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Andrade Silva CAD, Oka ML, da Silva PGP, Honma JM, Leite RSR, Fonseca GG. Physiological evaluation of yeast strains under anaerobic conditions using glucose, fructose, or sucrose as the carbon source. J Biosci Bioeng 2024; 137:420-428. [PMID: 38493064 DOI: 10.1016/j.jbiosc.2024.02.003] [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: 07/27/2023] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 03/18/2024]
Abstract
The aim of this study was to evaluate the physiology of 13 yeast strains by assessing their kinetic parameters under anaerobic conditions. They included Saccharomyces cerevisiae CAT-1 and 12 isolated yeasts from different regions in Brazil. The study aimed to enhance understanding of the metabolism of these strains for more effective applications. Measurements included quantification of sugars, ethanol, glycerol, and organic acids. Various kinetic parameters were analyzed, such as specific substrate utilization rate (qS), maximum specific growth rate (μmax), doubling time, biomass yield, product yield, maximum cell concentration, ethanol productivity (PEth), biomass productivity, and CO2 concentration. S. cerevisiae CAT-1 exhibited the highest values in glucose for μmax (0.35 h-1), qS (3.06 h-1), and PEth (0.69 gEth L-1 h-1). Candida parapsilosis Recol 37 did not fully consume the substrate. In fructose, S. cerevisiae CAT-1 stood out with higher values for μmax (0.25 h-1), qS (2.24 h-1), and PEth (0.60 gEth L-1 h-1). Meyerozyma guilliermondii Recol 09 and C. parapsilosis Recol 37 had prolonged fermentation times and residual substrate. In sucrose, only S. cerevisiae CAT-1, S. cerevisiae BB9, and Pichia kudriavzevii Recol 39 consumed all the substrate, displaying higher PEth (0.72, 0.51, and 0.44 gEth L-1 h-1, respectively) compared to other carbon sources.
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Affiliation(s)
- Cinthia Aparecida de Andrade Silva
- Center for Studies in Natural Resources, State University of Mato Grosso do Sul, Dourados, MS, Brazil; Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Marta Ligia Oka
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Pedro Garcia Pereira da Silva
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Janaina Mayumi Honma
- Laboratory of Bioengineering, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Rodrigo Simões Ribeiro Leite
- Laboratory of Enzymology and Fermentation Processes, Faculty of Biological and Environmental Sciences, Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Gustavo Graciano Fonseca
- Faculty of Natural Resource Sciences, School of Health, Business and Science, University of Akureyri, Akureyri, Iceland.
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2
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Horkai D, Hadj-Moussa H, Whale AJ, Houseley J. Dietary change without caloric restriction maintains a youthful profile in ageing yeast. PLoS Biol 2023; 21:e3002245. [PMID: 37643155 PMCID: PMC10464975 DOI: 10.1371/journal.pbio.3002245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 07/12/2023] [Indexed: 08/31/2023] Open
Abstract
Caloric restriction increases lifespan and improves ageing health, but it is unknown whether these outcomes can be separated or achieved through less severe interventions. Here, we show that an unrestricted galactose diet in early life minimises change during replicative ageing in budding yeast, irrespective of diet later in life. Average mother cell division rate is comparable between glucose and galactose diets, and lifespan is shorter on galactose, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing that these are not intrinsic aspects of replicative ageing but rather associated processes. Respiration on galactose is critical for minimising hallmarks of ageing, and forced respiration during ageing on glucose by overexpression of the mitochondrial biogenesis factor Hap4 also has the same effect though only in a fraction of cells. This fraction maintains Hap4 activity to advanced age with low senescence and a youthful gene expression profile, whereas other cells in the same population lose Hap4 activity, undergo dramatic dysregulation of gene expression and accumulate fragments of chromosome XII (ChrXIIr), which are tightly associated with senescence. Our findings support the existence of two separable ageing trajectories in yeast. We propose that a complete shift to the healthy ageing mode can be achieved in wild-type cells through dietary change in early life without caloric restriction.
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Affiliation(s)
- Dorottya Horkai
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
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3
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Qiu Y, Lei P, Wang R, Sun L, Luo Z, Li S, Xu H. Kluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications. Biotechnol Adv 2023; 64:108125. [PMID: 36870581 DOI: 10.1016/j.biotechadv.2023.108125] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.
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Affiliation(s)
- Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Zhengshan Luo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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Postigo V, O’Sullivan T, Elink Schuurman T, Arroyo T. Non-Conventional Yeast: Behavior under Pure Culture, Sequential and Aeration Conditions in Beer Fermentation. Foods 2022; 11:foods11223717. [PMID: 36429309 PMCID: PMC9689477 DOI: 10.3390/foods11223717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The use of wild yeasts, isolated from different environments, is becoming the most interesting option for the production of new beers. The objective of this study is to evaluate the potential of seven non-conventional yeast strains from five different species (Saccharomyces cerevisiae, Hanseniaspora guilliermondii, Metschnikowia pulcherrima, Torulaspora delbrueckii, and Zygosaccharomyces bailii) isolated from Madrid agriculture to produce type ale beer. Wild yeast strains were evaluated at laboratory and pilot plant scales under different fermentation conditions (pure, aerated, and sequential culture). Strain S. cerevisiae SafAle S-04 was used as a reference. Throughout the fermentation of beer, volatile compounds were determined by GC and residual sugars by HPLC, among other parameters. The yeast strains used for the fermentation in pure culture conditions were unable to ferment maltose and maltotriose (0.73-1.18% v/v of ethanol). The results of the study under aerated conditions showed varying levels of higher alcohol and ester concentrations. It should be noted that the strain CLI 1057 (S. cerevisiae) fermented maltose in the presence of oxygen (Kluyver effect). This strain also showed a high production of 4-vinyl guaiacol, making it suitable for producing beers with a phenolic profile. Finally, three strains (H. guilliermondii, Z. bailii, and T. delbrueckii) were evaluated in sequential culture together with commercial strain and found to improve the organoleptic characteristics of the brewed beer. These approaches offer the opportunity to add new product characteristics to the beers.
