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Zhang X, Zhang X, Lin L, Wang K, Ji XJ. Advances in the biosynthesis of tetraacetyl phytosphingosine, a key substrate of ceramides. Synth Syst Biotechnol 2024; 10:1-9. [PMID: 39193251 PMCID: PMC11347041 DOI: 10.1016/j.synbio.2024.07.005] [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: 07/07/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
Ceramides, formed by the dehydration of long-chain fatty acids with phytosphingosine and its derivatives, are widely used in skincare, cosmetics, and pharmaceuticals. Due to the exceedingly low concentration of phytosphingosine in plant seeds, relying on the extraction method is highly challenging. Currently, the primary method for obtaining phytosphingosine is the deacetylation of tetraacetyl phytosphingosine (TAPS) derived from fermentation. Wickerhamomyces ciferrii, an unconventional yeast from the pods of Dipteryx odorata, is the only known microorganism capable of naturally secreting TAPS, which is of great industrial value. In recent years, research and applications focused on modifying W. ciferrii for TAPS overproduction have increased rapidly. This review first describes the discovery history, applications, microbial synthesis pathway of TAPS. Research progress in using haploid breeding, mutagenesis breeding, and metabolic engineering to improve TAPS production is then summarized. In addition, the future prospects of TAPS production using the W. ciferrii platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future researches are also emphasized.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Xiaochen Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Kaifeng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
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Angstenberger M, de Signori F, Vecchi V, Dall’Osto L, Bassi R. Cell Synchronization Enhances Nuclear Transformation and Genome Editing via Cas9 Enabling Homologous Recombination in Chlamydomonas reinhardtii. ACS Synth Biol 2020; 9:2840-2850. [PMID: 32916053 PMCID: PMC8011982 DOI: 10.1021/acssynbio.0c00390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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In Chlamydomonas reinhardtii, the model organism
for eukaryotic green algae and plants, the processes of nuclear transformation
and genome editing in particular are still marked by a low level of
efficiency, and so intensive work is required in order to create and
identify mutants for the investigation of basic physiological processes,
as well as the implementation of biotechnological applications. In
this work, we show that cell synchronization during the stages of
the cell cycle, obtained from long-term cultivation under specific
growth conditions, greatly enhances the efficiency of transformation
and allows the identification of DNA repair mechanisms that occur
preferentially at different stages of the cell cycle. We demonstrate
that the transformation of synchronized cells at different times was
differentially associated with nonhomologous end joining (NHEJ) and/or
homologous recombination (HR), and makes it possible to knock-in specific
foreign DNA at the genomic nuclear location desired by exploiting
HR. This optimization greatly reduces the overall complexity of the
genome editing procedure and creates new opportunities for altering
genes and their products.
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Affiliation(s)
- Max Angstenberger
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Francesco de Signori
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Valeria Vecchi
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Luca Dall’Osto
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Roberto Bassi
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
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Contribution of the mitogen-activated protein kinase Hog1 to the halotolerance of the marine yeast Debaryomyces hansenii. Curr Genet 2020; 66:1135-1153. [PMID: 32719935 DOI: 10.1007/s00294-020-01099-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Halotolerant species are adapted to dealing continually with hyperosmotic environments, having evolved strategies that are uncommon in other organisms. The HOG pathway is the master system that regulates the cellular adaptation under these conditions; nevertheless, apart from the importance of Debaryomyces hansenii as an organism representative of the halotolerant class, its HOG1 pathway has been poorly studied, due to the difficulty of applying conventional recombinant DNA technology. Here we describe for the first time the phenotypic characterisation of a null HOG1 mutant of D. hansenii. Dhhog1Δ strain was found moderately resistant to 1 M NaCl and sensitive to higher concentrations. Under hyperosmotic shock, DhHog1 fully upregulated transcription of DhSTL1 and partially upregulated that of DhGPD1. High osmotic stress lead to long-term inner glycerol accumulation that was partially dependent on DhHog1. These observations indicated that the HOG pathway is required for survival under high external osmolarity but dispensable under low and mid-osmotic conditions. It was also found that DhHog1 can regulate response to alkali stress during hyperosmotic conditions and that it plays a role in oxidative and endoplasmic reticulum stress. Taken together, these results provide new insight into the contribution of this MAPK in halotolerance of this yeast.
