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Xie L, Yu W, Gao J, Wang H, Zhou YJ. Ogataea polymorpha as a next-generation chassis for industrial biotechnology. Trends Biotechnol 2024:S0167-7799(24)00086-6. [PMID: 38622041 DOI: 10.1016/j.tibtech.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.
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Affiliation(s)
- Linfeng Xie
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Haoyu Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China.
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Branduardi P, Barroso L, Dato L, Louis EJ, Porro D. Molecular Tools for Leveraging the Potential of the Acid-Tolerant Yeast Zygosaccharomyces bailii as Cell Factory. Methods Mol Biol 2022; 2513:179-204. [PMID: 35781206 DOI: 10.1007/978-1-0716-2399-2_11] [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] [Indexed: 06/15/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycete budding yeast, is widely known for its peculiar tolerance to different stresses, among which are organic acids. Moreover, the recent reclassification of the species, including diverse hybrids, is further expanding both fundamental and applied interests. It is therefore reasonable that despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here we describe in detail the methods for determining chromosome number, size, and aneuploidy, transformation, classical target gene disruption or gene integration, and designing of episomal expression plasmids helpful for engineering the yeast Z. bailii .
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
| | - Liliane Barroso
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Laura Dato
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Edward J Louis
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Wu L, Wen Y, Chen W, Yan T, Tian X, Zhou S. Simultaneously deleting ADH2 and THI3 genes of Saccharomyces cerevisiae for reducing the yield of acetaldehyde and fusel alcohols. FEMS Microbiol Lett 2021; 368:6354780. [PMID: 34410369 DOI: 10.1093/femsle/fnab094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
The reduced yields of acetaldehyde and fusel alcohols through fermentation by Saccharomyces cerevisiae is of significance for the improvement of the flavor and health of alcoholic beverages. In this study, the ADH2 (encode alcohol dehydrogenase) and THI3 (encode decarboxylase) genes of the industrial diploid strain S. cerevisiae XF1 were deleted. Results showed that single-gene-deletion mutants by separate gene deletion of ADH2 or THI3 led to a reduced production of the acetaldehyde or fusel alcohols, respectively. In the meantime, the double-gene-deletion mutant S. cerevisiae XF1-AT was constructed by deleting the ADH2 and THI3 simultaneously. An equivalent level of the ethanol production by the S. cerevisiae XF1-AT could be achieved but with the yields of acetaldehyde, isoamyl alcohol and iso-butanol reduced by 42.09%, 15.65% and 20.16%, respectively. In addition, there was no interaction between the ADH2 deletion and THI3 deletion in reducing the production of acetaldehyde and fusel alcohols. The engineered S. cerevisiae XF1-AT provided a new strategy to alcoholic beverages brewing industry for reducing the production of acetaldehyde as well as the fusel alcohols.
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Affiliation(s)
- Liang Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yongdi Wen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Wenying Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Tongshuai Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaofei Tian
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.,Guangxi Key Laboratory of Clean Pulp and Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning, Guangxi 530004, China
| | - Shishui Zhou
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
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Manfrão-Netto JHC, Gomes AMV, Parachin NS. Advances in Using Hansenula polymorpha as Chassis for Recombinant Protein Production. Front Bioeng Biotechnol 2019; 7:94. [PMID: 31119131 PMCID: PMC6504786 DOI: 10.3389/fbioe.2019.00094] [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: 01/18/2019] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
The methylotrophic yeast Hansenula polymorpha, known as a non-conventional yeast, is used for the last 30 years for the production of recombinant proteins, including enzymes, vaccines, and biopharmaceuticals. Although a large number of reviews have been published elucidating the applications of this yeast as a cell factory, the latest was released about 10 years ago. Therefore, this review aimed at summarizing available information on the use of H. polymorpha as a host for recombinant protein production in the last decade. Examples of chemicals and virus-like particles produced using this yeast also are discussed. Firstly, the aspects that feature this yeast as a host for recombinant protein production are highlighted including the techniques available for its genetic manipulation as well as strategies for cultivation in bioreactors. Special attention is given to the novel genomic editing tools, mainly CRISPR/Cas9 that was recently established in this yeast. Finally, recent examples of using H. polymorpha as an expression platform are presented and discussed. The production of human Parathyroid Hormone (PTH) and Staphylokinase (SAK) in H. polymorpha are described as case studies for process establishment in this yeast. Altogether, this review is a guideline for this yeast utilization as an expression platform bringing a thorough analysis of the genetic aspects and fermentation protocols used up to date, thus encouraging the production of novel biomolecules in H. polymorpha.
