1
|
Wang W, Wang X, Tan Y, Zhao S, Zhao L, Zhu Z. CRISPR-Cas9 mediated genome editing of Kluyveromyces marxianus for iterative, multiplexed gene disruption and pathway integration. Biotechnol Bioeng 2024. [PMID: 38778433 DOI: 10.1002/bit.28736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/19/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Kluyveromyces marxianus, a thermotolerant, fast-growing, Crabtree-negative yeast, is a promising chassis for the manufacture of various bioproducts. Although several genome editing tools are available for this yeast, these tools still require refinement to enable more convenient and efficient genetic modification. In this study, we engineered the K. marxianus NBRC 104275 strain by impairing the nonhomologous end joining and enhancing the homologous recombination machinery, which resulted in improved homology-directed repair effective on homology arms of up to 40 bp in length. Additionally, we simplified the CRISPR-Cas9 editing system by constructing a strain for integrative expression of Cas9 nuclease and plasmids bearing different selection markers for gRNA expression, thereby facilitating iterative genome editing without the need for plasmid curing. We demonstrated that tRNA was more effective than the hammerhead ribozyme for processing gRNA primary transcripts, and readily assembled tRNA-gRNA arrays were used for multiplexed editing of at least four targets. This editing tool was further employed for simultaneous scarless in vivo assembly of a 12-kb cassette from three fragments and marker-free integration for expressing a fusion variant of fatty acid synthase, as well as the integration of genes for starch hydrolysis. Together, the genome editing tool developed in this study makes K. marxianus more amenable to genetic modification and will facilitate more extensive engineering of this nonconventional yeast for chemical production.
Collapse
Affiliation(s)
- Wenliang Wang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Xinkai Wang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Yadi Tan
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Shuo Zhao
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Liqian Zhao
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, Liaoning, China
| | - Zhiwei Zhu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
- Ningbo Institute of Dalian University of Technology, Ningbo, Zhejiang, China
| |
Collapse
|
2
|
Yamada M. Molecular basis and functional development of membrane-based microbial metabolism. Biosci Biotechnol Biochem 2024; 88:461-474. [PMID: 38366612 DOI: 10.1093/bbb/zbae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
My research interest has so far been focused on metabolisms related to the "membrane" of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.
Collapse
Affiliation(s)
- Mamoru Yamada
- Graduate School of Sciences and Technology for Innovation, and Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| |
Collapse
|
3
|
Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
Collapse
Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
4
|
Muñoz-Miranda LA, Zepeda-Peña AC, Casas-Godoy L, Pereira-Santana A, Méndez-Zamora A, Barrera-Martínez I, Rodríguez-Zapata L, Gschaedler-Mathis AC, Figueroa-Yáñez LJ. CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3. World J Microbiol Biotechnol 2024; 40:121. [PMID: 38441729 DOI: 10.1007/s11274-023-03811-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/18/2023] [Indexed: 03/07/2024]
Abstract
Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.
Collapse
Affiliation(s)
- Luis A Muñoz-Miranda
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Andrea Catalina Zepeda-Peña
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Leticia Casas-Godoy
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Alejandro Pereira-Santana
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. Subsede Sureste, Parque Científico y Tecnológico de Yucatán, Mérida, Yucatán, México
| | - Andrés Méndez-Zamora
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México
| | - Iliana Barrera-Martínez
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Subsede Zapopan, Zapopan, Jalisco, México
| | - Luis Rodríguez-Zapata
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Mérida, Yucatán, México
| | - Anne Christine Gschaedler-Mathis
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
| | - Luis J Figueroa-Yáñez
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Subsede Zapopan, Zapopan, Jalisco, México.
| |
Collapse
|
5
|
Kik SK, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551061. [PMID: 37546789 PMCID: PMC10402146 DOI: 10.1101/2023.07.28.551061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
Collapse
Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | | | - Jared A. M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | | | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL
| |
Collapse
|
6
|
Li Y, Hou S, Ren Z, Fu S, Wang S, Chen M, Dang Y, Li H, Li S, Li P. Transcriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation. STRESS BIOLOGY 2023; 3:26. [PMID: 37676394 PMCID: PMC10441953 DOI: 10.1007/s44154-023-00108-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/11/2023] [Indexed: 09/08/2023]
Abstract
The thermotolerant yeast Kluyveromyces marxianus is known for its potential in high-temperature ethanol fermentation, yet it suffers from excess acetic acid production at elevated temperatures, which hinders ethanol production. To better understand how the yeast responds to acetic acid stress during high-temperature ethanol fermentation, this study investigated its transcriptomic changes under this condition. RNA sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) and enriched gene ontology (GO) terms and pathways under acetic acid stress. The results showed that 611 genes were differentially expressed, and GO and pathway enrichment analysis revealed that acetic acid stress promoted protein catabolism but repressed protein synthesis during high-temperature fermentation. Protein-protein interaction (PPI) networks were also constructed based on the interactions between proteins coded by the DEGs. Hub genes and key modules in the PPI networks were identified, providing insight into the mechanisms of this yeast's response to acetic acid stress. The findings suggest that the decrease in ethanol production is caused by the imbalance between protein catabolism and protein synthesis. Overall, this study provides valuable insights into the mechanisms of K. marxianus's response to acetic acid stress and highlights the importance of maintaining a proper balance between protein catabolism and protein synthesis for high-temperature ethanol fermentation.
Collapse
Affiliation(s)
- Yumeng Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Shiqi Hou
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Ziwei Ren
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Shaojie Fu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Sunhaoyu Wang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Mingpeng Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Hongshen Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084, China
| | - Shizhong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084, China
| | - Pengsong Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
- Engineering Research Center for Water Pollution Source Control & Eco-Remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Pham A, Bassett S, Chen W, Da Silva NA. Assembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding. ACS Synth Biol 2023; 12:1164-1174. [PMID: 36920425 DOI: 10.1021/acssynbio.2c00650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.
Collapse
Affiliation(s)
- Anhuy Pham
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
| | - Shane Bassett
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
| |
Collapse
|
9
|
Kruasuwan W, Puseenam A, Am-in S, Trakarnpaiboon S, Sornlek W, Kocharin K, Jindamorakot S, Tanapongpipat S, Bai FY, Roongsawang N. Evaluation of thermotolerant and ethanol-tolerant Saccharomyces cerevisiae as an alternative strain for bioethanol production from industrial feedstocks. 3 Biotech 2023; 13:23. [PMID: 36573155 PMCID: PMC9789288 DOI: 10.1007/s13205-022-03436-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/26/2022] [Indexed: 12/25/2022] Open
Abstract
Despite the fact that yeast Saccharomyces cerevisiae is by far the most commonly used in ethanol fermentation, few have been reported to be resistant to high ethanol concentrations at high temperatures. Hence, in this study, 150 S. cerevisiae strains from the Thailand Bioresource Research Center (TBRC) were screened for ethanol production based on their glucose utilization capability at high temperatures. Four strains, TBRC 12149, 12150, 12151, and 12153, exhibited the most outstanding ethanol production at high temperatures in shaking-flask culture. Among these, strain TBRC 12151 demonstrated a high ethanol tolerance of up to 12% at 40 °C. Compared to industrial and laboratory strains, TBRC 12149 displayed strong sucrose fermentation capacity whereas TBRC 12153 and 12151, respectively, showed the greatest ethanol production from molasses and cassava starch hydrolysate at high temperatures in shaking-flask conditions. In 5-L batch fermentation, similarly to both industrial strains, strain TBRC 12153 yielded an ethanol concentration of 66.5 g L-1 (58.4% theoretical yield) from molasses after 72 h at 40 °C. In contrast, strain TBRC12151 outperformed other industrial strains in cell growth and ethanol production from cassava starch hydrolysis at 40 °C with an ethanol production of 65 g L-1 (77.7% theoretical yield) after 72 h. Thus, the thermotolerant and ethanol-tolerant S. cerevisiae TBRC 12151 displayed great potential and possible uses as an alternative strain for industrial ethanol fermentation using cassava starch hydrolysate. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03436-4.
