1
|
Cai W, Wan Y, Chen Y, Fan H, Li M, Wu S, Lin P, Zeng T, Luo H, Huang D, Fu G. Transcriptomics to evaluate the influence mechanisms of ethanol on the ester production of Wickerhamomyces anomalus with the induction of lactic acid. Food Microbiol 2024; 122:104556. [PMID: 38839235 DOI: 10.1016/j.fm.2024.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 06/07/2024]
Abstract
Wickerhamomyces anomalus is one of the most important ester-producing strains in Chinese baijiu brewing. Ethanol and lactic acid are the main metabolites produced during baijiu brewing, but their synergistic influence on the growth and ester production of W. anomalus is unclear. Therefore, in this paper, based on the contents of ethanol and lactic acid during Te-flavor baijiu brewing, the effects of different ethanol concentrations (3, 6, and 9% (v/v)) combined with 1% lactic acid on the growth and ester production of W. anomalus NCUF307.1 were studied and their influence mechanisms were analyzed by transcriptomics. The results showed that the growth of W. anomalus NCUF307.1 under the induction of lactic acid was inhibited by ethanol. Although self-repair mechanism of W. anomalus NCUF307.1 induced by lactic acid was initiated at all concentrations of ethanol, resulting in significant up-regulation of genes related to the Genetic Information Processing pathway, such as cell cycle-yeast, meiosis-yeast, DNA replication and other pathways. However, the accumulation of reactive oxygen species and the inhibition of pathways associated with carbohydrate and amino acid metabolism may be the main reason for the inhibition of growth in W. anomalus NCUF307.1. In addition, 3% and 6% ethanol combined with 1% lactic acid could promote the ester production of W. anomalus NCUF307.1, which may be related to the up-regulation of EAT1, ADH5 and TGL5 genes, while the inhibition in 9% ethanol may be related to down-regulation of ATF2, EAT1, ADH2, ADH5, and TGL3 genes.
Collapse
Affiliation(s)
- Wenqin Cai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Yin Wan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Yanru Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Haowei Fan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China
| | - Mengxiang Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Shengwen Wu
- Sitir Liquor Co., Ltd, Zhangshu, 331200, PR, China
| | - Pei Lin
- Sitir Liquor Co., Ltd, Zhangshu, 331200, PR, China
| | | | - Huibo Luo
- Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Dan Huang
- Liquor Making Biological Technology and Application Key Laboratory of Sichuan Province, Yibin, 644000, PR, China
| | - Guiming Fu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR, China; International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, 330299, PR, China.
| |
Collapse
|
2
|
Tafrishi A, Trivedi V, Xing Z, Li M, Mewalal R, Cutler SR, Blaby I, Wheeldon I. Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library. Metab Eng 2024; 85:73-83. [PMID: 39019250 DOI: 10.1016/j.ymben.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/06/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
CRISPR-based high-throughput genome-wide loss-of-function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold coverage genome-wide sgRNA library for this biotechnologically important yeast containing 30,848 active sgRNAs targeting over 99% of its coding sequences. Conducting fitness screens in the absence of functional non-homologous end joining (NHEJ), the dominant DNA repair mechanism in K. phaffii, provides a quantitative means to assess the activity of each sgRNA in the library. This approach allows for the experimental validation of each guide's targeting activity, leading to more precise screening outcomes. We used this approach to conduct growth screens with glucose as the sole carbon source and identify essential genes. Comparative analysis of the called gene sets identified a core set of K. phaffii essential genes, many of which relate to metabolic engineering targets, including protein production, secretion, and glycosylation. The high activity, genome-wide CRISPR library developed here enables functional genomic screening in K. phaffii, applied here to gene essentiality classification, and promises to enable other genetic screens.
Collapse
Affiliation(s)
- Aida Tafrishi
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Varun Trivedi
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Zenan Xing
- Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA
| | - Mengwan Li
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Ritesh Mewalal
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sean R Cutler
- Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA
| | - Ian Blaby
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA; Center for Industrial Biotechnology, University of California-Riverside, Riverside, CA, 92521, USA.
| |
Collapse
|
3
|
Zhou H, Tian T, Liu J, Lu H, Yu Y, Wang Y. Efficient and markerless gene integration with SlugCas9-HF in Kluyveromyces marxianus. Commun Biol 2024; 7:797. [PMID: 38956406 PMCID: PMC11219867 DOI: 10.1038/s42003-024-06487-w] [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: 01/31/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The nonconventional yeast Kluyveromyces marxianus has potential for industrial production, but the lack of advanced synthetic biology tools for precise engineering hinders its rapid development. Here, we introduce a CRISPR-Cas9-mediated multilocus integration method for assembling multiple exogenous genes. Using SlugCas9-HF, a high-fidelity Cas9 nuclease, we enhance gene editing precision. Specific genomic loci predisposed to efficient integration and expression of heterologous genes are identified and combined with a set of paired CRISPR-Cas9 expression plasmids and donor plasmids to establish a CRISPR-based biosynthesis toolkit. This toolkit enables genome integration of large gene modules over 12 kb and achieves simultaneous quadruple-locus integration in a single step with 20% efficiency. As a proof-of-concept, we apply the toolkit to screen for gene combinations that promote heme production, revealing the importance of HEM4Km and HEM12Sc. This CRISPR-based toolkit simplifies the reconstruction of complex pathways in K. marxianus, broadening its application in synthetic biology.
Collapse
Affiliation(s)
- Huanyu Zhou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, 201399, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Tian Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Jingtong Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, 201399, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| | - Yongming Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, 201399, China.
