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Xia H, Song N, Liu D, Zhou R, Shangguan L, Chen X, Dai J. Exploring the stress response mechanisms to 2-phenylethanol conferred by Pdr1p mutation in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:109. [PMID: 39090744 PMCID: PMC11295549 DOI: 10.1186/s13068-024-02559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND The 2-phenylethanol (2-PE) tolerance phenotype is crucial to the production of 2-PE, and Pdr1p mutation can significantly increase the tolerance of 2-PE in Saccharomyces cerevisiae. However, its underlying molecular mechanisms are still unclear, hindering the rational design of superior 2-PE tolerance performance. RESULTS Here, the physiology and biochemistry of the PDR1_862 and 5D strains were analyzed. At 3.5 g/L 2-PE, the ethanol concentration of PDR1_862 decreased by 21%, and the 2-PE production of PDR1_862 increased by 16% than those of 5D strain. Transcriptome analysis showed that at 2-PE stress, Pdr1p mutation increased the expression of genes involved in the Ehrlich pathway. In addition, Pdr1p mutation attenuated sulfur metabolism and enhanced the one-carbon pool by folate to resist 2-PE stress. These metabolic pathways were closely associated with amino acids metabolism. Furthermore, at 3.5 g/L 2-PE, the free amino acids content of PDR1_862 decreased by 31% than that of 5D strain, among the free amino acids, cysteine was key amino acid for the enhancement of 2-PE stress tolerance conferred by Pdr1p mutation. CONCLUSIONS The above results indicated that Pdr1p mutation enhanced the Ehrlich pathway to improve 2-PE production of S. cerevisiae, and Pdr1p mutation altered the intracellular amino acids contents, in which cysteine might be a biomarker in response to Pdr1p mutation under 2-PE stress. The findings help to elucidate the molecular mechanisms for 2-PE stress tolerance by Pdr1p mutation in S. cerevisiae, identify key metabolic pathway responsible for 2-PE stress tolerance.
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Affiliation(s)
- Huili Xia
- College of Biological and Food Engineering, Huanghuai University, Zhumadian, 463000, Henan, China
| | - Na Song
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, 430068, Hubei, People's Republic of China
| | - Daoqi Liu
- College of Biological and Food Engineering, Huanghuai University, Zhumadian, 463000, Henan, China
| | - Rong Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, 430068, Hubei, People's Republic of China
| | - Lingling Shangguan
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, 430068, Hubei, People's Republic of China
| | - Xiong Chen
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, 430068, Hubei, People's Republic of China
| | - Jun Dai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, 430068, Hubei, People's Republic of China.
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2
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Patriarcheas D, Momtareen T, Gallagher JEG. Yeast of Eden: microbial resistance to glyphosate from a yeast perspective. Curr Genet 2023; 69:203-212. [PMID: 37269314 PMCID: PMC10716058 DOI: 10.1007/s00294-023-01272-4] [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: 04/07/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023]
Abstract
First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.
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Affiliation(s)
- Dionysios Patriarcheas
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA
| | - Taizina Momtareen
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA
| | - Jennifer E G Gallagher
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA.
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3
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Xiao Q, Li J, Chen J, Tan Q, Chen X, Li H, Zhao X, Zhang X. Uba1: A Potential Ubiquitin-like Activator Protein of Urm1 in Toxoplasma gondii. Int J Mol Sci 2022; 23:ijms231810298. [PMID: 36142209 PMCID: PMC9499322 DOI: 10.3390/ijms231810298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
We had shown in our previous study that TgUrm1 (ubiquitin-related Modifier 1) was involved in the regulation of anti-oxidant stress in Toxoplasma gondii by conjugating with TgAhp1. It is generally believed that Urm1 binds to target proteins through a mechanism involving Uba (ubiquitin-like activator protein). Here, we identified the TgUrm1-exclusive ubiquitin-like activator-TgUba1, which was located in the cytoplasm of Toxoplasma. TgUba1 contained three domains, including the atrophin-1 domain (ANT1), the E1-like domain (AD), and the rhodanese homology domain (RHD). We explored the interaction of TgUba1 with TgUrm1, and the AD domain was essential for the interaction of the two proteins. The TgUba1 knockout and complementary mutants were obtained based on CRISPR/Cas9 gene editing technology. The knockout of TgUba1 attenuated parasite proliferation and virulence in mice, but not invasion and egress processes, revealing the pivotal role played by TgUba1 in T. gondii survival. Meanwhile, the conjugate band of TgUrm1 was significantly reduced under oxidative stress stimulation without TgUba1, indicating that TgUba1 enhanced the targeted conjugation ability of TgUrm1 in response to oxidative stress, especially under diamide (Dia) stimulation. Furthermore, eleven TgUba1-interacting proteins were identified by proximity-based protein labeling techniques, relating them to ubiquitin-like modifications, anti-oxidative stress and metabolic regulation processes. In conclusion, TgUba1 was essential for T. gondii survival and might be a potential ubiquitin-like activator protein for TgUrm1.