Collapse
Affiliation(s)
- Worarat Kruasuwan
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
- Present Address: Siriraj Long-Read Laboratory (Si-LoL), Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700 Thailand
| | - Aekkachai Puseenam
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Somjit Am-in
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Srisakul Trakarnpaiboon
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Warasirin Sornlek
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Kanokarn Kocharin
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Sasitorn Jindamorakot
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Sutipa Tanapongpipat
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Niran Roongsawang
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, 12120 Pathum Thani Thailand
| |
Collapse
|
10
|
Molecular and Physiological Diversity of Indigenous Yeasts Isolated from Spontaneously Fermented Wine Wort from Ilfov County, Romania. Microorganisms 2022; 11:microorganisms11010037. [PMID: 36677329 PMCID: PMC9861077 DOI: 10.3390/microorganisms11010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Wine yeast research offers the possibility of isolating new strains with distinct metabolic properties due to the geographical location of the vineyard and the processes used in winemaking. Our study deals with the isolation and identification of six yeasts from spontaneously fermented wine wort from Romania and their characterization as new potential starter culture for traditional beverages, for food industry or biomedicine. (2) Materials and methods: The isolates were identified using conventional taxonomy tests, phenotypic phylogeny analysis (Biolog YT), MALDI-TOF mass spectrometry, PCR-RFLP, and sequencing of the ITS1-5,8S-ITS2 rDNA region. The capacity of the yeasts to grow under thermal, ionic, and osmotic stress was determined. The safe status was confirmed by testing virulence and pathogenicity factors. Assays were performed in order to evaluate the growth inhibition of Candida strains and determine the antimicrobial mechanism of action. (3) Results and discussions: The yeast isolates were identified as belonging to the Metschinikowia, Hanseniaspora, Torulaspora, Pichia, and Saccharomyces genera. All the isolates were able to develop under the tested stress conditions and were confirmed as safe. With the exception of S. cerevisiae CMGB-MS1-1, all the isolates showed good antimicrobial activity based on competition for iron ions or production of killer toxins. (4) Conclusions: The results revealed the resistance of our yeasts to environmental conditions related to industrial and biomedical applications and their high potential as starter cultures and biocontrol agents, respectively.
Collapse
|
11
|
Bever D, Wheeldon I, Da Silva N. RNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of Kluyveromyces marxianus. Metab Eng Commun 2022; 15:e00208. [PMID: 36249306 PMCID: PMC9558044 DOI: 10.1016/j.mec.2022.e00208] [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: 06/16/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus, there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K. marxianus strains. The use of a strong RNA polymerase II promoter allows efficient expression of gRNAs flanked by the self-cleaving RNA structures, tRNA and HDV ribozyme, from a single plasmid co-expressing a codon optimized Cas9. Implementing this system resulted in nearly 100% efficiency of gene disruptions in both NHEJ-functional and NHEJ-deficient K. marxianus strains, with donor integration efficiencies reaching 50% and 100% in the two strains, respectively. The high gRNA targeting performance also proved instrumental for selection of engineered strains with lower growth rate but improved polyketide biosynthesis by avoiding an extended outgrowth period, a common method used to enrich for edited cells but that fails to recover advantageous mutants with even slightly impaired fitness. Finally, we provide the first demonstration of simultaneous, markerless integrations at multiple loci in K. marxianus using a 2.6 kb and a 7.6 kb donor, achieving a dual integration efficiency of 25.5% in a NHEJ-deficient strain. These results highlight both the ease of use and general robustness of this system for rapid and flexible metabolic engineering in this non-conventional yeast. RNAP II-driven tRNA-gRNA-HDV ribozyme cassette built for K. marxianus genome editing. Gene integrations up to 7.6 kb were achieved with only 40 bp homology sequences. Recovery of growth-biased modifications achievable as extended outgrowth not required. Application (ZWF1 and GPD1 knockouts) increased polyketide specific titers. Expressing two unique gRNAs from one cassette enabled integrations at separate loci.
Collapse
|
12
|
Triple gene expressions in yeast, Escherichia coli, and mammalian cells by transferring DNA fragments amplified from a mother yeast expression plasmid. J Biosci Bioeng 2022; 133:587-595. [DOI: 10.1016/j.jbiosc.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 11/22/2022]
|
13
|
Bilal M, Ji L, Xu Y, Xu S, Lin Y, Iqbal HMN, Cheng H. Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology. Front Bioeng Biotechnol 2022; 10:851768. [PMID: 35519613 PMCID: PMC9065261 DOI: 10.3389/fbioe.2022.851768] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Kluyveromyces marxianus is an emerging non-conventional food-grade yeast that is generally isolated from diverse habitats, like kefir grain, fermented dairy products, sugar industry sewage, plants, and sisal leaves. A unique set of beneficial traits, such as fastest growth, thermotolerance, and broad substrate spectrum (i.e., hemi-cellulose hydrolysates, xylose, l-arabinose, d-mannose, galactose, maltose, sugar syrup molasses, cellobiose, and dairy industry) makes this yeast a particularly attractive host for applications in a variety of food and biotechnology industries. In contrast to Saccharomyces cerevisiae, most of the K. marxianus strains are apparently Crabtree-negative or having aerobic-respiring characteristics, and unlikely to endure aerobic alcoholic fermentation. This is a desirable phenotype for the large-scale biosynthesis of products associated with biomass formation because the formation of ethanol as an undesirable byproduct can be evaded under aerobic conditions. Herein, we discuss the current insight into the potential applications of K. marxianus as a robust yeast cell factory to produce various industrially pertinent enzymes, bioethanol, cell proteins, probiotic, fructose, and fructo-oligosaccharides, and vaccines, with excellent natural features. Moreover, the biotechnological improvement and development of new biotechnological tools, particularly CRISPR-Cas9-assisted precise genome editing in K. marxianus are delineated. Lastly, the ongoing challenges, concluding remarks, and future prospects for expanding the scope of K. marxianus utilization in modern biotechnology, food, feed, and pharmaceutical industries are also thoroughly vetted. In conclusion, it is critical to apprehend knowledge gaps around genes, metabolic pathways, key enzymes, and regulation for gaining a complete insight into the mechanism for producing relevant metabolites by K. marxianus.
Collapse
Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- *Correspondence: Hairong Cheng, ; Muhammad Bilal,
| | - Liyun Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yirong Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuping Lin
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Hairong Cheng, ; Muhammad Bilal,
| |
Collapse
|
14
|
Zhang N, Shang Y, Wang F, Wang D, Hong J. Influence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors. Microb Cell Fact 2021; 20:224. [PMID: 34906148 PMCID: PMC8672639 DOI: 10.1186/s12934-021-01715-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance. RESULTS In this study, the disruption of the prefoldin subunit 4 gene (KmPFD4) led to increased concentration of intracellular reactive oxygen species (ROS) and disturbed the assembly of actin and tubulin in the presence of inhibitors, resulting in reduced inhibitor tolerance. Nuclear localization of KmPFD4 indicated that it could regulate gene expression. Transcriptomic analysis showed that upregulated gene expression related to ROS elimination, ATP production, and NAD+ synthesis, which is a response to the presence of inhibitors, disappeared in KmPFD4-disrupted cells. Thus, KmPFD4 impacts inhibitor tolerance by maintaining integration of the cytoskeleton and directly or indirectly affecting the expression of genes in response to inhibitors. Finally, overexpression of KmPFD4 enhanced ethanol fermentation with a 46.27% improvement in productivity in presence of the inhibitors. CONCLUSION This study demonstrated that KmPFD4 plays a positive role in the inhibitor tolerance and can be applied for the development of inhibitor-tolerant platform strains.
Collapse
Affiliation(s)
- Nini Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Yingying Shang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Feier Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China.