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
4
|
Bassett S, Da Silva NA. Engineering a carbon source-responsive promoter for improved biosynthesis in the non-conventional yeast Kluyveromyces marxianus. Metab Eng Commun 2024; 18:e00238. [PMID: 38845682 PMCID: PMC11153928 DOI: 10.1016/j.mec.2024.e00238] [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: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Many desired biobased chemicals exhibit a range of toxicity to microbial cell factories, making industry-level biomanufacturing more challenging. Separating microbial growth and production phases is known to be beneficial for improving production of toxic products. Here, we developed a novel synthetic carbon-responsive promoter for use in the rapidly growing, stress-tolerant yeast Kluyveromyces marxianus, by fusing carbon-source responsive elements of the native ICL1 promoter to the strong S. cerevisiae TDH3 or native NC1 promoter cores. Two hybrids, P IT350 and P IN450 , were validated via EGFP fluorescence and demonstrated exceptional strength, partial repression during growth, and late phase activation in glucose- and lactose-based medium, respectively. Expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for synthesis of the polyketide triacetic acid lactone (TAL) under the control of P IN450 increased TAL more than 50% relative to the native NC1 promoter, and additional promoter engineering further increased TAL titer to 1.39 g/L in tube culture. Expression of the Penicillium griseofulvum 6-methylsalicylic acid synthase (6-MSAS) under the control of P IN450 resulted in a 6.6-fold increase in 6-MSA titer to 1.09 g/L and a simultaneous 1.5-fold increase in cell growth. Finally, we used P IN450 to express the Pseudomonas savastanoi IaaM and IaaH proteins and the Salvia pomifera sabinene synthase protein to improve production of the auxin hormone indole-3-acetic acid and the monoterpene sabinene, respectively, both extremely toxic to yeast. The development of carbon-responsive promoters adds to the synthetic biology toolbox and available metabolic engineering strategies for K. marxianus, allowing greater control over heterologous protein expression and improved production of toxic metabolites.
Collapse
Affiliation(s)
- Shane Bassett
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
| | - Nancy A. Da Silva
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
| |
Collapse
|
5
|
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
|
6
|
Wei S, Li M, Lang X, Robertson NR, Park SY, Cutler SR, Wheeldon I. Repurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast. Metab Eng 2024; 83:102-109. [PMID: 38554744 DOI: 10.1016/j.ymben.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1ABA/HAB1 and PYR1*MANDI/HAB1*) for high dynamic-range gene activation and repression controlled by either abscisic acid (ABA) or mandipropamid (mandi). To redirect metabolic flux towards ethyl acetate biosynthesis, we simultaneously repress pyruvate dehydrogenase (PDA1) and activate pyruvate decarboxylase (PDC1) to enhance ethyl acetate titers. Thus, we have developed new tools for chemically tuning gene expression in K. marxianus and S. cerevisiae that should be deployable across many non-conventional eukaryotic hosts.
Collapse
Affiliation(s)
- Shuang Wei
- Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, USA
| | - Mengwan Li
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Xuye Lang
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Nicholas R Robertson
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Sang-Youl Park
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Sean R Cutler
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
| |
Collapse
|
7
|
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
|
8
|
Wang Y, Du Y, Jin X, Xia Y, Zhao Y, Wu Z, Gomi K, Zhang W. Temperature-dependent alcohol acyltransferase reactions as the main enzymatic way to produce short-chain (C4-C8) and medium-chain (C9-C13) esters over the whole Daqu-making process. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:3939-3949. [PMID: 36352497 DOI: 10.1002/jsfa.12327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/01/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND The ester-synthesis enzymes influenced by environmental factors during Daqu-making process largely determine the flavor of Chinese liquor, but the main ester-synthesis enzyme and its key influencer remain unclear. Here, the volatile ester profiles over the whole Daqu-making process, under different treatments, for at least 90 days, were carefully analyzed, and the potential ester-synthesis enzymes, as well as their dependently environmental factors, were explored. RESULTS In the detected 46 volatile esters, only the short-chain (C4-C8) and medium-chain (C9-C13) ester content obviously changed, as the primary contributor discriminating different samples. Their trends were both consistent with that of the alcohols and the primary metabolism, which included alcohol acyltransferases (AATs) reaction with alcohols and acyl-CoAs as the substrates. Among the potential ester-synthesis enzymes, the typical AAT activity also exhibited the highest correlation with the short- and medium-chain esters (r > 0.78, P < 0.05). The Mantel test between environmental factors and ester production showed that temperature of Daqu was directly correlated with the short-chain esters (r = 0.58, P < 0.01) and AAT activity (r = 0.56, P < 0.01). Further, the short- and medium-chain ester content in Daqu under the treatment nearer to the reported optimal temperature of 40-50 °C of AATs reaction was overall higher than that of the other treatment Daqu. CONCLUSION This study revealed that the temperature-dependent AATs reaction was the main enzymatic method producing the short- and medium-chain esters over the whole Daqu-making process. The results could contribute to the flavor improvement of Baijiu. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yan Wang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Yake Du
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Xuelian Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Yu Xia
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Yajiao Zhao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Zhengyun Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Katsuya Gomi
- Laboratory of Fermentation Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Wenxue Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- School of Liquor-Brewing Engineering, Sichuan University of Jinjiang College, Meishan, China
| |
Collapse
|
9
|
Sun J, Zhu Z, Lin Q, Qi S, Li Q, Zhou Y, Li R. Metabolic Engineering of Escherichia coli for the Biosynthesis of 3-Phenylpropionic Acid and 3-Phenylpropyl Acetate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7451-7458. [PMID: 37146254 DOI: 10.1021/acs.jafc.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
3-Phenylpropionic acid (3PPA) and its derivative 3-phenylpropyl acetate (3PPAAc) are important aromatic compounds with broad applications in the cosmetics and food industries. In this study, we constructed a plasmid-free 3PPA-producing Escherichia coli strain and designed a novel 3PPAAc biosynthetic pathway. A module containing tyrosine ammonia lyase and enoate reductase, evaluated under the control of different promoters, was combined with phenylalanine-overproducing strain E. coli ATCC31884, enabling the plasmid-free de novo production of 218.16 ± 43.62 mg L-1 3PPA. The feasibility of the pathway was proved by screening four heterologous alcohol acetyltransferases, which catalyzed the transformation of 3-phenylpropyl alcohol into 3PPAAc. Afterward, 94.59 ± 16.25 mg L-1 3PPAAc was achieved in the engineered E. coli strain. Overall, we have not only demonstrated the potential of de novo synthesis of 3PPAAc in microbes for the first time but also provided a platform for the future of biosynthesis of other aromatic compounds.