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Britton CS, Sorrells TR, Johnson AD. Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit. Science 2020; 367:96-100. [PMID: 31896718 DOI: 10.1126/science.aax5217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Abstract
Changes in both the coding sequence of transcriptional regulators and in the cis-regulatory sequences recognized by these regulators have been implicated in the evolution of transcriptional circuits. However, little is known about how they evolved in concert. We describe an evolutionary pathway in fungi where a new transcriptional circuit (a-specific gene repression by the homeodomain protein Matα2) evolved by coding changes in this ancient regulator, followed millions of years later by cis-regulatory sequence changes in the genes of its future regulon. By analyzing a group of species that has acquired the coding changes but not the cis-regulatory sites, we show that the coding changes became necessary for the regulator's deeply conserved function, thereby poising the regulator to jump-start formation of the new circuit.
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Affiliation(s)
- Candace S Britton
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Trevor R Sorrells
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.
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Cen YK, Lin JG, Wang YL, Wang JY, Liu ZQ, Zheng YG. The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit. Front Bioeng Biotechnol 2020; 8:232. [PMID: 32292777 PMCID: PMC7118215 DOI: 10.3389/fbioe.2020.00232] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
In recent years, there has been a noticeable increase in research interests on the Fusarium species, which includes prevalent plant pathogens and human pathogens, common microbial food contaminants and industrial microbes. Taken the advantage of gibberellin synthesis, Fusarium fujikuroi succeed in being a prevalent plant pathogen. At the meanwhile, F. fujikuroi was utilized for industrial production of gibberellins, a group of extensively applied phytohormone. F. fujikuroi has been known for its outstanding performance in gibberellin production for almost 100 years. Research activities relate to this species has lasted for a very long period. The slow development in biological investigation of F. fujikuroi is largely due to the lack of efficient research technologies and molecular tools. During the past decade, technologies to analyze the molecular basis of host-pathogen interactions and metabolic regulations have been developed rapidly, especially on the aspects of genetic manipulation. At the meanwhile, the industrial fermentation technologies kept sustained development. In this article, we reviewed the currently available research tools/methods for F. fujikuroi research, focusing on the topics about genetic engineering and gibberellin production.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Guang Lin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - You-Liang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jun-You Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Ito Y, Watanabe T, Aikawa S, Nishi T, Nishiyama T, Nakamura Y, Hasunuma T, Okubo Y, Ishii J, Kondo A. Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii. FEMS Yeast Res 2019; 18:5054040. [PMID: 30010892 DOI: 10.1093/femsyr/foy074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/12/2018] [Indexed: 01/24/2023] Open
Abstract
The non-conventional yeast Komagataella phaffii, formerly Pichia pastoris, is a popular host for recombinant protein production. The relatively lower gene targeting efficiency observed in this species occurs due to high levels of non-homologous recombination activity. In the current study, we explored the function of the K. phaffii homolog of DNA ligase IV (Dnl4p) by creating a DNL4-disrupted strain. To assess the roles of non-homologous end joining (NHEJ)-related proteins in this species, strains deleted for either or both genes encoding Dnl4p or the telomeric Ku complex subunit (Ku70p) were generated. These deletions were constructed by either of two distinct marker-recycling methods (yielding either a seamless gene deletion or a Cre-loxP-mediated gene deletion). The resulting dnl4- and/or ku70-deleted K. phaffii strains were used to evaluate gene targeting efficiency in gene knock-out and gene knock-in experiments. The Dnl4p-defective strain showed improved gene targeting efficiency for homologous recombination compared to the wild-type and Ku70p-deffective strains. The dnl4 ku70 double knock-out strain exhibited a further improvement in gene targeting efficiency. Thus, the K. phaffii dnl4 and dnl4 ku70 deletion strains are expected to serve as useful platforms for functional analysis and strain development in this species.
