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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.
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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
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2
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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.
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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.
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3
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Wu L, Lyu Y, Wu P, Luo T, Zeng J, Shi T, Zhou J, Yu Y, Lu H. Meiosis-Based Laboratory Evolution of the Thermal Tolerance in Kluyveromyces marxianus. Front Bioeng Biotechnol 2022; 9:799756. [PMID: 35087802 PMCID: PMC8786734 DOI: 10.3389/fbioe.2021.799756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
Kluyveromyces marxianus is the fastest-growing eukaryote and a promising host for producing bioethanol and heterologous proteins. To perform a laboratory evolution of thermal tolerance in K. marxianus, diploid, triploid and tetraploid strains were constructed, respectively. Considering the genetic diversity caused by genetic recombination in meiosis, we established an iterative cycle of “diploid/polyploid - meiosis - selection of spores at high temperature” to screen thermotolerant strains. Results showed that the evolution of thermal tolerance in diploid strain was more efficient than that in triploid and tetraploid strains. The thermal tolerance of the progenies of diploid and triploid strains after a two-round screen was significantly improved than that after a one-round screen, while the thermal tolerance of the progenies after the one-round screen was better than that of the initial strain. After a two-round screen, the maximum tolerable temperature of Dip2-8, a progeny of diploid strain, was 3°C higher than that of the original strain. Whole-genome sequencing revealed nonsense mutations of PSR1 and PDE2 in the thermotolerant progenies. Deletion of either PSR1 or PDE2 in the original strain improved thermotolerance and two deletions displayed additive effects, suggesting PSR1 and PDE2 negatively regulated the thermotolerance of K. marxianus in parallel pathways. Therefore, the iterative cycle of “meiosis - spore screening” developed in this study provides an efficient way to perform the laboratory evolution of heat resistance in yeast.
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Affiliation(s)
- Li Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yilin Lyu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Tongyu Luo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Junyuan Zeng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
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4
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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5
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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.
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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
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6
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Zhang W, Kang J, Wang C, Ping W, Ge J. Effects of pyruvate decarboxylase ( pdc1, pdc5) gene knockout on the production of metabolites in two haploid Saccharomyces cerevisiae strains. Prep Biochem Biotechnol 2021; 52:62-69. [PMID: 33881948 DOI: 10.1080/10826068.2021.1910958] [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] [Indexed: 01/31/2023]
Abstract
Saccharomyces cerevisiae has good reproductive ability in both haploid and diploid forms, a pyruvate decarboxylase plays an important role in S. cerevisiae cell metabolism. In this study, pdc1 and pdc5 double knockout strains of S. cerevisiae H14-02 (MATa type) and S. cerevisiae H5-02 (MATα type) were obtained by the Cre/loxP technique. The effects of the deletion of pdc1 and pdc5 on the metabolites of the two haploid S. cerevisiae strains were consistent. In S. cerevisiae H14-02, the ethanol conversion decreased by 30.19%, the conversion of glycerol increased by 40.005%, the concentration of acetic acid decreased by 43.54%, the concentration of acetoin increased by 12.79 times, and the activity of pyruvate decarboxylase decreased by 40.91% compared to those in the original H14 strain. The original S. cerevisiae haploid strain H14 produced a small amount of acetoin but produced very little 2,3-butanediol. However, S. cerevisiae H14-02 produced 1.420 ± 0.063 g/L 2,3-BD. This study not only provides strain selection for obtaining haploid strains with a high yield of 2,3-BD but also lays a foundation for haploid S. cerevisiae to be used as a new tool for genetic research and breeding programs.