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Affiliation(s)
| | - Antônio Milton Vieira Gomes
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
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Wang L, Deng A, Zhang Y, Liu S, Liang Y, Bai H, Cui D, Qiu Q, Shang X, Yang Z, He X, Wen T. Efficient CRISPR-Cas9 mediated multiplex genome editing in yeasts. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:277. [PMID: 30337956 PMCID: PMC6180501 DOI: 10.1186/s13068-018-1271-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/26/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND The thermotolerant methylotrophic yeast Ogataea polymorpha has been regarded as an important organism for basic research and biotechnological applications. It is generally recognized as an efficient and safe cell factory in fermentative productions of chemicals, biofuels and other bio-products. However, it is difficult to genetically engineer for the deficiency of an efficient and versatile genome editing technology. RESULTS In this study, we developed a CRISPR-Cas9-assisted multiplex genome editing (CMGE) approach including multiplex genes knock-outs, multi-locus (ML) and multi-copy (MC) integration methods in yeasts. Based on CMGE, various genome modifications, including gene deletion, integration, and precise point mutation, were performed in O. polymorpha. Using the CMGE-ML integration method, three genes TAL from Herpetosiphon aurantiacus, 4CL from Arabidopsis thaliana and STS from Vitis vinifera of resveratrol biosynthetic pathway were simultaneously integrated at three different loci, firstly achieving the biosynthesis of resveratrol in O. polymorpha. Using the CMGE-MC method, ∼ 10 copies of the fusion expression cassette P ScTEF1 -TAL-P ScTPI1 -4CL-P ScTEF2 -STS were integrated into the genome. Resveratrol production was increased ~ 20 fold compared to the one copy integrant and reached 97.23 ± 4.84 mg/L. Moreover, the biosynthesis of human serum albumin and cadaverine were achieved in O. polymorpha using CMGE-MC to integrate genes HSA and cadA, respectively. In addition, the CMGE-MC method was successfully developed in Saccharomyces cerevisiae. CONCLUSIONS An efficient and versatile multiplex genome editing method was developed in yeasts. The method would provide an efficient toolkit for genetic engineering and synthetic biology researches of O. polymorpha and other yeast species.
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Affiliation(s)
- Laiyou Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yong Liang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Di Cui
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qidi Qiu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhao Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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Duan X, Gao J, Zhou YJ. Advances in engineering methylotrophic yeast for biosynthesis of valuable chemicals from methanol. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Efficient genome editing by CRISPR/Cas9 with a tRNA-sgRNA fusion in the methylotrophic yeast Ogataea polymorpha. J Biosci Bioeng 2017; 124:487-492. [PMID: 28666889 DOI: 10.1016/j.jbiosc.2017.06.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/02/2017] [Accepted: 06/02/2017] [Indexed: 11/30/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha (syn. Hansenula polymorpha) is an attractive industrial non-conventional yeast showing high thermo-tolerance (up to 50°C) and xylose assimilation. However, genetic manipulation of O. polymorpha is often laborious and time-consuming because it has lower homologous recombination efficiency relative to Saccharomyces cerevisiae. To overcome this disadvantage, we applied the CRISPR/Cas9 system as a powerful genome editing tool in O. polymorpha. In this system, both single guide RNA (sgRNA) and endonuclease Cas9 were expressed by a single autonomously-replicable plasmid and the sgRNA portion could be easily changed by using PCR and In-Fusion cloning techniques. Because the mutation efficiency of the CRISPR/Cas9 system was relatively low when the sgRNA was expressed under the control of the OpSNR6 promoter, the tRNACUG gene was used for sgRNA expression. The editing efficiency of this system ranged from 17% to 71% of transformants in several target genes tested (ADE12, PHO1, PHO11, and PHO84). These findings indicate that genetic manipulation of O. polymorpha will be more convenient and accelerated by using this CRISPR/Cas9 system.
