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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: 2] [Impact Index Per Article: 2.0] [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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Shikina E, Kovalevsky R, Shirkovskaya A, Toukach P. Prospective bacterial and fungal sources of hyaluronic acid: A review. Comput Struct Biotechnol J 2022; 20:6214-6236. [PMID: 36420162 PMCID: PMC9676211 DOI: 10.1016/j.csbj.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
The unique biological and rheological properties make hyaluronic acid a sought-after material for medicine and cosmetology. Due to very high purity requirements for hyaluronic acid in medical applications, the profitability of streptococcal fermentation is reduced. Production of hyaluronic acid by recombinant systems is considered a promising alternative. Variations in combinations of expressed genes and fermentation conditions alter the yield and molecular weight of produced hyaluronic acid. This review is devoted to the current state of hyaluronic acid production by recombinant bacterial and fungal organisms.
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Insights into the Structures, Inhibitors, and Improvement Strategies of Glucose Oxidase. Int J Mol Sci 2022; 23:ijms23179841. [PMID: 36077243 PMCID: PMC9456440 DOI: 10.3390/ijms23179841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Glucose oxidase, which uses molecular oxygen as an electron acceptor to specifically catalyze the conversion of β-d-glucose to gluconic acid and hydrogen peroxide (H2O2), has been considered an important enzyme in increasing environmental sustainability and food security. However, achieving the high yield, low price and high activity required for commercial viability remains challenging. In this review, we first present a brief introduction, looking at the sources, characteristics, catalytic process, and applications of glucose oxidase. Then, the predictive structures of glucose oxidase from two different sources are comparatively discussed. We summarize the inhibitors of glucose oxidase. Finally, we highlight how the production of glucose oxidase can be improved by optimizing the culture conditions and microbial metabolic engineering.
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Liang Z, Yan Y, Zhang W, Luo H, Yao B, Huang H, Tu T. Review of glucose oxidase as a feed additive: production, engineering, applications, growth-promoting mechanisms, and outlook. Crit Rev Biotechnol 2022:1-18. [PMID: 35723581 DOI: 10.1080/07388551.2022.2057275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The regulation and prohibition of antibiotics used as growth promoters (AGP) in the feed field are increasing because they cause antimicrobial resistance and drug residue issues and threaten community health. Recently, glucose oxidase (GOx) has attracted increasing interest in the feed industry as an alternative to antibiotics. GOx specifically catalyzes the production of gluconic acid (GA) and hydrogen peroxide (H2O2) by consuming molecular oxygen, and plays an important role in relieving oxidative stress, preserving health, and promoting animal growth. To expand the application of GOx in the feed field, considerable efforts have been made to mine new genetic resources. Efforts have also been made to heterologously overexpress relevant genes to reduce production costs and to engineer proteins by modifying enzyme properties, both of which are bottleneck problems that limit industrial feed applications. Herein, the: different sources, diverse biochemical properties, distinct structural features, and various strategies of GOx engineering and heterologous overexpression are summarized. The mechanism through which GOx promotes growth in animal production, including the improvement of antioxidant capacity, maintenance of intestinal microbiota homeostasis, and enhancement of gut function, are also systematically addressed. Finally, a new perspective is provided for the future development of GOx applications in the feed field.
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Affiliation(s)
- Ziqi Liang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yaru Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up. Microb Cell Fact 2021; 20:124. [PMID: 34193127 PMCID: PMC8246677 DOI: 10.1186/s12934-021-01617-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.
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Wang Y, Wang J, Leng F, Ma J, Bagadi A. Expression of Aspergillus niger glucose oxidase in Pichia pastoris and its antimicrobial activity against Agrobacterium and Escherichia coli. PeerJ 2020; 8:e9010. [PMID: 32832258 PMCID: PMC7413082 DOI: 10.7717/peerj.9010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
The gene encoding glucose oxidase from Aspergillus niger ZM-8 was cloned and transferred to Pichia pastoris GS115, a transgenic strain P. pastoris GS115-His-GOD constructed. The growth curve of P. pastoris GS115-His-GOD was consistent with that of Pichia pastoris GS115-pPIC9K under non-induced culture conditions. Under methanol induction conditions, the growth of the GOD-transgenic strain was significantly lowered than P. pastoris GS115-pPIC9K with the induced-culture time increase, and the optical densities of GOD-transgenic strain reached one-third of that of the P. pastoris GS115-pPIC9K at 51 h. The activity of glucose oxidase in the cell-free supernatant, the supernatant of cell lysate, and the precipitation of cell lysate was 14.3 U/mL, 18.2 U/mL and 0.48 U/mL, respectively. The specific activity of glucose oxidase was 8.3 U/mg, 6.52 U/mg and 0.73 U/mg, respectively. The concentration of hydrogen peroxide formed by glucose oxidase from supernatant of the fermentation medium, the supernatant of the cell lysate, and the precipitation of cell lysate catalyzing 0.2 M glucose was 14.3 μg/mL, 18.2 μg/mL, 0.48 μg/mL, respectively. The combination of different concentrations of glucose oxidase and glucose could significantly inhibit the growth of Agrobacterium and Escherichia coli in logarithmic phase. The filter article containing supernatant of the fermentation medium, supernatant of the cell lysate, and precipitation of cell lysate had no inhibitory effect on Agrobacterium and E. coli. The minimum inhibitory concentration of hydrogen peroxide on the plate culture of Agrobacterium and E. coli was 5.6 × 103 μg/mL and 6.0 × 103 μg/mL, respectively.