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Affiliation(s)
- Vanesa Postigo
- Department of Agri-Food, Madrid Institute for Rural, Agriculture and Food Research and Development (IMIDRA), El Encín, A-2, km 38.2, 28805 Alcalá de Henares, Spain
- Brewery La Cibeles, Petróleo 34, 28918 Leganés, Spain
| | - Tadhg O’Sullivan
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH Zoeterwoude, The Netherlands
| | - Tom Elink Schuurman
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH Zoeterwoude, The Netherlands
| | - Teresa Arroyo
- Department of Agri-Food, Madrid Institute for Rural, Agriculture and Food Research and Development (IMIDRA), El Encín, A-2, km 38.2, 28805 Alcalá de Henares, Spain
- Correspondence:
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Yang P, Jiang S, Lu S, Jiang S, Jiang S, Deng Y, Lu J, Wang H, Zhou Y. Ethanol yield improvement in Saccharomyces cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta mutant and molecular mechanism exploration based on the metabolic flux and transcriptomics approaches. Microb Cell Fact 2022; 21:160. [PMID: 35964044 PMCID: PMC9375381 DOI: 10.1186/s12934-022-01885-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Saccharomyces cerevisiae generally consumes glucose to produce ethanol accompanied by the main by-products of glycerol, acetic acid, and lactic acid. The minimization of the formation of by-products in S. cerevisiae was an effective way to improve the economic viability of the bioethanol industry. In this study, S. cerevisiae GPD2, FPS1, ADH2, and DLD3 genes were knocked out by the Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) approach. The mechanism of gene deletion affecting ethanol metabolism was further elucidated based on metabolic flux and transcriptomics approaches. Results The engineered S. cerevisiae with gene deletion of GPD2, FPS1, ADH2, and DLD3 was constructed by the CRISPR-Cas9 approach. The ethanol content of engineered S. cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta increased by 18.58% with the decrease of glycerol, acetic acid, and lactic acid contents by 22.32, 8.87, and 16.82%, respectively. The metabolic flux analysis indicated that the carbon flux rethanol in engineered strain increased from 60.969 to 63.379. The sequencing-based RNA-Seq transcriptomics represented 472 differential expression genes (DEGs) were identified in engineered S. cerevisiae, in which 195 and 277 genes were significantly up-regulated and down-regulated, respectively. The enriched pathways of up-regulated genes were mainly involved in the energy metabolism of carbohydrates, while the down-regulated genes were mainly enriched in acid metabolic pathways. Conclusions The yield of ethanol in engineered S. cerevisiae increased with the decrease of the by-products including glycerol, acetic acid, and lactic acid. The deletion of genes GPD2, FPS1, ADH2, and DLD3 resulted in the redirection of carbon flux. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01885-3.
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Affiliation(s)
- Peizhou Yang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China.
| | - Shuying Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Shuhua Lu
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Suwei Jiang
- Department of Biological, Food and Environment Engineering, Hefei University, 158 Jinxiu Avenue, Hefei, 230601, China
| | - Shaotong Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Yanhong Deng
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Jiuling Lu
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Hu Wang
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Yong Zhou
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
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6
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Lyutova LV, Naumov GI, Shnyreva AV, Naumova ES. Molecular Polymorphism of β-Galactosidase LAC4 Genes in Dairy and Natural Strains of Kluyveromyces Yeasts. Mol Biol 2021. [DOI: 10.1134/s0026893321010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Haploinsufficiency due to a novel ACO2 deletion causes mitochondrial dysfunction in fibroblasts from a patient with dominant optic nerve atrophy. Sci Rep 2020; 10:16736. [PMID: 33028849 PMCID: PMC7541502 DOI: 10.1038/s41598-020-73557-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
ACO2 is a mitochondrial protein, which is critically involved in the function of the tricarboxylic acid cycle (TCA), the maintenance of iron homeostasis, oxidative stress defense and the integrity of mitochondrial DNA (mtDNA). Mutations in the ACO2 gene were identified in patients suffering from a broad range of symptoms, including optic nerve atrophy, cortical atrophy, cerebellar atrophy, hypotonia, seizures and intellectual disabilities. In the present study, we identified a heterozygous 51 bp deletion (c.1699_1749del51) in ACO2 in a family with autosomal dominant inherited isolated optic atrophy. A complementation assay using aco1-deficient yeast revealed a growth defect for the mutant ACO2 variant substantiating a pathogenic effect of the deletion. We used patient-derived fibroblasts to characterize cellular phenotypes and found a decrease of ACO2 protein levels, while ACO2 enzyme activity was not affected compared to two age- and gender-matched control lines. Several parameters of mitochondrial function, including mitochondrial morphology, mitochondrial membrane potential or mitochondrial superoxide production, were not changed under baseline conditions. However, basal respiration, maximal respiration, and spare respiratory capacity were reduced in mutant cells. Furthermore, we observed a reduction of mtDNA copy number and reduced mtDNA transcription levels in ACO2-mutant fibroblasts. Inducing oxidative stress led to an increased susceptibility for cell death in ACO2-mutant fibroblasts compared to controls. Our study reveals that a monoallelic mutation in ACO2 is sufficient to promote mitochondrial dysfunction and increased vulnerability to oxidative stress as main drivers of cell death related to optic nerve atrophy.