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, 230026, People's Republic of China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China.
| |
Collapse
|
15
|
Abdel-Banat BMA, Hoshida H, Akada R. Various short autonomously replicating sequences from the yeast Kluyveromyces marxianus seemingly without canonical consensus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100053. [PMID: 34841344 PMCID: PMC8610295 DOI: 10.1016/j.crmicr.2021.100053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/08/2021] [Accepted: 07/27/2021] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic autonomously replicating sequences (ARSs) are composed of three domains, A, B, and C. Domain A is comprised of an ARS consensus sequence (ACS), while the B domain has the DNA unwinding element and the C domain is important for DNA-protein interactions. In Saccharomyces cerevisiae and Kluyveromyces lactis ARS101, the ACS is commonly composed of 11 bp, 5ˊ-(A/T)AAA(C/T)ATAAA(A/T)-3ˊ. This core sequence is essential for S. cerevisiae and K. lactis ARS activity. In this study, we identified ARS-containing sequences from genomic libraries of the yeast Kluyveromyces marxianus DMKU3-1042 and validated their replication activities. The identified K. marxianus DMKU3-1042 ARSs (KmARSs) have very effective replication ability but their sequences are divergent and share no common consensus. We have carried out point mutations, deletions, and base pairs substitutions within the sequences of some of the KmARSs to identify the sequence(s) that influence the replication activity. Consensus sequences same as the 11 bp ACS of S. cerevisiae and K. lactis were not found in all minimum functional KmARSs reported here except KmARS7. Moreover, partial sequences from different KmARSs are interchangeable among each other to retain the ARS activity. We have also specifically identified the essential nucleotides, which are indispensable for replication, within some of the KmARSs. Our deletions analysis revealed that only 21 bp in KmARS18 could retain the ARS activity. The identified KmARSs in this study are unique compared to other yeasts’ ARSs, do not share common ACS, and are interchangeable. Identification of minimal autonomously replicating sequences (ARSs) from the yeast Kluyveromyces marxianus DMKU3-1042. The identities of the isolated ARSs are divergent and have no common consensus with the ARSs of other yeasts. A short ARS sequence of twenty-one nucleotides functions as an effective replicator in K. marxianus DMKU3-1042. Segments of ARSs from the yeast K. marxianus are interchangeable among each other. Functional ARSs are found in both the intergenic and coding sequences of the strain DMKU3-1042.
Collapse
Affiliation(s)
- Babiker M A Abdel-Banat
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa 31982, Saudi Arabia.,Department of Crop Protection, University of Khartoum, Shambat 13314, Sudan
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Tokiwadai, Ube, Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Tokiwadai, Ube, Japan
| |
Collapse
|
16
|
Lan Q, Duan Y, Wu P, Li X, Yu Y, Shi B, Zhou J, Lu H. Coordinately express hemicellulolytic enzymes in Kluyveromyces marxianus to improve the saccharification and ethanol production from corncobs. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:220. [PMID: 34809677 PMCID: PMC8607645 DOI: 10.1186/s13068-021-02070-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Hemicellulose acts as one factor contributing to the recalcitrance of lignocellulose that prevents cellulases to degrade the cellulose efficiently even in low quantities. Supplement of hemicellulases can enhance the performance of commercial cellulases in the enzymatic hydrolyses of lignocellulose. Kluyveromyce marxianus is an attractive yeast for cellulosic ethanol fermentation, as well as a promising host for heterologous protein production, since it has remarkable thermotolerance, high growth rate, and broad substrate spectrum etc. In this study, we attempted to coordinately express multiple hemicellulases in K. marxianus through a 2A-mediated ribosome skipping to self-cleave polyproteins, and investigated their capabilities for saccharification and ethanol production from corncobs. RESULTS Two polycistronic genes IMPX and IMPαX were constructed to test the self-cleavage of P2A sequence from the Foot-and-Mouth Disease virus (FMDV) in K. marxianus. The IMPX gene consisted of a β-mannanase gene M330 (without the stop codon), a P2A sequence and a β-xylanase gene Xyn-CDBFV in turn. In the IMPαX gene, there was an additional α-factor signal sequence in frame with the N-terminus of Xyn-CDBFV. The extracellular β-mannanase activities of the IMPX and IMPαX strains were 21.34 and 15.50 U/mL, respectively, but the extracellular β-xylanase activity of IMPαX strain was much higher than that of the IMPX strain, which was 136.17 and 42.07 U/mL, respectively. Subsequently, two recombinant strains, the IXPαR and IMPαXPαR, were constructed to coordinately and secretorily express two xylantic enzymes, Xyn-CDBFV and β-D-xylosidase RuXyn1, or three hemicellulolytic enzymes including M330, Xyn-CDBFV and RuXyn1. In fed-batch fermentation, extracellular activities of β-xylanase and β-xylosidase in the IXPαR strain were 1664.2 and 0.90 U/mL. Similarly, the IMPαXPαR strain secreted the three enzymes, β-mannanase, β-xylanase, and β-xylosidase, with the activities of 159.8, 2210.5, and 1.25 U/mL, respectively. Hemicellulolases of both strains enhanced the yields of glucose and xylose from diluted acid pretreated (DAP) corncobs when acted synergistically with commercial cellulases. In hybrid saccharification and fermentation (HSF) of DAP corncobs, hemicellulases of the IMPαXPαR strain increased the ethanol yield by 8.7% at 144 h compared with the control. However, both ethanol and xylose yields were increased by 12.7 and 18.2%, respectively, at 120 h in HSF of aqueous ammonia pretreated (AAP) corncobs with this strain. Our results indicated that coordinate expression of hemicellulolytic enzymes in K. marxianus promoted the saccharification and ethanol production from corncobs. CONCLUSIONS The FMDV P2A sequence showed high efficiency in self-cleavage of polyproteins in K. marxianus and could be used for secretory expression of multiple enzymes in the presence of their signal sequences. The IMPαXPαR strain coexpressed three hemicellulolytic enzymes improved the saccharification and ethanol production from corncobs, and could be used as a promising strain for ethanol production from lignocelluloses.
Collapse
Affiliation(s)
- Qing Lan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Yitong Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Xueyin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Bo Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China.
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China.
- Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| |
Collapse
|
17
|
Hu M, Li M, Jiang B, Zhang T. Bioproduction of D-allulose: Properties, applications, purification, and future perspectives. Compr Rev Food Sci Food Saf 2021; 20:6012-6026. [PMID: 34668314 DOI: 10.1111/1541-4337.12859] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/07/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022]
Abstract
D-allulose is the C-3 epimer of D-fructose, which rarely exists in nature, and can be biosynthesized from D-fructose by the catalysis of D-psicose 3-epimerase. D-allulose is safe for human consumption and was recently approved by the United States Food and Drug Administration for food applications. It is not only able be used in food and dietary supplements as a low-calorie sweetener, but also modulates a variety of physiological functions. D-allulose has gained increasing attention owing to its excellent properties. This article presents a review of recent progress on the properties, applications, and bioproduction progress of D-allulose.
Collapse
Affiliation(s)
- Mengying Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
| |
Collapse
|
18
|
Binati RL, Salvetti E, Bzducha-Wróbel A, Bašinskienė L, Čižeikienė D, Bolzonella D, Felis GE. Non-conventional yeasts for food and additives production in a circular economy perspective. FEMS Yeast Res 2021; 21:6380488. [PMID: 34601574 DOI: 10.1093/femsyr/foab052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Yeast species have been spontaneously participating in food production for millennia, but the scope of applications was greatly expanded since their key role in beer and wine fermentations was clearly acknowledged. The workhorse for industry and scientific research has always been Saccharomyces cerevisiae. It occupies the largest share of the dynamic yeast market, that could further increase thanks to the better exploitation of other yeast species. Food-related 'non-conventional' yeasts (NCY) represent a treasure trove for bioprospecting, with their huge untapped potential related to a great diversity of metabolic capabilities linked to niche adaptations. They are at the crossroad of bioprocesses and biorefineries, characterized by low biosafety risk and produce food and additives, being also able to contribute to production of building blocks and energy recovered from the generated waste and by-products. Considering that the usual pattern for bioprocess development focuses on single strains or species, in this review we suggest that bioprospecting at the genus level could be very promising. Candida, Starmerella, Kluyveromyces and Lachancea were briefly reviewed as case studies, showing that a taxonomy- and genome-based rationale could open multiple possibilities to unlock the biotechnological potential of NCY bioresources.
