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Christensen KE, Duarte A, Ma Z, Edwards JL, Brem RB. Dissecting an ancient stress resistance trait syndrome in the compost yeast Kluyveromyces marxianus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572915. [PMID: 38187519 PMCID: PMC10769334 DOI: 10.1101/2023.12.21.572915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In the search to understand how evolution builds new traits, ancient events are often the hardest to dissect. Species-unique traits pose a particular challenge for geneticists-cases in which a character arose long ago and, in the modern day, is conserved within a species, distinguishing it from reproductively isolated relatives. In this work, we have developed the budding yeast genus Kluyveromyces as a model for mechanistic dissection of trait variation across species boundaries. Phenotypic profiling revealed robust heat and chemical-stress tolerance phenotypes that distinguished the compost yeast K. marxianus from the rest of the clade. We used culture-based, transcriptomic, and genetic approaches to characterize the metabolic requirements of the K. marxianus trait syndrome. We then generated a population-genomic resource for K. marxianus and harnessed it in molecular-evolution analyses, which found hundreds of housekeeping genes with evidence for adaptive protein variation unique to this species. Our data support a model in which, in the distant past, K. marxianus underwent a vastly complex remodeling of its proteome to achieve stress resistance. Such a polygenic architecture, involving nucleotide-level allelic variation on a massive scale, is consistent with theoretical models of the mechanisms of long-term adaptation, and suggests principles of broad relevance for interspecies trait genetics.
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Affiliation(s)
- Kaylee E. Christensen
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720
| | - Abel Duarte
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720
| | - Zhenzhen Ma
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720
- Current address: Department of Biology, Stanford University, Stanford, CA, 94305
| | - Judith L. Edwards
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720
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Lamas-Maceiras M, Vizoso-Vázquez Á, Barreiro-Alonso A, Cámara-Quílez M, Cerdán ME. Thanksgiving to Yeast, the HMGB Proteins History from Yeast to Cancer. Microorganisms 2023; 11:microorganisms11040993. [PMID: 37110415 PMCID: PMC10142021 DOI: 10.3390/microorganisms11040993] [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: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Yeasts have been a part of human life since ancient times in the fermentation of many natural products used for food. In addition, in the 20th century, they became powerful tools to elucidate the functions of eukaryotic cells as soon as the techniques of molecular biology developed. Our molecular understandings of metabolism, cellular transport, DNA repair, gene expression and regulation, and the cell division cycle have all been obtained through biochemistry and genetic analysis using different yeasts. In this review, we summarize the role that yeasts have had in biological discoveries, the use of yeasts as biological tools, as well as past and on-going research projects on HMGB proteins along the way from yeast to cancer.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Cámara-Quílez
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - María Esperanza Cerdán
- Centro Interdisciplinar de Química y Biología (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Facultad de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
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Fonseca GG. Metabolic engineering of Kluyveromyces marxianus for biomass-based applications. 3 Biotech 2022; 12:259. [PMID: 36068842 PMCID: PMC9440961 DOI: 10.1007/s13205-022-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/22/2022] [Indexed: 11/01/2022] Open
Abstract
Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03324-x.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Business and Science, University of Akureyri, Borgir v. Nordurslod, 600 Akureyri, Iceland
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Betinova V, Toth Hervay N, Elias D, Horvathova A, Gbelska Y. The UPC2 gene in Kluyveromyces lactis stress adaptation. Folia Microbiol (Praha) 2022; 67:641-647. [PMID: 35352326 DOI: 10.1007/s12223-022-00968-3] [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: 01/12/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
KlUpc2p, a transcription factor belonging to the fungal binuclear cluster family, is an important regulator of ergosterol biosynthesis and azole drug resistance in Kluyveromyces lactis. In this work, we show that the absence of KlUpc2p generates Rag- phenotype and modulates the K. lactis susceptibility to oxidants and calcofuor white. The KlUPC2 deletion leads to increased expression of KlMGA2 gene, encoding an important regulator of hypoxic and lipid biosynthetic genes in K. lactis and also KlHOG1 gene. The absence of KlUpc2p does not lead to statistically significant changes in glycerol, corroborating the expression of KlGPD1 gene, encoding NAD+-dependent glycerol-3-phosphate dehydrogenase, that is similar in both the deletion mutant and the parental wild-type strain. Increased sensitivity of Klupc2 mutant cells to brefeldin A accompanied with significant increase in KlARF2 gene expression point to the involvement of KlUpc2p in intracellular signaling. Our observations highlight the connections between ergosterol and fatty acid metabolism to modulate membrane properties and point to the possible involvement of KlUpc2p in K. lactis oxidative stress response.
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Affiliation(s)
- Veronika Betinova
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Nora Toth Hervay
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Daniel Elias
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Agnes Horvathova
- Centre for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovak Republic
| | - Yvetta Gbelska
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic.
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Dekker WJC, Jürgens H, Ortiz-Merino RA, Mooiman C, van den Berg R, Kaljouw A, Mans R, Pronk JT. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6523363. [PMID: 35137036 PMCID: PMC8862043 DOI: 10.1093/femsyr/foac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Hannes Jürgens
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Remon van den Berg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Corresponding author: Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands. Tel: +31 15 2783214; E-mail:
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Dekker WJC, Ortiz-Merino RA, Kaljouw A, Battjes J, Wiering FW, Mooiman C, Torre PDL, Pronk JT. Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth. Metab Eng 2021; 67:347-364. [PMID: 34303845 DOI: 10.1016/j.ymben.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Julius Battjes
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Frank W Wiering
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Pilar de la Torre
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands.
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7
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Zain Ul Arifeen M, Chu C, Yang X, Liu J, Huang X, Ma Y, Liu X, Xue Y, Liu C. The anaerobic survival mechanism of Schizophyllum commune 20R-7-F01, isolated from deep sediment 2 km below the seafloor. Environ Microbiol 2020; 23:1174-1185. [PMID: 33215844 DOI: 10.1111/1462-2920.15332] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/27/2022]
Abstract
Fungi dominated the eukaryotic group in the anaerobic sedimentary environment below the ocean floor where they play an essential ecological role. However, the adaptive mechanism of fungi to these anaerobic environments is still unclear. Here, we reported the anaerobic adaptive mechanism of Schizophyllum commune 20R-7-F01, isolated from deep coal-bearing sediment down to ~2 km below the seafloor, through biochemical, metabolomic and transcriptome analyses. The fungus grows well, but the morphology changes obviously and the fruit body develops incompletely under complete hypoxia. Compared with aerobic conditions, the fungus has enhanced branched-chain amino acid biosynthesis and ethanol fermentation under anaerobic conditions, and genes related to these metabolisms have been significantly up-regulated. Additionally, the fungus shows novel strategies for synthesizing ethanol by utilizing both glycolysis and ethanol fermentation pathways. These findings suggest that the subseafloor fungi may adopt multiple mechanisms to cope with lack of oxygen.