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Affiliation(s)
- Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China.,Key Laboratory of Drug Screening and Deep Processing for Traditional Chinese and Tibetan Medicine of Gansu Province, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jiangqin Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China.,Key Laboratory of Drug Screening and Deep Processing for Traditional Chinese and Tibetan Medicine of Gansu Province, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China.,Key Laboratory of Drug Screening and Deep Processing for Traditional Chinese and Tibetan Medicine of Gansu Province, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China.,Key Laboratory of Drug Screening and Deep Processing for Traditional Chinese and Tibetan Medicine of Gansu Province, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Alnoor Bagadi
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
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7
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Wu L, Wang M, Zha G, Zhou J, Yu Y, Lu H. Improving the expression of a heterologous protein by genome shuffling in Kluyveromyces marxianus. J Biotechnol 2020; 320:11-16. [DOI: 10.1016/j.jbiotec.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
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8
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Rai DK, Gurusaran M, Urban V, Aran K, Ma L, Li P, Qian S, Narayanan TN, Ajayan PM, Liepmann D, Sekar K, Álvarez-Cao ME, Escuder-Rodríguez JJ, Cerdán ME, González-Siso MI, Viswanathan S, Paulmurugan R, Renugopalakrishnan V. Structural determination of Enzyme-Graphene Nanocomposite Sensor Material. Sci Rep 2019; 9:15519. [PMID: 31664095 PMCID: PMC6820869 DOI: 10.1038/s41598-019-51882-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.
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Affiliation(s)
- Durgesh K Rai
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York, 14853, USA.
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne-NE1 7RU, UK
| | - Volker Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA.
| | - Kiana Aran
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Lulu Ma
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Pingzuo Li
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA
| | - Tharangattu N Narayanan
- Tata Institute of Fundamental Research - Center for Interdisciplinary Sciences, Hyderabad, 500107, India
| | - Pulickel M Ajayan
- Department of Mechanical Engineering and Materials Science, Rice University, Houston, Texas, 77005, USA
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94709, USA
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - María-Efigenia Álvarez-Cao
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Juan-José Escuder-Rodríguez
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Esperanza Cerdán
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - María-Isabel González-Siso
- Universidade da Coruña, Grupo EXPRELA, F. Ciencias & Centro de Investigacións Científicas Avanzadas (CICA) & Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, 15011, Spain
| | - Sowmya Viswanathan
- Newton Wellesley Hospital/Partners Healthcare System, Newton, Massachusetts, 02462, USA
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Dept. of Radiology, Stanford University School of Medicine, 3155 Porter Drive, Suite 2236, Palo Alto, California, 94304, USA
| | - Venkatesan Renugopalakrishnan
- Center for Life Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115, USA.
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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.
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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.