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Affiliation(s)
- Qianqian Xiao
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Jinxuan Li
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Junpeng Chen
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Qianqian Tan
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Xiao Chen
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Hongmei Li
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Xiaomin Zhao
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: (X.Z.); (X.Z.)
| | - Xiao Zhang
- Room 115, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: (X.Z.); (X.Z.)
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4
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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5
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Horikiri S, Harada M, Asada R, J Sakamoto J, Furuta M, Tsuchido T. Low Temperature Heating-Induced Death and Vacuole Injury in Cladosporium sphaerospermum Conidia. Biocontrol Sci 2022; 27:107-115. [PMID: 35753793 DOI: 10.4265/bio.27.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The mechanism of thermal death of mold conidia has not been understood in detail. The purpose of this study is to analyze the death kinetics of heated conidia of Cladosporium sphaerospermum and to ascertain the expectant cell injury responsible for the death. The death of the dormant (resting) conidia of Cladosporium sphaerospermum was examined at temperatures of between 43 and 54℃ with the conventional colony count method. The death reaction apparently followed the first order kinetics, but the Arrhenius plot of the death rate constant demonstrated seemingly a break. The linearity at temperatures higher than that at the break was lost at lower temperatures, suggesting the involvement of an unusual mechanism in the latter temperatures. In the cell morphology, we observed with quinacrine staining the vacuole rupture at a lower temperature but not at a high temperature. Interestingly, the vacuole rupture by low-temperature heating was found to correlate with the viability loss. Furthermore, active protease originally locating in vacuoles was detected in the cytoplasm of the conidia after heated at a low temperature. The results obtained suggest the involvement of potent autophagic cell death induced by low temperature heating of C. sphaerospermum conidia.
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Affiliation(s)
- Shigetoshi Horikiri
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Panasonic Ecology Systems Co., Ltd
| | - Mami Harada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University
| | - Ryoko Asada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Research Center of Microorganism Control, Organization for Research Promotion
| | - Jin J Sakamoto
- Research Center of Microorganism Control, Organization for Research Promotion.,Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Masakazu Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University.,Research Center of Microorganism Control, Organization for Research Promotion
| | - Tetsuaki Tsuchido
- Research Center of Microorganism Control, Organization for Research Promotion
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6
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Zeng L, Huang J, Feng P, Zhao X, Si Z, Long X, Cheng Q, Yi Y. Transcriptomic analysis of formic acid stress response in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2022; 38:34. [PMID: 34989900 DOI: 10.1007/s11274-021-03222-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/26/2021] [Indexed: 12/23/2022]
Abstract
Formic acid is a representative small molecule acid in lignocellulosic hydrolysate that can inhibit the growth of Saccharomyces cerevisiae cells during alcohol fermentation. However, the mechanism of formic acid cytotoxicity remains largely unknown. In this study, RNA-Seq technology was used to study the response of S. cerevisiae to formic acid stress at the transcriptional level. Scanning electron microscopy and Fourier transform infrared spectroscopy were conducted to observe the surface morphology of yeast cells. A total of 1504 genes were identified as being differentially expressed, with 797 upregulated and 707 downregulated genes. Transcriptomic analysis showed that most genes related to glycolysis, glycogen synthesis, protein degradation, the cell cycle, the MAPK signaling pathway, and redox regulation were significantly induced under formic acid stress and were involved in protein translation and synthesis amino acid synthesis genes were significantly suppressed. Formic acid stress can induce oxidative stress, inhibit protein biosynthesis, cause cells to undergo autophagy, and activate the intracellular metabolic pathways of energy production. The increase of glycogen and the decrease of energy consumption metabolism may be important in the adaptation of S. cerevisiae to formic acid. In addition, formic acid can also induce sexual reproduction and spore formation. This study through transcriptome analysis has preliminarily reveal the molecular response mechanism of S. cerevisiae to formic acid stress and has provided a basis for further research on methods used to improve the tolerance to cell inhibitors in lignocellulose hydrolysate.