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Affiliation(s)
- Yoichiro Ito
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Toru Watanabe
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Shimpei Aikawa
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Teruyuki Nishi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Tozo Nishiyama
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Yasuyuki Nakamura
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuji Okubo
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Zhang YT, Jiang JY, Shi TQ, Sun XM, Zhao QY, Huang H, Ren LJ. Application of the CRISPR/Cas system for genome editing in microalgae. Appl Microbiol Biotechnol 2019; 103:3239-3248. [PMID: 30877356 DOI: 10.1007/s00253-019-09726-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022]
Abstract
Microalgae are arguably the most abundant single-celled eukaryotes and are widely distributed in oceans and freshwater lakes. Moreover, microalgae are widely used in biotechnology to produce bioenergy and high-value products such as polyunsaturated fatty acids (PUFAs), bioactive peptides, proteins, antioxidants and so on. In general, genetic editing techniques were adapted to increase the production of microalgal metabolites. The main genome editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas nuclease system. Due to its high genome editing efficiency, the CRISPR/Cas system is emerging as the most important genome editing method. In this review, we summarized the available literature on the application of CRISPR/Cas in microalgal genetic engineering, including transformation methods, strategies for the expression of Cas9 and sgRNA, the CRISPR/Cas9-mediated gene knock-in/knock-out strategies, and CRISPR interference expression modification strategies.
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Affiliation(s)
- Yu-Ting Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Jia-Yi Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Tian-Qiong Shi
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Xiao-Man Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Quan-Yu Zhao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - He Huang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing, 210009, People's Republic of China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Lu-Jing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.
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Angstenberger M, Krischer J, Aktaş O, Büchel C. Knock-Down of a ligIV Homologue Enables DNA Integration via Homologous Recombination in the Marine Diatom Phaeodactylum tricornutum. ACS Synth Biol 2019; 8:57-69. [PMID: 30525458 DOI: 10.1021/acssynbio.8b00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic engineering of Phaeodactylum tricornutum as a model organism for diatoms is the basis of molecular and biochemical research, and can also be used in biotechnological approaches. So far, integration of foreign DNA into the genome happens randomly by nonhomologous end joining (NHEJ), if the classical method of particle bombardment is used, with the danger of negative physiological side effects. Here we show that a putative gene for a DNA ligase IV homologue ( ligIV) in P. tricornutum codes for a functional LigIV. The knock-down of ligIV in P. tricornutum via antisense RNA drastically enhances homologous recombination (HR) by interfering with the NHEJ pathway at its central DNA ligation step done by LigIV. This enables a specific integration of DNA at desired locations, greatly enhanced transformation rates and provides a new way of specifically altering the genome of P. tricornutum.
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Affiliation(s)
- Max Angstenberger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Julia Krischer
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Ozan Aktaş
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
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Lee H, Han C, Lee HW, Park G, Jeon W, Ahn J, Lee H. Development of a promising microbial platform for the production of dicarboxylic acids from biorenewable resources. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:310. [PMID: 30455739 PMCID: PMC6225622 DOI: 10.1186/s13068-018-1310-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND As a sustainable industrial process, the production of dicarboxylic acids (DCAs), used as precursors of polyamides, polyesters, perfumes, plasticizers, lubricants, and adhesives, from vegetable oil has continuously garnered interest. Although the yeast Candida tropicalis has been used as a host for DCA production, additional strains are continually investigated to meet productivity thresholds and industrial needs. In this regard, the yeast Wickerhamiella sorbophila, a potential candidate strain, has been screened. However, the lack of genetic and physiological information for this uncommon strain is an obstacle that merits further research. To overcome this limitation, we attempted to develop a method to facilitate genetic recombination in this strain and produce high amounts of DCAs from methyl laurate using engineered W. sorbophila. RESULTS In the current study, we first developed efficient genetic engineering tools for the industrial application of W. sorbophila. To increase homologous recombination (HR) efficiency during transformation, the cell cycle of the yeast was synchronized to the S/G2 phase using hydroxyurea. The HR efficiency at POX1 and POX2 loci increased from 56.3% and 41.7%, respectively, to 97.9% in both cases. The original HR efficiency at URA3 and ADE2 loci was nearly 0% during the early stationary and logarithmic phases of growth, and increased to 4.8% and 25.6%, respectively. We used the developed tools to construct W. sorbophila UHP4, in which β-oxidation was completely blocked. The strain produced 92.5 g/l of dodecanedioic acid (DDDA) from methyl laurate over 126 h in 5-l fed-batch fermentation, with a productivity of 0.83 g/l/h. CONCLUSIONS Wickerhamiella sorbophila UHP4 produced more DDDA methyl laurate than C. tropicalis. Hence, we demonstrated that W. sorbophila is a powerful microbial platform for vegetable oil-based DCA production. In addition, by using the developed genetic engineering tools, this emerging yeast could be used for the production of a variety of fatty acid derivatives, such as fatty alcohols, fatty aldehydes, and ω-hydroxy fatty acids.
