1
|
de Moura Ferreira MA, da Silveira FA, da Silveira WB. Ethanol stress responses in Kluyveromyces marxianus: current knowledge and perspectives. Appl Microbiol Biotechnol 2022; 106:1341-1353. [DOI: 10.1007/s00253-022-11799-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/02/2022]
|
2
|
Leonel LV, Arruda PV, Chandel AK, Felipe MGA, Sene L. Kluyveromyces marxianus: a potential biocatalyst of renewable chemicals and lignocellulosic ethanol production. Crit Rev Biotechnol 2021; 41:1131-1152. [PMID: 33938342 DOI: 10.1080/07388551.2021.1917505] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Kluyveromyces marxianus is an ascomycetous yeast which has shown promising results in cellulosic ethanol and renewable chemicals production. It can survive on a variety of carbon sources under industrially favorable conditions due to its fast growth rate, thermotolerance, and acid tolerance. K. marxianus, is generally regarded as a safe (GRAS) microorganism, is widely recognized as a powerhouse for the production of heterologous proteins and is accepted by the US Food and Drug Administration (USFDA) for its pharmaceutical and food applications. Since lignocellulosic hydrolysates are comprised of diverse monomeric sugars, oligosaccharides and potential metabolism inhibiting compounds, this microorganism can play a pivotal role as it can grow on lignocellulosic hydrolysates coping with vegetal cell wall derived inhibitors. Furthermore, advancements in synthetic biology, for example CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, will enable development of an engineered yeast for the production of biochemicals and biopharmaceuticals having a myriad of industrial applications. Genetic engineering companies such as Cargill, Ginkgo Bioworks, DuPont, Global Yeast, Genomatica, and several others are actively working to develop designer yeasts. Given the important traits and properties of K. marxianus, these companies may find it to be a suitable biocatalyst for renewable chemicals and fuel production on the large scale. This paper reviews the recent progress made with K. marxianus biotechnology for sustainable production of ethanol, and other products utilizing lignocellulosic sugars.
Collapse
Affiliation(s)
- L V Leonel
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
| | - P V Arruda
- Department of Bioprocess Engineering and Biotechnology - COEBB/TD, Federal University of Technology - Paraná (UTFPR), Toledo, Brazil
| | - A K Chandel
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - M G A Felipe
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - L Sene
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
| |
Collapse
|
3
|
Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
Collapse
Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| |
Collapse
|
4
|
Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.
Collapse
|
5
|
Suzuki T, Hoshino T, Matsushika A. High-temperature ethanol production by a series of recombinant xylose-fermenting Kluyveromyces marxianus strains. Enzyme Microb Technol 2019; 129:109359. [DOI: 10.1016/j.enzmictec.2019.109359] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022]
|
6
|
Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
Collapse
Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
| |
Collapse
|
7
|
Yang P, Wu Y, Zheng Z, Cao L, Zhu X, Mu D, Jiang S. CRISPR-Cas9 Approach Constructing Cellulase sestc-Engineered Saccharomyces cerevisiae for the Production of Orange Peel Ethanol. Front Microbiol 2018; 9:2436. [PMID: 30364071 PMCID: PMC6191481 DOI: 10.3389/fmicb.2018.02436] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022] Open
Abstract
The development of lignocellulosic bioethanol plays an important role in the substitution of petrochemical energy and high-value utilization of agricultural wastes. The safe and stable expression of cellulase gene sestc was achieved by applying the clustered regularly interspaced short palindromic repeats-Cas9 approach to the integration of sestc expression cassette containing Agaricus biporus glyceraldehyde-3-phosphate-dehydrogenase gene (gpd) promoter in the Saccharomyces cerevisiae chromosome. The target insertion site was found to be located in the S. cerevisiae hexokinase 2 by designing a gRNA expression vector. The recombinant SESTC protein exhibited a size of approximately 44 kDa in the engineered S. cerevisiae. By using orange peel as the fermentation substrate, the filter paper, endo-1,4-β-glucanase, exo-1,4-β-glucanase activities of the transformants were 1.06, 337.42, and 1.36 U/mL, which were 35.3-fold, 23.03-fold, and 17-fold higher than those from wild-type S. cerevisiae, respectively. After 6 h treatment, approximately 20 g/L glucose was obtained. Under anaerobic conditions the highest ethanol concentration reached 7.53 g/L after 48 h fermentation and was 37.7-fold higher than that of wild-type S. cerevisiae (0.2 g/L). The engineered strains may provide a valuable material for the development of lignocellulosic ethanol.