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Affiliation(s)
- Lingjie Zeng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Jinxiang Huang
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Pixue Feng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Xuemei Zhao
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Zaiyong Si
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Xiufeng Long
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Qianwei Cheng
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China
| | - Yi Yi
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, China.
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Liuzhou, 545006, China.
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Chaperonin point mutation enhances cadmium endurance in Saccharomyces cerevisiae. Biotechnol Lett 2021; 43:1735-1745. [PMID: 34047865 DOI: 10.1007/s10529-021-03151-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To study the effect of the mutation in conserved G412E in Cct7p subunit of CCT complex on its cellular fate. RESULTS TriC/CCT is a dynamic multimeric protein that assists in protein folding in an energy-dependent manner. A point mutation in the ATP binding pocket in the equatorial domain of the Cct7p subunit delays the doubling time. The cell size was twice the wild type, and the formation of protein aggregates suggests disturbed folding of the proteins. Upon growing in stressful conditions of arsenous acid and cadmium chloride, the mutant was lethal in As3+ but grew well in Cd2+ with 10.5 µg cadmium uptake mg-1 compared to the wild type. The increased expression of vacuole transporters YCF1 and BPT1 by ten-fold and two-fold in mutant indicates the metal transportation to the vacuole. CONCLUSION CCT complex was vulnerable to the mutation in G412E in the Cct7p subunit of protein folding molecular machinery. Interestingly, already stressed cells provided robustness against oxidative stress and cadmium sequestration in the vacuole.
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8
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Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
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9
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Rogers CM, Veatch D, Covey A, Staton C, Bochman ML. Terminal acidic shock inhibits sour beer bottle conditioning by Saccharomyces cerevisiae. Food Microbiol 2016; 57:151-8. [DOI: 10.1016/j.fm.2016.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/29/2016] [Accepted: 02/27/2016] [Indexed: 10/22/2022]
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10
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Stauffer B, Powers T. Target of rapamycin signaling mediates vacuolar fragmentation. Curr Genet 2016; 63:35-42. [PMID: 27233284 DOI: 10.1007/s00294-016-0616-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 11/26/2022]
Abstract
In eukaryotic cells, cellular homeostasis requires that different organelles respond to intracellular as well as environmental signals and modulate their behavior as conditions demand. Understanding the molecular mechanisms required for these changes remains an outstanding goal. One such organelle is the lysosome/vacuole, which undergoes alterations in size and number in response to environmental and physiological stimuli. Changes in the morphology of this organelle are mediated in part by the equilibrium between fusion and fission processes. While the fusion of the yeast vacuole has been studied intensively, the regulation of vacuolar fission remains poorly characterized by comparison. In recent years, a number of studies have incorporated genome-wide visual screens and high-throughput microscopy to identify factors required for vacuolar fission in response to diverse cellular insults, including hyperosmotic and endoplasmic reticulum stress. Available evidence now demonstrates that the rapamycin-sensitive TOR network, a master regulator of cell growth, is required for vacuolar fragmentation in response to stress. Importantly, many of the genes identified in these studies provide new insights into potential links between the vacuolar fission machinery and TOR signaling. Together these advances both extend our understanding of the regulation of vacuolar fragmentation in yeast as well as underscore the role of analogous events in mammalian cells.
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Affiliation(s)
- Bobbiejane Stauffer
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Ted Powers
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA.