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Branduardi P, Dato L, Porro D. Molecular tools and protocols for engineering the acid-tolerant yeast Zygosaccharomyces bailii as a potential cell factory. Methods Mol Biol 2014; 1152:63-85. [PMID: 24744027 DOI: 10.1007/978-1-4939-0563-8_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycetales budding yeast, is widely known for its peculiar tolerance to various stresses, among which are organic acids. Despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here, we describe in detail protocols for transformation, for target gene disruption or gene integration, and for designing episomal expression plasmids helpful for developing and further studying the yeast Z. bailii.
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2 - 20126, Milan, Italy,
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9
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Nitrogen-dependent calcineurin activation in the yeast Hansenula polymorpha. Fungal Genet Biol 2013; 53:34-41. [PMID: 23403359 DOI: 10.1016/j.fgb.2013.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 11/23/2022]
Abstract
Non-preferred nitrogen sources, unlike preferred ones, raised total cell Ca(2+) content and expression of ENA1, a very well-known calcineurin-regulated gene. This indicates calcineurin activation is regulated by nitrogen source. Nitrogen catabolite repression (NCR) and nitrate induction mechanisms, both regulating nitrate assimilation in Hansenula polymorpha, are controlled by calcineurin. Concerning NCR, lack of calcineurin (cnb1 mutant) decreased nitrate-assimilation gene expression, levels of the transcription factor Gat1 and growth in several nitrogen sources. We found that the role of calcineurin in NCR was mediated by Crz1 via Gat1. Regarding nitrate induction, calcineurin also affects the levels of transcription factors Gat2 and Yna2 involved in this process. We conclude that Ca(2+) and calcineurin play a central role in nitrogen signalling and assimilation. Thus, the nitrogen source modulates Ca(2+) content and calcineurin activation. Calcineurin in turn regulates nitrogen assimilation genes.
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Cabrera E, Álvarez MC, Martín Y, Siverio JM, Ramos J. K+ uptake systems in the yeast Hansenula polymorpha. Transcriptional and post-translational mechanisms involved in high-affinity K+ transporter regulation. Fungal Genet Biol 2012; 49:755-63. [DOI: 10.1016/j.fgb.2012.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/14/2012] [Accepted: 06/19/2012] [Indexed: 11/28/2022]
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Dato L, Branduardi P, Passolunghi S, Cattaneo D, Riboldi L, Frascotti G, Valli M, Porro D. Advances in molecular tools for the use of Zygosaccharomyces bailii as host for biotechnological productions and construction of the first auxotrophic mutant. FEMS Yeast Res 2010; 10:894-908. [DOI: 10.1111/j.1567-1364.2010.00668.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Agaphonov M, Romanova N, Choi ES, Ter-Avanesyan M. A novel kanamycin/G418 resistance marker for direct selection of transformants in Escherichia coli and different yeast species. Yeast 2010; 27:189-95. [PMID: 20014045 DOI: 10.1002/yea.1741] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We have developed a set of cloning vectors possessing a modified Tn903 kanamycin resistance gene that enables the selection of both kanamycin-resistant transformants in Escherichia coli and G418-resistant transformants in the yeasts Saccharomyces cerevisiae, Hansenula polymorpha and Pichia pastoris. Expression of this gene in yeast is controlled by the H. polymorpha glyceraldehyde-3-phosphate dehydrogenase promoter, while expression in E. coli is governed by an upstream E. coli lacZ promoter. Applicability of the vectors for gene disruption in H. polymorpha and S. cerevisiae was demonstrated by inactivation of the HpMAL1 and URA3 genes, respectively. One of the vectors possesses a H. polymorpha ARS allowing plasmid maintenance in an episomal state. The small size of the vectors (2-2.5 kb) makes them convenient for routine DNA cloning. In addition, we report a novel approach for construction of gene disruption cassettes.
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Affiliation(s)
- Michael Agaphonov
- Institute of Experimental Cardiology, Cardiology Research Centre, 121552 Moscow, Russia.