Collapse
Affiliation(s)
- Jing Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Zhi Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Qingfang Lin
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Shilian Qi
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Qianqian Li
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Yang Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Rongpeng Li
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| |
Collapse
|
10
|
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
|
11
|
Hoffmann A, Franz A, Walther T, Löser C. Utilization of delactosed whey permeate for the synthesis of ethyl acetate with Kluyveromyces marxianus. Appl Microbiol Biotechnol 2023; 107:1635-1648. [PMID: 36786916 PMCID: PMC10006051 DOI: 10.1007/s00253-023-12419-1] [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: 11/07/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
Ethyl acetate is an important organic solvent and currently produced from fossil carbon resources. Microbial synthesis of this ester from sugar-rich waste could be an interesting alternative. Therefore, synthesis of ethyl acetate by Kluyveromyces marxinanus DSM 5422 from delactosed whey permeate (DWP) was studied in an aerated stirred bioreactor at 40 °C. DWP is mainly composed of residual lactose and minerals. The minerals inhibited yeast growth, as witnessed by an increased lag period, a reduced growth rate, and an extended process duration. All experiments were therefore carried out with diluted DWP. In a series of batch experiments, the pH of iron-deficient DWP medium varied between 4.8 and 5.9. The pH of the cultivation medium significantly influenced cell growth and product syntheses, with the highest ethyl acetate yield of 0.347 g g-1 and lowest by-product formation achieved at pH 5.1. It is likely that this effect is due to pH-dependent iron chelation, which affects the iron bioavailability and the intracellular iron content, thus affecting growth and metabolite synthesis. The viability of yeast cells was always high despite the harsh conditions in DWP medium, which enabled extended usage of the biomass in repeated-batch and fed-batch cultivations. These two culture techniques increased the volume of DWP processed per time by 32 and 84% for the repeated-batch and the fed-batch cultivation, respectively, without a drop of the ester yield. KEY POINTS: • Delactosed whey permeate was converted to ethyl acetate with a high rate and yield. • The formation of ethyl acetate in DWP medium at iron limitation is pH-dependent. • Highly active yeasts from batch processes enabled extension as fed and repeated batch.
Collapse
Affiliation(s)
- Andreas Hoffmann
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Alexander Franz
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
- Biophysical Chemistry, Institute of Biochemistry, University of Leipzig, 04103, Leipzig, Germany
| | - Thomas Walther
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christian Löser
- Bioprocess Engineering, Institute of Natural Materials Technology, Technische Universität Dresden, 01062, Dresden, Germany.
| |
Collapse
|
12
|
Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
Collapse
Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
| |
Collapse
|
13
|
Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet 2023; 13:989199. [PMID: 36685866 PMCID: PMC9845283 DOI: 10.3389/fgene.2022.989199] [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: 07/08/2022] [Accepted: 11/15/2022] [Indexed: 01/05/2023] Open
Abstract
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
Collapse
Affiliation(s)
- Sakshi Dharmendra Kor
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India,*Correspondence: Palakolanu Sudhakar Reddy, ,
| |
Collapse
|
14
|
Liu N, Qin L, Hu L, Miao S. Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
15
|
Prospects of thermotolerant Kluyveromyces marxianus for high solids ethanol fermentation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:134. [PMID: 36474296 PMCID: PMC9724321 DOI: 10.1186/s13068-022-02232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
Simultaneous saccharification and fermentation (SSF) is effective for minimizing sugar inhibition during high solids fermentation of biomass solids to ethanol. However, fungal enzymes used during SSF are optimal between 50 and 60 °C, whereas most fermentative yeast, such as Saccharomyces cerevisiae, do not tolerate temperatures above 37 °C. Kluyveromyces marxianus variant CBS 6556 is a thermotolerant eukaryote that thrives at 43 °C, thus potentially serving as a promising new host for SSF operation in biorefineries. Here, we attempt to leverage the thermotolerance of the strain to demonstrate the application of CBS 6556 in a high solids (up to 20 wt% insoluble solid loading) SSF configuration to understand its capabilities and limitations as compared to a proven SSF strain, S. cerevisiae D5A. For this study, we first pretreated hardwood poplar chips using Co-Solvent Enhanced Lignocellulosic Fractionation (CELF) to remove lignin and hemicellulose and to produce cellulose-enriched pretreated solids for SSF. Our results demonstrate that although CBS 6556 could not directly outperform D5A, it demonstrated similar tolerance to high gravity sugar solutions, superior growth rates at higher temperatures and higher early stage ethanol productivity. We discovered that CBS 6556's membrane was particularly sensitive to higher ethanol concentrations causing it to suffer earlier fermentation arrest than D5A. Cross-examination of metabolite data between CBS 6556 and D5A and cell surface imaging suggests that the combined stresses of high ethanol concentrations and temperature to CBS 6556's cell membrane was a primary factor limiting its ethanol productivity. Hence, we believe K. marxianus to be an excellent host for future genetic engineering efforts to improve membrane robustness especially at high temperatures in order to achieve higher ethanol productivity and titers, serving as a viable alternative to D5A.