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11
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Narayanan A, Pullepu D, Reddy PK, Uddin W, Kabir MA. Defects in Protein Folding Machinery Affect Cell Wall Integrity and Reduce Ethanol Tolerance in S. cerevisiae. Curr Microbiol 2016; 73:38-45. [DOI: 10.1007/s00284-016-1024-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/05/2016] [Indexed: 11/28/2022]
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12
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Berterame NM, Porro D, Ami D, Branduardi P. Protein aggregation and membrane lipid modifications under lactic acid stress in wild type and OPI1 deleted Saccharomyces cerevisiae strains. Microb Cell Fact 2016; 15:39. [PMID: 26887851 PMCID: PMC4756461 DOI: 10.1186/s12934-016-0438-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/02/2016] [Indexed: 11/12/2022] Open
Abstract
Background Lactic acid is a versatile chemical platform with many different industrial applications. Yeasts have been demonstrated as attractive alternative to natural lactic acid producers since they can grow at low pH, allowing the direct purification of the product in the desired acidic form. However, when very high concentrations of organic acids are reached, the major limitation for a viable production is the toxic effect of the product. The accumulation in the cytosol of H+ and of the weak organic counter-anions triggers a cellular reprogramming. Here, the effects of lactic acid exposure on Saccharomycescerevisiae have been evaluated by Fourier transform infrared (FTIR) microspectroscopy. In addition to -omic techniques, describing these responses in terms of systems and networks, FTIR microspectroscopy allows a rapid acquisition of the cellular biochemical fingerprint, providing information on the major classes of macromolecules. Results FTIR analyses on Saccharomyces cerevisiae cells under lactic acid stress at low pH revealed some still uncharacterized traits: (1) a direct correlation between lactic acid exposure and a rearrangement in lipid hydrocarbon tails, together with a decrease in the signals of phosphatidylcholine (PC), one of the main components of cell membrane; (2) a rearrangement in the cell wall carbohydrates, including glucans and mannans (3) a significant yet transient protein aggregation, possibly responsible for the observed transient decrease of the growth rate. When repeated on the isogenic strain deleted in OPI1, encoding for a transcriptional repressor of genes involved in PC biosynthesis, FTIR analysis revealed that not only the PC levels were affected but also the cell membrane/wall composition and the accumulation of protein aggregates, resulting in higher growth rate in the presence of the stressing agent. Conclusions This work revealed novel effects evoked by lactic acid on cell membrane/wall composition and protein aggregation in S. cerevisiae cells. We consequently demonstrated that the targeted deletion of OPI1 resulted in improved lactic acid tolerance. Considering that stress response involves many and different cellular networks and regulations, most of which are still not implemented in modelling, these findings constitute valuable issues for interpreting cellular rewiring and for tailoring ameliorated cell factories for lactic acid production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0438-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy. .,SYSBIO - Centre of Systems Biology, Milano and Roma, Italy.
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy. .,Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, Milan, 20126, Italy. .,Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia (CNISM) UdR Milano-Bicocca, Milan, 20126, Italy.
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.
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Song JY, Park JS, Kang CD, Cho HY, Yang D, Lee S, Cho KM. Introduction of a bacterial acetyl-CoA synthesis pathway improves lactic acid production in Saccharomyces cerevisiae. Metab Eng 2015; 35:38-45. [PMID: 26384570 DOI: 10.1016/j.ymben.2015.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 11/19/2022]
Abstract
Acid-tolerant Saccharomyces cerevisiae was engineered to produce lactic acid by expressing heterologous lactate dehydrogenase (LDH) genes, while attenuating several key pathway genes, including glycerol-3-phosphate dehydrogenase1 (GPD1) and cytochrome-c oxidoreductase2 (CYB2). In order to increase the yield of lactic acid further, the ethanol production pathway was attenuated by disrupting the pyruvate decarboxylase1 (PDC1) and alcohol dehydrogenase1 (ADH1) genes. Despite an increase in lactic acid yield, severe reduction of the growth rate and glucose consumption rate owing to the absence of ADH1 caused a considerable decrease in the overall productivity. In Δadh1 cells, the levels of acetyl-CoA, a key precursor for biologically applicable components, could be insufficient for normal cell growth. To increase the cellular supply of acetyl-CoA, we introduced bacterial acetylating acetaldehyde dehydrogenase (A-ALD) enzyme (EC 1.2.1.10) genes into the lactic acid-producing S. cerevisiae. Escherichia coli-derived A-ALD genes, mhpF and eutE, were expressed and effectively complemented the attenuated acetaldehyde dehydrogenase (ALD)/acetyl-CoA synthetase (ACS) pathway in the yeast. The engineered strain, possessing a heterologous acetyl-CoA synthetic pathway, showed an increased glucose consumption rate and higher productivity of lactic acid fermentation. The production of lactic acid was reached at 142g/L with production yield of 0.89g/g and productivity of 3.55gL(-1)h(-1) under fed-batch fermentation in bioreactor. This study demonstrates a novel approach that improves productivity of lactic acid by metabolic engineering of the acetyl-CoA biosynthetic pathway in yeast.