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Ma Y, Chi Z, Li YF, Jiang H, Liu GL, Hu Z, Chi ZM. Cloning, deletion, and overexpression of a glucose oxidase gene in Aureobasidium sp. P6 for Ca2+-gluconic acid overproduction. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1393-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Liu Y, Mo WJ, Shi TF, Wang MZ, Zhou JG, Yu Y, Yew WS, Lu H. Mutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus. Microb Cell Fact 2018; 17:144. [PMID: 30217195 PMCID: PMC6138896 DOI: 10.1186/s12934-018-0993-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/08/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The yeast Kluyveromyces marxianus is an emerging cell factory for heterologous protein biosynthesis and its use holds tremendous advantages for multiple applications. However, which genes influence the productivity of desired proteins in K. marxianus has so far been investigated by very few studies. RESULTS In this study, we constructed a K. marxianus recombinant (FIM1/Est1E), which expressed the heterologous ruminal feruloyl esterase Est1E as reporter. UV-60Co-γ irradiation mutagenesis was performed on this recombinant, and one mutant (be termed as T1) was screened and reported, in which the productivity of heterologous Est1E was increased by at least tenfold compared to the parental FIM1/Est1E recombinant. Transcriptional perturbance was profiled and presented that the intracellular vesicle trafficking was enhanced while autophagy be weakened in the T1 mutant. Moreover, whole-genome sequencing combined with CRISPR/Cas9 mediated gene-editing identified a novel functional protein Mtc6p, which was prematurely terminated at Tyr251 by deletion of a single cytosine at 755 loci of its ORF in the T1 mutant. We found that deleting C755 of MTC6 in FIM1 led to 4.86-fold increase in the production of Est1E compared to FIM1, while the autophagy level decreased by 47%; on the contrary, when reinstating C755 of MTC6 in the T1 mutant, the production of Est1E decreased by 66% compared to T1, while the autophagy level increased by 124%. Additionally, in the recombinant with attenuated autophagy (i.e., FIM1 mtc6C755Δ and T1) or interdicted autophagy (i.e., FIM1 atg1Δ and T1 atg1Δ), the productivity of three other heterologous proteins was also increased, specifically the heterologous mannase Man330, the β-1,4-endoxylanase XynCDBFV or the conventional EGFP. CONCLUSIONS Our results demonstrated that Mtc6p was involved in regulating autophagy; attenuating or interdicting autophagy would dramatically improve the yields of desired proteins in K. marxianus, and this modulation could be achieved by focusing on the premature mutation of Mtc6p target.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Wen-Juan Mo
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Tian-Fang Shi
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Meng-Zhu Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Jun-Gang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China
| | - Wen-Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, People's Republic of China. .,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, People's Republic of China.
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Zhou J, Zhu P, Hu X, Lu H, Yu Y. Improved secretory expression of lignocellulolytic enzymes in Kluyveromyces marxianus by promoter and signal sequence engineering. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:235. [PMID: 30279722 PMCID: PMC6116501 DOI: 10.1186/s13068-018-1232-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/20/2018] [Indexed: 06/05/2023]
Abstract
BACKGROUND Taking into account its thermotolerance, high growth rate, and broad substrate spectrum, Kluyveromyces marxianus can be considered an ideal consolidated bioprocessing (CBP). A major obstacle to ethanol production using K. marxianus is the low production of lignocellulolytic enzymes, which reduces the cellulose hydrolysis and ethanol production. Thus, further improvement of enzyme expression and secretion is essential. RESULTS To improve the expression of lignocellulolytic enzymes, the inulinase promoter and signal sequence from K. marxianus was optimized through mutagenesis. A T(-361)A mutation inside the promoter, a deletion of AT-rich region inside 5'UTR (UTR∆A), and a P10L substitution in the signal sequence increased the secretory expression of the feruloyl esterase Est1E by up to sixfold. T(-361)A and UTR∆A increased the mRNA expression, while the P10L substitution extended the hydrophobic core of signal sequence and promoted secretion of mature protein. P10L and T(-361)A mutations increased secretory expressions of other types of lignocellulolytic enzymes by up to threefold, including endo-1,4-β-glucanase RuCelA, endo-1,4-β-endoxylanase Xyn-CDBFV, and endo-1,4-β-mannanase MAN330. During the fed-batch fermentation of strains carrying optimized modules, the peak activities of RuCelA, Xyn-CDBFV, MAN330, and Est1E reached 24 U/mL, 25,600 U/mL, 10,200 U/mL, and 1220 U/mL, respectively. Importantly, higher yield of enzymes by optimized promoter and signal sequence were achieved in all tested carbon sources, including the major end products of lignocellulose saccharification and fermentation, with growth on xylose resulting in the highest production. CONCLUSIONS The engineered promoter and signal sequence presented increased secretory expressions of different lignocellulolytic enzymes in K. marxianus by means of various carbon resources. Activities of lignocellulolytic enzymes in fed-batch fermentation were the highest activities reported for K. marxianus so far. Our engineered modules are valuable in producing lignocellulolytic enzymes by K. marxianus and in constructing efficient CBP strains for cellulosic ethanol production.