Collapse
Affiliation(s)
- Renato L Binati
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Anna Bzducha-Wróbel
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159c St., 02-776 Warsaw, Poland
| | - Loreta Bašinskienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - Dalia Čižeikienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - David Bolzonella
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| |
Collapse
|
19
|
Hoshida H, Kagawa S, Ogami K, Akada R. Anoxia-induced mitophagy in the yeast Kluyveromyces marxianus. FEMS Yeast Res 2021; 20:5932265. [PMID: 33130889 DOI: 10.1093/femsyr/foaa057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Abstract
Kluyveromyces marxianus is a thermotolerant, ethanol-producing yeast that requires oxygen for efficient ethanol fermentation. Under anaerobic conditions, glucose consumption and ethanol production are retarded, suggesting that oxygen affects the metabolic state of K. marxianus. Mitochondria require oxygen to function, and their forms and number vary according to environmental conditions. In this study, the effect of anoxia on mitochondrial behavior in K. marxianus was examined. Under aerobic growth conditions, mitochondria-targeted GFP exhibited a tubular and dotted localization, representing a typical mitochondrial morphology, but under anaerobic conditions, GFP localized in vacuoles, suggesting that mitophagy occurs under anaerobic conditions. To confirm mitophagy induction, the ATG32, ATG8, ATG11 and ATG19 genes were disrupted. Vacuolar localization of mitochondria-targeted GFP under anaerobic conditions was interrupted in the Δatg32 and Δatg8 strains but not the Δatg11 and Δatg19 strains. Electron microscopy revealed mitochondria-like membrane components in the vacuoles of wild-type cells grown under anaerobic conditions. Quantitative analyses using mitochondria-targeted Pho8 demonstrated that mitophagy was induced in K. marxianus by anoxia but not nitrogen starvation. To the best of our knowledge, this is the first demonstration of anoxia-induced mitophagy in yeasts.
Collapse
Affiliation(s)
- Hisashi Hoshida
- Division of Applied Chemistry, Graduate School of Science and Technology for Innovation, 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
| | - Shota Kagawa
- Division of Applied Chemistry, Graduate School of Science and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan
| | - Kentaro Ogami
- Department of Applied Chemistry, Faculty of Engineering, Yamaguchi University, Ube 755-8611, Japan
| | - Rinji Akada
- Division of Applied Chemistry, Graduate School of Science and Technology for Innovation, 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
|
20
|
Xia Y, Cheng Q, Mu W, Hu X, Sun Z, Qiu Y, Liu X, Wang Z. Research Advances of d-allulose: An Overview of Physiological Functions, Enzymatic Biotransformation Technologies, and Production Processes. Foods 2021; 10:2186. [PMID: 34574296 PMCID: PMC8467252 DOI: 10.3390/foods10092186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/08/2021] [Accepted: 09/12/2021] [Indexed: 02/02/2023] Open
Abstract
d-allulose has a significant application value as a sugar substitute, not only as a food ingredient and dietary supplement, but also with various physiological functions, such as improving insulin resistance, anti-obesity, and regulating glucolipid metabolism. Over the decades, the physiological functions of d-allulose and the corresponding mechanisms have been studied deeply, and this product has been applied to various foods to enhance food quality and prolong shelf life. In recent years, biotransformation technologies for the production of d-allulose using enzymatic approaches have gained more attention. However, there are few comprehensive reviews on this topic. This review focuses on the recent research advances of d-allulose, including (1) the physiological functions of d-allulose; (2) the major enzyme families used for the biotransformation of d-allulose and their microbial origins; (3) phylogenetic and structural characterization of d-allulose 3-epimerases, and the directed evolution methods for the enzymes; (4) heterologous expression of d-allulose ketose 3-epimerases and biotransformation techniques for d-allulose; and (5) production processes for biotransformation of d-allulose based on the characterized enzymes. Furthermore, the future trends on biosynthesis and applications of d-allulose in food and health industries are discussed and evaluated in this review.
Collapse
Affiliation(s)
- Yu Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.M.); (Z.W.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Qianqian Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.M.); (Z.W.)
| | - Xiuyu Hu
- China Biotech Fermentation Industry Association, Beijing 100833, China;
| | - Zhen Sun
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
| | - Yangyu Qiu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
| | - Ximing Liu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (W.M.); (Z.W.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.C.); (Z.S.); (Y.Q.); (X.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
21
|
Hoffman SM, Alvarez M, Alfassi G, Rein DM, Garcia-Echauri S, Cohen Y, Avalos JL. Cellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:157. [PMID: 34274018 PMCID: PMC8285809 DOI: 10.1186/s13068-021-02008-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/05/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Future expansion of corn-derived ethanol raises concerns of sustainability and competition with the food industry. Therefore, cellulosic biofuels derived from agricultural waste and dedicated energy crops are necessary. To date, slow and incomplete saccharification as well as high enzyme costs have hindered the economic viability of cellulosic biofuels, and while approaches like simultaneous saccharification and fermentation (SSF) and the use of thermotolerant microorganisms can enhance production, further improvements are needed. Cellulosic emulsions have been shown to enhance saccharification by increasing enzyme contact with cellulose fibers. In this study, we use these emulsions to develop an emulsified SSF (eSSF) process for rapid and efficient cellulosic biofuel production and make a direct three-way comparison of ethanol production between S. cerevisiae, O. polymorpha, and K. marxianus in glucose and cellulosic media at different temperatures. RESULTS In this work, we show that cellulosic emulsions hydrolyze rapidly at temperatures tolerable to yeast, reaching up to 40-fold higher conversion in the first hour compared to microcrystalline cellulose (MCC). To evaluate suitable conditions for the eSSF process, we explored the upper temperature limits for the thermotolerant yeasts Kluyveromyces marxianus and Ogataea polymorpha, as well as Saccharomyces cerevisiae, and observed robust fermentation at up to 46, 50, and 42 °C for each yeast, respectively. We show that the eSSF process reaches high ethanol titers in short processing times, and produces close to theoretical yields at temperatures as low as 30 °C. Finally, we demonstrate the transferability of the eSSF technology to other products by producing the advanced biofuel isobutanol in a light-controlled eSSF using optogenetic regulators, resulting in up to fourfold higher titers relative to MCC SSF. CONCLUSIONS The eSSF process addresses the main challenges of cellulosic biofuel production by increasing saccharification rate at temperatures tolerable to yeast. The rapid hydrolysis of these emulsions at low temperatures permits fermentation using non-thermotolerant yeasts, short processing times, low enzyme loads, and makes it possible to extend the process to chemicals other than ethanol, such as isobutanol. This transferability establishes the eSSF process as a platform for the sustainable production of biofuels and chemicals as a whole.
Collapse
Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
| | - Maria Alvarez
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
- Department of Chemical Engineering, University of Vigo, 36310, Vigo, Spain
| | - Gilad Alfassi
- Department of Biotechnology Engineering, ORT Braude College, Karmiel, Israel
| | - Dmitry M Rein
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sergio Garcia-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
| | - Yachin Cohen
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA.