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Affiliation(s)
- Ji-Yoon Song
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Joon-Song Park
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Chang Duk Kang
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Hwa-Young Cho
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Dongsik Yang
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Seunghyun Lee
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea
| | - Kwang Myung Cho
- Biomaterials Laboratory, Material Research Center, Samsung Advanced Institute of Technology, Gyeonggi-do, Republic of Korea.
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14
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PEP3 overexpression shortens lag phase but does not alter growth rate in Saccharomyces cerevisiae exposed to acetic acid stress. Appl Microbiol Biotechnol 2015; 99:8667-80. [PMID: 26051671 DOI: 10.1007/s00253-015-6708-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/22/2015] [Accepted: 05/19/2015] [Indexed: 12/12/2022]
Abstract
In fungi, two recognized mechanisms contribute to pH homeostasis: the plasma membrane proton-pumping ATPase that exports excess protons and the vacuolar proton-pumping ATPase (V-ATPase) that mediates vacuolar proton uptake. Here, we report that overexpression of PEP3 which encodes a component of the HOPS and CORVET complexes involved in vacuolar biogenesis, shortened lag phase in Saccharomyces cerevisiae exposed to acetic acid stress. By confocal microscopy, PEP3-overexpressing cells stained with the vacuolar membrane-specific dye, FM4-64 had more fragmented vacuoles than the wild-type control. The stained overexpression mutant was also found to exhibit about 3.6-fold more FM4-64 fluorescence than the wild-type control as determined by flow cytometry. While the vacuolar pH of the wild-type strain grown in the presence of 80 mM acetic acid was significantly higher than in the absence of added acid, no significant difference was observed in vacuolar pH of the overexpression strain grown either in the presence or absence of 80 mM acetic acid. Based on an indirect growth assay, the PEP3-overexpression strain exhibited higher V-ATPase activity. We hypothesize that PEP3 overexpression provides protection from acid stress by increasing vacuolar surface area and V-ATPase activity and, hence, proton-sequestering capacity.
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15
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Sheibani S, Jones NK, Eid R, Gharib N, Arab NTT, Titorenko V, Vali H, Young PA, Greenwood MT. Inhibition of stress mediated cell death by human lactate dehydrogenase B in yeast. FEMS Yeast Res 2015; 15:fov032. [DOI: 10.1093/femsyr/fov032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/19/2015] [Indexed: 12/11/2022] Open
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16
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Nugroho RH, Yoshikawa K, Shimizu H. Metabolomic analysis of acid stress response in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:396-404. [PMID: 25795572 DOI: 10.1016/j.jbiosc.2015.02.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/24/2022]
Abstract
Acid stress has been reported to inhibit cell growth and decrease productivity during bio-production processes. In this study, a metabolomics approach was conducted to understand the effect of lactic acid induced stress on metabolite pools in Saccharomyces cerevisiae. Cells were cultured with lactic acid as the acidulant, with or without initial pH control, i.e., at pH 6 or pH 2.5, respectively. Under conditions of low pH, lactic acid led to a decrease in the intracellular pH and specific growth rate; however, these parameters remained unaltered in the cultures with pH control. Capillary electrophoresis-mass spectrometry followed by a statistical principal component analysis was used to identify the metabolites and measure the increased concentrations of ATP, glutathione and proline during severe acid stress. Addition of proline to the acidified cultures improved the specific growth rates. We hypothesized that addition of proline protected the cells from acid stress by combating acid-induced oxidative stress. Lactic acid diffusion into the cell resulted in intracellular acidification, which elicited an oxidative stress response and resulted in increased glutathione levels.