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Affiliation(s)
- Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Peixia Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Xiaoyue Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, 200237 China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
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da Silveira FA, Diniz RHS, Sampaio GMS, Brandão RL, da Silveira WB, Castro IM. Sugar transport systems in Kluyveromyces marxianus CCT 7735. Antonie van Leeuwenhoek 2018; 112:211-223. [DOI: 10.1007/s10482-018-1143-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/11/2018] [Indexed: 11/30/2022]
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14
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Darvishi F, Zarei A, Madzak C. In silico and in vivo analysis of signal peptides effect on recombinant glucose oxidase production in nonconventional yeast Yarrowia lipolytica. World J Microbiol Biotechnol 2018; 34:128. [PMID: 30083963 DOI: 10.1007/s11274-018-2512-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Signal peptide (SP) is an important factor and biobrick in the production and secretion of recombinant proteins. The aim of this study was in silico and in vivo analysis of SPs effect on the production of recombinant glucose oxidase (GOX) in Yarrowia lipolytica. Several in silico softwares, namely SignalP4, Signal-CF, Phobius, WolfPsort 0.2, SOLpro and ProtParam, were used to analyse the potential of 15 endogenous and exogenous SPs for the secretion of recombinant GOX in Y. lipolytica. According to in silico results, the SP of GOX was predicted as suitable in terms of high secretory potential and of protein solubility and stability which is chosen for in vivo analysis. The recombinant Y. lipolytica strain produced 280 U/L of extracellular GOX after 7 days in YPD medium. The results show that the SP of GOX can be applied to efficient production of extracellular heterologous proteins and metabolic engineering in Y. lipolytica.
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Affiliation(s)
- Farshad Darvishi
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, 55181-83111, Iran.
| | - Amin Zarei
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, 55181-83111, Iran
| | - Catherine Madzak
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
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15
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Gao J, Yuan W, Li Y, Bai F, Jiang Y. Characterization of inulinase promoter from Kluyveromyces marxianus for intensive protein expression in industrial biotechnology. FEMS Yeast Res 2018; 17:4082735. [PMID: 28922844 DOI: 10.1093/femsyr/fox062] [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: 04/27/2017] [Accepted: 08/10/2017] [Indexed: 11/12/2022] Open
Abstract
Inulinase from Kluyveromyces marxianus (KmINU1) has wide application in industrial biotechnology, and it is supposed that its expression is regulated at the transcriptional level via the promoter. Therefore, in this study, the KmINU1 promoter, fused to the reporter EGFP gene, was analyzed to determine its fundamental regulatory mechanisms in Saccharomyces cerevisiae S288C (ATCC 204508). Induction by inulin and repression by high glucose concentrations of KmINU1 promoters are reported, and the promoter with a length of 353 bp was shown to have the highest strength with the weakest responses to high glucose concentration. Responses of the KmINU1 promoter to carbon source were shown to be related to the Mig1 binding site extending from -496 to -485 bp. Hence, we propose clear regulation mechanisms of the inulinase promoter, which may provide a powerful theoretical reference for its application in protein production.
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Affiliation(s)
- Jiaoqi Gao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Wenjie Yuan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Yimin Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Fengwu Bai
- School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Yu Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, PA 15261, USA
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16
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Transcriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress. Appl Microbiol Biotechnol 2017; 101:6969-6980. [DOI: 10.1007/s00253-017-8432-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/11/2017] [Accepted: 07/19/2017] [Indexed: 12/11/2022]
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17
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Khadivi Derakshan F, Darvishi F, Dezfulian M, Madzak C. Expression and Characterization of Glucose Oxidase from Aspergillus niger in Yarrowia lipolytica. Mol Biotechnol 2017. [DOI: 10.1007/s12033-017-0017-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Dubey MK, Zehra A, Aamir M, Meena M, Ahirwal L, Singh S, Shukla S, Upadhyay RS, Bueno-Mari R, Bajpai VK. Improvement Strategies, Cost Effective Production, and Potential Applications of Fungal Glucose Oxidase (GOD): Current Updates. Front Microbiol 2017; 8:1032. [PMID: 28659876 PMCID: PMC5468390 DOI: 10.3389/fmicb.2017.01032] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 01/15/2023] Open
Abstract
Fungal glucose oxidase (GOD) is widely employed in the different sectors of food industries for use in baking products, dry egg powder, beverages, and gluconic acid production. GOD also has several other novel applications in chemical, pharmaceutical, textile, and other biotechnological industries. The electrochemical suitability of GOD catalyzed reactions has enabled its successful use in bioelectronic devices, particularly biofuel cells, and biosensors. Other crucial aspects of GOD such as improved feeding efficiency in response to GOD supplemental diet, roles in antimicrobial activities, and enhancing pathogen defense response, thereby providing induced resistance in plants have also been reported. Moreover, the medical science, another emerging branch where GOD was recently reported to induce several apoptosis characteristics as well as cellular senescence by downregulating Klotho gene expression. These widespread applications of GOD have led to increased demand for more extensive research to improve its production, characterization, and enhanced stability to enable long term usages. Currently, GOD is mainly produced and purified from Aspergillus niger and Penicillium species, but the yield is relatively low and the purification process is troublesome. It is practical to build an excellent GOD-producing strain. Therefore, the present review describes innovative methods of enhancing fungal GOD production by using genetic and non-genetic approaches in-depth along with purification techniques. The review also highlights current research progress in the cost effective production of GOD, including key advances, potential applications and limitations. Therefore, there is an extensive need to commercialize these processes by developing and optimizing novel strategies for cost effective GOD production.