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8
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Gomes AMV, Orlandi ACAL, Parachin NS. Deletion of the trehalose tps1 gene in Kluyveromyces lactis does not impair growth in glucose. FEMS Microbiol Lett 2020; 367:5823741. [PMID: 32319521 DOI: 10.1093/femsle/fnaa072] [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: 10/24/2019] [Accepted: 04/20/2020] [Indexed: 11/14/2022] Open
Abstract
Trehalose is a non-reducing disaccharide composed of two α-glucose molecules and synthesized by an enzyme complex containing four subunits TPS1 (EC 2.4.1.15), TPS2 (EC 3.1.3.12), TPS3 and TSL1. First reports about trehalose classified this sugar as an energy reserve compound like glycogen. However, lately, trehalose is known to assist yeast cells during heat, osmotic and starvation stresses. In Saccharomyces cerevisiae, the deletion of the tps1 encoding gene eliminated the yeast ability to grow on glucose as the sole carbon source. Kluyveromyces lactis is a yeast present in various dairy products and is currently utilized for the synthesis of more than 40 industrial heterologous products. In this study, the deletion of the tps1 gene in K. lactis showed that unlike S. cerevisiae, tps1 gene disruption does not cause growth failure in glucose, galactose, or fructose. The µMAX rate values of K. lactis tps1Δ strains were equal than the non-disrupted strains, showing that the gene deletion does not affect the yeast growth. After gene disruption, the absence of trehalose into the metabolism of K. lactis was also confirmed.
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Affiliation(s)
- Antonio M V Gomes
- Grupo de Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Campus Darcy Ribeiro, Bloco K. 70.790-900. Brasilia, Federal District, Brazil
| | - Ana Carolina A L Orlandi
- Grupo de Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Campus Darcy Ribeiro, Bloco K. 70.790-900. Brasilia, Federal District, Brazil
| | - Nádia S Parachin
- Grupo de Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Campus Darcy Ribeiro, Bloco K. 70.790-900. Brasilia, Federal District, Brazil
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9
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Abstract
Non-alcoholic beer (NAB) is enjoying growing demand and popularity due to consumer lifestyle trends and improved production methods. In recent years in particular, research into the application of non-Saccharomyces yeasts to produce NAB via limited fermentation has gained momentum. Non-Saccharomyces yeasts are known to produce fruity aromas, owing to a high ester production. This trait could be harnessed to mask the often-criticized wort-like off-flavor of NAB produced via limited fermentation. Six Cyberlindnera strains were characterized and screened in wort extract. Four of the six strains produced a pleasant, fruity aroma while exhibiting low ethanol production. The strain Cyberlindnera subsufficiens C6.1 was chosen for fermentation optimization via response surface methodology (RSM) and a pilot-scale (60 L) brewing trial with subsequent sensory evaluation. A low fermentation temperature and low pitching rate enhanced the fruitiness and overall acceptance of the NAB. The NAB (0.36% ABV) produced on pilot-scale was significantly more fruity and exhibited a significantly reduced wort-like off-flavor compared to two commercial NABs. This study demonstrated the suitability of Cyberlindnera subsufficiens to produce a fruity NAB, which can compete with commercial NABs. The outcome strengthens the position of non-Saccharomyces yeasts as a serious and applicable alternative to established methods in NAB brewing.
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Varela JA, Puricelli M, Ortiz-Merino RA, Giacomobono R, Braun-Galleani S, Wolfe KH, Morrissey JP. Origin of Lactose Fermentation in Kluyveromyces lactis by Interspecies Transfer of a Neo-functionalized Gene Cluster during Domestication. Curr Biol 2019; 29:4284-4290.e2. [PMID: 31813610 PMCID: PMC6926475 DOI: 10.1016/j.cub.2019.10.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022]
Abstract
Humans have used yeasts to make cheese and kefir for millennia, but the ability to ferment the milk sugar lactose is found in only a few yeast species, of which the foremost is Kluyveromyces lactis [1]. Two genes, LAC12 (lactose permease) and LAC4 (lactase), are sufficient for lactose uptake and hydrolysis to glucose and galactose [2]. Here, we show that these genes have a complex evolutionary history in the genus Kluyveromyces that is likely the result of human activity during domestication. We show that the ancestral Lac12 was bifunctional, able to import both lactose and cellobiose into the cell. These disaccharides were then hydrolyzed by Lac4 in the case of lactose or Cel2 in the case of cellobiose. A second cellobiose transporter, Cel1, was also present ancestrally. In the K. lactis lineage, the ancestral LAC12 and LAC4 were lost and a separate upheaval in the sister species K. marxianus resulted in loss of CEL1 and quadruplication of LAC12. One of these LAC12 genes became neofunctionalized to encode an efficient lactose transporter capable of supporting fermentation, specifically in dairy strains of K. marxianus, where it formed a LAC4-LAC12-CEL2 gene cluster, although another remained a cellobiose transporter. Then, the ability to ferment lactose was acquired very recently by K. lactis var. lactis by introgression of LAC12 and LAC4 on a 15-kb subtelomeric region from a dairy strain of K. marxianus. The genomic history of the LAC genes shows that strong selective pressures were imposed on yeasts by early dairy farmers.
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Affiliation(s)
- Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | - Martina Puricelli
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 Delft, the Netherlands
| | - Romina Giacomobono
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | | | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4 D04 C7X2, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland.
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da Silva JM, da Silva GHTG, Parente DC, Leite FCB, Silva CS, Valente P, Ganga AM, Simões DA, de Morais MA. Biological diversity of carbon assimilation among isolates of the yeast Dekkera bruxellensis from wine and fuel-ethanol industrial processes. FEMS Yeast Res 2019; 19:5372417. [PMID: 30848782 DOI: 10.1093/femsyr/foz022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Dekkera bruxellensis is considered a spoilage yeast in winemaking, brewing and fuel-ethanol production. However, there is growing evidence in the literature of its biotechnological potential. In this work, we surveyed 29 D. bruxellensis isolates from three countries and two different industrial origins (winemaking and fuel-ethanol production) for the metabolization of industrially relevant sugars. The isolates were characterized by the determination of their maximum specific growth rates, and by testing their ability to grow in the presence of 2-deoxy-d-glucose and antimycin A. Great diversity was observed among the isolates, with fuel-ethanol isolates showing overall higher specific growth rates than wine isolates. Preferences for galactose (three wine isolates) and for cellobiose or lactose (some fuel-ethanol isolates) were observed. Fuel-ethanol isolates were less sensitive than wine isolates to glucose catabolite repression (GCR) induction by 2-deoxy-d-glucose. In strictly anaerobic conditions, isolates selected for having high aerobic growth rates were able to ferment glucose, sucrose and cellobiose at fairly high rates without supplementation of casamino acids or yeast extract in the culture medium. The phenotypic diversity found among wine and fuel-ethanol isolates suggests adaptation to these environments. A possible application of some of the GCR-insensitive, fast-growing isolates in industrial processes requiring co-assimilation of different sugars is considered.