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13
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Qian W, Song H, Liu Y, Zhang C, Niu Z, Wang H, Qiu B. Improved gene disruption method and Cre-loxP mutant system for multiple gene disruptions in Hansenula polymorpha. J Microbiol Methods 2009; 79:253-9. [PMID: 19765620 DOI: 10.1016/j.mimet.2009.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 08/17/2009] [Accepted: 09/02/2009] [Indexed: 11/27/2022]
Abstract
In H. polymorpha, there is still a lack of a highly efficient gene disruption method. To help address this issue, we presented a simple and efficient method for both single and multiple gene disruptions in H. polymorpha. The knockout system combined a variation of sticky-end polymerase chain reaction method (SEP), split marker deletion method, co-transformation of single-stranded DNA and mutant Cre-loxP system. Using a slightly modified LiAc/SS-DNA/PEG procedure, the co-transformation double-stranded split marker constructs together with single-stranded split marker constructs resulted in at least 70% homologous recombination events when the homologous genomic DNA fragment had a size of approximately 500bp. Our evidence suggested that single-stranded DNA may be responsible for the increased gene disruption efficiency. We demonstrated the effectiveness of the method for gene disruption by constructing both single and double gene disruptions at the ALG3 and URA5 loci in the same genetic background. The method described here presents an improved strategy for gene disruption and a potential application for investigation of biological processes in other yeast strains.
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Affiliation(s)
- Weidong Qian
- Center for Agricultural Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, People's Republic of China
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Xiong AS, Peng RH, Zhuang J, Gao F, Li Y, Cheng ZM, Yao QH. Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 2008; 32:522-40. [DOI: 10.1111/j.1574-6976.2008.00109.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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15
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Meng Y, Patel G, Heist M, Betts MF, Tucker SL, Galadima N, Donofrio NM, Brown D, Mitchell TK, Li L, Xu JR, Orbach M, Thon M, Dean RA, Farman ML. A systematic analysis of T-DNA insertion events in Magnaporthe oryzae. Fungal Genet Biol 2007; 44:1050-64. [PMID: 17544743 DOI: 10.1016/j.fgb.2007.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 03/19/2007] [Accepted: 04/04/2007] [Indexed: 01/24/2023]
Abstract
We describe here the analysis of random T-DNA insertions that were generated as part of a large-scale insertional mutagenesis project for Magnaporthe oryzae. Chromosomal regions flanking T-DNA insertions were rescued by inverse PCR, sequenced and used to search the M. oryzae genome assembly. Among the 175 insertions for which at least one flank was rescued, 137 had integrated in single-copy regions of the genome, 17 were in repeated sequences, one had no match to the genome, and the remainder were unassigned due to illegitimate T-DNA integration events. These included in order of abundance: head-to-tail tandem insertions, right border excision failures, left border excision failures and insertion of one T-DNA into another. The left borders of the T-DNA were frequently truncated and inserted in sequences with micro-homology to the left terminus. By contrast the right borders were less prone to degradation and appeared to have been integrated in a homology-independent manner. Gross genome rearrangements rarely occurred when the T-DNAs integrated in single-copy regions, although most insertions did cause small deletions at the target site. Significant insertion bias was detected, with promoters receiving two times more T-DNA hits than expected, and open reading frames receiving three times fewer. In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed.
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Affiliation(s)
- Yan Meng
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
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16
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Hwang GW, Furuchi T, Naganuma A. Ubiquitin-conjugating enzyme Cdc34 mediates cadmium resistance in budding yeast through ubiquitination of the transcription factor Met4. Biochem Biophys Res Commun 2007; 363:873-8. [PMID: 17904100 DOI: 10.1016/j.bbrc.2007.09.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 09/16/2007] [Indexed: 11/25/2022]
Abstract
Overexpression of the ubiquitin-conjugating enzyme Cdc34 conferred strong cadmium resistance on budding yeast. Proteasome activity, which is involved in the degradation of ubiquitinated proteins, was not essential for the acquisition of resistance to cadmium. The overexpression of Cdc34 accelerated the ubiquitination of the transcription factor Met4 and reduced expression of MET25 gene, which is a target of Met4. A MET25-disrupted strain of yeast was more resistant to cadmium than was the wild-type strain, but overexpression of Cdc34 in the MET25-disrupted cells did not affect sensitivity to cadmium. Met25 is an enzyme that catalyzes the synthesis of homocysteine from sulfide (S(2-)) and O-acetylhomocysteine and we detected the increased production of S(2-) upon overexpression of Cdc34. Our results suggest that overexpression of Cdc34 inactivates Met4 and interferes with expression of the MET25, with subsequent production of CdS, which has low toxicity, and, thus, a decrease in the cadmium toxicity.