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Affiliation(s)
- Riyanto Heru Nugroho
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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17
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Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus. BMC Genomics 2014; 15:521. [PMID: 24965678 PMCID: PMC4082610 DOI: 10.1186/1471-2164-15-521] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse expression in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions. Results Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition-specific anti-sense transcription levels is higher than that in condition-specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse expression in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse expression, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes. Conclusions By performing a genome-scale computational analysis, we have tried to evaluate the role of antisense transcription in mediating sense transcription under different environmental conditions across and in two related yeast species. Our findings suggest that antisense regulation could control expression of the corresponding sense transcript via inverse expression under a range of different circumstances. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-521) contains supplementary material, which is available to authorized users.
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18
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Kubo R, Ohta K, Funakawa S, Kitabatake N, Araki S, Izawa S. Isolation of lactic acid-tolerant Saccharomyces cerevisiae from Cameroonian alcoholic beverage. J Biosci Bioeng 2014; 118:657-60. [PMID: 24910259 DOI: 10.1016/j.jbiosc.2014.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/10/2014] [Accepted: 05/09/2014] [Indexed: 11/18/2022]
Abstract
We investigated yeast strains used in Cameroonian microbreweries, and identified a Saccharomyces cerevisiae strain (OCY3) with an excellent capacity for alcoholic fermentation. OCY3 showed higher tolerance to lactic acid and better fermentation performance under acidic conditions than a representative Japanese sake yeast, Kyokai No. 7, and a wine yeast, EC1118.
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Affiliation(s)
- Ryosuke Kubo
- Department of Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Kyoto 606-8501, Japan
| | - Keisuke Ohta
- Department of Microbiology, Wakayama Medical University, Kimiidera, Wakayama 641-8509, Japan
| | - Shinya Funakawa
- Department of Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Kyoto 606-8501, Japan; Division of Environmental Science and Technology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Naofumi Kitabatake
- Faculty of Human Life Sciences, Notre Dame Seishin University, 9-16-2 Ifuku-cho, Okayama 700-8516, Japan; Graduate School of Asian and African Area Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Kyoto 606-8501, Japan
| | - Shigeru Araki
- Graduate School of Asian and African Area Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Kyoto 606-8501, Japan
| | - Shingo Izawa
- Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan.
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Potent l-lactic acid assimilation of the fermentative and heterothallic haploid yeast Saccharomyces cerevisiae NAM34-4C. J Biosci Bioeng 2014; 117:65-70. [DOI: 10.1016/j.jbiosc.2013.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 05/10/2013] [Accepted: 06/03/2013] [Indexed: 11/22/2022]
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20
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Suzuki T, Sakamoto T, Sugiyama M, Ishida N, Kambe H, Obata S, Kaneko Y, Takahashi H, Harashima S. Disruption of multiple genes whose deletion causes lactic-acid resistance improves lactic-acid resistance and productivity in Saccharomyces cerevisiae. J Biosci Bioeng 2013; 115:467-74. [PMID: 23290995 DOI: 10.1016/j.jbiosc.2012.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 10/19/2012] [Accepted: 11/19/2012] [Indexed: 11/28/2022]
Abstract
To create strains that have high productivity of lactic acid without neutralization, a genome-wide screening for strains showing hyper-resistance to 6% l-lactic acid (pH 2.6) was performed using the gene deletion collection of Saccharomyces cerevisiae. We identified 94 genes whose disruption led to resistance to 6% lactic acid in rich medium. We also found that multiple combinations of Δdse2, Δscw11, Δeaf3, and/or Δsed1 disruption led to enhanced resistance to lactic acid depending upon their combinations. In particular, the quadruple disruptant Δdse2Δscw11Δeaf3Δsed1 grew well in 6% lactic acid with the shortest lag phase. We then introduced an exogenous lactate dehydrogenase gene (LDH) into those single and multiple disruptants to evaluate their productivity of lactic acid. It was found that the quadruple disruptant displaying highest lactic-acid resistance showed a 27% increase of lactic-acid productivity as compared with the LDH-harboring wild-type strain. These observations suggest that disruption of multiple genes whose deletion leads to lactic-acid resistance is an effective way to enhance resistance to lactic acid, leading to high lactic-acid productivity without neutralization.
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Affiliation(s)
- Toshihiro Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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