Collapse
|
16
|
Ren L, Liu Y, Xia Y, Huang Y, Liu Y, Wang Y, Li P, Chang K, Xu D, Li F, Zhang B. Improving glycerol utilization during high-temperature xylitol production with Kluyveromyces marxianus using a transient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system. BIORESOURCE TECHNOLOGY 2022; 365:128179. [PMID: 36283669 DOI: 10.1016/j.biortech.2022.128179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Glycerol is an ideal co-substrate for xylitol production with Kluyveromyces marxianus. This study demonstrated that K. marxianus catabolizes glycerol through the Gut1-Gut2 pathway instead of the previously speculated NADPH-dependent Gcy1-Dak1 pathway using the transient clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system. Additionally, Utr1p was demonstrated to mediate NADPH generation through NADH phosphorylation. YZB392, which was constructed by integrating Utr1 into the Ypr1 site in the strain overexpressing NcXyl1 and CiGxf1 and harboring disrupted Xyl2, exhibited enhanced glycerol utilization for xylitol production (from 2.50- to 3.30- g/L after consuming 1 g/L glycerol). Fed-batch fermentation at 42 °C with YZB392 yielded 322.07 g/L xylitol, which is the highest known xylitol titer obtained via biological method. Feeding crude glycerol, xylose mother liquor, and corn steep liquor powder into a bioreactor resulted in the production of 235.69 g/L xylitol. This study developed a platform for xylitol production from industrial by-products.
Collapse
Affiliation(s)
- Lili Ren
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Yanyan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Yitong Xia
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Yi Huang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Yu Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Youming Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Pengfei Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Kechao Chang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Dayong Xu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China
| | - Biao Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, PR China.
| |
Collapse
|
17
|
Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.
Collapse
|
18
|
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
|
19
|
CRISPR-based metabolic engineering in non-model microorganisms. Curr Opin Biotechnol 2022; 75:102698. [PMID: 35217297 DOI: 10.1016/j.copbio.2022.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
Non-model microorganisms possess unique and versatile metabolic characteristics, offering great opportunities as cell factories for biosynthesis of target products. However, lack of efficient genetic tools for pathway engineering represents a big challenge to unlock the full production potential of these microbes. Over the past years, CRISPR systems have been extensively developed and applied to domesticate non-model microorganisms. In this paper, we summarize the current significant advances in designing and constructing CRISPR-mediated genetic modification systems in non-model microorganisms, such as bacteria, fungi and cyanobacteria. We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools. Moreover, the current barriers and future perspectives on improving the editing efficiency of CRISPR systems in non-model microorganisms are also discussed.
Collapse
|
20
|
Baisya D, Ramesh A, Schwartz C, Lonardi S, Wheeldon I. Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nat Commun 2022; 13:922. [PMID: 35177617 PMCID: PMC8854577 DOI: 10.1038/s41467-022-28540-0] [Citation(s) in RCA: 4] [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: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide's ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
Collapse
Affiliation(s)
- Dipankar Baisya
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
21
|
Rajkumar AS, Morrissey JP. Protocols for marker-free gene knock-out and knock-down in Kluyveromyces marxianus using CRISPR/Cas9. FEMS Yeast Res 2022; 22:foab067. [PMID: 34928332 PMCID: PMC8800938 DOI: 10.1093/femsyr/foab067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/16/2021] [Indexed: 12/03/2022] Open
Abstract
There is increased interest in strain engineering in the food and industrial yeast Kluyveromyces marxianus and a number of CRISPR/Cas9 systems have been described and used by different groups. The methods that we developed allow for very rapid and efficient inactivation of target genes using the endogenous DNA repair mechanisms of the cell. The strains and plasmids that we use are freely available, and here we provide a set of integrated protocols to easily inactivate genes and to precisely integrate DNA fragments into the genome, for example for promoter replacement, allelic swaps or introduction of point mutations. The protocols use the Cas9/gRNA expression plasmid pUCC001 and Golden Gate assembly for molecular cloning of targeting sequences. A genome-wide set of target sequences is provided. Using these plasmids in wild-type strains or in strains lacking non-homologous end-joining (NHEJ) DNA repair, the first set of protocols explain how to introduce indels (NHEJ-mediated) or precise deletions (homology-dependent repair (HDR)-mediated) at precise targets. The second set of protocols describe how to swap a promoter or coding sequence to yield a reprogrammed gene. The methods do not require the use of dominant or auxotrophic marker genes and thus the strains generated are marker-free. The protocols have been tested in multiple K. marxianus strains, are straightforward and can be carried out in any molecular biology laboratory without specialized equipment.
Collapse
Affiliation(s)
- Arun S Rajkumar
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, SUSFERM Fermentation Centre, University College Cork, Cork T12 K8AF, Ireland
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, SUSFERM Fermentation Centre, University College Cork, Cork T12 K8AF, Ireland
| |
Collapse
|
22
|
Study on the construction and aroma-producing characteristics of the recombinant Saccharomyces cerevisiae strain W303-EAT. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-021-03890-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Ploessl D, Zhao Y, Cao M, Ghosh S, Lopez C, Sayadi M, Chudalayandi S, Severin A, Huang L, Gustafson M, Shao Z. A repackaged CRISPR platform increases homology-directed repair for yeast engineering. Nat Chem Biol 2022; 18:38-46. [PMID: 34711982 DOI: 10.1038/s41589-021-00893-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Inefficient homology-directed repair (HDR) constrains CRISPR-Cas9 genome editing in organisms that preferentially employ nonhomologous end joining (NHEJ) to fix DNA double-strand breaks (DSBs). Current strategies used to alleviate NHEJ proficiency involve NHEJ disruption. To confer precision editing without NHEJ disruption, we identified the shortcomings of the conventional CRISPR platforms and developed a CRISPR platform-lowered indel nuclease system enabling accurate repair (LINEAR)-which enhanced HDR rates (to 67-100%) compared to those in previous reports using conventional platforms in four NHEJ-proficient yeasts. With NHEJ preserved, we demonstrate its ability to survey genomic landscapes, identifying loci whose spatiotemporal genomic architectures yield favorable expression dynamics for heterologous pathways. We present a case study that deploys LINEAR precision editing and NHEJ-mediated random integration to rapidly engineer and optimize a microbial factory to produce (S)-norcoclaurine. Taken together, this work demonstrates how to leverage an antagonizing pair of DNA DSB repair pathways to expand the current collection of microbial factories.