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Affiliation(s)
- Manish K. Dubey
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Andleeb Zehra
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Mohd Aamir
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Mukesh Meena
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Laxmi Ahirwal
- Laboratory of Molecular Biology, Department of Botany, Dr. Hari Singh Gour UniversitySagar, India
| | - Siddhartha Singh
- Laboratory of Molecular Biology, Department of Botany, Dr. Hari Singh Gour UniversitySagar, India
| | - Shruti Shukla
- Department of Energy and Materials Engineering, Dongguk UniversitySeoul, South Korea
| | - Ram S. Upadhyay
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Ruben Bueno-Mari
- Research and Development (R+D) Department, Laboratorios LokímicaValencia, Spain
| | - Vivek K. Bajpai
- Department of Applied Microbiology and Biotechnology, Yeungnam UniversityGyeongsan, South Korea
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19
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Löbs AK, Engel R, Schwartz C, Flores A, Wheeldon I. CRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:164. [PMID: 28652865 PMCID: PMC5483312 DOI: 10.1186/s13068-017-0854-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/16/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND The thermotolerant yeast Kluyveromyces marxianus shows promise as an industrial host for the biochemical production of fuels and chemicals. Wild-type strains are known to ferment high titers of ethanol and can effectively convert a wide range of C5, C6, and C12 sugars into the volatile short-chain ester ethyl acetate. Strain engineering, however, has been limited due to a lack of advanced genome-editing tools and an incomplete understanding of ester and ethanol biosynthesis. RESULTS Enabled by the design of hybrid RNA polymerase III promoters, this work adapts the CRISPR-Cas9 system from Streptococcus pyogenes for use in K. marxianus. The system was used to rapidly create functional disruptions to alcohol dehydrogenase (ADH) and alcohol-O-acetyltransferase (ATF) genes with putative function in ethyl acetate and ethanol biosynthesis. Screening of the KmATF disrupted strain revealed that Atf activity contributes to ethyl acetate biosynthesis, but the knockout reduced ethyl acetate titers by only ~15%. Overexpression experiments revealed that KmAdh7 can catalyze the oxidation of hemiacetal to ethyl acetate. Finally, analysis of the KmADH2 disrupted strain showed that the knockout almost completely eliminated ethanol production and resulted in the accumulation of acetaldehyde. CONCLUSIONS Newly designed RNA polymerase III promoters for sgRNA expression in K. marxianus enable a CRISPR-Cas9 genome-editing system for the thermotolerant yeast. This system was used to disrupt genes involved in ethyl acetate biosynthesis, specifically KmADH1-7 and KmATF. KmAdh2 was found to be critical for aerobic and anaerobic ethanol production. Aerobically produced ethanol supplies the biosynthesis of ethyl acetate catalyzed by KmAtf. KmAdh7 was found to exhibit activity toward the oxidation of hemiacetal, a possible alternative route for the synthesis of ethyl acetate.
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Affiliation(s)
- Ann-Kathrin Löbs
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ronja Engel
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
- Mannheim University of Applied Sciences, Mannheim, Germany
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Andrew Flores
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, 92521 USA
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20
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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.
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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.