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Affiliation(s)
- Heeseok Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
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Qin X, Li R, Luo X, Lin Y, Feng JX. Deletion of ligD significantly improves gene targeting frequency in the lignocellulolytic filamentous fungus Penicillium oxalicum. Fungal Biol 2017; 121:615-623. [PMID: 28606356 DOI: 10.1016/j.funbio.2017.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/29/2017] [Accepted: 04/17/2017] [Indexed: 01/05/2023]
Abstract
To improve the gene targeting frequency (GTF) in the lignocellulolytic filamentous fungus Penicillium oxalicum HP7-1, the non-homologous end-joining (NHEJ) gene ligD was deleted. The obtained PoligD deletion mutant ΔPoligD showed no apparent defect in cellulase production, growth rate, and sensitivity towards osmotic stress and mutagen ethyl methanesulphonate (EMS), while increased sensitivity to high concentrations of methyl methanesulfonate (MMS). Deletion of PoligD gene resulted in significantly increased GTFs at three different loci in P. oxalicum, which are even higher than those in Poku70 deletion mutant. The GTF in ΔPoligD at PoargB (reached 97 %) and PoagaA (reached 90 %) loci increased 5.1- and 1.2-fold compared with that in wild-type strain (WT), while at the Podpp4 locus GTF was up to 27 % in ΔPoligD but close to 0 % in WT, with 0.5 kb homologous flanking regions. Furthermore, the argB and agaA nutritional selection in P. oxalicum was demonstrated and the PoargB and PoagaA genes could be used as selective markers in this fungus. Thus, the PoligD deletion mutant can be an important tool for the functional analysis of genes in P. oxalicum.
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Affiliation(s)
- Xiulin Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Ruijie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Xiang Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Yanmei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
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Oguro Y, Yamazaki H, Ara S, Shida Y, Ogasawara W, Takagi M, Takaku H. Efficient gene targeting in non-homologous end-joining-deficient Lipomyces starkeyi strains. Curr Genet 2017; 63:751-763. [DOI: 10.1007/s00294-017-0679-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/21/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
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12
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Abstract
Ceramide 3 is used mainly as a moisturizer in various cosmetic products. Although several safety studies on formulations containing pseudo-ceramide or ceramide have been conducted at the preclinical and clinical levels for regulatory approval, no studies have evaluated the systemic toxicity of ceramide 3. To address this issue, we conducted a risk assessment and comprehensive toxicological review of ceramide and pseudo-ceramide. We assumed that ceramide 3 is present in various personal and cosmetic products at concentrations of 0.5-10%. Based on previously reported exposure data, the margin of safety (MOS) was calculated for product type, use pattern, and ceramide 3 concentration. Lipsticks with up to 10% ceramide 3 (MOS = 4111) are considered safe, while shampoos containing 0.5% ceramide 3 (MOS = 148) are known to be safe. Reported MOS values for body lotion applied to the hands (1% ceramide 3) and back (5% ceramide 3) were 103 and 168, respectively. We anticipate that face cream would be safe up to a ceramide 3 concentration of 3% (MOS = 149). Collectively, the MOS approach indicated no safety concerns for cosmetic products containing less than 1% ceramide 3.
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Affiliation(s)
- Seul Min Choi
- Division of Toxicology, College of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Changan-ku, Suwon, Gyeonggi-do, 440-746, Republic of Korea
| | - Byung-Mu Lee
- Division of Toxicology, College of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Changan-ku, Suwon, Gyeonggi-do, 440-746, Republic of Korea.
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13
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Deletion of the DNA Ligase IV Gene in Candida glabrata Significantly Increases Gene-Targeting Efficiency. EUKARYOTIC CELL 2015; 14:783-91. [PMID: 26048009 DOI: 10.1128/ec.00281-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/28/2015] [Indexed: 11/20/2022]
Abstract
Candida glabrata is reported as the second most prevalent human opportunistic fungal pathogen in the United States. Over the last decades, its incidence increased, whereas that of Candida albicans decreased slightly. One of the main reasons for this shift is attributed to the inherent tolerance of C. glabrata toward the commonly used azole antifungal drugs. Despite a close phylogenetic distance to Saccharomyces cerevisiae, homologous recombination works with poor efficiency in C. glabrata compared to baker's yeast, in fact limiting targeted genetic alterations of the pathogen's genome. It has been shown that nonhomologous DNA end joining is dominant over specific gene targeting in C. glabrata. To improve the homologous recombination efficiency, we have generated a strain in which the LIG4 gene has been deleted, which resulted in a significant increase in correct gene targeting. The very specific function of Lig4 in mediating nonhomologous end joining is the reason for the absence of clear side effects, some of which affect the ku80 mutant, another mutant with reduced nonhomologous end joining. We also generated a LIG4 reintegration cassette. Our results show that the lig4 mutant strain may be a valuable tool for the C. glabrata research community.