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Affiliation(s)
- Gi-Wook Hwang
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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17
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Wang Q, He P, Lu D, Shen A, Jiang N. Metabolic engineering of Torulopsis glabrata for improved pyruvate production. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2005.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Furuchi T, Takahashi T, Tanaka S, Nitta K, Naganuma A. Functions of yeast helicase Ssl2p that are essential for viability are also involved in protection from the toxicity of adriamycin. Nucleic Acids Res 2004; 32:2578-85. [PMID: 15141027 PMCID: PMC419470 DOI: 10.1093/nar/gkh582] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Revised: 04/13/2004] [Accepted: 04/13/2004] [Indexed: 11/15/2022] Open
Abstract
We have found that, in the yeast Saccharomyces cerevisiae, overexpression of the DNA helicase Ssl2p confers resistance to adriamycin. Ssl2p is involved, as a subunit of the basic transcription factor TFIIH, in the initiation of transcription and in nucleotide-excision repair (NER), and this helicase is essential for the survival of yeast cells. An examination of the relationship between the known functions of Ssl2p and adriamycin resistance indicated that overexpression of Ssl2p caused little or no increase in the rate of RNA synthesis and in NER. The absence of any involvement of NER in adriamycin resistance was supported by the finding that yeast cells that overexpressed the mutant form of Ssl2p that lacked the carboxy-terminal region, which is necessary for NER, remained resistant to adriamycin. When we examined the effects of overexpression in yeast of other mutant forms of Ssl2p with various deletions, we found that, of the 843 amino acids of Ssl2p, the entire amino acid sequence from position 81 to position 750 was necessary for adriamycin resistance. This region is identical to the region of Ssl2p that is necessary for the survival of yeast cells. Although this region contains helicase motifs, the overexpression of other yeast helicases, such as Rad3 and Sgs1, had little or no effect on adriamycin resistance, indicating that a mere increase in the intracellular level of helicases does not result in adriamycin resistance. Our results suggest that the functions of Ssl2p that are essential for yeast survival are also required for protection against adriamycin toxicity.
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Affiliation(s)
- Takemitsu Furuchi
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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Takahashi T, Furuchi T, Naganuma A. A novel role for Bsd2 in the resistance of yeast to adriamycin. J Cell Physiol 2004; 202:100-4. [PMID: 15389553 DOI: 10.1002/jcp.20082] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In a search for undiscovered mechanisms of resistance to adriamycin, we screened a genomic library derived from Saccharomyces cerevisiae for genes related to adriamycin resistance. To our surprise, we found that overexpression of BSD2 rendered yeast cells resistant to adriamycin. Downregulation of the metal transporters Smf1 and Smf2 is the only activity of Bsd2 reported to date, and Bsd2 deficiency increases intracellular levels of Smf1 and Smf2. SMF2-disrupted cells exhibited significantly greater resistance to adriamycin, whereas the resistance of SMF1-disrupted cells was only slightly improved. The sensitivity of the SMF1- and SMF2-disrupted yeast cell line overexpressing BSD2 was almost the same as that of the BSD2-overexpressing parental yeast cell. Thus the overexpression of BSD2 and the disruption of SMF1 and SMF2 might be involved in the same mechanism that confers resistance to adriamycin. Although both SMF1- and SMF2-disrupted cells were very sensitive to EGTA, overexpression of BSD2 had little or no effect on sensitivity to EGTA. However, a partial decrease in the intracellular level of FLAG-Smf2 was observed by overexpression of BSD2. Thus, the resistance to adriamycin acquired by overexpression of BSD2 might be partially explained by down-regulation of Smf2, but in addition to Smf2, other as of yet unidentified targets of Bsd2 must also be responsible for the resistance.