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Affiliation(s)
- Muhammad Zain Ul Arifeen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinyi Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Junzhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xin Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yunan Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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Evolution of Distinct Responses to Low NAD + Stress by Rewiring the Sir2 Deacetylase Network in Yeasts. Genetics 2020; 214:855-868. [PMID: 32071196 DOI: 10.1534/genetics.120.303087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/12/2020] [Indexed: 01/20/2023] Open
Abstract
Evolutionary adaptation increases the fitness of a species in its environment. It can occur through rewiring of gene regulatory networks, such that an organism responds appropriately to environmental changes. We investigated whether sirtuin deacetylases, which repress transcription and require NAD+ for activity, serve as transcriptional rewiring points that facilitate the evolution of potentially adaptive traits. If so, bringing genes under the control of sirtuins could enable organisms to mount appropriate responses to stresses that decrease NAD+ levels. To explore how the genomic targets of sirtuins shift over evolutionary time, we compared two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, that display differences in cellular metabolism and life cycle timing in response to nutrient availability. We identified sirtuin-regulated genes through a combination of chromatin immunoprecipitation and RNA expression. In both species, regulated genes were associated with NAD+ homeostasis, mating, and sporulation, but the specific genes differed. In addition, regulated genes in K. lactis were associated with other processes, including utilization of nonglucose carbon sources, detoxification of arsenic, and production of the siderophore pulcherrimin. Consistent with the species-restricted regulation of these genes, sirtuin deletion affected relevant phenotypes in K. lactis but not S. cerevisiae Finally, sirtuin-regulated gene sets were depleted for broadly conserved genes, consistent with sirtuins regulating processes restricted to a few species. Taken together, these results are consistent with the notion that sirtuins serve as rewiring points that allow species to evolve distinct responses to low NAD+ stress.
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da Costa BLV, Raghavendran V, Franco LFM, Chaves Filho ADB, Yoshinaga MY, Miyamoto S, Basso TO, Gombert AK. Forever panting and forever growing: physiology of Saccharomyces cerevisiae at extremely low oxygen availability in the absence of ergosterol and unsaturated fatty acids. FEMS Yeast Res 2019; 19:5551481. [DOI: 10.1093/femsyr/foz054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/02/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
We sought to investigate how far the growth of Saccharomyces cerevisiae under full anaerobiosis is dependent on the widely used anaerobic growth factors (AGF) ergosterol and oleic acid. A continuous cultivation setup was employed and, even forcing ultrapure N2 gas through an O2 trap upstream of the bioreactor, neither cells from S. cerevisiae CEN.PK113–7D (a lab strain) nor from PE-2 (an industrial strain) washed out after an aerobic-to-anaerobic switch in the absence of AGF. S. cerevisiae PE-2 seemed to cope better than the laboratory strain with this extremely low O2 availability, since it presented higher biomass yield, lower specific rates of glucose consumption and CO2 formation, and higher survival at low pH. Lipid (fatty acid and sterol) composition dramatically altered when cells were grown anaerobically without AGF: saturated fatty acid, squalene and lanosterol contents increased, when compared to either cells grown aerobically or anaerobically with AGF. We concluded that these lipid alterations negatively affect cell viability during exposure to low pH or high ethanol titers.
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Affiliation(s)
- Bruno Labate Vale da Costa
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, 13083-862 Campinas-SP, Brazil
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, Av. Prof. Lineu Prestes, 580, 05424-970 São Paulo-SP, Brazil
| | - Vijayendran Raghavendran
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, 13083-862 Campinas-SP, Brazil
| | - Luís Fernando Mercier Franco
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, Av. Prof. Lineu Prestes, 580, 05424-970 São Paulo-SP, Brazil
| | | | - Marcos Yukio Yoshinaga
- Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo-SP, Brazil
| | - Sayuri Miyamoto
- Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo-SP, Brazil
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, Av. Prof. Lineu Prestes, 580, 05424-970 São Paulo-SP, Brazil
| | - Andreas Karoly Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, 13083-862 Campinas-SP, Brazil
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Sewsynker-Sukai Y, Gueguim Kana EB. Simultaneous saccharification and bioethanol production from corn cobs: Process optimization and kinetic studies. BIORESOURCE TECHNOLOGY 2018; 262:32-41. [PMID: 29689438 DOI: 10.1016/j.biortech.2018.04.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the simultaneous saccharification and fermentation (SSF) process for bioethanol production from corn cobs with prehydrolysis (PSSF) and without prehydrolysis (OSSF). Two response surface models were developed with high coefficients of determination (>0.90). Process optimization gave high bioethanol concentrations and bioethanol conversions for the PSSF (36.92 ± 1.34 g/L and 62.36 ± 2.27%) and OSSF (35.04 ± 0.170 g/L and 58.13 ± 0.283%) models respectively. Additionally, the logistic and modified Gompertz models were used to study the kinetics of microbial cell growth and ethanol formation under microaerophilic and anaerobic conditions. Cell growth in the OSSFmicroaerophilic process gave the highest maximum specific growth rate (µmax) of 0.274 h-1. The PSSFmicroaerophilic bioprocess gave the highest potential maximum bioethanol concentration (Pm) (42.24 g/L). This study demonstrated that microaerophilic rather than anaerobic culture conditions enhanced cell growth and bioethanol production, and that additional prehydrolysis steps do not significantly impact on the bioethanol concentration and conversion in SSF process.
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Affiliation(s)
| | - E B Gueguim Kana
- University of KwaZulu-Natal, School of Life Sciences, Pietermaritzburg, South Africa.
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11
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Molecular and functional characterization of two pyruvate decarboxylase genes, PDC1 and PDC5, in the thermotolerant yeast Kluyveromyces marxianus. Appl Microbiol Biotechnol 2018; 102:3723-3737. [DOI: 10.1007/s00253-018-8862-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/01/2018] [Accepted: 02/08/2018] [Indexed: 10/17/2022]
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12
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Anaerobiosis revisited: growth of Saccharomyces cerevisiae under extremely low oxygen availability. Appl Microbiol Biotechnol 2018; 102:2101-2116. [DOI: 10.1007/s00253-017-8732-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022]
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13
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Dias O, Basso TO, Rocha I, Ferreira EC, Gombert AK. Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates. Antonie van Leeuwenhoek 2017; 111:183-195. [PMID: 28900755 DOI: 10.1007/s10482-017-0940-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The yeast Kluyveromyces lactis has received attention both from academia and industry due to some important features, such as its capacity to grow in lactose-based media, its safe status, its suitability for large-scale cultivation and for heterologous protein synthesis. It has also been considered as a model organism for genomics and metabolic regulation. Despite this, very few studies were carried out hitherto under strictly controlled conditions, such as those found in a chemostat. Here we report a set of quantitative physiological data generated during chemostat cultivations with the K. lactis CBS 2359 strain, obtained under glucose-limiting and fully aerobic conditions. This dataset serves [corrected] as a basis for the comparison of K. lactis with the model yeast Saccharomyces cerevisiae in terms of their elemental compositions, as well as for future metabolic flux analysis and metabolic modelling studies with K. lactis.
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Affiliation(s)
- Oscar Dias
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil
| | - Thiago O Basso
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil.
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Eugénio C Ferreira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas K Gombert
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil.,School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
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14
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A Pichia anomala Strain (P. anomala M1) Isolated from Traditional Greek Sausage is an Effective Producer of Extracellular Lipolytic Enzyme in Submerged Fermentation. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Pentjuss A, Stalidzans E, Liepins J, Kokina A, Martynova J, Zikmanis P, Mozga I, Scherbaka R, Hartman H, Poolman MG, Fell DA, Vigants A. Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. J Ind Microbiol Biotechnol 2017; 44:1177-1190. [PMID: 28444480 DOI: 10.1007/s10295-017-1946-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/16/2017] [Indexed: 12/11/2022]
Abstract
The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism's potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.