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Affiliation(s)
- Jackeline Maria da Silva
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Denise Castro Parente
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Carolina Santos Silva
- Department of Chemical Engineering, Federal University of Pernambuco, Recife, Brazil
| | - Patrícia Valente
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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12
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Construction and characterization of a Saccharomyces cerevisiae strain able to grow on glucosamine as sole carbon and nitrogen source. Sci Rep 2018; 8:16949. [PMID: 30446667 PMCID: PMC6240059 DOI: 10.1038/s41598-018-35045-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/29/2018] [Indexed: 01/31/2023] Open
Abstract
Saccharomyces cerevisiae can transport and phosphorylate glucosamine, but cannot grow on this amino sugar. While an enzyme catalyzing the reaction from glucosamine-6-phosphate to fructose-6-phosphate, necessary for glucosamine catabolism, is present in yeasts using N-acetylglucosamine as carbon source, a sequence homology search suggested that such an enzyme is absent from Saccharomyces cerevisiae. The gene YlNAG1 encoding glucosamine-6-phosphate deaminase from Yarrowia lipolytica was introduced into S. cerevisiae and growth in glucosamine tested. The constructed strain grew in glucosamine as only carbon and nitrogen source. Growth on the amino sugar required respiration and caused an important ammonium excretion. Strains overexpressing YlNAG1 and one of the S. cerevisiae glucose transporters HXT1, 2, 3, 4, 6 or 7 grew in glucosamine. The amino sugar caused catabolite repression of different enzymes to a lower extent than that produced by glucose. The availability of a strain of S. cerevisiae able to grow on glucosamine opens new possibilities to investigate or manipulate pathways related with glucosamine metabolism in a well-studied organism.
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13
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Perez-Samper G, Cerulus B, Jariani A, Vermeersch L, Barrajón Simancas N, Bisschops MMM, van den Brink J, Solis-Escalante D, Gallone B, De Maeyer D, van Bael E, Wenseleers T, Michiels J, Marchal K, Daran-Lapujade P, Verstrepen KJ. The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources. mBio 2018; 9:e01331-18. [PMID: 30377274 PMCID: PMC6212832 DOI: 10.1128/mbio.01331-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/20/2018] [Indexed: 12/16/2022] Open
Abstract
When faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the genetic network that determines the duration of the lag phase has not been studied in much detail. Here, we performed a genome-wide Bar-Seq screen to identify genetic determinants of the Saccharomyces cerevisiae glucose-to-galactose lag phase. The results show that genes involved in respiration, and specifically those encoding complexes III and IV of the electron transport chain, are needed for efficient growth resumption after the lag phase. Anaerobic growth experiments confirmed the importance of respiratory energy conversion in determining the lag phase duration. Moreover, overexpression of the central regulator of respiration, HAP4, leads to significantly shorter lag phases. Together, these results suggest that the glucose-induced repression of respiration, known as the Crabtree effect, is a major determinant of microbial fitness in fluctuating carbon environments.IMPORTANCE The lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox of S. cerevisiae combined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.
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Affiliation(s)
- Gemma Perez-Samper
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Bram Cerulus
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Abbas Jariani
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Lieselotte Vermeersch
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | | | - Markus M M Bisschops
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Joost van den Brink
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Brigida Gallone
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Dries De Maeyer
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Elise van Bael
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jan Michiels
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Kevin J Verstrepen
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
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14
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Factors Influencing the Production of Sensory Active Substances in Brewer's and Wine Yeast. KVASNY PRUMYSL 2017. [DOI: 10.18832/kp201720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Meurer M, Chevyreva V, Cerulus B, Knop M. The regulatableMAL32promoter inSaccharomyces cerevisiae: characteristics and tools to facilitate its use. Yeast 2016; 34:39-49. [DOI: 10.1002/yea.3214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/01/2016] [Accepted: 09/23/2016] [Indexed: 11/09/2022] Open
Affiliation(s)
- Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg; University of Heidelberg; Im Neuenheimer Feld 282 69120 Heidelberg Germany
| | - Veronika Chevyreva
- Zentrum für Molekulare Biologie der Universität Heidelberg; University of Heidelberg; Im Neuenheimer Feld 282 69120 Heidelberg Germany
| | - Bram Cerulus
- KU Leuven Department Microbiële en Moleculaire Systemen; CMPG Laboratory of Genetics and Genomics; Gaston Geenslaan 1 3001 Leuven Belgium
- VIB Laboratory of Systems Biology; Gaston Geenslaan 1 3001 Leuven Belgium
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg; University of Heidelberg; Im Neuenheimer Feld 282 69120 Heidelberg Germany
- Deutsches Krebsforschungszentrum (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
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16
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Sarris D, Papanikolaou S. Biotechnological production of ethanol: Biochemistry, processes and technologies. Eng Life Sci 2016. [DOI: 10.1002/elsc.201400199] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Dimitris Sarris
- Laboratory of Food Microbiology and Biotechnology Department of Food Science and Human Nutrition, Agricultural University of Athens Athens Greece
| | - Seraphim Papanikolaou
- Laboratory of Food Microbiology and Biotechnology Department of Food Science and Human Nutrition, Agricultural University of Athens Athens Greece
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17
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Legrand J, Bolotin-Fukuhara M, Bourgais A, Fairhead C, Sicard D. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res 2015; 16:fov112. [PMID: 26684721 DOI: 10.1093/femsyr/fov112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.