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Affiliation(s)
- Wen Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Changli Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wenxiang Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, China
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7
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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8
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Wu L, Wang M, Zha G, Zhou J, Yu Y, Lu H. A protocol of rapid laboratory evolution by genome shuffling in Kluyveromyces marxianus. MethodsX 2020; 7:101138. [PMID: 33294397 PMCID: PMC7701259 DOI: 10.1016/j.mex.2020.101138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/07/2020] [Indexed: 11/16/2022] Open
Abstract
Genome shuffling is a process to combine advantage traits by the recombination of the entire genome and it has been successfully applied in the laboratory evolution of various industrial microorganisms. However, genome shuffling has not been described in Kluyveromyces marxianus (KM), a promising yeast host for the expression of heterologous proteins. In this protocol, genome shuffling in KM is performed by sexual reproduction and is combined with high-throughput screening to obtain high-yielding strains. Notably, the screening of diploid clones risen from one mating mixture is carried out to improve the effectiveness of evolution. Mating-sporulation-mating cycles are repeated to obtain KM strain with ideal traits. •The method combines genome shuffling with high-throughput to achieve strains displaying high yielding of heterologous proteins.•This method can be applied to the genome shuffling of other species when only a few starting strains are available for sexual reproduction.
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Affiliation(s)
- Li Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Mengzhu Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Genhan Zha
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China.,Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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9
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Yang Z, Blenner M. Genome editing systems across yeast species. Curr Opin Biotechnol 2020; 66:255-266. [PMID: 33011454 DOI: 10.1016/j.copbio.2020.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [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.
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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.
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10
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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.
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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
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11
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Martins LC, Monteiro CC, Semedo PM, Sá-Correia I. Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges. Appl Microbiol Biotechnol 2020; 104:6527-6547. [PMID: 32474799 PMCID: PMC7347521 DOI: 10.1007/s00253-020-10697-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/19/2020] [Indexed: 01/29/2023]
Abstract
Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular d-galacturonic acid and l-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed.Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. |
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Affiliation(s)
- Luís C Martins
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina C Monteiro
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Paula M Semedo
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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12
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Lee MH, Hsu TL, Lin JJ, Lin YJ, Kao YY, Chang JJ, Li WH. Constructing a human complex type N-linked glycosylation pathway in Kluyveromyces marxianus. PLoS One 2020; 15:e0233492. [PMID: 32469948 PMCID: PMC7259728 DOI: 10.1371/journal.pone.0233492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 11/18/2022] Open
Abstract
Glycosylation can affect various protein properties such as stability, biological activity, and immunogenicity. To produce human therapeutic proteins, a host that can produce glycoproteins with correct glycan structures is required. Microbial expression systems offer economical, rapid and serum-free production and are more amenable to genetic manipulation. In this study, we developed a protocol for CRISPR/Cas9 multiple gene knockouts and knockins in Kluyveromyces marxianus, a probiotic yeast with a rapid growth rate. As hyper-mannosylation is a common problem in yeast, we first knocked out the α-1,3-mannosyltransferase (ALG3) and α-1,6-mannosyltransferase (OCH1) genes to reduce mannosylation. We also knocked out the subunit of the telomeric Ku domain (KU70) to increase the homologous recombination efficiency of K. marxianus. In addition, we knocked in the MdsI (α-1,2-mannosidase) gene to reduce mannosylation and the GnTI (β-1,2-N-acetylglucosaminyltransferase I) and GnTII genes to produce human N-glycan structures. We finally obtained two strains that can produce low amounts of the core N-glycan Man3GlcNAc2 and the human complex N-glycan Man3GlcNAc4, where Man is mannose and GlcNAc is N-acetylglucosamine. This study lays a cornerstone of glycosylation engineering in K. marxianus toward producing human glycoproteins.