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Affiliation(s)
- A Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - E Stalidzans
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia.
| | - J Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - A Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - J Martynova
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - P Zikmanis
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - I Mozga
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - R Scherbaka
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - H Hartman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - M G Poolman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - D A Fell
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - A Vigants
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
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16
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Wellenbeck W, Mampel J, Naumer C, Knepper A, Neubauer P. Fast-track development of a lactase production process with Kluyveromyces lactis by a progressive parameter-control workflow. Eng Life Sci 2016; 17:1185-1194. [PMID: 32624746 DOI: 10.1002/elsc.201600031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/12/2016] [Accepted: 09/07/2016] [Indexed: 11/12/2022] Open
Abstract
The time-to-market challenge is key to success for consumer goods affiliated industries. In recent years, the dairy industry faces a fast and constantly growing demand for enzymatically produced lactose-free milk products, mainly driven by emerging markets in South America and Asia. In order to take advantage of this opportunity, we developed a fermentation process for lactase (β-galactosidase) from Kluyveromyces lactis within short time. Here, we describe the process of stepwise increasing the level of control over relevant process parameters during scale-up that established a highly efficient and stable production system. Process development started with evolutionary engineering to generate catabolite-derepressed variants of the K. lactis wild-type strain. A high-throughput screening mimicking fed-batch cultivation identified a constitutive lactase overproducer with 260-fold improved activity of 4.4 U per milligram dry cell weight when cultivated in glucose minimal medium. During scale-up, process control was progressively increased up to the level of conventional, fully controlled fed-batch cultivations by simulating glucose feed, applying pH- and dissolved oxygen tension (DOT)-sensor technology to small scale, and by the use of a milliliter stirred tank bioreactor. Additionally, process development was assisted by design-of-experiments optimization of the growth medium employing the response surface methodology.
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Affiliation(s)
- Wenzel Wellenbeck
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Christian Naumer
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Andreas Knepper
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
| | - Peter Neubauer
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
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17
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Usage of different aerobic non-Saccharomyces yeasts and experimental conditions as a tool for reducing the potential ethanol content in wines. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2703-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances. Fungal Genet Biol 2016; 89:126-136. [DOI: 10.1016/j.fgb.2015.12.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/18/2015] [Accepted: 12/05/2015] [Indexed: 12/16/2022]
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19
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Homola P, Kurák T, Illeová V, Polakovič M. Cultivation of Pichia capsulata as a whole-cell biocatalyst with NADH-dependent alcohol dehydrogenase activity for R -1-phenylethanol production. FOOD AND BIOPRODUCTS PROCESSING 2015. [DOI: 10.1016/j.fbp.2015.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Ottaviano D, Montanari A, De Angelis L, Santomartino R, Visca A, Brambilla L, Rinaldi T, Bello C, Reverberi M, Bianchi MM. Unsaturated fatty acids-dependent linkage between respiration and fermentation revealed by deletion of hypoxic regulatory KlMGA2 gene in the facultative anaerobe-respiratory yeast Kluyveromyces lactis. FEMS Yeast Res 2015; 15:fov028. [PMID: 26019145 DOI: 10.1093/femsyr/fov028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2015] [Indexed: 01/03/2023] Open
Abstract
In the yeast Kluyveromyces lactis, the inactivation of structural or regulatory glycolytic and fermentative genes generates obligate respiratory mutants which can be characterized by sensitivity to the mitochondrial drug antimycin A on glucose medium (Rag(-) phenotype). Rag(-) mutations can occasionally be generated by the inactivation of genes not evidently related to glycolysis or fermentation. One such gene is the hypoxic regulatory gene KlMGA2. In this work, we report a study of the many defects, in addition to the Rag(-) phenotype, generated by KlMGA2 deletion. We analyzed the fermentative and respiratory metabolism, mitochondrial functioning and morphology in the Klmga2Δ strain. We also examined alterations in the regulation of the expression of lipid biosynthetic genes, in particular fatty acids, ergosterol and cardiolipin, under hypoxic and cold stress and the phenotypic suppression by unsaturated fatty acids of the deleted strain. Results indicate that, despite the fact that the deleted mutant strain had a typical glycolytic/fermentative phenotype and KlMGA2 is a hypoxic regulatory gene, the deletion of this gene generated defects linked to mitochondrial functions suggesting new roles of this protein in the general regulation and cellular fitness of K. lactis. Supplementation of unsaturated fatty acids suppressed or modified these defects suggesting that KlMga2 modulates membrane functioning or membrane-associated functions, both cytoplasmic and mitochondrial.
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Affiliation(s)
- Daniela Ottaviano
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo De Angelis
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Rosa Santomartino
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Visca
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, Bicocca University of Milan, p.zza Della Scienza 2, 20126 Milan, Italy
| | - Teresa Rinaldi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy Pasteur Institut Cenci-Bolognetti Foundation, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Cristiano Bello
- Departement of Environmental Biology, Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Massimo Reverberi
- Departement of Environmental Biology, Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Michele M Bianchi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, p.le Aldo Moro 5, 00185 Rome, Italy
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21
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Akanni GB, du Preez JC, Steyn L, Kilian SG. Protein enrichment of an Opuntia ficus-indica cladode hydrolysate by cultivation of Candida utilis and Kluyveromyces marxianus. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:1094-1102. [PMID: 25371280 PMCID: PMC4402007 DOI: 10.1002/jsfa.6985] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/18/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND The cladodes of Opuntia ficus-indica (prickly pear cactus) have a low protein content; for use as a balanced feed, supplementation with other protein sources is therefore desirable. We investigated protein enrichment by cultivation of the yeasts Candida utilis and Kluyveromyces marxianus in an enzymatic hydrolysate of the cladode biomass. RESULTS Dilute acid pretreatment and enzymatic hydrolysis of sun-dried cladodes resulted in a hydrolysate containing (per litre) 45.5 g glucose, 6.3 g xylose, 9.1 g galactose, 10.8 g arabinose and 9.6 g fructose. Even though K. marxianus had a much higher growth rate and utilized l-arabinose and d-galactose more completely than C. utilis, its biomass yield coefficient was lower due to ethanol and ethyl acetate production despite aerobic cultivation. Yeast cultivation more than doubled the protein content of the hydrolysate, with an essential amino acid profile superior to sorghum and millet grains. CONCLUSIONS This K. marxianus strain was weakly Crabtree positive. Despite its low biomass yield, its performance compared well with C. utilis. This is the first report showing that the protein content and quality of O. ficus-indica cladode biomass could substantially be improved by yeast cultivation, including a comparative evaluation of C. utilis and K. marxianus.
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Affiliation(s)
| | - James C du Preez
- *Correspondence to: James du Preez, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa. E-mail:
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22
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Dashko S, Zhou N, Compagno C, Piškur J. Why, when, and how did yeast evolve alcoholic fermentation? FEMS Yeast Res 2014; 14:826-32. [PMID: 24824836 PMCID: PMC4262006 DOI: 10.1111/1567-1364.12161] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 05/07/2014] [Accepted: 05/07/2014] [Indexed: 11/28/2022] Open
Abstract
The origin of modern fruits brought to microbial communities an abundant source of rich food based on simple sugars. Yeasts, especially Saccharomyces cerevisiae, usually become the predominant group in these niches. One of the most prominent and unique features and likely a winning trait of these yeasts is their ability to rapidly convert sugars to ethanol at both anaerobic and aerobic conditions. Why, when, and how did yeasts remodel their carbon metabolism to be able to accumulate ethanol under aerobic conditions and at the expense of decreasing biomass production? We hereby review the recent data on the carbon metabolism in Saccharomycetaceae species and attempt to reconstruct the ancient environment, which could promote the evolution of alcoholic fermentation. We speculate that the first step toward the so-called fermentative lifestyle was the exploration of anaerobic niches resulting in an increased metabolic capacity to degrade sugar to ethanol. The strengthened glycolytic flow had in parallel a beneficial effect on the microbial competition outcome and later evolved as a “new” tool promoting the yeast competition ability under aerobic conditions. The basic aerobic alcoholic fermentation ability was subsequently “upgraded” in several lineages by evolving additional regulatory steps, such as glucose repression in the S. cerevisiae clade, to achieve a more precise metabolic control.