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21
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Spohner SC, Schaum V, Quitmann H, Czermak P. Kluyveromyces lactis: An emerging tool in biotechnology. J Biotechnol 2016; 222:104-16. [DOI: 10.1016/j.jbiotec.2016.02.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 02/04/2023]
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22
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Yang C, Hu S, Zhu S, Wang D, Gao X, Hong J. Characterizing yeast promoters used in Kluyveromyces marxianus. World J Microbiol Biotechnol 2015; 31:1641-6. [PMID: 26164057 DOI: 10.1007/s11274-015-1899-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
Fermentation at higher temperatures can potentially reduce the cooling cost in large-scale fermentation and reduce the contamination risk. Thus, the thermotolerant yeast, Kluyveromyces marxianus, which can grow and ferment at elevated temperatures, is a promising biotechnological tool for future applications. However, the promoters used in K. marxianus are not well characterized, especially at elevated temperatures, which is important in efficient metabolic pathway construction. In this study, six constitutive promoters (P(TDH3), P(PGK), and P(ADH1) from both Saccharomyces cerevisiae and K. marxianus) were evaluated in K. marxianus through the heterologous expression of the KlLAC4, GUSA, and SH BLE genes at various temperatures, with various carbon sources and oxygen conditions. The expression was evaluated at the transcription and protein level using real-time PCR and protein activity determination to eliminate the effect of heterologous protein stability. While the transcription of all the promoters decreased at higher temperatures, the order of their promoting strength at various temperatures with glucose as the carbon source was P(KmPGK) > P(KmTDH3) > P(ScPGK) > P(ScTDH3) > P(KmADH1) > P(ScADH1). When glycerol or xylose was supplied as the carbon source at 42 °C, the order of promoter strength was P(KmPGK) > P(ScPGK) > P(KmADH1) > P(ScADH1) > P(ScTDH3) > P(KmTDH3). The promoter activity of P TDH3 decreased significantly, while the promoter activity of both of the P(ADH1) promoters increased. Oxygen conditions had non-significant effect. The results of this study provide important information for fine-tuned pathway construction for the metabolic engineering of K. marxianus.
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Affiliation(s)
- Chun Yang
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Shenglin Hu
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Songli Zhu
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Xiaolian Gao
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China.,Department of Biology and Biochemistry, University of Houston, Houston, 77004-5001, USA
| | - Jiong Hong
- School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China. .,Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China.
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23
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Lertwattanasakul N, Kosaka T, Hosoyama A, Suzuki Y, Rodrussamee N, Matsutani M, Murata M, Fujimoto N, Tsuchikane K, Limtong S, Fujita N, Yamada M. Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:47. [PMID: 25834639 PMCID: PMC4381506 DOI: 10.1186/s13068-015-0227-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/19/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis. RESULTS The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions. CONCLUSIONS This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.
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Affiliation(s)
- Noppon Lertwattanasakul
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Tomoyuki Kosaka
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
| | - Akira Hosoyama
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Yutaka Suzuki
- />Department of Medical Genome Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Nadchanok Rodrussamee
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Minenosuke Matsutani
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
| | - Masayuki Murata
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Naoko Fujimoto
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Keiko Tsuchikane
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Savitree Limtong
- />Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Nobuyuki Fujita
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Mamoru Yamada
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
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High-Level Extracellular Production of Glucose Oxidase by Recombinant Pichia Pastoris Using a Combined Strategy. Appl Biochem Biotechnol 2014; 175:1429-47. [DOI: 10.1007/s12010-014-1387-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
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25
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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26
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Bragança CRS, Colombo LT, Roberti AS, Alvim MCT, Cardoso SA, Reis KCP, de Paula SO, da Silveira WB, Passos FML. Construction of recombinant Kluyveromyces marxianus UFV-3 to express dengue virus type 1 nonstructural protein 1 (NS1). Appl Microbiol Biotechnol 2014; 99:1191-203. [PMID: 25085614 DOI: 10.1007/s00253-014-5963-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
Abstract
The yeast Kluyveromyces marxianus is a convenient host for industrial synthesis of biomolecules. However, despite its potential, there are few studies reporting the expression of heterologous proteins using this yeast. Here, we report expression of a dengue virus protein in K. marxianus for the first time. The dengue virus type 1 nonstructural protein 1 (NS1) was integrated into the K. marxianus UFV-3 genome at the LAC4 locus using an adapted integrative vector designed for high-level expression of recombinant protein in Kluyveromyces lactis. The NS1 gene sequence was codon-optimized to increase the level of protein expression in yeast. The synthetic gene was cloned in frame with K. lactis α-mating factor signal peptide, and the recombinant plasmid obtained was used to transform K. marxianus UFV-3 by electroporation. The transformed cells, selected in yeast extract peptone dextrose containing 200 μg mL(-1) Geneticin, were mitotically stable. Analysis of recombinant strains by RT-PCR and protein detection using blot analysis confirmed both transcription and expression of extracellular NS1 polypeptide. After induction with galactose, the NS1 protein was analyzed by sodium dodecyl sulfate-PAGE and immunogenic detection. Protein production was investigated under two conditions: with galactose and biotin pulses at 24-h intervals during 96 h of induction and without galactose and biotin supplementation. Protease activity was not detected in post-growth medium. Our results indicate that recombinant K. marxianus is a good host for the production of dengue virus NS1 protein, which has potential for diagnostic applications.