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Affiliation(s)
- Judith Legrand
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Monique Bolotin-Fukuhara
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Aurélie Bourgais
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Cécile Fairhead
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France INRA, UMR 1083 Sciences pour l'oenologie, 34060 Montpellier Cedex 2, France
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18
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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: 1.3] [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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19
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Kuloyo OO, du Preez JC, García-Aparicio MDP, Kilian SG, Steyn L, Görgens J. Opuntia ficus-indica cladodes as feedstock for ethanol production by Kluyveromyces marxianus and Saccharomyces cerevisiae. World J Microbiol Biotechnol 2014; 30:3173-83. [PMID: 25248867 PMCID: PMC4210634 DOI: 10.1007/s11274-014-1745-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 09/17/2014] [Indexed: 11/05/2022]
Abstract
The feasibility of ethanol production using an enzymatic hydrolysate of pretreated cladodes of Opuntia ficus-indica (prickly pear cactus) as carbohydrate feedstock was investigated, including a comprehensive chemical analysis of the cladode biomass and the effects of limited aeration on the fermentation profiles and sugar utilization. The low xylose and negligible mannose content of the cladode biomass used in this study suggested that the hemicellulose structure of the O. ficus-indica cladode was atypical of hardwood or softwood hemicelluloses. Separate hydrolysis and fermentation and simultaneous saccharification and fermentation procedures using Kluyveromyces marxianus and Saccharomyces cerevisiae at 40 and 35 °C, respectively, gave similar ethanol yields under non-aerated conditions. In oxygen-limited cultures K. marxianus exhibited almost double the ethanol productivity compared to non-aerated cultures, although after sugar depletion utilization of the produced ethanol was evident. Ethanol concentrations of up to 19.5 and 20.6 g l−1 were obtained with K. marxianus and S. cerevisiae, respectively, representing 66 and 70 % of the theoretical yield on total sugars in the hydrolysate. Because of the low xylan content of the cladode biomass, a yeast capable of xylose fermentation might not be a prerequisite for ethanol production. K. marxianus, therefore, has potential as an alternative to S. cerevisiae for bioethanol production. However, the relatively low concentration of fermentable sugars in the O. ficus-indica cladode hydrolysate presents a technical constraint for commercial exploitation.
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Affiliation(s)
- Olukayode O Kuloyo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
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20
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Santos AM, Silveira WB, Fietto LG, Brandão RL, Castro IM. Kinetics and regulation of lactose transport and metabolism in Kluyveromyces lactis JA6. World J Microbiol Biotechnol 2014; 30:1977-83. [DOI: 10.1007/s11274-014-1620-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 01/31/2014] [Indexed: 11/29/2022]
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21
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Rodicio R, Heinisch JJ. Yeast on the milky way: genetics, physiology and biotechnology of Kluyveromyces lactis. Yeast 2013; 30:165-77. [PMID: 23576126 DOI: 10.1002/yea.2954] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 11/08/2022] Open
Abstract
The milk yeast Kluyveromyces lactis has a life cycle similar to that of Saccharomyces cerevisiae and can be employed as a model eukaryote using classical genetics, such as the combination of desired traits, by crossing and tetrad analysis. Likewise, a growing set of vectors, marker cassettes and tags for fluorescence microscopy are available for manipulation by genetic engineering and investigating its basic cell biology. We here summarize these applications, as well as the current knowledge regarding its central metabolism, glucose and extracellular stress signalling pathways. A short overview on the biotechnological potential of K. lactis concludes this review.
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Affiliation(s)
- Rosaura Rodicio
- Departamento de Bioquímica y Biología Molecular and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, Spain
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22
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Streefland M, Martens DE, Beuvery EC, Wijffels RH. Process analytical technology (PAT) tools for the cultivation step in biopharmaceutical production. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200025] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Mathieu Streefland
- Bioprocess Engineering; Wageningen University; Wageningen; The Netherlands
| | - Dirk E. Martens
- Bioprocess Engineering; Wageningen University; Wageningen; The Netherlands
| | | | - René H. Wijffels
- Bioprocess Engineering; Wageningen University; Wageningen; The Netherlands
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23
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Huberts DHEW, Niebel B, Heinemann M. A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 2011; 12:118-28. [DOI: 10.1111/j.1567-1364.2011.00767.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/28/2011] [Accepted: 11/16/2011] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daphne H. E. W. Huberts
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Bastian Niebel
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
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24
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Genetics and Regulation of Glycogen and Trehalose Metabolism in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-3-642-21467-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Physiological and metabolic diversity in the yeast Kluyveromyces marxianus. Antonie van Leeuwenhoek 2011; 100:507-19. [DOI: 10.1007/s10482-011-9606-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022]
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26
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Grabek-Lejko D, Kurylenko OO, Sibirny VA, Ubiyvovk VM, Penninckx M, Sibirny AA. Alcoholic fermentation by wild-type Hansenula polymorpha and Saccharomyces cerevisiae versus recombinant strains with an elevated level of intracellular glutathione. J Ind Microbiol Biotechnol 2011; 38:1853-9. [DOI: 10.1007/s10295-011-0974-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 04/07/2011] [Indexed: 11/24/2022]
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27
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Growth and ethanol fermentation ability on hexose and pentose sugars and glucose effect under various conditions in thermotolerant yeast Kluyveromyces marxianus. Appl Microbiol Biotechnol 2011; 90:1573-86. [PMID: 21476140 DOI: 10.1007/s00253-011-3218-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 02/13/2011] [Accepted: 02/24/2011] [Indexed: 10/18/2022]
Abstract
Ethanol fermentation ability of the thermotolerant yeast Kluyveromyces marxianus, which is able to utilize various sugars including glucose, mannose, galactose, xylose, and arabinose, was examined under shaking and static conditions at high temperatures. The yeast was found to produce ethanol from all of these sugars except for arabinose under a shaking condition but only from hexose sugars under a static condition. Growth and sugar utilization rate under a static condition were slower than those under a shaking condition, but maximum ethanol yield was slightly higher. Even at 40°C, a level of ethanol production similar to that at 30°C was observed except for galactose under a static condition. Glucose repression on utilization of other sugars was observed, and it was more evident at elevated temperatures. Consistent results were obtained by the addition of 2-deoxyglucose. The glucose effect was further examined at a transcription level, and it was found that KmGAL1 for galactokinase and KmXYL1 for xylose reductase for galactose and xylose/arabinose utilization, respectively, were repressed by glucose at low and high temperatures, but KmHXK2 for hexokinase was not repressed. We discuss the possible mechanism of glucose repression and the potential for utilization of K. marxianus in high-temperature fermentation with mixed sugars containing glucose.