Collapse
Affiliation(s)
- Peizhou Yang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, China
| | | | | | | | | | | | | |
Collapse
|
8
|
Kwon DH, Park JB, Hong E, Ha SJ. Ethanol production from xylose is highly increased by the Kluyveromyces marxianus mutant 17694-DH1. Bioprocess Biosyst Eng 2018; 42:63-70. [DOI: 10.1007/s00449-018-2014-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
|
9
|
Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production. ACTA ACUST UNITED AC 2017; 44:879-891. [DOI: 10.1007/s10295-017-1912-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
Abstract
Abstract
The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S. cerevisiae) at 30 °C and over-expression of all PPP genes at 36 °C resulted in the highest ethanol productivities. Furthermore, combinatorial over-expression of PPP genes derived from S. cerevisiae and a thermostable yeast Kluyveromyces marxianus allowed the strain to ferment xylose with ethanol productivity of 0.51 g/L/h, even at 38 °C. These results clearly demonstrate that xylose metabolism can be improved by the utilization of appropriate combinations of thermostable PPP genes in high-temperature production of ethanol.
Collapse
|
10
|
Zong H, Zhang C, Zhuge B, Lu X, Fang H, Sun J. Effects of xylitol dehydrogenase (XYL2) on xylose fermentation by engineeredCandida glycerinogenes. Biotechnol Appl Biochem 2017; 64:590-599. [DOI: 10.1002/bab.1514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 05/21/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hong Zong
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Cheng Zhang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Huiying Fang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Jin Sun
- Zhejiang Condiments Industry Research Center; Zhejiang Zhengwei Food Co., Ltd.; Yiwu People's Republic of China
| |
Collapse
|
11
|
Bischof RH, Ramoni J, Seiboth B. Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei. Microb Cell Fact 2016; 15:106. [PMID: 27287427 PMCID: PMC4902900 DOI: 10.1186/s12934-016-0507-6] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
More than 70 years ago, the filamentous ascomycete Trichoderma reesei was isolated on the Solomon Islands due to its ability to degrade and thrive on cellulose containing fabrics. This trait that relies on its secreted cellulases is nowadays exploited by several industries. Most prominently in biorefineries which use T. reesei enzymes to saccharify lignocellulose from renewable plant biomass in order to produce biobased fuels and chemicals. In this review we summarize important milestones of the development of T. reesei as the leading production host for biorefinery enzymes, and discuss emerging trends in strain engineering. Trichoderma reesei has very recently also been proposed as a consolidated bioprocessing organism capable of direct conversion of biopolymeric substrates to desired products. We therefore cover this topic by reviewing novel approaches in metabolic engineering of T. reesei.
Collapse
Affiliation(s)
- Robert H Bischof
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | - Jonas Ramoni
- Molecular Biotechnology, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | - Bernhard Seiboth
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Molecular Biotechnology, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
| |
Collapse
|
12
|
Gombert AK, Madeira JV, Cerdán ME, González-Siso MI. Kluyveromyces marxianus as a host for heterologous protein synthesis. Appl Microbiol Biotechnol 2016; 100:6193-6208. [PMID: 27260286 DOI: 10.1007/s00253-016-7645-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/22/2016] [Accepted: 05/25/2016] [Indexed: 01/08/2023]
Abstract
The preferentially respiring and thermotolerant yeast Kluyveromyces marxianus is an emerging host for heterologous protein synthesis, surpassing the traditional preferentially fermenting yeast Saccharomyces cerevisiae in some important aspects: K . marxianus can grow at temperatures 10 °C higher than S. cerevisiae, which may result in decreased costs for cooling bioreactors and reduced contamination risk; has ability to metabolize a wider variety of sugars, such as lactose and xylose; is the fastest growing eukaryote described so far; and does not require special cultivation techniques (such as fed-batch) to avoid fermentative metabolism. All these advantages exist together with a high secretory capacity, performance of eukaryotic post-translational modifications, and with a generally regarded as safe (GRAS) status. In the last years, replication origins from several Kluyveromyces spp. have been used for the construction of episomal vectors, and also integrative strategies have been developed based on the tendency for non-homologous recombination displayed by K. marxianus. The recessive URA3 auxotrophic marker and the dominant Kan(R) are mostly used for selection of transformed cells, but other markers have been made available. Homologous and heterologous promoters and secretion signals have been characterized, with the K. marxianus INU1 expression and secretion system being of remarkable functionality. The efficient synthesis of roughly 50 heterologous proteins has been demonstrated, including one thermophilic enzyme. In this mini-review, we summarize the physiological characteristics of K. marxianus relevant for its use in the efficient synthesis of heterologous proteins, the efforts performed hitherto in the development of a molecular toolbox for this purpose, and some successful examples.