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Affiliation(s)
- Sofia Dashko
- Wine Research Centre, University of Nova Gorica, Vipava, Slovenia; Department of Biology, Lund University, Lund, Sweden
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23
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Dias O, Pereira R, Gombert AK, Ferreira EC, Rocha I. iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis. Biotechnol J 2014; 9:776-90. [DOI: 10.1002/biot.201300242] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/07/2014] [Accepted: 04/23/2014] [Indexed: 11/08/2022]
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24
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Löser C, Urit T, Bley T. Perspectives for the biotechnological production of ethyl acetate by yeasts. Appl Microbiol Biotechnol 2014; 98:5397-415. [DOI: 10.1007/s00253-014-5765-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 12/18/2022]
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25
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Ottaviano D, Micolonghi C, Tizzani L, Lemaire M, Wésolowski-Louvel M, De Stefano ME, Ranieri D, Bianchi MM. Autoregulation of the Kluyveromyces lactis pyruvate decarboxylase gene KlPDC1 involves the regulatory gene RAG3. MICROBIOLOGY-SGM 2014; 160:1369-1378. [PMID: 24763423 DOI: 10.1099/mic.0.078543-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the yeast Kluyveromyces lactis, the pyruvate decarboxylase gene KlPDC1 is strongly regulated at the transcription level by different environmental factors. Sugars and hypoxia act as inducers of transcription, while ethanol acts as a repressor. Their effects are mediated by gene products, some of which have been characterized. KlPDC1 transcription is also strongly repressed by its product--KlPdc1--through a mechanism called autoregulation. We performed a genetic screen that allowed us to select and identify the regulatory gene RAG3 as a major factor in the transcriptional activity of the KlPDC1 promoter in the absence of the KlPdc1 protein, i.e. in the autoregulatory mechanism. We also showed that the two proteins Rag3 and KlPdc1 interact, co-localize in the cell and that KlPdc1 may control Rag3 nuclear localization.
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Affiliation(s)
- Daniela Ottaviano
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Chiara Micolonghi
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Lorenza Tizzani
- Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Marc Lemaire
- CNRS, Villeurbanne, France.,Université Lyon1, Lyon, France.,Génétique Moléculaire des Levures, UMR5240 Microbiologie, Adaptation et Pathogénie, Université de Lyon, Lyon, France
| | - Micheline Wésolowski-Louvel
- CNRS, Villeurbanne, France.,Université Lyon1, Lyon, France.,Génétique Moléculaire des Levures, UMR5240 Microbiologie, Adaptation et Pathogénie, Université de Lyon, Lyon, France
| | - Maria Egle De Stefano
- Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy.,Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
| | - Danilo Ranieri
- Dip. Medicina clinica e molecolare, Sapienza Università di Roma, via di Grottarossa 1035, 00189 Roma, Italy
| | - Michele M Bianchi
- Istituto Pasteur Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Roma, Italy.,Dip. Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, p.le Aldo Moro 5, 00185 Roma, Italy
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26
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Moshtanska V, Kujumdzieva A, Petrova V, Beeumen JV, Voelter W, Devreese B, Dolashka-Angelova P. Glycosylated CU/ZN-Superoxide Dismutase fromKluyveromycesYeast, Determined by Mass Spectrometry. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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27
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Fonseca GG, de Carvalho NMB, Gombert AK. Growth of the yeast Kluyveromyces marxianus CBS 6556 on different sugar combinations as sole carbon and energy source. Appl Microbiol Biotechnol 2013; 97:5055-67. [PMID: 23435899 DOI: 10.1007/s00253-013-4748-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/31/2013] [Accepted: 01/31/2013] [Indexed: 12/01/2022]
Abstract
The yeast Kluyveromyces marxianus has been pointed out as a promising microorganism for a variety of industrial bioprocesses. Although genetic tools have been developed for this yeast and different potential applications have been investigated, quantitative physiological studies have rarely been reported. Here, we report and discuss the growth, substrate consumption, metabolite formation, and respiratory parameters of K. marxianus CBS 6556 during aerobic batch bioreactor cultivations, using a defined medium with different sugars as sole carbon and energy source, at 30 and 37 °C. Cultivations were carried out both on single sugars and on binary sugar mixtures. Carbon balances closed within 95 to 101 % in all experiments. Biomass and CO2 were the main products of cell metabolism, whereas by-products were always present in very low proportion (<3 % of the carbon consumed), as long as full aerobiosis was guaranteed. On all sugars tested as sole carbon and energy source (glucose, fructose, sucrose, lactose, and galactose), the maximum specific growth rate remained between 0.39 and 0.49 h(-1), except for galactose at 37 °C, which only supported growth at 0.31 h(-1). Different growth behaviors were observed on the binary sugar mixtures investigated (glucose and lactose, glucose and galactose, lactose and galactose, glucose and fructose, galactose and fructose, fructose and lactose), and the observations were in agreement with previously published data on the sugar transport systems in K. marxianus. We conclude that K. marxianus CBS 6556 does not present any special nutritional requirements; grows well in the range of 30 to 37 °C on different sugars; is capable of growing on sugar mixtures in a shorter period of time than Saccharomyces cerevisiae, which is interesting from an industrial point of view; and deviates tiny amounts of carbon towards metabolite formation, as long as full aerobiosis is maintained.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Department of Chemical Engineering, University of São Paulo, PO Box 61548, CEP 05424-970 São Paulo, SP, Brazil
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28
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Yeast respiration of sugars by non-Saccharomyces yeast species: A promising and barely explored approach to lowering alcohol content of wines. Trends Food Sci Technol 2013. [DOI: 10.1016/j.tifs.2012.06.015] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Leite FCB, Basso TO, Pita WDB, Gombert AK, Simões DA, de Morais MA. Quantitative aerobic physiology of the yeast Dekkera bruxellensis, a major contaminant in bioethanol production plants. FEMS Yeast Res 2012; 13:34-43. [PMID: 23078341 DOI: 10.1111/1567-1364.12007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 08/07/2012] [Accepted: 09/07/2012] [Indexed: 12/01/2022] Open
Abstract
Dekkera bruxellensis has been described as the major contaminant yeast of industrial ethanol production, although little is known about its physiology. The aim of this study was to investigate the growth of this yeast in diverse carbon sources and involved conducting shake-flask and glucose- or sucrose-limited chemostats experiments, and from the chemostat data, the stoichiometry of biomass formation during aerobic growth was established. As a result of the shake-flask experiments with hexoses or disaccharides, the specific growth rates were calculated, and a different behavior in rich and mineral medium was observed concerning to profile of acetate and ethanol production. In C-limited chemostats conditions, the metabolism of this yeast was completely respiratory, and the biomass yields reached values of 0.62 gDW gS(-1) . In addition, glucose pulses were applied to the glucose- or sucrose-limited chemostats. These results showed that D. bruxellensis has a short-term Crabtree effect. While the glucose pulse was at the sucrose-limited chemostat, sucrose accumulated at the reactor, indicating the presence of a glucose repression mechanism in D. bruxellensis.