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
22
|
Monteiro de Oliveira P, Aborneva D, Bonturi N, Lahtvee PJ. Screening and Growth Characterization of Non-conventional Yeasts in a Hemicellulosic Hydrolysate. Front Bioeng Biotechnol 2021; 9:659472. [PMID: 33996782 PMCID: PMC8116571 DOI: 10.3389/fbioe.2021.659472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
Lignocellulosic biomass is an attractive raw material for the sustainable production of chemicals and materials using microbial cell factories. Most of the existing bioprocesses focus on second-generation ethanol production using genetically modified Saccharomyces cerevisiae, however, this microorganism is naturally unable to consume xylose. Moreover, extensive metabolic engineering has to be carried out to achieve high production levels of industrially relevant building blocks. Hence, the use of non-Saccharomyces species, or non-conventional yeasts, bearing native metabolic routes, allows conversion of a wide range of substrates into different products, and higher tolerance to inhibitors improves the efficiency of biorefineries. In this study, nine non-conventional yeast strains were selected and screened on a diluted hemicellulosic hydrolysate from Birch. Kluyveromyces marxianus CBS 6556, Scheffersomyces stipitis CBS 5773, Lipomyces starkeyi DSM 70295, and Rhodotorula toruloides CCT 7815 were selected for further characterization, where their growth and substrate consumption patterns were analyzed under industrially relevant substrate concentrations and controlled environmental conditions in bioreactors. K. marxianus CBS 6556 performed poorly under higher hydrolysate concentrations, although this yeast was determined among the fastest-growing yeasts on diluted hydrolysate. S. stipitis CBS 5773 demonstrated a low growth and biomass production while consuming glucose, while during the xylose-phase, the specific growth and sugar co-consumption rates were among the highest of this study (0.17 h–1 and 0.37 g/gdw*h, respectively). L. starkeyi DSM 70295 and R. toruloides CCT 7815 were the fastest to consume the provided sugars at high hydrolysate conditions, finishing them within 54 and 30 h, respectively. R. toruloides CCT 7815 performed the best of all four studied strains and tested conditions, showing the highest specific growth (0.23 h–1), substrate co-consumption (0.73 ± 0.02 g/gdw*h), and xylose consumption (0.22 g/gdw*h) rates. Furthermore, R. toruloides CCT 7815 was able to produce 10.95 ± 1.37 gL–1 and 1.72 ± 0.04 mgL–1 of lipids and carotenoids, respectively, under non-optimized cultivation conditions. The study provides novel information on selecting suitable host strains for biorefinery processes, provides detailed information on substrate consumption patterns, and pinpoints to bottlenecks possible to address using metabolic engineering or adaptive evolution experiments.
Collapse
Affiliation(s)
| | - Daria Aborneva
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | |
Collapse
|
23
|
Ha-Tran DM, Lai RY, Nguyen TTM, Huang E, Lo SC, Huang CC. Construction of engineered RuBisCO Kluyveromyces marxianus for a dual microbial bioethanol production system. PLoS One 2021; 16:e0247135. [PMID: 33661900 PMCID: PMC7932148 DOI: 10.1371/journal.pone.0247135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/02/2021] [Indexed: 11/28/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes play important roles in CO2 fixation and redox balancing in photosynthetic bacteria. In the present study, the kefir yeast Kluyveromyces marxianus 4G5 was used as host for the transformation of form I and form II RubisCO genes derived from the nonsulfur purple bacterium Rhodopseudomonas palustris using the Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO) method. Hungateiclostridium thermocellum ATCC 27405, a well-known bacterium for its efficient solubilization of recalcitrant lignocellulosic biomass, was used to degrade Napier grass and rice straw to generate soluble fermentable sugars. The resultant Napier grass and rice straw broths were used as growth media for the engineered K. marxianus. In the dual microbial system, H. thermocellum degraded the biomass feedstock to produce both C5 and C6 sugars. As the bacterium only used hexose sugars, the remaining pentose sugars could be metabolized by K. marxianus to produce ethanol. The transformant RubisCO K. marxianus strains grew well in hydrolyzed Napier grass and rice straw broths and produced bioethanol more efficiently than the wild type. Therefore, these engineered K. marxianus strains could be used with H. thermocellum in a bacterium-yeast coculture system for ethanol production directly from biomass feedstocks.
Collapse
Affiliation(s)
- Dung Minh Ha-Tran
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Rou-Yin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Trinh Thi My Nguyen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Eugene Huang
- College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Shou-Chen Lo
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (SCL); (CCH)
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (SCL); (CCH)
| |
Collapse
|
24
|
Domenzain I, Li F, Kerkhoven EJ, Siewers V. Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. FEMS Yeast Res 2021; 21:foab002. [PMID: 33428734 PMCID: PMC7943257 DOI: 10.1093/femsyr/foab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public.
Collapse
Affiliation(s)
- Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Feiran Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| |
Collapse
|
25
|
Li P, Tan X, Fu X, Dang Y, Li S. Metabolomic analysis reveals Kluyveromyces marxianus’s stress responses during high-temperature ethanol fermentation. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
26
|
Li M, Lang X, Moran Cabrera M, De Keyser S, Sun X, Da Silva N, Wheeldon I. CRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:3. [PMID: 33407831 PMCID: PMC7788952 DOI: 10.1186/s13068-020-01852-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND 2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material. RESULTS We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 33-factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7G141S, results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L. The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures. CONCLUSIONS The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.
Collapse
Affiliation(s)
- Mengwan Li
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xuye Lang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Marcos Moran Cabrera
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Sawyer De Keyser
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Xiyan Sun
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Nancy Da Silva
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California Riverside, Riverside, CA, 92527, USA.
| |
Collapse
|
27
|
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
|
28
|
Chupaza MH, Park YR, Kim SH, Yang JW, Jeong GT, Kim SK. Bioethanol Production from Azolla filiculoides by Saccharomyces cerevisiae, Pichia stipitis, Candida lusitaniae, and Kluyveromyces marxianus. Appl Biochem Biotechnol 2020; 193:502-514. [PMID: 33026615 DOI: 10.1007/s12010-020-03437-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Ethanol was produced by separate hydrolysis and fermentation using Azolla filiculoides as a biomass. Thermal acid hydrolysis and enzymatic saccharification were used as pretreatment methods to produce monosaccharides from Azolla. The optimal content for thermal acid hydrolysis of 14% (w/v) Azolla weed slurry produced 16.7-g/L monosaccharides by using 200 mM H2SO4 at 121 °C for 60 min. Enzymatic saccharification using 16 U/mL Viscozyme produced 61.6 g/L monosaccharide at 48 h. Ethanol productions with ethanol yield coefficients from Azolla weed hydrolysate using Kluyveromyces marxianus, Candida lusitaniae Saccharomyces cerevisiae, and Pichia stipitis were 26.8 g/L (YEtOH = 0.43), 23.2 g/L (YEtOH = 0.37), 18.2 g/L (YEtOH = 0.29), and 13.7 g/L (YEtOH = 0.22), respectively. Saccharomyces cerevisiae produces the lowest yield as it utilized only glucose. Bioethanol from Azolla weed hydrolysate can be successfully produced by using Kluyveromyces marxianus because it consumed the mixture of glucose and xylose completely within 60 h.
Collapse
Affiliation(s)
- Mariam H Chupaza
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea.,KOICA-PKNU International Graduate Program of Fisheries Science, Pukyong National University, Busan, 48513, Republic of Korea.,Department of Fishing and Fish Processing, Fisheries Education and Training Agency, P.O. Box 83, Bagamoyo, Costal Region, Tanzania
| | - Yu-Rim Park
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea
| | - So Hee Kim
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea
| | - Ji Won Yang
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea
| | - Gwi-Teak Jeong
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea
| | - Sung-Koo Kim
- School of Marine Fisheries, and Life Science (Major in Biotechnology), Pukyong National University, 48513, Busan, Republic of Korea.
| |
Collapse
|
29
|
Ding L, Macdonald HD, Smith HO, Hutchison CA, Merryman C, Michael TP, Abramson BW, Kannan K, Liang J, Gill J, Gibson DG, Glass JI. Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing. Int J Mol Sci 2020; 21:ijms21197112. [PMID: 32993167 PMCID: PMC7582981 DOI: 10.3390/ijms21197112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022] Open
Abstract
Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus otherwise wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the gross chromosomal rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research.