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Affiliation(s)
- Ming-Hsuan Lee
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Nankang, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jinn-Jy Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yi-Ying Kao
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Anandharaj M, Lin YJ, Rani RP, Nadendla EK, Ho MC, Huang CC, Cheng JF, Chang JJ, Li WH. Constructing a yeast to express the largest cellulosome complex on the cell surface. Proc Natl Acad Sci U S A 2020; 117:2385-2394. [PMID: 31953261 PMCID: PMC7007581 DOI: 10.1073/pnas.1916529117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cellulosomes, which are multienzyme complexes from anaerobic bacteria, are considered nature's finest cellulolytic machinery. Thus, constructing a cellulosome in an industrial yeast has long been a goal pursued by scientists. However, it remains highly challenging due to the size and complexity of cellulosomal genes. Here, we overcame the difficulties by synthesizing the Clostridium thermocellum scaffoldin gene (CipA) and the anchoring protein gene (OlpB) using advanced synthetic biology techniques. The engineered Kluyveromyces marxianus, a probiotic yeast, secreted a mixture of dockerin-fused fungal cellulases, including an endoglucanase (TrEgIII), exoglucanase (CBHII), β-glucosidase (NpaBGS), and cellulase boosters (TaLPMO and MtCDH). The confocal microscopy results confirmed the cell-surface display of OlpB-ScGPI and fluorescence-activated cell sorting analysis results revealed that almost 81% of yeast cells displayed OlpB-ScGPI. We have also demonstrated the cellulosome complex formation using purified and crude cellulosomal proteins. Native polyacrylamide gel electrophoresis and mass spectrometric analysis further confirmed the cellulosome complex formation. Our engineered cellulosome can accommodate up to 63 enzymes, whereas the largest engineered cellulosome reported thus far could accommodate only 12 enzymes and was expressed by a plasmid instead of chromosomal integration. Interestingly, CipA 2B9C (with two cellulose binding modules, CBM) released significantly higher quantities of reducing sugars compared with other CipA variants, thus confirming the importance of cohesin numbers and CBM domain on cellulosome complex. The engineered yeast host efficiently degraded cellulosic substrates and released 3.09 g/L and 8.61 g/L of ethanol from avicel and phosphoric acid-swollen cellulose, respectively, which is higher than any previously constructed yeast cellulosome.
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Affiliation(s)
- Marimuthu Anandharaj
- Biodiversity Research Center, Academia Sinica, 11529 Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, 11529 Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, 40227 Taichung, Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, 11529 Taipei, Taiwan
| | | | | | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, 40227 Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 40227 Taichung, Taiwan
| | - Jan-Fang Cheng
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, 402 Taichung, Taiwan;
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, 11529 Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, 11529 Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, 40227 Taichung, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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14
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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Rajkumar AS, Varela JA, Juergens H, Daran JMG, Morrissey JP. Biological Parts for Kluyveromyces marxianus Synthetic Biology. Front Bioeng Biotechnol 2019; 7:97. [PMID: 31134195 PMCID: PMC6515861 DOI: 10.3389/fbioe.2019.00097] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
Kluyveromyces marxianus is a non-conventional yeast whose physiology and metabolism lends itself to diverse biotechnological applications. While the wild-type yeast is already in use for producing fragrances and fermented products, the lack of standardised tools for its genetic and metabolic engineering prevent it from being used as a next-generation cell factory for bio-based chemicals. In this paper, we bring together and characterise a set of native K. marxianus parts for the expression of multiple genes for metabolic engineering and synthetic biology. All parts are cloned and stored according to the MoClo/Yeast Tool Kit standard for quick sharing and rapid construction. Using available genomic and transcriptomic data, we have selected promoters and terminators to fine-tune constitutive and inducible gene expression. The collection includes a number of known centromeres and autonomously replication sequences (ARS). We also provide a number of chromosomal integration sites selected for efficiency or visible phenotypes for rapid screening. Finally, we provide a single-plasmid CRISPR/Cas9 platform for genome engineering and facilitated gene targeting, and rationally create auxotrophic strains to expand the common range of selection markers available to K. marxianus. The curated and characterised tools we have provided in this kit will serve as a base to efficiently build next-generation cell factories from this alternative yeast. Plasmids containing all parts are available at Addgene for public distribution.
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Affiliation(s)
- Arun S Rajkumar
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hannes Juergens
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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16
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Abstract
The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications. Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications. Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits—thermotolerance, lipid production, and facile transformation with exogenous DNA—into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.
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