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Affiliation(s)
- Tsutomu Takahashi
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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Navarro FJ, Perdomo G, Tejera P, Medina B, Machín F, Guillén RM, Lancha A, Siverio JM. The role of nitrate reductase in the regulation of the nitrate assimilation pathway in the yeast Hansenula polymorpha. FEMS Yeast Res 2003; 4:149-55. [PMID: 14613879 DOI: 10.1016/s1567-1356(03)00163-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of nitrate reductase (NR) in the regulation of the nitrate assimilation pathway was evaluated in the yeast Hansenula polymorpha. Posttranscriptional regulation of NR in response to reduced nitrogen sources and the effect of a heterologous NR on the transcriptional regulation of nitrate-assimilatory gene expression was examined. The strain bearing YNR1 (nitrate reductase gene) under the control of the methanol-induced MOX (methanol oxidase) promoter showed that NR is active in the presence of reduced nitrogen sources. In cells incubated with glutamine plus nitrate, rapamycin abolished nitrogen catabolite repression, NR activity being very similar to that in cells induced by nitrate alone. This reveals the involvement of the Tor-signalling pathway in the transcriptional regulation of H. polymorpha nitrate assimilation genes. To assess the role of NR in nitrate-assimilatory gene expression, different strains lacking YNR1, or both YNR1 and YNT1 (high-affinity nitrate transporter) genes, or expressing the tobacco NR under the YNR1 promoter, were used. Tobacco NR abolished the constitutive nitrate-assimilatory gene induction shown by an NR gene disruptant strain. Moreover, in strains lacking the high-affinity nitrate transporter and NR this deregulation disappeared. These facts discard the role of NR protein in the transcriptional induction of the nitrate-assimilatory genes and point out the involvement of the high-affinity nitrate transporter as a part of the nitrate-signalling pathway.
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Affiliation(s)
- Francisco J Navarro
- Departamento de Bioquímica y Biología Molecular, Grupo del Metabolismo del Nitrógeno, Universidad de La Laguna, E-38206 La Laguna, Canarias, Tenerife, Spain
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21
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Affiliation(s)
- Mark Johnston
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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22
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Affiliation(s)
- Marie E Petracek
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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Lau PCY, Sung CK, Lee JH, Morrison DA, Cvitkovitch DG. PCR ligation mutagenesis in transformable streptococci: application and efficiency. J Microbiol Methods 2002; 49:193-205. [PMID: 11830305 DOI: 10.1016/s0167-7012(01)00369-4] [Citation(s) in RCA: 268] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PCR ligation mutagenesis is a novel technique that can easily be adapted for many gene modification purposes. Successful application of this versatile technique involves sequence identification of the target gene region, creation of a mutagenic construct consisting of two gene-flanking proximal sequences specifically ligated to a selectable marker, and incorporation of this construct into the genome via genetic transformation and homologous recombination. In this study, we demonstrate the use of PCR, followed by restriction digestion and re-ligation to generate transforming constructs for the rapid deletion of open reading frames in transformable streptococci. Moreover, we characterized the dependence of transformation efficiency for mutant generation on the length of the homologous regions harbored by the mutagenic construct. Our results indicated that PCR ligation mutagenesis could be reliably employed for the systematic generation of gene deletion mutants in both highly transformable Streptococcus mutans and S. pneumoniae. Evaluation of the method showed a strong influence of the length of homologous flanking region on integration efficiency.
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Affiliation(s)
- Peter C Y Lau
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, Ontorio, Canada
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24
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Gellissen G, Veenhuis M. The methylotrophic yeast Hansenula polymorpha: its use in fundamental research and as a cell factory. Yeast 2001; 18:i-iii. [PMID: 11180462 DOI: 10.1002/1097-0061(200102)18:3<::aid-yea695>3.0.co;2-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- G Gellissen
- Rhein Biotech GmbH, Eichsfelder Strasse 11, 40595 Düsseldorf, Germany.
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Current awareness on yeast. Yeast 2000. [DOI: 10.1002/1097-0061(20000115)16:1<89::aid-yea563>3.0.co;2-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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