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30
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Intracellular NADPH levels affect the oligomeric state of the glucose 6-phosphate dehydrogenase. EUKARYOTIC CELL 2012; 11:1503-11. [PMID: 23064253 DOI: 10.1128/ec.00211-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the yeast Kluyveromyces lactis, glucose 6-phosphate dehydrogenase (G6PDH) is detected as two differently migrating forms on native polyacrylamide gels. The pivotal metabolic role of G6PDH in K. lactis led us to investigate the mechanism controlling the two activities in respiratory and fermentative mutant strains. An extensive analysis of these mutants showed that the NAD(+)(H)/NADP(+)(H)-dependent cytosolic alcohol (ADH) and aldehyde (ALD) dehydrogenase balance affects the expression of the G6PDH activity pattern. Under fermentative/ethanol growth conditions, the concomitant activation of ADH and ALD activities led to cytosolic accumulation of NADPH, triggering an alteration in the oligomeric state of the G6PDH caused by displacement/release of the structural NADP(+) bound to each subunit of the enzyme. The new oligomeric G6PDH form with faster-migrating properties increases as a consequence of intracellular redox unbalance/NADPH accumulation, which inhibits G6PDH activity in vivo. The appearance of a new G6PDH-specific activity band, following incubation of Saccharomyces cerevisiae and human cellular extracts with NADP(+), also suggests that a regulatory mechanism of this activity through NADPH accumulation is highly conserved among eukaryotes.
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31
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Kluyveromyces lactis: a suitable yeast model to study cellular defense mechanisms against hypoxia-induced oxidative stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:634674. [PMID: 22928082 PMCID: PMC3425888 DOI: 10.1155/2012/634674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/22/2012] [Indexed: 11/17/2022]
Abstract
Studies about hypoxia-induced oxidative stress in human health disorders take advantage from the use of unicellular eukaryote models. A widely extended model is the fermentative yeast Saccharomyces cerevisiae. In this paper, we describe an overview of the molecular mechanisms induced by a decrease in oxygen availability and their interrelationship with the oxidative stress response in yeast. We focus on the differential characteristics between S. cerevisiae and the respiratory yeast Kluyveromyces lactis, a complementary emerging model, in reference to multicellular eukaryotes.
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32
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Micolonghi C, Ottaviano D, Di Silvio E, Damato G, Heipieper HJ, Bianchi MM. A dual signalling pathway for the hypoxic expression of lipid genes, dependent on the glucose sensor Rag4, is revealed by the analysis of the KlMGA2 gene in Kluyveromyces lactis. MICROBIOLOGY-SGM 2012; 158:1734-1744. [PMID: 22516223 DOI: 10.1099/mic.0.059402-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the respiratory yeast Kluyveromyces lactis, little is known about the factors regulating the metabolic response to oxygen shortage. After searching for homologues of characterized Saccharomyces cerevisiae regulators of the hypoxic response, we identified a gene that we named KlMGA2, which is homologous to MGA2. The deletion of KlMGA2 strongly reduced both the fermentative and respiratory growth rate and altered fatty acid composition and the unsaturation index of membranes. The reciprocal heterologous expression of MGA2 and KlMGA2 in the corresponding deletion mutant strains suggested that Mga2 and KlMga2 are functional homologues. KlMGA2 transcription was induced by hypoxia and the glucose sensor Rag4 mediated the hypoxic induction of KlMGA2. Transcription of lipid biosynthetic genes KlOLE1, KlERG1, KlFAS1 and KlATF1 was induced by hypoxia and was dependent on KlMga2, except for KlOLE1. Rag4 was required for hypoxic induction of transcription for both KlMga2-dependent (KlERG1) and KlMga2-independent (KlOLE1) structural genes.
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Affiliation(s)
- Chiara Micolonghi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Ottaviano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Eva Di Silvio
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe Damato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Michele M Bianchi
- Pasteur Institut Cenci-Bolognetti Foundation, Sapienza University of Rome, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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Rodríguez Torres AM, Lamas Maceiras M, Rodríguez Belmonte E, Núñez Naveira L, Blanco Calvo M, Cerdán ME. KlRox1p contributes to yeast resistance to metals and is necessary for KlYCF1 expression in the presence of cadmium. Gene 2012; 497:27-37. [DOI: 10.1016/j.gene.2012.01.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 01/21/2012] [Indexed: 11/29/2022]
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Grahl N, Puttikamonkul S, Macdonald JM, Gamcsik MP, Ngo LY, Hohl TM, Cramer RA. In vivo hypoxia and a fungal alcohol dehydrogenase influence the pathogenesis of invasive pulmonary aspergillosis. PLoS Pathog 2011; 7:e1002145. [PMID: 21811407 PMCID: PMC3141044 DOI: 10.1371/journal.ppat.1002145] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/17/2011] [Indexed: 01/09/2023] Open
Abstract
Currently, our knowledge of how pathogenic fungi grow in mammalian host environments is limited. Using a chemotherapeutic murine model of invasive pulmonary aspergillosis (IPA) and (1)H-NMR metabolomics, we detected ethanol in the lungs of mice infected with Aspergillus fumigatus. This result suggests that A. fumigatus is exposed to oxygen depleted microenvironments during infection. To test this hypothesis, we utilized a chemical hypoxia detection agent, pimonidazole hydrochloride, in three immunologically distinct murine models of IPA (chemotherapeutic, X-CGD, and corticosteroid). In all three IPA murine models, hypoxia was observed during the course of infection. We next tested the hypothesis that production of ethanol in vivo by the fungus is involved in hypoxia adaptation and fungal pathogenesis. Ethanol deficient A. fumigatus strains showed no growth defects in hypoxia and were able to cause wild type levels of mortality in all 3 murine models. However, lung immunohistopathology and flow cytometry analyses revealed an increase in the inflammatory response in mice infected with an alcohol dehydrogenase null mutant strain that corresponded with a reduction in fungal burden. Consequently, in this study we present the first in vivo observations that hypoxic microenvironments occur during a pulmonary invasive fungal infection and observe that a fungal alcohol dehydrogenase influences fungal pathogenesis in the lung. Thus, environmental conditions encountered by invading pathogenic fungi may result in substantial fungal metabolism changes that influence subsequent host immune responses.
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Affiliation(s)
- Nora Grahl
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
| | - Srisombat Puttikamonkul
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
| | - Jeffrey M. Macdonald
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michael P. Gamcsik
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, United States of America
| | - Lisa Y. Ngo
- Infectious Disease Sciences, Vaccine and Infectious Disease Division, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tobias M. Hohl
- Infectious Disease Sciences, Vaccine and Infectious Disease Division, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Robert A. Cramer
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana, United States of America
- * E-mail:
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Rocha SN, Abrahão-Neto J, Gombert AK. Physiological diversity within the Kluyveromyces marxianus species [corrected]. Antonie van Leeuwenhoek 2011; 100:619-30. [PMID: 21732033 DOI: 10.1007/s10482-011-9617-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/21/2011] [Indexed: 11/30/2022]
Abstract
The Kluyveromyces marxianus strains CBS 6556, CBS 397 and CBS 712(T) were cultivated on a defined medium with either glucose, lactose or sucrose as the sole carbon source, at 30 and 37°C. The aim of this work was to evaluate the diversity within this species, in terms of the macroscopic physiology. The main properties evaluated were: intensity of the Crabtree effect, specific growth rate, biomass yield on substrate, metabolite excretion and protein secretion capacity, inferred by measuring extracellular inulinase activity. The strain Kluyveromyces lactis CBS 2359 was evaluated in parallel, since it is the best described Kluyveromyces yeast and thus can be used as a control for the experimental setup. K. marxianus CBS 6556 presented the highest specific growth rate (0.70 h(-1)) and the highest specific inulinase activity (1.65 U mg(-1) dry cell weight) among all strains investigated, when grown at 37°C with sucrose as the sole carbon source. The lowest metabolite formation and highest biomass yield on substrate (0.59 g dry cell weight g sucrose(-1)) was achieved by K. marxianus CBS 712(T) at 37°C. Taken together, the results show a systematic comparison of carbon and energy metabolism among three of the best known K. marxianus strains, in parallel to K. lactis CBS 2359.