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28
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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: 0.1] [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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29
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Fang ZA, Wang GH, Chen AL, Li YF, Liu JP, Li YY, Bolotin-Fukuhara M, Bao WG. Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast. PLoS One 2009; 4:e7561. [PMID: 19855843 PMCID: PMC2763219 DOI: 10.1371/journal.pone.0007561] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 09/16/2009] [Indexed: 11/18/2022] Open
Abstract
The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae—its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the ‘non-WGD’ Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the ‘post-WGD’ genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae.
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Affiliation(s)
- Zi-An Fang
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guang-Hui Wang
- School of Mathematics, Shandong University, Jinan, Shandong, China
- Laboratoire Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Châtenay-Malabry, France
| | - Ai-Lian Chen
- Department of Mathematics, Fuzhou University, Fuzhou, Fujian, China
| | - You-Fang Li
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
| | - Jian-Ping Liu
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Yang Li
- Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Wei-Guo Bao
- Université Paris Sud-11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- * E-mail:
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30
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van den Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P. Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions. MICROBIOLOGY-SGM 2009; 155:1340-1350. [PMID: 19332835 DOI: 10.1099/mic.0.025775-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glucose is the favoured carbon source for Saccharomyces cerevisiae, and the Leloir pathway for galactose utilization is only induced in the presence of galactose during glucose-derepressed conditions. The goal of this study was to investigate the dynamics of glucose-galactose transitions. To this end, well-controlled, glucose-limited chemostat cultures were switched to galactose-excess conditions. Surprisingly, galactose was not consumed upon a switch to galactose excess under anaerobic conditions. However, the transcripts of the Leloir pathway were highly increased upon galactose excess under both aerobic and anaerobic conditions. Protein and enzyme-activity assays showed that impaired galactose consumption under anaerobiosis coincided with the absence of the Leloir-pathway proteins. Further results showed that absence of protein synthesis was not caused by glucose-mediated translation inhibition. Analysis of adenosine nucleotide pools revealed a fast decrease of the energy charge after the switch from glucose to galactose under anaerobic conditions. Similar results were obtained when glucose-galactose transitions were analysed under aerobic conditions with a respiratory-deficient strain. It is concluded that under fermentative conditions, the energy charge was too low to allow synthesis of the Leloir proteins. Hence, this study conclusively shows that the intracellular energy status is an important factor in the metabolic flexibility of S. cerevisiae upon changes in its environment.
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Affiliation(s)
- J van den Brink
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - M Akeroyd
- DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - J T Pronk
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J H de Winde
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - P Daran-Lapujade
- Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Merico A, Galafassi S, Piskur J, Compagno C. The oxygen level determines the fermentation pattern in Kluyveromyces lactis. FEMS Yeast Res 2009; 9:749-56. [PMID: 19500150 DOI: 10.1111/j.1567-1364.2009.00528.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Yeasts belonging to the lineage that underwent whole-genome duplication (WGD) possess a good fermentative potential and can proliferate in the absence of oxygen. In this study, we analyzed the pre-WGD yeast Kluyveromyces lactis and its ability to grow under oxygen-limited conditions. Under these conditions, K. lactis starts to increase the glucose metabolism and accumulates ethanol and glycerol. However, under more limited conditions, the fermentative metabolism decreases, causing a slow growth rate. In contrast, Saccharomyces cerevisiae and Saccharomyces kluyveri in anaerobiosis exhibit almost the same growth rate as in aerobiosis. In this work, we showed that in K. lactis, under oxygen-limited conditions, a decreased expression of RAG1 occurred. The activity of glucose-6-phosphate dehydrogenase also decreased, likely causing a reduced flux in the pentose phosphate pathway. Comparison of related and characterized yeasts suggests that the behavior observed in K. lactis could reflect the lack of an efficient mechanism to maintain a high glycolytic flux and to balance the redox homeostasis under hypoxic conditions. This could be a consequence of a recent specialization of K. lactis toward living in a niche where the ethanol accumulation at high oxygen concentrations and the ability to survive at a low oxygen concentration do not represent an advantage.