Collapse
Affiliation(s)
- Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, Campinas, SP, 13083-862, Brazil
| | - José Valdo Madeira
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato, 80, Campinas, SP, 13083-862, Brazil
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Coruña, 15071, A Coruña, Spain.
| |
Collapse
|
13
|
Shabbir Hussain M, Gambill L, Smith S, Blenner MA. Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica. ACS Synth Biol 2016; 5:213-23. [PMID: 26635071 DOI: 10.1021/acssynbio.5b00100] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic promoters have a complex architecture to control both the strength and timing of gene transcription spanning up to thousands of bases from the initiation site. This complexity makes rational fine-tuning of promoters in fungi difficult to predict; however, this very same complexity enables multiple possible strategies for engineering promoter strength. Here, we studied promoter architecture in the oleaginous yeast, Yarrowia lipolytica. While recent studies have focused on upstream activating sequences, we systematically examined various components common in fungal promoters. Here, we examine several promoter components including upstream activating sequences, proximal promoter sequences, core promoters, and the TATA box in autonomously replicating expression plasmids and integrated into the genome. Our findings show that promoter strength can be fine-tuned through the engineering of the TATA box sequence, core promoter, and upstream activating sequences. Additionally, we identified a previously unreported oleic acid responsive transcription enhancement in the XPR2 upstream activating sequences, which illustrates the complexity of fungal promoters. The promoters engineered here provide new genetic tools for metabolic engineering in Y. lipolytica and provide promoter engineering strategies that may be useful in engineering other non-model fungal systems.
Collapse
Affiliation(s)
- Murtaza Shabbir Hussain
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Lauren Gambill
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Spencer Smith
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Mark A. Blenner
- Department of Chemical and Biomolecular Engineering and ‡Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| |
Collapse
|
14
|
Suzuki A, Fujii H, Hoshida H, Akada R. Gene expression analysis using strains constructed by NHEJ-mediated one-step promoter cloning in the yeast Kluyveromyces marxianus. FEMS Yeast Res 2015; 15:fov059. [PMID: 26136515 DOI: 10.1093/femsyr/fov059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 01/02/2023] Open
Abstract
Gene expression analysis provides valuable information to evaluate cellular state. Unlike quantitative mRNA analysis techniques like reverse-transcription PCR and microarray, expression analysis using a reporter gene has not been commonly used for multiple-gene analysis, probably due to the difficulty in preparing multiple reporter-gene constructs. To circumvent this problem, we developed a novel one-step reporter-gene construction system mediated by non-homologous end joining (NHEJ) in the yeast Kluyveromyces marxianus. As a selectable reporter gene, the ScURA3 selection marker was fused in frame with a red fluorescent gene yEmRFP (ScURA3:yEmRFP). The N-terminally truncated ScURA3:yEmRFP fragment was prepared by PCR. Promoter sequences were also prepared by PCR using primers containing the sequence of the deleted ScURA3 N-terminus to attach at their 3(') ends. The two DNA fragments were used for the transformation of a ura3(-) strain of K. marxianus, in which two DNA fragments are randomly joined and integrated into the chromosome through NHEJ. Only the correctly aligned fragments produced transformants on uracil-deficient medium and expressed red fluorescence under the control of the introduced promoters. A total of 36 gene promoters involved in glycolysis and other pathways were analyzed. Fluorescence measurements of these strains allowed real-time gene expression analysis in different culture conditions.