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Affiliation(s)
- Saul Nitsche Rocha
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil.
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Corrales Escobosa AR, Rangel Porras RA, Meza Carmen V, Gonzalez Hernandez GA, Torres Guzman JC, Wrobel K, Wrobel K, Roncero MIG, Gutierrez Corona JF. Fusarium oxysporum Adh1 has dual fermentative and oxidative functions and is involved in fungal virulence in tomato plants. Fungal Genet Biol 2011; 48:886-95. [PMID: 21704720 DOI: 10.1016/j.fgb.2011.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 05/30/2011] [Accepted: 06/02/2011] [Indexed: 11/29/2022]
Abstract
An alcohol dehydrogenase gene, adh1, has been identified in the vascular wilt fungus Fusarium oxysporum f. sp. lycopersici. Reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that adh1 is highly expressed in mycelia grown in potato dextrose liquid medium (PDB) under hypoxic conditions, as compared to mycelia grown under aerobic conditions. One spontaneous allyl alcohol-resistant (Ally(R)) mutant exhibited insertion of an incomplete F.oxysporum transposable element, while another mutant contained a short (13 nucleotide) deletion, in both cases interrupting the coding region of the adh1 gene. These mutations caused deficiency in Adh activity due to loss of the main constitutive isoform of Adh1, as well as alteration of different physiological parameters related to carbon and energy metabolism, including the ability to use ethanol as a carbon source under aerobic conditions; impaired growth under hypoxic conditions with glucose as the carbon source; and diminished production of ethanol in glucose-containing medium. Interestingly, the adh1 mutations resulted in a significant delay in fungal disease development in tomato plants. Complementation with the wild-type adh1 allele repaired all defects caused by mutation, indicating that the product of the adh1 gene has dual enzymatic functions (fermentative and oxidative), depending on culture conditions, and is also required for full fungal virulence.
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Affiliation(s)
- Alma Rosa Corrales Escobosa
- Departamento de Biología y, DCNyE, Universidad de Guanajuato. Noria Alta s/n, Guanajuato, México 36000, Mexico
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Rozpędowska E, Galafassi S, Johansson L, Hagman A, Piškur J, Compagno C. Candida albicans--a pre-whole genome duplication yeast--is predominantly aerobic and a poor ethanol producer. FEMS Yeast Res 2011; 11:285-91. [PMID: 21205163 DOI: 10.1111/j.1567-1364.2010.00715.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Yeast species belonging to the lineage that underwent the whole genome duplication (WGD), and including Saccharomyces cerevisiae, can grow under anaerobiosis and accumulate ethanol in the presence of glucose and oxygen. The pre-WGD yeasts, which branched from the S. cerevisiae lineage just before the WGD event, including Kluyveromyces lactis, are more dependent on oxygen and do not accumulate large amounts of ethanol in the presence of excess oxygen. Yeasts that belong to the so-called 'lower branches' of the yeast phylogenetic tree and diverged from S. cerevisiae more than 200 million years ago have so far not been thoroughly investigated for their physiology and carbon metabolism. Here, we have studied several isolates of Candida albicans and Debaryomyces hansenii for their dependence on oxygen. Candida albicans grew very poorly at an oxygen concentration <1 p.p.m. and D. hansenii could not grow at all. In aerobic batch cultivations, C. albicans exhibited a predominantly aerobic metabolism, accumulating only small amounts of ethanol (0.01-0.09 g g(-1) glucose). Apparently, C. albicans and several other pre-WGD yeasts still exhibit the original traits of the yeast progenitor: poor accumulation of ethanol under aerobic conditions and strong dependence on the presence of oxygen.
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Christen S, Sauer U. Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics. FEMS Yeast Res 2011; 11:263-72. [PMID: 21205161 DOI: 10.1111/j.1567-1364.2010.00713.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Key distinguishing characteristics of yeast glucose metabolism are the relative proportions of fermentation and respiration. Crabtree-positive yeast species exhibit a respirofermentative metabolism, whereas aerobic species respire fully without secretion of fermentation byproducts. Physiological data suggest a gradual transition in different species between these two states. Here, we investigate whether this gradual transition also occurs at the intracellular level by quantifying the intracellular metabolism of Saccharomyces cerevisiae, Saccharomyces bayanus, Saccharomyces exiguus, Kluyveromyces thermotolerans, Yarrowia lipolytica, Pichia angusta and Candida rugosa by (13)C-flux analysis and metabolomics. Different from the extracellular physiology, the intracellular fluxes through the tricarboxylic acid cycle fall into two classes where the aerobic species exhibit much higher respiratory fluxes at otherwise similar glycolytic fluxes. More generally, we found the intracellular metabolite concentrations to be primarily species-specific. The sole exception of a metabolite-flux correlation in a species-overarching manner was found for fructose-1,6-bisphosphate and dihydroxyacetone-phosphate, indicating a conservation of the functional properties around these two metabolites.
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Affiliation(s)
- Stefan Christen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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Anders A, Breunig KD. Evolutionary aspects of a genetic network: studying the lactose/galactose regulon of Kluyveromyces lactis. Methods Mol Biol 2011; 734:259-277. [PMID: 21468994 DOI: 10.1007/978-1-61779-086-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The budding yeast Kluyveromyces lactis has diverged from the Saccharomyces lineage before the whole-genome duplication and its genome sequence reveals lower redundancy of many genes. Moreover, it shows lower preference for fermentative carbon metabolism and a broader substrate spectrum making it a particularly rewarding system for comparative and evolutionary studies of carbon-regulated genetic networks. The lactose/galactose regulon of K. lactis, which is regulated by the prototypic transcription activator Gal4 exemplifies important aspects of network evolution when compared with the model GAL regulon of Saccharomyces cerevisiae. Differences in physiology relate to different subcellular compartmentation of regulatory components and, importantly, to quantitative differences in protein-protein interactions rather than major differences in network architecture. Here, we introduce genetic and biochemical tools to study K. lactis in general and the lactose/galactose regulon in particular. We present methods to quantify relevant protein-protein interactions in that network and to visualize such differences in simple plate assays allowing for genetic approaches in further studies.
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Affiliation(s)
- Alexander Anders
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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Rocha SN, Abrahão-Neto J, Cerdán ME, Gombert AK, González-Siso MI. Heterologous expression of a thermophilic esterase in Kluyveromyces yeasts. Appl Microbiol Biotechnol 2010; 89:375-85. [PMID: 20862582 DOI: 10.1007/s00253-010-2869-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/13/2010] [Accepted: 09/07/2010] [Indexed: 11/26/2022]
Abstract
In the present work, a thermophilic esterase from Thermus thermophilus HB27 was cloned into Kluyveromyces marxianus and into Kluyveromyces lactis using two different expression systems, yielding four recombinant strains. K. lactis showed the highest esterase expression levels (294 units per gram dry cell weight, with 65% of cell-bound enzyme) using an episomal system with the PGK promoter and terminator from Saccharomyces cerevisiae combined with the K. lactis k1 secretion signal. K. marxianus showed higher secretion efficiency of the heterologous esterase (56.9 units per gram dry cell weight, with 34% of cell-bound enzyme) than K. lactis. Hydrolytic activities for the heterologous esterases were maximum at pH values between 8.0 and 9.0 for both yeast species and at temperatures of 50 °C and 45 °C for K. marxianus and K. lactis, respectively. When compared to previously published data on this same esterase produced in the original host or in S. cerevisiae, our results indicate that Kluyveromyces yeasts can be considered good hosts for the heterologous secretion of thermophilic esterases, which have a potential application in biodiesel production or in resolving racemates.