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Affiliation(s)
- Annamaria Merico
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, via Celoria 26, Milan, Italy
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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: 1.1] [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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Viigand K, Alamäe T. Further study of theHansenula polymorpha MALlocus: characterization of the α-glucoside permease encoded by theHpMAL2gene. FEMS Yeast Res 2007; 7:1134-44. [PMID: 17559409 DOI: 10.1111/j.1567-1364.2007.00257.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The HpMAL2 gene of the MAL gene cluster of Hansenula polymorpha codes for a permease similar to yeast maltose and alpha-glucoside transporters. Genomic disruption of HpMAL2 resulted in an inability of cells to grow on maltose, sucrose, trehalose, maltotriose and turanose, as well as a lack of p-nitrophenyl-alpha-D-glucopyranoside (PNPG) transport. PNPG uptake was competitively inhibited by all these substrates, with Ki values between 0.23 and 1.47 mM. Transport by HpMal2p was sensitive to pH and a protonophore carbonyl cyanide-m-chlorophenylhydrazone (CCCP), revealing its energization by the proton gradient over the cell membrane. Although HpMAL2 was responsible for trehalose uptake, its expression was not induced during trehalose growth. A maltase disruption mutant did not grow on maltotriose and turanose, whereas it showed normal growth on trehalose, demonstrating the dispensability of maltase for intracellular hydrolysis of trehalose. In a Genolevures clone pBB0AA011B12, the promoter region and the N-terminal fragment of the putative transactivator of MAL genes is located adjacent to HpMAL2. A reporter gene assay showed that expression from that promoter was induced by maltose and sucrose, repressed by glucose, and derepressed during glycerol and trehalose growth. Therefore, we presume that the gene encodes a functional regulator.
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Affiliation(s)
- Katrin Viigand
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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34
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Merico A, Sulo P, Piskur J, Compagno C. Fermentative lifestyle in yeasts belonging to the Saccharomyces complex. FEBS J 2007; 274:976-89. [PMID: 17239085 DOI: 10.1111/j.1742-4658.2007.05645.x] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast Saccharomyces cerevisiae is characterized by its ability to: (a) degrade glucose or fructose to ethanol, even in the presence of oxygen (Crabtree effect); (b) grow in the absence of oxygen; and (c) generate respiratory-deficient mitochondrial mutants, so-called petites. How unique are these properties among yeasts in the Saccharomyces clade, and what is their origin? Recent progress in genome sequencing has elucidated the phylogenetic relationships among yeasts in the Saccharomyces complex, providing a framework for the understanding of the evolutionary history of several modern traits. In this study, we analyzed over 40 yeasts that reflect over 150 million years of evolutionary history for their ability to ferment, grow in the absence of oxygen, and generate petites. A great majority of isolates exhibited good fermentation ability, suggesting that this trait could already be an intrinsic property of the progenitor yeast. We found that lineages that underwent the whole-genome duplication, in general, exhibit a fermentative lifestyle, the Crabtree effect, and the ability to grow without oxygen, and can generate stable petite mutants. Some of the pre-genome duplication lineages also exhibit some of these traits, but a majority of the tested species are petite-negative, and show a reduced Crabtree effect and a reduced ability to grow in the absence of oxygen. It could be that the ability to accumulate ethanol in the presence of oxygen, a gradual independence from oxygen and/or the ability to generate petites were developed later in several lineages. However, these traits have been combined and developed to perfection only in the lineage that underwent the whole-genome duplication and led to the modern Saccharomyces cerevisiae yeast.
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Affiliation(s)
- Annamaria Merico
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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35
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Naumov GI. Why does the yeast Kluyveromyces wickerhamii assimilates but not ferments lactose? DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2006; 403:310-2. [PMID: 16358582 DOI: 10.1007/s10630-005-0121-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- G I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Pervyi Dorozhnyi pr. 1, Moscow, 113545 Russia
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Rubio-Texeira M. A comparative analysis of the GAL genetic switch between not-so-distant cousins: Saccharomyces cerevisiae versus Kluyveromyces lactis. FEMS Yeast Res 2005; 5:1115-28. [PMID: 16014343 DOI: 10.1016/j.femsyr.2005.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 05/12/2005] [Accepted: 05/18/2005] [Indexed: 11/21/2022] Open
Abstract
Despite their close phylogenetic relationship, Kluyveromyces lactis and Saccharomyces cerevisiae have adapted their carbon utilization systems to different environments. Although they share identities in the arrangement, sequence and functionality of their GAL gene set, both yeasts have evolved important differences in the GAL genetic switch in accordance to their relative preference for the utilization of galactose as a carbon source. This review provides a comparative overview of the GAL-specific regulatory network in S. cerevisiae and K. lactis, discusses the latest models proposed to explain the transduction of the galactose signal, and describes some of the particularities that both microorganisms display in their regulatory response to different carbon sources. Emphasis is placed on the potential for improved strategies in biotechnological applications using yeasts.
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Affiliation(s)
- Marta Rubio-Texeira
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Regev-Rudzki N, Karniely S, Ben-Haim NN, Pines O. Yeast aconitase in two locations and two metabolic pathways: seeing small amounts is believing. Mol Biol Cell 2005; 16:4163-71. [PMID: 15975908 PMCID: PMC1196327 DOI: 10.1091/mbc.e04-11-1028] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The distribution of identical enzymatic activities between different subcellular compartments is a fundamental process of living cells. At present, the Saccharomyces cerevisiae aconitase enzyme has been detected only in mitochondria, where it functions in the tricarboxylic acid (TCA) cycle and is considered a mitochondrial matrix marker. We developed two strategies for physical and functional detection of aconitase in the yeast cytosol: 1) we fused the alpha peptide of the beta-galactosidase enzyme to aconitase and observed alpha complementation in the cytosol; and 2) we created an ACO1-URA3 hybrid gene, which allowed isolation of strains in which the hybrid protein is exclusively targeted to mitochondria. These strains display a specific phenotype consistent with glyoxylate shunt elimination. Together, our data indicate that yeast aconitase isoenzymes distribute between two distinct subcellular compartments and participate in two separate metabolic pathways; the glyoxylate shunt in the cytosol and the TCA cycle in mitochondria. We maintain that such dual distribution phenomena have a wider occurrence than recorded currently, the reason being that in certain cases there is a small fraction of one of the isoenzymes, in one of the locations, making its detection very difficult. We term this phenomenon of highly uneven isoenzyme distribution "eclipsed distribution."