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Affiliation(s)
- Caio Roberto Soares Bragança
- Laboratório de Fisiologia de Micro-organismos, Departamento de Microbiologia, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Weinhandl K, Winkler M, Glieder A, Camattari A. Carbon source dependent promoters in yeasts. Microb Cell Fact 2014; 13:5. [PMID: 24401081 PMCID: PMC3897899 DOI: 10.1186/1475-2859-13-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/16/2013] [Indexed: 11/22/2022] Open
Abstract
Budding yeasts are important expression hosts for the production of recombinant proteins. The choice of the right promoter is a crucial point for efficient gene expression, as most regulations take place at the transcriptional level. A wide and constantly increasing range of inducible, derepressed and constitutive promoters have been applied for gene expression in yeasts in the past; their different behaviours were a reflection of the different needs of individual processes. Within this review we summarize the majority of the large available set of carbon source dependent promoters for protein expression in yeasts, either induced or derepressed by the particular carbon source provided. We examined the most common derepressed promoters for Saccharomyces cerevisiae and other yeasts, and described carbon source inducible promoters and promoters induced by non-sugar carbon sources. A special focus is given to promoters that are activated as soon as glucose is depleted, since such promoters can be very effective and offer an uncomplicated and scalable cultivation procedure.
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Affiliation(s)
| | | | | | - Andrea Camattari
- Institute of Molecular Biotechnology, Technical University Graz, Graz, Austria.
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Yuan W, Zhao X, Chen L, Bai F. Improved ethanol production in Jerusalem artichoke tubers by overexpression of inulinase gene in Kluyveromyces marxianus. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0026-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Raimondi S, Zanni E, Amaretti A, Palleschi C, Uccelletti D, Rossi M. Thermal adaptability of Kluyveromyces marxianus in recombinant protein production. Microb Cell Fact 2013; 12:34. [PMID: 23587421 PMCID: PMC3655038 DOI: 10.1186/1475-2859-12-34] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/26/2013] [Indexed: 01/16/2023] Open
Abstract
Background Kluyveromyces marxianus combines the ease of genetic manipulation and fermentation with the ability to efficiently secrete high molecular weight proteins, performing eukaryotic post-translational modifications. It is able to grow efficiently in a wide range of temperatures. The secretion performances were analyzed in the host K. marxianus L3 in the range between 5°C and 40°C by means of 3 different reporter proteins, since temperature appears a key parameter for production and secretion of recombinant proteins. Results The recombinant strains were able to grow up to 40°C and, along the tested temperature interval (5-40°C), the specific growth rates (μ) were generally lower as compared to those of the untransformed strain. Biomass yields were slightly affected by temperature, with the highest values reached at 15°C and 30°C. The secretion of the endogenous β-fructofuranosidase, used as an internal control, was efficient in the range of the tested temperature, as evaluated by assaying the enzyme activity in the culture supernatants. The endogenous β-fructofuranosidase production was temperature dependent, with the highest yield at 30°C. The heterologous proteins HSA, GAA and Sod1p were all successfully produced and secreted between 5°C and 40°C, albeit each one presented a different optimal production temperature (15, 40, 5-30°C for HSA, GAA and Sod1p, respectively). Conclusions K. marxianus L3 has been identified as a promising and flexible cell factory. In a sole host, the optimization of growth temperatures for the efficient secretion of each individual protein can be carried out over a wide range of temperatures.
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Affiliation(s)
- Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Fonseca GG, de Carvalho NMB, Gombert AK. Growth of the yeast Kluyveromyces marxianus CBS 6556 on different sugar combinations as sole carbon and energy source. Appl Microbiol Biotechnol 2013; 97:5055-67. [PMID: 23435899 DOI: 10.1007/s00253-013-4748-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/31/2013] [Accepted: 01/31/2013] [Indexed: 12/01/2022]
Abstract
The yeast Kluyveromyces marxianus has been pointed out as a promising microorganism for a variety of industrial bioprocesses. Although genetic tools have been developed for this yeast and different potential applications have been investigated, quantitative physiological studies have rarely been reported. Here, we report and discuss the growth, substrate consumption, metabolite formation, and respiratory parameters of K. marxianus CBS 6556 during aerobic batch bioreactor cultivations, using a defined medium with different sugars as sole carbon and energy source, at 30 and 37 °C. Cultivations were carried out both on single sugars and on binary sugar mixtures. Carbon balances closed within 95 to 101 % in all experiments. Biomass and CO2 were the main products of cell metabolism, whereas by-products were always present in very low proportion (<3 % of the carbon consumed), as long as full aerobiosis was guaranteed. On all sugars tested as sole carbon and energy source (glucose, fructose, sucrose, lactose, and galactose), the maximum specific growth rate remained between 0.39 and 0.49 h(-1), except for galactose at 37 °C, which only supported growth at 0.31 h(-1). Different growth behaviors were observed on the binary sugar mixtures investigated (glucose and lactose, glucose and galactose, lactose and galactose, glucose and fructose, galactose and fructose, fructose and lactose), and the observations were in agreement with previously published data on the sugar transport systems in K. marxianus. We conclude that K. marxianus CBS 6556 does not present any special nutritional requirements; grows well in the range of 30 to 37 °C on different sugars; is capable of growing on sugar mixtures in a shorter period of time than Saccharomyces cerevisiae, which is interesting from an industrial point of view; and deviates tiny amounts of carbon towards metabolite formation, as long as full aerobiosis is maintained.