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Affiliation(s)
- Saul Nitsche Rocha
- Department of Chemical Engineering, University of São Paulo, C.P. 61548, 05424-970 São Paulo, SP, Brazil.
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Rocha SN, Abrahão-Neto J, Cerdán ME, González-Siso MI, Gombert AK. Heterologous expression of glucose oxidase in the yeast Kluyveromyces marxianus. Microb Cell Fact 2010; 9:4. [PMID: 20092622 PMCID: PMC2817671 DOI: 10.1186/1475-2859-9-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 01/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In spite of its advantageous physiological properties for bioprocess applications, the use of the yeast Kluyveromyces marxianus as a host for heterologous protein production has been very limited, in constrast to its close relative Kluyveromyces lactis. In the present work, the model protein glucose oxidase (GOX) from Aspergillus niger was cloned into K. marxianus CBS 6556 and into K. lactis CBS 2359 using three different expression systems. We aimed at verifying how each expression system would affect protein expression, secretion/localization, post-translational modification, and biochemical properties. RESULTS The highest GOX expression levels (1552 units of secreted protein per gram dry cell weight) were achieved using an episomal system, in which the INU1 promoter and terminator were used to drive heterologous gene expression, together with the INU1 prepro sequence, which was employed to drive secretion of the enzyme. In all cases, GOX was mainly secreted, remaining either in the periplasmic space or in the culture supernatant. Whereas the use of genetic elements from Saccharomyces cerevisiae to drive heterologous protein expression led to higher expression levels in K. lactis than in K. marxianus, the use of INU1 genetic elements clearly led to the opposite result. The biochemical characterization of GOX confirmed the correct expression of the protein and showed that K. marxianus has a tendency to hyperglycosylate the protein, in a similar way as already observed for other yeasts, although this tendency seems to be smaller than the one of e.g. K. lactis and S. cerevisiae. Hyperglycosylation of GOX does not seem to affect its affinity for the substrate, nor its activity. CONCLUSIONS Taken together, our results indicate that K. marxianus is indeed a good host for the expression of heterologous proteins, not only for its physiological properties, but also because it correctly secretes and folds these proteins.
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Affiliation(s)
- Saul N Rocha
- Department of Chemical Engineering, Polytechnic School of Engineering, University of São Paulo, CP 61548, 05424-970 São Paulo-SP, Brazil
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Abstract
Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose-fermenting yeast Pichia stipitis. These studies have provided an insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the result of several gene products acting together. When coinheritance is necessary for the overall physiological function, recombination and selection favor colocation of these genes in a cluster. These are particularly evident in strongly conserved and idiomatic traits. In some cases, the functional clusters consist of multiple gene families. Phylogenetic analyses of the members in each family show that once formed, functional clusters undergo duplication and differentiation. Genome-wide expression analysis reveals that regulatory patterns of clusters are similar after they have duplicated and that the expression profiles evolve along with functional differentiation of the clusters. Orthologous gene families appear to arise through tandem gene duplication, followed by differentiation in the regulatory and coding regions of the gene. Genome-wide expression analysis combined with cross-species comparisons of functional gene clusters should reveal many more aspects of eukaryotic physiology.
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Oxygen-dependent transcriptional regulator Hap1p limits glucose uptake by repressing the expression of the major glucose transporter gene RAG1 in Kluyveromyces lactis. EUKARYOTIC CELL 2008; 7:1895-905. [PMID: 18806211 DOI: 10.1128/ec.00018-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The HAP1 (CYP1) gene product of Saccharomyces cerevisiae is known to regulate the transcription of many genes in response to oxygen availability. This response varies according to yeast species, probably reflecting the specific nature of their oxidative metabolism. It is suspected that a difference in the interaction of Hap1p with its target genes may explain some of the species-related variation in oxygen responses. As opposed to the fermentative S. cerevisiae, Kluyveromyces lactis is an aerobic yeast species which shows different oxygen responses. We examined the role of the HAP1-equivalent gene (KlHAP1) in K. lactis. KlHap1p showed a number of sequence features and some gene targets (such as KlCYC1) in common with its S. cerevisiae counterpart, and KlHAP1 was capable of complementing the hap1 mutation. However, the KlHAP1 disruptant showed temperature-sensitive growth on glucose, especially at low glucose concentrations. At normal temperature, 28 degrees C, the mutant grew well, the colony size being even greater than that of the wild type. The most striking observation was that KlHap1p repressed the expression of the major glucose transporter gene RAG1 and reduced the glucose uptake rate. This suggested an involvement of KlHap1p in the regulation of glycolytic flux through the glucose transport system. The DeltaKlhap1 mutant showed an increased ability to produce ethanol during aerobic growth, indicating a possible transformation of its physiological property to Crabtree positivity or partial Crabtree positivity. Dual roles of KlHap1p in activating respiration and repressing fermentation may be seen as a basis of the Crabtree-negative physiology of K. lactis.
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Fonseca GG, Heinzle E, Wittmann C, Gombert AK. The yeast Kluyveromyces marxianus and its biotechnological potential. Appl Microbiol Biotechnol 2008; 79:339-54. [PMID: 18427804 DOI: 10.1007/s00253-008-1458-6] [Citation(s) in RCA: 307] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 03/12/2008] [Accepted: 03/13/2008] [Indexed: 11/26/2022]
Abstract
Strains belonging to the yeast species Kluyveromyces marxianus have been isolated from a great variety of habitats, which results in a high metabolic diversity and a substantial degree of intraspecific polymorphism. As a consequence, several different biotechnological applications have been investigated with this yeast: production of enzymes (beta-galactosidase, beta-glucosidase, inulinase, and polygalacturonases, among others), of single-cell protein, of aroma compounds, and of ethanol (including high-temperature and simultaneous saccharification-fermentation processes); reduction of lactose content in food products; production of bioingredients from cheese-whey; bioremediation; as an anticholesterolemic agent; and as a host for heterologous protein production. Compared to its congener and model organism, Kluyveromyces lactis, the accumulated knowledge on K. marxianus is much smaller and spread over a number of different strains. Although there is no publicly available genome sequence for this species, 20% of the CBS 712 strain genome was randomly sequenced (Llorente et al. in FEBS Lett 487:71-75, 2000). In spite of these facts, K. marxianus can envisage a great biotechnological future because of some of its qualities, such as a broad substrate spectrum, thermotolerance, high growth rates, and less tendency to ferment when exposed to sugar excess, when compared to K. lactis. To increase our knowledge on the biology of this species and to enable the potential applications to be converted into industrial practice, a more systematic approach, including the careful choice of (a) reference strain(s) by the scientific community, would certainly be of great value.