Collapse
Affiliation(s)
- Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Carmen Lopez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA
| | - Maryam Sayadi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Siva Chudalayandi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Andrew Severin
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Lei Huang
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Marissa Gustafson
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA. .,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA. .,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA. .,Bioeconomy Institute, Iowa State University, Ames, IA, USA. .,The Ames Laboratory, Ames, IA, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
24
|
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
|
25
|
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
|
26
|
Shan L, Dai Z, Wang Q. Advances and Opportunities of CRISPR/Cas Technology in Bioengineering Non-conventional Yeasts. Front Bioeng Biotechnol 2021; 9:765396. [PMID: 34708030 PMCID: PMC8542773 DOI: 10.3389/fbioe.2021.765396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Non-conventional yeasts have attracted a growing interest on account of their excellent characteristics. In recent years, the emerging of CRISPR/Cas technology has improved the efficiency and accuracy of genome editing. Utilizing the advantages of CRISPR/Cas in bioengineering of non-conventional yeasts, quite a few advancements have been made. Due to the diversity in their genetic background, the ways for building a functional CRISPR/Cas system of various species non-conventional yeasts were also species-specific. Herein, we have summarized the different strategies for optimizing CRISPR/Cas systems in different non-conventional yeasts and their biotechnological applications in the construction of cell factories. In addition, we have proposed some potential directions for broadening and improving the application of CRISPR/Cas technology in non-conventional yeasts.
Collapse
Affiliation(s)
- Lu Shan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| |
Collapse
|
27
|
Cui DY, Ge JL, Song YM, Feng PP, Lin LC, Guo LY, Zhang CY. Regulating the ratio of higher alcohols to esters by simultaneously overexpressing ATF1 and deleting BAT2 in brewer's yeast Saccharomyces pastorianus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
28
|
Godinho CP, Palma M, Oliveira J, Mota MN, Antunes M, Teixeira MC, Monteiro PT, Sá-Correia I. The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts. FEMS Yeast Res 2021; 21:6356955. [PMID: 34427650 DOI: 10.1093/femsyr/foab045] [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: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract (http://yeastract-plus.org/ncyeastract/) was associated to YEASTRACT + (http://yeastract-plus.org/). The YEASTRACT + portal is a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. N.C.Yeastract gathers all published regulatory associations and TF-binding sites for Komagataellaphaffii (formerly Pichia pastoris), the oleaginous yeast Yarrowia lipolytica, the lactose fermenting species Kluyveromyces lactis and Kluyveromyces marxianus, and the remarkably weak acid-tolerant food spoilage yeast Zygosaccharomyces bailii. The objective of this review paper is to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on these species, exploring all the information available in the global YEASTRACT + portal. Using simple and widely used examples, a guided exploitation is offered for several tools: (i) inference of orthologous genes; (ii) search for putative TF binding sites and (iii) inter-species comparison of transcription regulatory networks and prediction of TF-regulated networks based on documented regulatory associations available in YEASTRACT + for well-studied species. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed.
Collapse
Affiliation(s)
- Cláudia P Godinho
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Palma
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | - Marta N Mota
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Antunes
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel C Teixeira
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro T Monteiro
- INESC-ID, Lisbon, Portugal.,Department of Computer Science and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
29
|
Wang Q, Al Makishah NH, Li Q, Li Y, Liu W, Sun X, Wen Z, Yang S. Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production. Front Bioeng Biotechnol 2021; 9:661694. [PMID: 34164382 PMCID: PMC8215697 DOI: 10.3389/fbioe.2021.661694] [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: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.
Collapse
Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Naief H Al Makishah
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wenzheng Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
30
|
Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [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: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
Collapse
Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
31
|
Leonel LV, Arruda PV, Chandel AK, Felipe MGA, Sene L. Kluyveromyces marxianus: a potential biocatalyst of renewable chemicals and lignocellulosic ethanol production. Crit Rev Biotechnol 2021; 41:1131-1152. [PMID: 33938342 DOI: 10.1080/07388551.2021.1917505] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Kluyveromyces marxianus is an ascomycetous yeast which has shown promising results in cellulosic ethanol and renewable chemicals production. It can survive on a variety of carbon sources under industrially favorable conditions due to its fast growth rate, thermotolerance, and acid tolerance. K. marxianus, is generally regarded as a safe (GRAS) microorganism, is widely recognized as a powerhouse for the production of heterologous proteins and is accepted by the US Food and Drug Administration (USFDA) for its pharmaceutical and food applications. Since lignocellulosic hydrolysates are comprised of diverse monomeric sugars, oligosaccharides and potential metabolism inhibiting compounds, this microorganism can play a pivotal role as it can grow on lignocellulosic hydrolysates coping with vegetal cell wall derived inhibitors. Furthermore, advancements in synthetic biology, for example CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, will enable development of an engineered yeast for the production of biochemicals and biopharmaceuticals having a myriad of industrial applications. Genetic engineering companies such as Cargill, Ginkgo Bioworks, DuPont, Global Yeast, Genomatica, and several others are actively working to develop designer yeasts. Given the important traits and properties of K. marxianus, these companies may find it to be a suitable biocatalyst for renewable chemicals and fuel production on the large scale. This paper reviews the recent progress made with K. marxianus biotechnology for sustainable production of ethanol, and other products utilizing lignocellulosic sugars.