Collapse
Affiliation(s)
- Lin Ding
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Harrison D. Macdonald
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Hamilton O. Smith
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
- Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA; (K.K.); (J.L.); (J.G.)
| | - Clyde A. Hutchison
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Chuck Merryman
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Todd P. Michael
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Bradley W. Abramson
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
| | - Krishna Kannan
- Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA; (K.K.); (J.L.); (J.G.)
| | - Joe Liang
- Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA; (K.K.); (J.L.); (J.G.)
| | - John Gill
- Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA; (K.K.); (J.L.); (J.G.)
| | - Daniel G. Gibson
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
- Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA; (K.K.); (J.L.); (J.G.)
| | - John I. Glass
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA; (L.D.); (H.D.M.); (H.O.S.); (C.A.H.III); (C.M.); (T.P.M.); (B.W.A.); (D.G.G.)
- Correspondence: ; Tel.: +1-858-200-1856
| |
Collapse
|
30
|
Chacón-Vargas K, Torres J, Giles-Gómez M, Escalante A, Gibbons JG. Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing. Sci Rep 2020; 10:15115. [PMID: 32934253 PMCID: PMC7493934 DOI: 10.1038/s41598-020-71864-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.
Collapse
Affiliation(s)
- Katherine Chacón-Vargas
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Julian Torres
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Martha Giles-Gómez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adelfo Escalante
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - John G Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA.
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA.
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA.
| |
Collapse
|
31
|
Lang X, Besada-Lombana PB, Li M, Da Silva NA, Wheeldon I. Developing a broad-range promoter set for metabolic engineering in the thermotolerant yeast Kluyveromyces marxianus. Metab Eng Commun 2020; 11:e00145. [PMID: 32995271 PMCID: PMC7508702 DOI: 10.1016/j.mec.2020.e00145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/17/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
Kluyveromyces marxianus is an emerging host for metabolic engineering. This thermotolerant yeast is the fastest growing eukaryote, has high flux through the TCA cycle, and can metabolize a broad range of C5, C6, and C12 carbon sources. In comparison to the common host Saccharomyces cerevisiae, this non-conventional yeast suffers from a lack of metabolic engineering tools to control gene expression over a wide transcriptional range. To address this issue, we designed a library of 25 native-derived promoters from K. marxanius CBS6556 that spans 87-fold transcriptional strength under glucose metabolism. Six promoters from the library were further characterized in both glucose and xylose as well as across various temperatures from 30 to 45 °C. The temperature study revealed that in most cases EGFP expression decreased with elevating temperature; however, two promoters, P SSA3 and P ADH1 , increased expression above 40 °C in both xylose and glucose. The six-promoter set was also validated in xylose for triacetic acid lactone (TAL) production. By controlling the expression level of heterologous 2-pyrone synthase (2-PS), the specific TAL titer increased over 8-fold at 37 °C. Cultures at 41 °C exhibited a similar TAL biosynthesis capability, while at 30 °C TAL levels were lower. Taken together, these results advance the metabolic engineering tool set in K. marxianus and further develop this new host for chemical biosynthesis.
Collapse
Affiliation(s)
- Xuye Lang
- Department of Chemical and Environmental Engineering, UC Riverside, United States
| | | | - Mengwan Li
- Department of Chemical and Environmental Engineering, UC Riverside, United States
| | - Nancy A. Da Silva
- Department of Chemical and Biomolecular Engineering, UC Irvine, United States
- Corresponding author. Department of Chemical and Biomolecular Engineering, UC Irvine, United States.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, UC Riverside, United States
- Center for Industrial Biotechnology, UC Riverside, United States
- Corresponding author. Department of Chemical and Environmental Engineering, UC Riverside, United States.
| |
Collapse
|
32
|
Karim A, Gerliani N, Aïder M. Kluyveromyces marxianus: An emerging yeast cell factory for applications in food and biotechnology. Int J Food Microbiol 2020; 333:108818. [PMID: 32805574 DOI: 10.1016/j.ijfoodmicro.2020.108818] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022]
Abstract
Several yeasts, which are eukaryotic microorganisms, have long been used in different industries due to their potential applications, both for fermentation and for the production of specific metabolites. Kluyveromyces marxianus is one of the most auspicious nonconventional yeasts, generally isolated from wide-ranging natural habitats such as fermented traditional dairy products, kefir grain, sewage from sugar industries, sisal leaves, and plants. This is a food-grade yeast with various beneficial traits, such as rapid growth rate and thermotolerance that make it appealing for different industrial food and biotechnological applications. K. marxianus is a respiro-fermentative yeast likely to produce energy by either respiration or fermentation pathways. It generates a wide-ranging specific metabolites and could contribute to a variety of different food and biotechnological industries. Although Saccharomyces cerevisiae is the most widely used dominant representative in all aspects, many applications of K. marxianus in biotechnology, food and environment have only started to emerge nowadays; some of the most promising applications are reviewed here. The general physiology of K. marxianus is outlined, and then the different applications are discussed: first, the applications of K. marxianus in biotechnology, and then the recent advances and possible applications in food, feed and environmental industries. Finally, this review provides a discussion of the main challenges and some perspectives for targeted applications of K. marxianus in the modern food technology and applied biotechnology in order to exploit the full potential of this yeast which can be used as a cell factory with great efficiency.
Collapse
Affiliation(s)
- Ahasanul Karim
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada
| | - Natela Gerliani
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada
| | - Mohammed Aïder
- Department of Soil Sciences and Agri-food Engineering, Université Laval, Quebec, QC G1V 0A6, Canada; Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC G1V 0A6, Canada.
| |
Collapse
|
33
|
Lee MH, Hsu TL, Lin JJ, Lin YJ, Kao YY, Chang JJ, Li WH. Constructing a human complex type N-linked glycosylation pathway in Kluyveromyces marxianus. PLoS One 2020; 15:e0233492. [PMID: 32469948 PMCID: PMC7259728 DOI: 10.1371/journal.pone.0233492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 11/18/2022] Open
Abstract
Glycosylation can affect various protein properties such as stability, biological activity, and immunogenicity. To produce human therapeutic proteins, a host that can produce glycoproteins with correct glycan structures is required. Microbial expression systems offer economical, rapid and serum-free production and are more amenable to genetic manipulation. In this study, we developed a protocol for CRISPR/Cas9 multiple gene knockouts and knockins in Kluyveromyces marxianus, a probiotic yeast with a rapid growth rate. As hyper-mannosylation is a common problem in yeast, we first knocked out the α-1,3-mannosyltransferase (ALG3) and α-1,6-mannosyltransferase (OCH1) genes to reduce mannosylation. We also knocked out the subunit of the telomeric Ku domain (KU70) to increase the homologous recombination efficiency of K. marxianus. In addition, we knocked in the MdsI (α-1,2-mannosidase) gene to reduce mannosylation and the GnTI (β-1,2-N-acetylglucosaminyltransferase I) and GnTII genes to produce human N-glycan structures. We finally obtained two strains that can produce low amounts of the core N-glycan Man3GlcNAc2 and the human complex N-glycan Man3GlcNAc4, where Man is mannose and GlcNAc is N-acetylglucosamine. This study lays a cornerstone of glycosylation engineering in K. marxianus toward producing human glycoproteins.
Collapse
Affiliation(s)
- Ming-Hsuan Lee
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Nankang, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jinn-Jy Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yi-Ying Kao
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
34
|
Villena GK, Kitazono AA, Hernández-Macedo M L. Bioengineering Fungi and Yeast for the Production of Enzymes, Metabolites, and Value-Added Compounds. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Navarrete C, L. Martínez J. Non-conventional yeasts as superior production platforms for sustainable fermentation based bio-manufacturing processes. AIMS BIOENGINEERING 2020. [DOI: 10.3934/bioeng.2020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
36
|
Nurcholis M, Lertwattanasakul N, Rodrussamee N, Kosaka T, Murata M, Yamada M. Integration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus. Appl Microbiol Biotechnol 2019; 104:475-488. [PMID: 31781815 DOI: 10.1007/s00253-019-10224-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/17/2022]
Abstract
Among the so-called non-conventional yeasts, Kluyveromyces marxianus has extremely potent traits that are suitable for industrial applications. Indeed, it has been used for the production of various enzymes, chemicals, and macromolecules in addition to utilization of cell biomass as nutritional materials, feed and probiotics. The yeast is expected to be an efficient ethanol producer with advantages over Saccharomyces cerevisiae in terms of high growth rate, thermotolerance and a wide sugar assimilation spectrum. Results of comprehensive analyses of its genome and transcriptome may accelerate studies for applications of the yeast and may further increase its potential by combination with recent biotechnological tools including the CRISPR/Cas9 system. We thus review published studies by merging with information obtained from comprehensive data including genomic and transcriptomic data, which would be useful for future applications of K. marxianus.