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Suzuki K, Inoue H. Recombination and Gene Targeting in Neurospora. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Liu Q, Liu H, Yang Y, Zhang X, Bai Y, Qiao M, Xu H. Scarless gene deletion using mazF as a new counter-selection marker and an improved deletion cassette assembly method in Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2014; 60:89-93. [DOI: 10.2323/jgam.60.89] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Abstract
Wickerhamomyces ciferrii is a microorganism characterized by the production and secretion of large amounts of acetylated sphingoid bases, in particular tetraacetyl phytosphingosine. Here, we present the 15.90-Mbp draft genome sequence of W. ciferrii NRRL Y-1031 F-60-10 generated by pyrosequencing and de novo assembly. The draft genome sequence comprising 364 contigs in 150 scaffolds was annotated and covered 6,702 protein-coding sequences. This information will contribute to the metabolic engineering of this yeast to improve the yield and spectrum of acetylated sphingoid bases in biotechnological production.
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17
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Biotechnological production of sphingoid bases and their applications. Appl Microbiol Biotechnol 2013; 97:4301-8. [DOI: 10.1007/s00253-013-4878-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 12/14/2022]
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18
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Efficient gene targeting in a Candida guilliermondii non-homologous end-joining pathway-deficient strain. Biotechnol Lett 2013; 35:1035-43. [DOI: 10.1007/s10529-013-1169-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/18/2013] [Indexed: 01/21/2023]
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19
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Production of tetraacetyl phytosphingosine (TAPS) in Wickerhamomyces ciferrii is catalyzed by acetyltransferases Sli1p and Atf2p. Appl Microbiol Biotechnol 2013; 97:8537-46. [PMID: 23318835 DOI: 10.1007/s00253-012-4670-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/03/2012] [Accepted: 12/19/2012] [Indexed: 10/27/2022]
Abstract
Wickerhamomyces ciferrii secretes tetraacetyl phytosphingosine (TAPS), and in this study, the catalyzing acetyltransferases were identified using mass spectrometry-based proteomics. The proteome of wild-type strain NRRL Y-1031 served as control and was compared to the tetraacetyl phytosphingosine defective mating type NRRL Y-1031-27. Acetylation of phytosphingosine in W. ciferrii is catalyzed by acetyltransferases Sli1p and Atf2p, encoded by genes similar to Saccharomyces cerevisiae YGR212W and YGR177C, respectively. Ablation of SLI1 resulted in an almost complete loss of tri- and tetraacetyl phytosphingosines, whereas the loss ATF2 resulted in an 15-fold increase in triacetyl phytosphingosine. Most likely, it is the concerted action of these two acetyltransferases that yields tetraacetyl phytosphingosine, in which Sli1p catalyzes initial O- and N-acetylation, producing triacetyl phytosphingosine. Finally, Atf2p catalyzes final O-acetylation to yield tetraacetyl phytosphingosine. The current study demonstrates that mass spectrometry-based proteomics can be employed to identify key steps in ill-explored metabolite biosynthesis pathways of nonconventional microorganisms. Furthermore, the identification of phytosphingosine as substrate for alcohol acetyltransferase Atf2p broadens the known substrate range of this enzyme. This interesting property of Atf2p may be exploited to enhance the secretion of heterologous compounds.