Collapse
Affiliation(s)
- L V Leonel
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
| | - P V Arruda
- Department of Bioprocess Engineering and Biotechnology - COEBB/TD, Federal University of Technology - Paraná (UTFPR), Toledo, Brazil
| | - A K Chandel
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - M G A Felipe
- Department of Biotechnology, School of Engineering of Lorena - EEL, University of São Paulo, Lorena, Brazil
| | - L Sene
- Center of Exact and Technological Sciences - CCET, State University of West Paraná, Cascavel, Brazil
| |
Collapse
|
32
|
Löser C, Kupsch C, Walther T, Hoffmann A. A new approach for balancing the microbial synthesis of ethyl acetate and other volatile metabolites during aerobic bioreactor cultivations. Eng Life Sci 2021; 21:137-153. [PMID: 33716613 PMCID: PMC7923609 DOI: 10.1002/elsc.202000047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Ethyl acetate is an organic solvent with many industrial applications, currently produced by energy-intensive chemical processes based on fossil carbon resources. Ethyl acetate can be synthesized from renewable sugars by yeasts like Kluyveromyces marxianus in aerobic processes. However, ethyl acetate is highly volatile and thus stripped from aerated cultivation systems which complicate the quantification of the produced ester. Synthesis of volatile metabolites is commonly monitored by repeated analysis of metabolite concentrations in both the gas and liquid phase. In this study, a model-based method for quantifying the synthesis and degradation of volatile metabolites was developed. This quantification of volatiles is solely based on repeatedly measured gas-phase concentrations and allows calculation of reaction rates and yields in high temporal resolution. Parameters required for these calculations were determined in abiotic stripping tests. The developed method was validated for ethyl acetate, ethanol and acetaldehyde which were synthesized by K. marxianus DSM 5422 during an iron-limited batch cultivation; it was shown that the presented method is more precise and less time-consuming than the conventional method. The biomass-specific synthesis rate and the yield of ethyl acetate varied over time and exhibited distinct momentary maxima of 0.50 g g‒1h‒1 and 0.38 g g‒1 at moderate iron limitation.
Collapse
Affiliation(s)
- Christian Löser
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Kupsch
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Thomas Walther
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Andreas Hoffmann
- Chair of Bioprocess Engineering, Institute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| |
Collapse
|
33
|
Hoffmann A, Kupsch C, Walther T, Löser C. Synthesis of ethyl acetate from glucose by Kluyveromyces marxianus, Cyberlindnera jadinii and Wickerhamomyces anomalus depending on the induction mode. Eng Life Sci 2021; 21:154-168. [PMID: 33716614 PMCID: PMC7923572 DOI: 10.1002/elsc.202000048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/28/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
Ethyl acetate is currently produced from fossil carbon resources. This ester could also be microbially synthesized from sugar-rich wastes of the food industry. Wild-type strains with GRAS status are preferred for such applications. Production of ethyl acetate by wild-type yeasts has been repeatedly reported, but comparative studies with several strains at various induction modes are largely missing. Here, synthesis of ethyl acetate by three yeasts with GRAS status, Kluyveromyces marxianus DSM 5422, Cyberlindnera jadinii DSM 2361 and Wickerhamomyces anomalus DSM 6766, was studied under identical and well-defined conditions in an aerated bioreactor, by inducing the ester synthesis via iron or oxygen limitation. Balancing the ester synthesis was based on measured concentrations of ethyl acetate in the exhaust gas, delivering masses of synthesized ester and synthesis rates in a high temporal resolution. All tested yeasts synthesized ethyl acetate under these conditions, but the intensity varied with the strain and induction mode. The highest yields were achieved under iron limitation with K. marxianus (0.182 g g-1) and under oxygen limitation with W. anomalus (0.053 g g-1). Iron limitation proved to be the better inducer for ester synthesis while oxygen limitation favored ethanol formation. K. marxianus DSM 5422 was the most potent producer of ethyl acetate exhibiting the highest biomass-specific synthesis rate of 0.5 g g-1h-1 under moderate iron limitation.
Collapse
Affiliation(s)
- Andreas Hoffmann
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Kupsch
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Thomas Walther
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| | - Christian Löser
- Chair of Bioprocess EngineeringInstitute of Natural Materials TechnologyTechnische Universität DresdenDresdenGermany
| |
Collapse
|
34
|
The identification of novel promoters and terminators for protein expression and metabolic engineering applications in Kluyveromyces marxianus. Metab Eng Commun 2021; 12:e00160. [PMID: 33489753 PMCID: PMC7808952 DOI: 10.1016/j.mec.2020.e00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 11/29/2022] Open
Abstract
The K. marxianus has emerged as a potential yeast strain for various biotechnological applications. However, the limited number of available genetic tools has hindered the widespread usage of this yeast. In the current study we have expanded the molecular tool box by identifying novel sets of promoters and terminators for increased recombinant protein expression in K. marxianus. The previously available transcriptomic data were analyzed to identify top 10 promoters of highest gene expression activity. We further characterized and compared strength of these identified promoters using eGFP as a reporter protein, at different temperatures and carbon sources. To examine the regulatory region driving protein expression, serially truncated shorter versions of two selected strong promoters were designed, and examined for their ability to drive eGFP protein expression. The activities of these two promoters were further enhanced using different combinations of native transcription terminators of K. marxianus. We further utilized the identified DNA cassette encoding strong promoter in metabolic engineering of K. marxianus for enhanced β-galactosidase activity. The present study thus provides novel sets of promoters and terminators as well as engineered K. marxianus strain for its wider utility in applications requiring lactose degradation such as in cheese whey and milk. Novel promoters and terminators for constitutive gene expression in K. marxianus. The promoters show constitutive expression at varying temperature and carbon source. K. marxianus strain with improved production of β-galactosidase.