Collapse
Affiliation(s)
- Ayako Suzuki
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Hiroshi Fujii
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan Yamaguchi University Biomedical Engineering Center, Ube 755-8611, Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan Yamaguchi University Biomedical Engineering Center, Ube 755-8611, Japan
| |
Collapse
|
15
|
Zhang J, Zhang B, Wang D, Gao X, Sun L, Hong J. Rapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H)-preferring xylose reductase-xylitol dehydrogenase pathway. Metab Eng 2015; 31:140-52. [PMID: 26253204 DOI: 10.1016/j.ymben.2015.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/22/2015] [Accepted: 07/27/2015] [Indexed: 11/17/2022]
Abstract
Conversion of xylose to ethanol by yeasts is a challenge because of the redox imbalances under oxygen-limited conditions. The thermotolerant yeast Kluyveromyces marxianus grows well with xylose as a carbon source at elevated temperatures, but its xylose fermentation ability is weak. In this study, a combination of the NADPH-preferring xylose reductase (XR) from Neurospora crassa and the NADP(+)-preferring xylitol dehydrogenase (XDH) mutant from Scheffersomyces stipitis (Pichia stipitis) was constructed. The xylose fermentation ability and redox balance of the recombinant strains were improved significantly by over-expression of several downstream genes. The intracellular concentrations of coenzymes and the reduced coenzyme/oxidized coenzyme ratio increased significantly in these metabolic strains. The byproducts, such as glycerol and acetic acid, were significantly reduced by the disruption of glycerol-3-phosphate dehydrogenase (GPD1). The resulting engineered K. marxianus YZJ088 strain produced 44.95 g/L ethanol from 118.39 g/L xylose with a productivity of 2.49 g/L/h at 42 °C. Additionally, YZJ088 realized glucose and xylose co-fermentation and produced 51.43 g/L ethanol from a mixture of 103.97 g/L xylose and 40.96 g/L glucose with a productivity of 2.14 g/L/h at 42 °C. These promising results validate the YZJ088 strain as an excellent producer of ethanol from xylose through the synthetic xylose assimilation pathway.
Collapse
Affiliation(s)
- Jia Zhang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China
| | - Biao Zhang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China
| | - Dongmei Wang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China
| | - Xiaolian Gao
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004-5001, USA; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China
| | - Lianhong Sun
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China
| | - Jiong Hong
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China; Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, PR China.
| |
Collapse
|
16
|
Kim JS, Park JB, Jang SW, Ha SJ. Enhanced Xylitol Production by Mutant Kluyveromyces marxianus 36907-FMEL1 Due to Improved Xylose Reductase Activity. Appl Biochem Biotechnol 2015; 176:1975-84. [DOI: 10.1007/s12010-015-1694-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/27/2015] [Indexed: 11/28/2022]
|
17
|
Sylvester K, Wang QM, James B, Mendez R, Hulfachor AB, Hittinger CT. Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species. FEMS Yeast Res 2015; 15:fov002. [PMID: 25743785 DOI: 10.1093/femsyr/fov002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 01/08/2023] Open
Abstract
Compared to its status as an experimental model system and importance to industry, the ecology and genetic diversity of the genus Saccharomyces has received less attention. To investigate systematically the biogeography, community members and habitat of these important yeasts, we isolated and identified nearly 600 yeast strains using sugar-rich enrichment protocols. Isolates were highly diverse and contained representatives of more than 80 species from over 30 genera, including eight novel species that we describe here: Kwoniella betulae f.a. (yHKS285(T) = NRRL Y-63732(T) = CBS 13896(T)), Kwoniella newhampshirensis f.a. (yHKS256(T) = NRRL Y-63731(T) = CBS 13917(T)), Cryptococcus wisconsinensis (yHKS301(T) = NRRL Y-63733(T) = CBS 13895(T)), Cryptococcus tahquamenonensis (yHAB242(T) = NRRL Y-63730(T) = CBS 13897(T)), Kodamaea meredithiae f.a. (yHAB239(T) = NRRL Y-63729(T) = CBS 13899(T)), Blastobotrys buckinghamii (yHAB196(T) = NRRL Y-63727(T) = CBS 13900(T)), Candida sungouii (yHBJ21(T) = NRRL Y-63726(T) = CBS 13907(T)) and Cyberlindnera culbertsonii f.a. (yHAB218(T) = NRRL Y-63728(T) = CBS 13898(T)), spp. nov. Saccharomyces paradoxus was one of the most frequently isolated species and was represented by three genetically distinct lineages in Wisconsin alone. We found a statistically significant association between Quercus (oak) samples and the isolation of S. paradoxus, as well as several novel associations. Variation in temperature preference was widespread across taxonomic ranks and evolutionary timescales. This survey highlights the genetic and taxonomic diversity of yeasts and suggests that host and temperature preferences are major ecological factors.
Collapse
Affiliation(s)
- Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi-Ming Wang
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Brielle James
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Russell Mendez
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
18
|
Integrative expression vectors for overexpression of xylitol dehydrogenase (XYL2) in Osmotolerant yeast, Candida glycerinogenes WL2002-5. J Ind Microbiol Biotechnol 2014; 42:113-24. [DOI: 10.1007/s10295-014-1530-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
|