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Solis-Escalante D, Kuijpers NGA, Bongaerts N, Bolat I, Bosman L, Pronk JT, Daran JM, Daran-Lapujade P. amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae. FEMS Yeast Res 2012; 13:126-39. [PMID: 23253382 PMCID: PMC3563226 DOI: 10.1111/1567-1364.12024] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/09/2012] [Accepted: 11/09/2012] [Indexed: 12/17/2022] Open
Abstract
Despite the large collection of selectable marker genes available for Saccharomyces cerevisiae, marker availability can still present a hurdle when dozens of genetic manipulations are required. Recyclable markers, counterselectable cassettes that can be removed from the targeted genome after use, are therefore valuable assets in ambitious metabolic engineering programs. In the present work, the new recyclable dominant marker cassette amdSYM, formed by the Ashbya gossypii TEF2 promoter and terminator and a codon-optimized acetamidase gene (Aspergillus nidulans amdS), is presented. The amdSYM cassette confers S. cerevisiae the ability to use acetamide as sole nitrogen source. Direct repeats flanking the amdS gene allow for its efficient recombinative excision. As previously demonstrated in filamentous fungi, loss of the amdS marker cassette from S. cerevisiae can be rapidly selected for by growth in the presence of fluoroacetamide. The amdSYM cassette can be used in different genetic backgrounds and represents the first counterselectable dominant marker gene cassette for use in S. cerevisiae. Furthermore, using astute cassette design, amdSYM excision can be performed without leaving a scar or heterologous sequences in the targeted genome. The present work therefore demonstrates that amdSYM is a useful addition to the genetic engineering toolbox for Saccharomyces laboratory, wild, and industrial strains.
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Börgel D, van den Berg M, Hüller T, Andrea H, Liebisch G, Boles E, Schorsch C, van der Pol R, Arink A, Boogers I, van der Hoeven R, Korevaar K, Farwick M, Köhler T, Schaffer S. Metabolic engineering of the non-conventional yeast Pichia ciferrii for production of rare sphingoid bases. Metab Eng 2012; 14:412-26. [PMID: 22449569 DOI: 10.1016/j.ymben.2012.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Revised: 02/19/2012] [Accepted: 03/09/2012] [Indexed: 12/13/2022]
Abstract
The study describes the identification of sphingolipid biosynthesis genes in the non-conventional yeast Pichia ciferrii, the development of tools for its genetic modification as well as their application for metabolic engineering of P. ciferrii with the goal to generate strains capable of producing the rare sphingoid bases sphinganine and sphingosine. Several canonical genes encoding ceramide synthase (encoded by PcLAG1 and PcLAF1), alkaline ceramidase (PcYXC1) and sphingolipid C-4-hydroxylase(PcSYR2), as well as structural genes for dihydroceramide Δ(4)-desaturase (PcDES1) and sphingolipid Δ(8)-desaturase (PcSLD1) were identified, indicating that P. ciferrii would be capable of synthesizing desaturated sphingoid bases, a property not ubiquitously found in yeasts. In order to convert the phytosphingosine-producing P. ciferrii wildtype into a strain capable of producing predominantly sphinganine, Syringomycin E-resistant mutants were isolated. A stable mutant almost exclusively producing high levels of acetylated sphinganine was obtained and used as the base strain for further metabolic engineering. A metabolic pathway required for the three-step conversion of sphinganine to sphingosine was implemented in the sphinganine producing P. ciferrii strain and subsequently enhanced by screening for the appropriate heterologous enzymes, improvement of gene expression and codon optimization. These combined efforts led to a strain capable of producing 240mgL(-1) triacetyl sphingosine in shake flask, with tri- and diacetyl sphinganine being the main by-products. Lab-scale fermentation of this strain resulted in production of up to 890mgkg(-1) triacetyl sphingosine. A third by-product was unequivocally identified as triacetyl sphingadienine. It could be shown that inactivation of the SLD1 gene in P. ciferrii efficiently suppresses triacetyl sphingadienine formation. Further improvement of the described P. ciferrii strains will enable a biotechnological route to produce sphinganine and sphingosine for cosmetic and pharmaceutical applications.
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Affiliation(s)
- Daniel Börgel
- Evonik Degussa, Project House ProFerm, Creavis Technologies & Innovation, Rodenbacher Chaussee 4, D-63457 Hanau, Germany.