Collapse
Affiliation(s)
- Mochamad Nurcholis
- Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan.,Department of Food Science and Technology, Faculty of Agricultural Technology, Brawijaya University, Malang, 65145, Indonesia
| | - Noppon Lertwattanasakul
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Nadchanok Rodrussamee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tomoyuki Kosaka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Masayuki Murata
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Mamoru Yamada
- Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan. .,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan.
| |
Collapse
|
37
|
Ahmed El-Imam AM, Greetham D, Du C, Dyer PS. The development of a biorefining strategy for the production of biofuel from sorghum milling waste. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
38
|
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]
|
39
|
Lehnen M, Ebert BE, Blank LM. Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts. BMC Microbiol 2019; 19:100. [PMID: 31101012 PMCID: PMC6525440 DOI: 10.1186/s12866-019-1453-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses. RESULTS To elaborate on the metabolic network response to increased fermentation temperatures of up to 49 °C, comprehensive physiological datasets of several Kluyveromyces and Ogataea strains were generated and used for 13C-metabolic flux analyses. While the maximum growth temperature was very similar in all investigated strains, the metabolic network response to elevated temperatures was not conserved among the different species. In fact, metabolic flux distributions were remarkably irresponsive to increasing temperatures in O. polymorpha, while the K. marxianus strains exhibited extensive flux rerouting at elevated temperatures. CONCLUSIONS While a clear mechanism of thermotolerance is not deducible from the fluxome level alone, the generated data can be valued as a knowledge repository for using temperature to modulate the metabolic activity towards engineering goals.
Collapse
Affiliation(s)
- Mathias Lehnen
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Birgitta E. Ebert
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Lars M. Blank
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| |
Collapse
|
40
|
Misumi Y, Nishioka S, Fukuda A, Uemura T, Nakamura M, Hoshida H, Akada R. YHp as a highly stable, hyper-copy, hyper-expression plasmid constructed using a full 2-μm circle sequence in cir 0 strains of Saccharomyces cerevisiae. Yeast 2019; 36:249-257. [PMID: 30537227 DOI: 10.1002/yea.3371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/20/2018] [Accepted: 11/24/2018] [Indexed: 11/07/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the yeast episomal plasmid (YEp), containing a partial sequence from a natural 2-μm plasmid, has been frequently used to induce high levels of gene expression. In this study, we used Japanese sake yeast natural cir0 strain as a host for constructing an entire 2-μm plasmid with an expression construct using the three-fragment gap-repair method without Escherichia coli manipulation. The 2-μm plasmid contains two long inverted repeats, which is problematic for the amplification by polymerase chain reaction. Therefore, we amplified it by dividing into two fragments, each containing a single repeat together with an overlapping sequence for homologous recombination. TDH3 promoter-driven yEmRFP (TDH3p-yEmRFP) and the URA3 were used as a reporter gene and a selection marker, respectively, and inserted at the 3' end of the RAF1 gene on the 2-μm plasmid. The three fragments were combined and used for the transformation of sake yeast cir0 ura3- strain. The resulting transformant colonies showed a red or purple coloration, which was significantly stronger than that of the cells transformed with YEp-TDH3p-yEmRFP. The 2-μm transformants were cultured in YPD medium and observed by fluorescence microscopy. Almost all cells showed strong fluorescence, suggesting that the plasmid was preserved during nonselective culture conditions. The constructed plasmid maintained a high copy state similar to that of the natural 2-μm plasmid, and the red fluorescent protein expression was 54 fold compared with the chromosomal integrant. This vector is named YHp, the Yeast Hyper expression plasmid.
Collapse
Affiliation(s)
- Yukie Misumi
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube, Japan
| | - Satoko Nishioka
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube, Japan
| | - Akira Fukuda
- JXTG Nippon Oil & Energy Corporation, Yokohama, Japan
| | | | - Mikiko Nakamura
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube, Japan
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube, Japan
| | - Rinji Akada
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube, Japan
| |
Collapse
|
41
|
Sakihama Y, Hidese R, Hasunuma T, Kondo A. Increased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions. Sci Rep 2019; 9:5319. [PMID: 30926897 PMCID: PMC6440987 DOI: 10.1038/s41598-019-41863-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/14/2019] [Indexed: 11/10/2022] Open
Abstract
Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.
Collapse
Affiliation(s)
- Yuri Sakihama
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Ryota Hidese
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Innovation, Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| |
Collapse
|
42
|
Alcazar-Valle M, Gschaedler A, Gutierrez-Pulido H, Arana-Sanchez A, Arellano-Plaza M. Fermentative capabilities of native yeast strains grown on juices from different Agave species used for tequila and mezcal production. Braz J Microbiol 2019; 50:379-388. [PMID: 30826999 DOI: 10.1007/s42770-019-00049-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 01/07/2019] [Indexed: 11/26/2022] Open
Abstract
The Asparagaceae family is endemic from America, being the Agave genus the most important. The Agave species possess economic relevance and are use as raw material to produce several distilled alcoholic beverages, as bacanora, tequila, and mezcal. The fermentation process has been carry out either spontaneously or by adding a selected yeast strain. The latter is generally responsible for the production of ethanol and volatile compounds. This study comprised five Agave species (A. angustifolia, A. cupreata, A. durangensis, A. salmiana, and A. tequilana) and eight endogenous yeast strains: five of them were non-Saccharomyces (Torulaspora delbrueckii, Zygosaccharomyces bisporus, Candida ethanolica, and two Kluyveromyces marxianus) and three Saccharomyces cerevisiae strains. The results showed that the S. cerevisiae strains were not able to grow on A. durangensis and A. salmiana juices. The Kluyveromyces marxianus strains grew and fermented all the agave juices and displayed high ethanol production (48-52 g L-1) and volatile compounds. The ethanol production was higher on A. angustifolia juice (1.1-2.8-fold), whereas the volatile compound was dependent on both yeast strain and the Agave species. The use of endogenous non-Saccharomyces yeast strains is feasible, as they may outperform S. cerevisiae regarding the production of fermented beverages from agave plants with a high content of ethanol and aromatic compounds. Graphical abstract.
Collapse
Affiliation(s)
- M Alcazar-Valle
- Biotecnología Industrial, CIATEJ, Camino Arenero 1227, El Bajío, 45019, Zapopan, Jalisco, Mexico
| | - A Gschaedler
- Biotecnología Industrial, CIATEJ, Camino Arenero 1227, El Bajío, 45019, Zapopan, Jalisco, Mexico
| | - H Gutierrez-Pulido
- Centro Universitarios de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, esq. Calzada Olímpica, 44430, Guadalajara, Jalisco, Mexico
| | - A Arana-Sanchez
- Biotecnología Industrial, CIATEJ, Camino Arenero 1227, El Bajío, 45019, Zapopan, Jalisco, Mexico
| | - M Arellano-Plaza
- Biotecnología Industrial, CIATEJ, Camino Arenero 1227, El Bajío, 45019, Zapopan, Jalisco, Mexico.
| |
Collapse
|
43
|
The production of ethanol from lignocellulosic biomass by Kluyveromyces marxianus CICC 1727-5 and Spathaspora passalidarum ATCC MYA-4345. Appl Microbiol Biotechnol 2019; 103:2845-2855. [DOI: 10.1007/s00253-019-09625-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/18/2018] [Accepted: 12/16/2018] [Indexed: 11/25/2022]
|
44
|
Dasgupta D, Junghare V, Nautiyal AK, Jana A, Hazra S, Ghosh D. Xylitol Production from Lignocellulosic Pentosans: A Rational Strain Engineering Approach toward a Multiproduct Biorefinery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1173-1186. [PMID: 30618252 DOI: 10.1021/acs.jafc.8b05509] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Kluyveromyces marxianus IIPE453 can utilize biomass-derived fermentable sugars for xylitol and ethanol fermentation. In this study, the xylitol production in the native strain was improved by overexpression of endogenous d-xylose reductase gene. A suitable expression cassette harboring the gene of interest was constructed and incorporated in the native yeast. qPCR analysis demonstrated the 2.1-fold enhancement in d-xylose reductase transcript levels in the modified strain with 1.62-fold enhancement in overall xylitol yield without affecting its ethanol fermenting capacity. Material balance analysis on 2 kg of sugar cane bagasse-derived fermentable sugars illustrated an excess of 58.62 ± 0.15 g of xylitol production by transformed strain in comparison to the wild variety with similar ethanol yield. The modified strain can be suitably used as a single biocatalyst for multiproduct biorefinery application.