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Affiliation(s)
- Gustavo Graciano Fonseca
- Department of Chemical Engineering, University of São Paulo, PO Box 61548, CEP 05424-970 São Paulo, SP, Brazil
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Novel post-translational modifications of the hemagglutinin and neuraminidase proteins of avian influenza virus expressed by Kluyveromyces lactis. J Virol Methods 2011; 175:175-81. [DOI: 10.1016/j.jviromet.2011.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/21/2011] [Accepted: 05/04/2011] [Indexed: 11/18/2022]
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Rocha SN, Abrahão-Neto J, Gombert AK. Physiological diversity within the Kluyveromyces marxianus species [corrected]. Antonie van Leeuwenhoek 2011; 100:619-30. [PMID: 21732033 DOI: 10.1007/s10482-011-9617-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/21/2011] [Indexed: 11/30/2022]
Abstract
The Kluyveromyces marxianus strains CBS 6556, CBS 397 and CBS 712(T) were cultivated on a defined medium with either glucose, lactose or sucrose as the sole carbon source, at 30 and 37°C. The aim of this work was to evaluate the diversity within this species, in terms of the macroscopic physiology. The main properties evaluated were: intensity of the Crabtree effect, specific growth rate, biomass yield on substrate, metabolite excretion and protein secretion capacity, inferred by measuring extracellular inulinase activity. The strain Kluyveromyces lactis CBS 2359 was evaluated in parallel, since it is the best described Kluyveromyces yeast and thus can be used as a control for the experimental setup. K. marxianus CBS 6556 presented the highest specific growth rate (0.70 h(-1)) and the highest specific inulinase activity (1.65 U mg(-1) dry cell weight) among all strains investigated, when grown at 37°C with sucrose as the sole carbon source. The lowest metabolite formation and highest biomass yield on substrate (0.59 g dry cell weight g sucrose(-1)) was achieved by K. marxianus CBS 712(T) at 37°C. Taken together, the results show a systematic comparison of carbon and energy metabolism among three of the best known K. marxianus strains, in parallel to K. lactis CBS 2359.
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Affiliation(s)
- Saul Nitsche Rocha
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil.
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Rocha SN, Abrahão-Neto J, Cerdán ME, Gombert AK, González-Siso MI. Heterologous expression of a thermophilic esterase in Kluyveromyces yeasts. Appl Microbiol Biotechnol 2010; 89:375-85. [PMID: 20862582 DOI: 10.1007/s00253-010-2869-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/13/2010] [Accepted: 09/07/2010] [Indexed: 11/26/2022]
Abstract
In the present work, a thermophilic esterase from Thermus thermophilus HB27 was cloned into Kluyveromyces marxianus and into Kluyveromyces lactis using two different expression systems, yielding four recombinant strains. K. lactis showed the highest esterase expression levels (294 units per gram dry cell weight, with 65% of cell-bound enzyme) using an episomal system with the PGK promoter and terminator from Saccharomyces cerevisiae combined with the K. lactis k1 secretion signal. K. marxianus showed higher secretion efficiency of the heterologous esterase (56.9 units per gram dry cell weight, with 34% of cell-bound enzyme) than K. lactis. Hydrolytic activities for the heterologous esterases were maximum at pH values between 8.0 and 9.0 for both yeast species and at temperatures of 50 °C and 45 °C for K. marxianus and K. lactis, respectively. When compared to previously published data on this same esterase produced in the original host or in S. cerevisiae, our results indicate that Kluyveromyces yeasts can be considered good hosts for the heterologous secretion of thermophilic esterases, which have a potential application in biodiesel production or in resolving racemates.
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Affiliation(s)
- Saul Nitsche Rocha
- Department of Chemical Engineering, University of São Paulo, C.P. 61548, 05424-970 São Paulo, SP, Brazil.
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