Collapse
|
35
|
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
|
36
|
Misa J, Schwartz C. CRISPR Interference and Activation to Modulate Transcription in Yarrowia lipolytica. Methods Mol Biol 2021; 2307:95-109. [PMID: 33847984 DOI: 10.1007/978-1-0716-1414-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent developments in RNA-guided nuclease technologies have advanced the engineering of a wide range of organisms, including the nonconventional yeast Yarrowia lipolytica. Y. lipolytica has been the focus of a range of synthetic biology and metabolic engineering studies due to its high capacity to synthesize and accumulate intracellular lipids. The CRISPR-Cas9 system from Streptococcus pyogenes has been successfully adapted and used for genome editing in Y. lipolytica. However, as engineered strains are moved closer to industrialization, the need for finer control of transcription is still present. To overcome this challenge, we have developed CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems to allow modulating the transcription of endogenous genes. We begin this protocol chapter by describing how to use the CRISPRi system to repress expression of any gene in Y. lipolytica. A second method describes how to use the CRISPRa system to increase expression of native Y. lipolytica genes. Finally, we describe how CRISPRi or CRISPRa vectors can be combined to enable multiplexed activation or repression of more than one gene. The implementation of CRISPRi and CRISPRa systems improves our ability to control gene expression in Y. lipolytica and promises to enable more advanced synthetic biology and metabolic engineering studies in this host.
Collapse
Affiliation(s)
- Joshua Misa
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA
| | - Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.
| |
Collapse
|
37
|
Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.
Collapse
|
38
|
Yang Z, Blenner M. Genome editing systems across yeast species. Curr Opin Biotechnol 2020; 66:255-266. [PMID: 33011454 PMCID: PMC7744358 DOI: 10.1016/j.copbio.2020.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 02/07/2023]
Abstract
Yeasts are used to produce a myriad of value-added compounds. Engineering yeasts into cost-efficient cell factories is greatly facilitated by the availability of genome editing tools. While traditional engineering techniques such as homologous recombination-based gene knockout and pathway integration continue to be widely used, novel genome editing systems including multiplexed approaches, bacteriophage integrases, CRISPR-Cas systems, and base editors are emerging as more powerful toolsets to accomplish rapid genome scale engineering and phenotype screening. In this review, we summarized the techniques which have been successfully implemented in model yeast Saccharomyces cerevisiae as well as non-conventional yeast species. The mechanisms and applications of various genome engineering systems are discussed and general guidelines to expand genome editing systems from S. cerevisiae to other yeast species are also highlighted.
Collapse
Affiliation(s)
- Zhiliang Yang
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, United States
| | - Mark Blenner
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, United States.
| |
Collapse
|
39
|
Lacerda MP, Oh EJ, Eckert C. The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels. Life (Basel) 2020; 10:E299. [PMID: 33233378 PMCID: PMC7700301 DOI: 10.3390/life10110299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.
Collapse
Affiliation(s)
- Maria Priscila Lacerda
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
| | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Carrie Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
- National Renewable Energy Laboratory (NREL), Biosciences Center, Golden, CO 80401, USA
| |
Collapse
|
40
|
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
|
41
|
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
|
42
|
Reyes-Sánchez FJ, Páez-Lerma JB, Rojas-Contreras JA, López-Miranda J, Soto-Cruz NÓ, Reinhart-Kirchmayr M. Study of the Enzymatic Capacity of Kluyveromyces marxianus for the Synthesis of Esters. J Mol Microbiol Biotechnol 2020; 29:1-9. [PMID: 32325454 DOI: 10.1159/000507551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
Recently, biotechnological opportunities have been found in non-Saccharomyces yeasts because they possess metabolic characteristics that lead to the production of compounds of interest. It has been observed that Kluyveromyces marxianus has a great potential in the production of esters, which are aromatic compounds of industrial importance. The genetic bases that govern the synthesis of esters include a large group of enzymes, among which the most important are alcohol acetyl transferases (AATases) and esterases (AEATases), and it is known that some are present in K. marxianus, because it has genetic characteristics like S. cerevisiae. It also has a physiology suitable for biotechnological use since it is the eukaryotic microorganism with the fastest growth rate and has a wide range of thermotolerance with respect to other yeasts. In this work, the enzymatic background of K. marxianus involved in the synthesis of esters is analyzed, based on the sequences reported in the NCBI database.
Collapse
Affiliation(s)
| | | | | | - Javier López-Miranda
- Chemistry and Biochemistry, TECNM/Instituto Tecnológico de Durango, Durango, Mexico
| | | | - Manuel Reinhart-Kirchmayr
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Guadalajara, Mexico
| |
Collapse
|
43
|
Ramesh A, Ong T, Garcia JA, Adams J, Wheeldon I. Guide RNA Engineering Enables Dual Purpose CRISPR-Cpf1 for Simultaneous Gene Editing and Gene Regulation in Yarrowia lipolytica. ACS Synth Biol 2020; 9:967-971. [PMID: 32208677 DOI: 10.1021/acssynbio.9b00498] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yarrowia lipolytica has fast become a biotechnologically significant yeast for its ability to accumulate lipids to high levels. While there exists a suite of synthetic biology tools for genetic engineering in this yeast, there is a need for multipurposed tools for rapid strain generation. Here, we describe a dual purpose CRISPR-Cpf1 system that is capable of simultaneous gene disruption and gene regulation. Truncating guide RNA spacer length to 16 nt inhibited nuclease activity but not binding to the target loci, enabling gene activation and repression with Cpf1-fused transcriptional regulators. Gene repression was demonstrated using a Cpf1-Mxi1 fusion achieving a 7-fold reduction in mRNA, while CRISPR-activation with Cpf1-VPR increased hrGFP expression by 10-fold. High efficiency disruptions were achieved with gRNAs 23-25 bp in length, and efficiency and repression levels were maintained with multiplexed expression of truncated and full-length gRNAs. The developed CRISPR-Cpf1 system should prove useful in metabolic engineering, genome wide screening, and functional genomics studies.