Collapse
Affiliation(s)
- Diptarka Dasgupta
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | | | - Abhilek K Nautiyal
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | - Arijit Jana
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | | | - Debashish Ghosh
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| |
Collapse
|
45
|
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
|
46
|
Fraberger V, Call LM, Domig KJ, D'Amico S. Applicability of Yeast Fermentation to Reduce Fructans and Other FODMAPs. Nutrients 2018; 10:E1247. [PMID: 30200589 PMCID: PMC6163668 DOI: 10.3390/nu10091247] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
A diet low in fermentable oligosaccharides, disaccharides, monosaccharides and, polyols (FODMAPs) is recommended for people affected by irritable bowel syndrome (IBS) and non-coeliac wheat sensitivity (NCWS) in order to reduce symptoms. Therefore, the aim of this study was to evaluate the impact of 13 sourdough-related yeasts on FODMAP degradation, especially fructans. First, a model system containing a typical wheat carbohydrate profile was applied to evaluate the growth rate of each yeast strain. Additionally, changes in the sugar composition, for up to four days, were monitored by high-pressure anion-exchange chromatography (HPAEC). A more realistic approach with a wheat flour suspension was used to characterize CO₂ production according to the Einhorn method. The reduction of the total fructans was analyzed using an enzymatic method. Furthermore, a fingerprint of the present fructans with different degrees of polymerization was analyzed by HPAEC. The results revealed strong differences in the examined yeast strains' ability to degrade fructans, in both the model system and wheat flour. Overall, Saccharomycescerevisiae isolated from Austrian traditional sourdough showed the highest degree of degradation of the total fructan content and the highest gas building capacity, followed by Torulasporadelbrueckii. Hence, this study provides novel knowledge about the FODMAP conversion of yeast strains.
Collapse
Affiliation(s)
- Vera Fraberger
- Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.
| | - Lisa-Maria Call
- Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.
| | - Konrad J Domig
- Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.
| | - Stefano D'Amico
- Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.
| |
Collapse
|
47
|
Li P, Fu X, Li S, Zhang L. Engineering TATA-binding protein Spt15 to improve ethanol tolerance and production in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:207. [PMID: 30061929 PMCID: PMC6058363 DOI: 10.1186/s13068-018-1206-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/16/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Low ethanol tolerance of Kluyveromyces marxianus limits its application in high-temperature ethanol fermentation. As a complex phenotype, ethanol tolerance involves synergistic actions of many genes that are widely distributed throughout the genome, thereby being difficult to engineer. TATA-binding protein is the most common target of global transcription machinery engineering for improvement of complex phenotypes. RESULTS A random mutagenesis library of K. marxianus TATA-binding protein Spt15 was constructed and subjected to screening under ethanol stress. Two mutant strains with improved ethanol tolerance were identified, one of which (denoted as M2) exhibited increased ethanol productivity. The mutant of Spt15 in strain M2 (denoted as Spt15-M2) has a single amino acid substitution at position 31 (Lys → Glu). RNA-Seq-based transcriptomic analysis revealed cellular transcription profile changes resulting from Spt15-M2. Spt15-M2 caused changes in transcriptional level of most of the genes in the central carbon metabolism network. Compared with control strain, 444 differentially expressed genes (DEGs) were identified in strain M2 (fold change > 2, Padj < 0.05), including 48 up-regulated and 396 down-regulated. The up-regulated DEGs are involved in amino acid transport, long-chain fatty acid biosynthesis and MAPK signaling pathway, while the down-regulated DEGs are related to ribosome biogenesis, translation and protein synthesis. Five candidate genes (GAP1, GNP1, FAR1, STE2 and TEC1), which were found to be up-regulated in M2 strain, were overexpressed for a gain-of-function assay. However, the overexpression of no single gene helped improve ethanol tolerance as SPT15-M2 did. CONCLUSIONS This work demonstrates that ethanol tolerance of K. marxianus can be improved by engineering its TATA-binding protein. A single amino acid substitution (K31E) of TATA-binding protein Spt15 is able to bring differential expression of hundreds of genes that acted as an interconnected network for the phenotype of ethanol tolerance. Future perspectives of this technique in K. marxianus were discussed.
Collapse
Affiliation(s)
- Pengsong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| |
Collapse
|
48
|
Paulino de Souza J, Dias do Prado C, Eleutherio EC, Bonatto D, Malavazi I, Ferreira da Cunha A. Improvement of Brazilian bioethanol production – Challenges and perspectives on the identification and genetic modification of new strains of Saccharomyces cerevisiae yeasts isolated during ethanol process. Fungal Biol 2018; 122:583-591. [DOI: 10.1016/j.funbio.2017.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
|
49
|
Hoshida H, Kidera K, Takishita R, Fujioka N, Fukagawa T, Akada R. Enhanced production of extracellular inulinase by the yeast Kluyveromyces marxianus in xylose catabolic state. J Biosci Bioeng 2018; 125:676-681. [DOI: 10.1016/j.jbiosc.2017.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/27/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
|
50
|
Varela JA, Montini N, Scully D, Van der Ploeg R, Oreb M, Boles E, Hirota J, Akada R, Hoshida H, Morrissey JP. Polymorphisms in the LAC12 gene explain lactose utilisation variability in Kluyveromyces marxianus strains. FEMS Yeast Res 2018; 17:3739724. [PMID: 28444380 DOI: 10.1093/femsyr/fox021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/16/2017] [Indexed: 01/29/2023] Open
Abstract
Kluyveromyces marxianus is a safe yeast used in the food and biotechnology sectors. One of the important traits that sets it apart from the familiar yeasts, Saccharomyces cerevisiae, is its capacity to grow using lactose as a carbon source. Like in its close relative, Kluyveromyces lactis, this requires lactose transport via a permease and intracellular hydrolysis of the disaccharide. Given the importance of the trait, it was intriguing that most, but not all, strains of K. marxianus are reported to consume lactose efficiently. In this study, primarily through heterologous expression in S. cerevisiae and K. marxianus, it was established that a single gene, LAC12, is responsible for lactose uptake in K. marxianus. Strains that failed to transport lactose showed variation in 13 amino acids in the Lac12p protein, rendering the protein non-functional for lactose transport. Genome analysis showed that the LAC12 gene is present in four copies in the subtelomeric regions of three different chromosomes but only the ancestral LAC12 gene encodes a functional lactose transporter. Other copies of LAC12 may be non-functional or have alternative substrates. The analysis raises some interesting questions regarding the evolution of sugar transporters in K. marxianus.
Collapse
Affiliation(s)
- Javier A Varela
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | - Noemi Montini
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | - Damhan Scully
- School of Microbiology, University College Cork, Cork T12YN60, Ireland
| | | | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Junya Hirota
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan
| | - Rinji Akada
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan.,Biomedical Engineering Center, Yamaguchi University, Ube 755-8611, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan
| | - Hisashi Hoshida
- Department of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Ube 755-8611, Japan.,Biomedical Engineering Center, Yamaguchi University, Ube 755-8611, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8315, Japan
| | - John P Morrissey
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| |
Collapse
|