
- Valentina Longo
- Department of Ecology and Biology, "La Tuscia" University, Viterbo, Italy
| | - Maša Ždralević
- Institute of Biomembrane and Bioenergetics, CNR, Bari, Italy
| | | | | | - Lello Zolla
- Department of Ecology and Biology, "La Tuscia" University, Viterbo, Italy.
| | | |
Collapse
|
46
|
Both BAT1 and ARO8 are responsible for unpleasant odor generation in halo-tolerant yeast Zygosaccharomyces rouxii. Appl Microbiol Biotechnol 2015; 99:7685-97. [DOI: 10.1007/s00253-015-6673-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/29/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
|
47
|
Xu B, Sowa N, Cardenas ME, Gerton JL. L-leucine partially rescues translational and developmental defects associated with zebrafish models of Cornelia de Lange syndrome. Hum Mol Genet 2014; 24:1540-55. [PMID: 25378554 PMCID: PMC4351377 DOI: 10.1093/hmg/ddu565] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cohesinopathies are human genetic disorders that include Cornelia de Lange syndrome (CdLS) and Roberts syndrome (RBS) and are characterized by defects in limb and craniofacial development as well as mental retardation. The developmental phenotypes of CdLS and other cohesinopathies suggest that mutations in the structure and regulation of the cohesin complex during embryogenesis interfere with gene regulation. In a previous project, we showed that RBS was associated with highly fragmented nucleoli and defects in both ribosome biogenesis and protein translation. l-leucine stimulation of the mTOR pathway partially rescued translation in human RBS cells and development in zebrafish models of RBS. In this study, we investigate protein translation in zebrafish models of CdLS. Our results show that phosphorylation of RPS6 as well as 4E-binding protein 1 (4EBP1) was reduced in nipbla/b, rad21 and smc3-morphant embryos, a pattern indicating reduced translation. Moreover, protein biosynthesis and rRNA production were decreased in the cohesin morphant embryo cells. l-leucine partly rescued protein synthesis and rRNA production in the cohesin morphants and partially restored phosphorylation of RPS6 and 4EBP1. Concomitantly, l-leucine treatment partially improved cohesinopathy embryo development including the formation of craniofacial cartilage. Interestingly, we observed that alpha-ketoisocaproate (α-KIC), which is a keto derivative of leucine, also partially rescued the development of rad21 and nipbla/b morphants by boosting mTOR-dependent translation. In summary, our results suggest that cohesinopathies are caused in part by defective protein synthesis, and stimulation of the mTOR pathway through l-leucine or its metabolite α-KIC can partially rescue development in zebrafish models for CdLS.
Collapse
Affiliation(s)
- Baoshan Xu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nenja Sowa
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA, Medical Faculty, University of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Maria E Cardenas
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA, Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA,
| |
Collapse
|
48
|
Förster J, Halbfeld C, Zimmermann M, Blank LM. A blueprint of the amino acid biosynthesis network of hemiascomycetes. FEMS Yeast Res 2014; 14:1090-100. [PMID: 25187056 DOI: 10.1111/1567-1364.12205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022] Open
Abstract
The structure and regulation of biosynthesis pathways in Saccharomyces cerevisiae have been detailed extensively. For other hemiascomycetes, genomic sequences are primarily available, whereas biochemical information on them is scarce. The resulting biochemical networks that are used for research in basic science and biotechnology are often biased by data from S. cerevisiae, assuming that there are often implicitly conserved structures between species. We examined the structure of the amino acid biosynthesis network in nine hemiascomycetes, spanning the phylogenetic clade. Differences in the genetic inventory included the presence and absence of isoenzymes and compartmentation of the pathways. Notably, no two hemiascomycetes had identical genetic inventories. For example, the lack of the mitochondrial αIPMS isoenzyme and presence of only one copy of the BCAA aminotransferase in Pichia pastoris indicate a disparately compartmented leucine biosynthesis pathway. Our findings suggest that αIPMS and BCAA aminotransferase are solely located in the cytosol of P. pastoris, requiring correction of the leucine biosynthesis pathway layout in this species. Our results argue for careful use of information from S. cerevisiae and for joint efforts to fill the knowledge gaps in other species. Such analysis will lead to contributions in biotechnology disciplines, such as protein production and compartment engineering.
Collapse
Affiliation(s)
- Jan Förster
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | | | | | | |
Collapse
|
49
|
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]
|
50
|
He Y, Dong J, Yin H, Zhao Y, Chen R, Wan X, Chen P, Hou X, Liu J, Chen L. Wort composition and its impact on the flavour-active higher alcohol and ester formation of beer - a review. JOURNAL OF THE INSTITUTE OF BREWING 2014. [DOI: 10.1002/jib.145] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yang He
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Jianjun Dong
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Yuxiang Zhao
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Rong Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Xiujuan Wan
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Peng Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Xiaoping Hou
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Jia Liu
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| | - Lu Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewing Ltd; Qingdao 266061 People's Republic of China
| |
Collapse
|