Collapse
Affiliation(s)
- Adithya Ramesh
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Thomas Ong
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Jaime A Garcia
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, Texas 78228, United States
| | - Jessica Adams
- Molecular and Cell Biology Department, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, California 92521, United States
| |
Collapse
|
44
|
Bohnenkamp AC, Kruis AJ, Mars AE, Wijffels RH, van der Oost J, Kengen SWM, Weusthuis RA. Multilevel optimisation of anaerobic ethyl acetate production in engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:65. [PMID: 32280373 PMCID: PMC7137189 DOI: 10.1186/s13068-020-01703-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/25/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ethyl acetate is a widely used industrial solvent that is currently produced by chemical conversions from fossil resources. Several yeast species are able to convert sugars to ethyl acetate under aerobic conditions. However, performing ethyl acetate synthesis anaerobically may result in enhanced production efficiency, making the process economically more viable. RESULTS We engineered an E. coli strain that is able to convert glucose to ethyl acetate as the main fermentation product under anaerobic conditions. The key enzyme of the pathway is an alcohol acetyltransferase (AAT) that catalyses the formation of ethyl acetate from acetyl-CoA and ethanol. To select a suitable AAT, the ethyl acetate-forming capacities of Atf1 from Saccharomyces cerevisiae, Eat1 from Kluyveromyces marxianus and Eat1 from Wickerhamomyces anomalus were compared. Heterologous expression of the AAT-encoding genes under control of the inducible LacI/T7 and XylS/Pm promoters allowed optimisation of their expression levels. CONCLUSION Engineering efforts on protein and fermentation level resulted in an E. coli strain that anaerobically produced 42.8 mM (3.8 g/L) ethyl acetate from glucose with an unprecedented efficiency, i.e. 0.48 C-mol/C-mol or 72% of the maximum pathway yield.
Collapse
Affiliation(s)
- Anna C. Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Aleksander J. Kruis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Astrid E. Mars
- Biobased Products, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
45
|
Zhang S, Guo F, Yan W, Dai Z, Dong W, Zhou J, Zhang W, Xin F, Jiang M. Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology. Front Bioeng Biotechnol 2020; 7:459. [PMID: 32047743 PMCID: PMC6997136 DOI: 10.3389/fbioe.2019.00459] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Industrial biology plays a crucial role in the fields of medicine, health, food, energy, and so on. However, the lack of efficient genetic engineering tools has restricted the rapid development of industrial biology. Recently, the emergence of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system brought a breakthrough in genome editing technologies due to its high orthogonality, versatility, and efficiency. In this review, we summarized the barriers of CRISPR/Cas9 and corresponding solutions for efficient genetic engineering in industrial microorganisms. In addition, the advances of industrial biology employing the CRISPR/Cas9 system were compared in terms of its application in bacteria, yeast, and filamentous fungi. Furthermore, the cooperation between CRISPR/Cas9 and synthetic biology was discussed to help build complex and programmable gene circuits, which can be used in industrial biotechnology.
Collapse
Affiliation(s)
- Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wei Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| |
Collapse
|
46
|
Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis. Nat Chem Biol 2020; 16:113-121. [DOI: 10.1038/s41589-019-0452-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
|
47
|
Kruis AJ, Bohnenkamp AC, Nap B, Nielsen J, Mars AE, Wijffels RH, van der Oost J, Kengen SWM, Weusthuis RA. From Eat to trEat: engineering the mitochondrial Eat1 enzyme for enhanced ethyl acetate production in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:76. [PMID: 32328168 PMCID: PMC7168974 DOI: 10.1186/s13068-020-01711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/04/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for a wide range of compounds. Ethyl acetate is an industrial solvent that is used in several applications, mainly as a biodegradable organic solvent with low toxicity. While ethyl acetate is produced by several natural yeast species, the main mechanism of production has remained elusive until the discovery of Eat1 in Wickerhamomyces anomalus. Unlike other yeast alcohol acetyl transferases (AATs), Eat1 is located in the yeast mitochondria, suggesting that the coding sequence contains a mitochondrial pre-sequence. For expression in prokaryotic hosts such as E. coli, expression of heterologous proteins with eukaryotic signal sequences may not be optimal. RESULTS Unprocessed and synthetically truncated eat1 variants of Kluyveromyces marxianus and Wickerhamomyces anomalus have been compared in vitro regarding enzyme activity and stability. While the specific activity remained unaffected, half-life improved for several truncated variants. The same variants showed better performance regarding ethyl acetate production when expressed in E. coli. CONCLUSION By analysing and predicting the N-terminal pre-sequences of different Eat1 proteins and systematically trimming them, the stability of the enzymes in vitro could be improved, leading to an overall improvement of in vivo ethyl acetate production in E. coli. Truncated variants of eat1 could therefore benefit future engineering approaches towards efficient ethyl acetate production.
Collapse
Affiliation(s)
- Aleksander J. Kruis
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna C. Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bram Nap
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jochem Nielsen
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Astrid E. Mars
- Biobased Products, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
48
|
Kruis AJ, Bohnenkamp AC, Patinios C, van Nuland YM, Levisson M, Mars AE, van den Berg C, Kengen SW, Weusthuis RA. Microbial production of short and medium chain esters: Enzymes, pathways, and applications. Biotechnol Adv 2019; 37:107407. [DOI: 10.1016/j.biotechadv.2019.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/24/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022]
|
49
|
Schwartz C, Cheng JF, Evans R, Schwartz CA, Wagner JM, Anglin S, Beitz A, Pan W, Lonardi S, Blenner M, Alper HS, Yoshikuni Y, Wheeldon I. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metab Eng 2019; 55:102-110. [PMID: 31216436 DOI: 10.1016/j.ymben.2019.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.
Collapse
Affiliation(s)
- Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Robert Evans
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Christopher A Schwartz
- Department of Civil and Mechanical Engineering, United States Military Academy, West Point, NY, 10996, USA
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Scott Anglin
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Adam Beitz
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Weihua Pan
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
| |
Collapse
|
50
|
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
|