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Affiliation(s)
- Neta Regev-Rudzki
- Department of Molecular Biology, Hebrew University Medical School, Jerusalem 91120, Israel
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38
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Lai LC, Kosorukoff AL, Burke PV, Kwast KE. Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 2005; 25:4075-91. [PMID: 15870279 PMCID: PMC1087712 DOI: 10.1128/mcb.25.10.4075-4091.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In contrast to previous steady-state analyses of the O(2)-responsive transcriptome, here we examined the dynamics of the response to short-term anaerobiosis (2 generations) in both catabolite-repressed (glucose) and derepressed (galactose) cells, assessed the specific role that Msn2 and Msn4 play in mediating the response, and identified gene networks using a novel clustering approach. Upon shifting cells to anaerobic conditions in galactose medium, there was an acute ( approximately 10 min) yet transient (<45 min) induction of Msn2- and/or Msn4-regulated genes associated with the remodeling of reserve energy and catabolic pathways during the switch from mixed respiro-fermentative to strictly fermentative growth. Concomitantly, MCB- and SCB-regulated networks associated with the G(1)/S transition of the cell cycle were transiently down-regulated along with rRNA processing genes containing PAC and RRPE motifs. Remarkably, none of these gene networks were differentially expressed when cells were shifted in glucose, suggesting that a metabolically derived signal arising from the abrupt cessation of respiration, rather than O(2) deprivation per se, elicits this "stress response." By approximately 0.2 generation of anaerobiosis in both media, more chronic, heme-dependent effects were observed, including the down-regulation of Hap1-regulated networks, derepression of Rox1-regulated networks, and activation of Upc2-regulated ones. Changes in these networks result in the functional remodeling of the cell wall, sterol and sphingolipid metabolism, and dissimilatory pathways required for long-term anaerobiosis. Overall, this study reveals that the acute withdrawal of oxygen can invoke a metabolic state-dependent "stress response" but that acclimatization to oxygen deprivation is a relatively slow process involving complex changes primarily in heme-regulated gene networks.
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Affiliation(s)
- Liang-Chuan Lai
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois 61801, USA
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39
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Mazzoni C, Serafini A, Falcone C. The inactivation of KlNOT4, a Kluyveromyces lactis gene encoding a component of the CCR4-NOT complex, reveals new regulatory functions. Genetics 2005; 170:1023-32. [PMID: 15879504 PMCID: PMC1451162 DOI: 10.1534/genetics.105.041863] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have isolated the KlNOT4 gene of the yeast Kluyveromyces lactis, which encodes a component of the evolutionarily conserved CCR4-NOT complex. We show that inactivation of the gene leads to pleiotropic defects that were differentially suppressed by the NOT4 gene of S. cerevisiae, indicating that these genes have overlapping, but not identical, functions. K. lactis strains lacking Not4p are defective in fermentation and show reduced transcription of glucose transporter and glycolytic genes, which are phenotypes that are not found in the corresponding mutant of S. cerevisiae. We also show that Not4 proteins control the respiratory pathway in both yeasts, although with some differences. They activate transcription of KlACS2 and KlCYC1, but repress KlICL1, ScICL1, ScACS1, and ScCYC1. Altogether, our results indicate that Not4p is a pivotal factor involved in the regulation of carbon metabolism in yeast.
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Affiliation(s)
- Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome La Sapienza, 00185 Rome, Italy.
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40
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Silveira W, Passos F, Mantovani H, Passos F. Ethanol production from cheese whey permeate by Kluyveromyces marxianus UFV-3: A flux analysis of oxido-reductive metabolism as a function of lactose concentration and oxygen levels. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2005.01.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Bolotin-Fukuhara M, Casaregola S, Aigle M. Genome evolution: Lessons from Genolevures. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/b136677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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42
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Barnett JA, Entian KD. A history of research on yeasts 9: regulation of sugar metabolism. Yeast 2005; 22:835-94. [PMID: 16134093 DOI: 10.1002/yea.1249] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- James A Barnett
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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43
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Jules M, Guillou V, François J, Parrou JL. Two distinct pathways for trehalose assimilation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2004; 70:2771-8. [PMID: 15128531 PMCID: PMC404389 DOI: 10.1128/aem.70.5.2771-2778.2004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Saccharomyces cerevisiae can synthesize trehalose and also use this disaccharide as a carbon source for growth. However, the molecular mechanism by which extracellular trehalose can be transported to the vacuole and degraded by the acid trehalase Ath1p is not clear. By using an adaptation of the assay of invertase on whole cells with NaF, we showed that more than 90% of the activity of Ath1p is extracellular, splitting of the disaccharide into glucose. We also found that Agt1p-mediated trehalose transport and the hydrolysis of the disaccharide by the cytosolic neutral trehalase Nth1p are coupled and represent a second, independent pathway, although there are several constraints on this alternative route. First, the AGT1/MAL11 gene is controlled by the MAL system, and Agt1p was active in neither non-maltose-fermenting nor maltose-inducible strains. Second, Agt1p rapidly lost activity during growth on trehalose, by a mechanism similar to the sugar-induced inactivation of the maltose permease. Finally, both pathways are highly pH sensitive and effective growth on trehalose occurred only when the medium was buffered at around pH 5.0. The catabolism of trehalose was purely oxidative, and since levels of Ath1p limit the glucose flux in the cells, batch cultures on trehalose may provide a useful alternative to glucose-limited chemostat cultures for investigation of metabolic responses in yeast.
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Affiliation(s)
- Matthieu Jules
- Centre de Bioingénierie Gilbert Durand, UMR-CNRS 5504, UMR-INRA 792, Complexe Scientifique de Rangueil, 31077 Toulouse Cedex 04, France
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44
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Current awareness on yeast. Yeast 2003; 20:1151-8. [PMID: 14598808 DOI: 10.1002/yea.949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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