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Werther T, Spinka M, Tittmann K, Schütz A, Golbik R, Mrestani-Klaus C, Hübner G, König S. Amino acids allosterically regulate the thiamine diphosphate-dependent alpha-keto acid decarboxylase from Mycobacterium tuberculosis. J Biol Chem 2007; 283:5344-54. [PMID: 18086676 DOI: 10.1074/jbc.m706569200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene rv0853c from Mycobacterium tuberculosis strain H37Rv codes for a thiamine diphosphate-dependent alpha-keto acid decarboxylase (MtKDC), an enzyme involved in the amino acid degradation via the Ehrlich pathway. Steady state kinetic experiments were performed to determine the substrate specificity of MtKDC. The mycobacterial enzyme was found to convert a broad spectrum of branched-chain and aromatic alpha-keto acids. Stopped-flow kinetics showed that MtKDC is allosterically activated by alpha-keto acids. Even more, we demonstrate that also amino acids are potent activators of this thiamine diphosphate-dependent enzyme. Thus, metabolic flow through the Ehrlich pathway can be directly regulated at the decarboxylation step. The influence of amino acids on MtKDC catalysis was investigated, and implications for other thiamine diphosphate-dependent enzymes are discussed.
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Affiliation(s)
- Tobias Werther
- Institute of Biochemistry and Biotechnology, Faculty for Biological Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle Saale, Germany
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Lamas-Maceiras M, Núñez L, Rodríguez-Belmonte E, González-Siso MI, Cerdán ME. Functional characterization of KlHAP1: a model to foresee different mechanisms of transcriptional regulation by Hap1p in yeasts. Gene 2007; 405:96-107. [PMID: 17942245 DOI: 10.1016/j.gene.2007.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 09/04/2007] [Accepted: 09/10/2007] [Indexed: 01/10/2023]
Abstract
In this work we have cloned and characterized the Kluyveromyces lactis HAP1 gene and we have found that, contrary to data previously described for the homologous gene of Saccharomyces cerevisiae, i.) the function of this gene does not affect growth in media with carbon sources used by fermentative or respiratory pathways ii) in aerobiosis, KlHap1p is not a transcriptional activator of the expression of genes related to respiration, cholesterol biosynthesis or oxidative stress defence analyzed in this study. The comparison of homology between specific regions of ScHap1p and KlHap1p reveals that the dimerization domain is poorly conserved and we have verified that this domain, cloned in the two plasmids of the two hybrid system, does not reconstitute S. cerevisiae Gal4p activity. Since the COOH-terminal transcriptional activation domain of KlHap1p is active when fused to the Gal4p-DNA binding domain, we hypothesize that differences in the capacity to form dimers could contribute to allow different functions of the protein in K. lactis and S. cerevisiae. Transcriptional expression of KlHAP1 is dependent on oxygen availability, increasing its expression in hypoxia. Deletion of KlHAP1 increases the resistance to oxidative stress or cadmium and the induction of KlYAP1 and KlTSA1 by the addition of 0.5 mM H(2)O(2) is repressed by KlHap1p. These data are discussed in reference to the evolution of respiro-fermentative metabolism in yeasts.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Dpto. Biología Celular y Molecular. Universidad de A Coruña, F. Ciencias, Campus de A Zapateira s/n 15075, A Coruña, Spain
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Camattari A, Bianchi MM, Branduardi P, Porro D, Brambilla L. Induction by hypoxia of heterologous-protein production with the KlPDC1 promoter in yeasts. Appl Environ Microbiol 2007; 73:922-9. [PMID: 17142360 PMCID: PMC1800783 DOI: 10.1128/aem.01764-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 11/24/2006] [Indexed: 11/20/2022] Open
Abstract
The control of promoter activity by oxygen availability appears to be an intriguing system for heterologous protein production. In fact, during cell growth in a bioreactor, an oxygen shortage is easily obtained simply by interrupting the air supply. The purpose of our work was to explore the possible use of hypoxic induction of the KlPDC1 promoter to direct heterologous gene expression in yeast. In the present study, an expression system based on the KlPDC1 promoter was developed and characterized. Several heterologous proteins, differing in size, origin, localization, and posttranslational modification, were successfully expressed in Kluyveromyces lactis under the control of the wild type or a modified promoter sequence, with a production ratio between 4 and more than 100. Yields were further optimized by a more accurate control of hypoxic physiological conditions. Production of as high as 180 mg/liter of human interleukin-1beta was obtained, representing the highest value obtained with yeasts in a lab-scale bioreactor to date. Moreover, the transferability of our system to related yeasts was assessed. The lacZ gene from Escherichia coli was cloned downstream of the KlPDC1 promoter in order to get beta-galactosidase activity in response to induction of the promoter. A centromeric vector harboring this expression cassette was introduced in Saccharomyces cerevisiae and in Zygosaccharomyces bailii, and effects of hypoxic induction were measured and compared to those already observed in K. lactis cells. Interestingly, we found that the induction still worked in Z. bailii; thus, this promotor constitutes a possible inducible system for this new nonconventional host.
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Affiliation(s)
- Andrea Camattari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, P.zza della Scienza 2, 20126 Milan, Italy
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Ishtar Snoek IS, Yde Steensma H. Factors involved in anaerobic growth ofSaccharomyces cerevisiae. Yeast 2007; 24:1-10. [PMID: 17192845 DOI: 10.1002/yea.1430] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Life in the absence of molecular oxygen requires several adaptations. Traditionally, the switch from respiratory metabolism to fermentation has attracted much attention in Saccharomyces cerevisiae, as this is the basis for the use of this yeast in the production of alcohol and in baking. It has also been clear that under anaerobic conditions the yeast is not able to synthesize sterols and unsaturated fatty acids and that for anaerobic growth these have to be added to the media. More recently it has been found that many more factors play a role. Several other biosynthetic reactions also require molecular oxygen and the yeast must have alternatives for these. In addition, the composition of the cell wall and cell membrane show major differences when aerobic and anaerobic cells are compared. All these changes are reflected by the observation that the transcription of more than 500 genes changes significantly between aerobically and anaerobically growing cultures. In this review we will give an overview of the factors that play a role in the survival in the absence of molecular oxygen.
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Affiliation(s)
- I S Ishtar Snoek
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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Suleau A, Gourdon P, Reitz-Ausseur J, Casaregola S. Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains. EUKARYOTIC CELL 2006; 5:1360-70. [PMID: 16896219 PMCID: PMC1539144 DOI: 10.1128/ec.00087-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Accepted: 05/17/2006] [Indexed: 11/20/2022]
Abstract
Genome-wide analysis of transcriptional regulation is generally carried out on well-characterized reference laboratory strains; hence, the characteristics of industrial isolates are therefore overlooked. In a previous study on the major cheese yeast Kluyveromyces lactis, we have shown that the reference strain and an industrial strain used in cheese making display a differential gene expression when grown on a single carbon source. Here, we have used more controlled conditions, i.e., growth in a fermentor with pH and oxygen maintained constant, to study how these two isolates grown in glucose reacted to an addition of lactose. The observed differences between sugar consumption and the production of various metabolites, ethanol, acetate, and glycerol, correlated with the response were monitored by the analysis of the expression of 482 genes. Extensive differences in gene expression between the strains were revealed in sugar transport, glucose repression, ethanol metabolism, and amino acid import. These differences were partly due to repression by glucose and another, yet-unknown regulation mechanism. Our results bring to light a new type of K. lactis strain with respect to hexose transport gene content and repression by glucose. We found that a combination of point mutations and variation in gene regulation generates a biodiversity within the K. lactis species that was not anticipated. In contrast to S. cerevisiae, in which there is a massive increase in the number of sugar transporter and fermentation genes, in K. lactis, interstrain diversity in adaptation to a changing environment is based on small changes at the level of key genes and cell growth control.
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Affiliation(s)
- Audrey Suleau
- Laboratoire de Microbiologie et Génétique Moléculaire, INRA UMR1238, CNRS/INA-PG UMR 2585, 78850 Thiverval-Grignon, France
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