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22
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High-level production of tetraacetyl phytosphingosine (TAPS) by combined genetic engineering of sphingoid base biosynthesis and L-serine availability in the non-conventional yeast Pichia ciferrii. Metab Eng 2012; 14:172-84. [DOI: 10.1016/j.ymben.2011.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/29/2011] [Accepted: 12/02/2011] [Indexed: 11/20/2022]
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23
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Takahashi T, Mizutani O, Shiraishi Y, Yamada O. Development of an efficient gene-targeting system in Aspergillus luchuensis by deletion of the non-homologous end joining system. J Biosci Bioeng 2011; 112:529-34. [DOI: 10.1016/j.jbiosc.2011.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 11/16/2022]
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24
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Alshahni MM, Yamada T, Takatori K, Sawada T, Makimura K. Insights into a nonhomologous integration pathway in the dermatophyte Trichophyton mentagrophytes: efficient targeted gene disruption by use of mutants lacking ligase IV. Microbiol Immunol 2011; 55:34-43. [PMID: 21175772 DOI: 10.1111/j.1348-0421.2010.00283.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted gene disruption experiments in Trichophyton mentagrophytes are impeded by the dominant of repair of DNA double strand breaks through a nonhomologous end joining pathway (NHEJ). Inactivation of human DNA ligase IV homologs, which is involved in the final step of the NHEJ pathway, has been shown to enhance homologous recombination (HR) frequency in filamentous fungi. To improve the frequency of HR in T. mentagrophytes, the lig4 homolog (TmLIG4) was disrupted. T. mentagrophytes lacking TmLIG4 showed no discernable phenotypic differences when compared to wild-type controls. Both mutant and parent strains had almost identical growth ability, sporulation rate and sensitivity to DNA damaging agents. When four different loci were disrupted in the TMLIG4-deficient mutant, HR frequencies reached as high as 93% depending on the locus, whereas they ranged from 0%-40% in the wild-type. These results suggest that studies in strains lacking TmLIG4 would help to improve our understanding of dermatophytosis by facilitating the genetic manipulation of dermatophytes.
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25
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de Boer P, Bastiaans J, Touw H, Kerkman R, Bronkhof J, van den Berg M, Offringa R. Highly efficient gene targeting in Penicillium chrysogenum using the bi-partite approach in deltalig4 or deltaku70 mutants. Fungal Genet Biol 2010; 47:839-46. [PMID: 20659576 DOI: 10.1016/j.fgb.2010.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/15/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
Abstract
Inactivating the non-homologous end-joining (NHEJ) pathway is a well established method to increase gene targeting (GT) efficiencies in filamentous fungi. In this study we have compared the effect of inactivating the NHEJ genes ku70 or lig4 on GT in the industrial penicillin producer Penicillium chrysogenum. Deletion of both genes resulted in strongly increased GT efficiencies at three different loci but not higher than 70%, implying that other, yet uncharacterized, recombination pathways are still active causing a part of the DNA to be integrated via non-homologous recombination. To further increase the GT efficiency we applied the bi-partite approach, in which the DNA fragment for integration was split in two non-functional overlapping parts that via homologous recombination invivo can form a functional selection marker. The combined NHEJ mutant and bi-partite approach further increased GT frequencies up to approximately 90%, which will enable the efficient high throughput engineering of the P. chrysogenum genome. We expect that this combined approach will function with similar high efficiencies in other filamentous fungi.
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Affiliation(s)
- Paulo de Boer
- Add2X Biosciences B.V., Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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26
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Li HM, Virtudazo EV, Toh-e A, Yamaguchi M, Kawamoto S, Shimizu K. Non-homologous end joining pathway of the human pathogen Cryptococcus neoformans influences homologous integration efficiency but not virulence. MYCOSCIENCE 2010. [DOI: 10.1007/s10267-010-0038-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Słabicki M, Theis M, Krastev DB, Samsonov S, Mundwiller E, Junqueira M, Paszkowski-Rogacz M, Teyra J, Heninger AK, Poser I, Prieur F, Truchetto J, Confavreux C, Marelli C, Durr A, Camdessanche JP, Brice A, Shevchenko A, Pisabarro MT, Stevanin G, Buchholz F. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. PLoS Biol 2010; 8:e1000408. [PMID: 20613862 PMCID: PMC2893954 DOI: 10.1371/journal.pbio.1000408] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 05/19/2010] [Indexed: 12/26/2022] Open
Abstract
We have identified a novel gene in a genome-wide, double-strand break DNA repair RNAi screen and show that is involved in the neurological disease hereditary spastic paraplegia. DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair. All cells in our bodies have to cope with numerous lesions to their DNA. Cells use a battery of genes to repair DNA and maintain genome integrity. Given the importance of an intact genome, it is not surprising that genes with roles in DNA repair are mutated in many human diseases. Here, we present the results of a genome-scale DNA repair screen in human cells and discover 61 genes that have a potential role in this process. We studied in detail a previously uncharacterized gene (KIAA0415/SPG48) and demonstrated its importance for efficient DNA double strand break repair. Further analyses revealed mutations in the SPG48 gene in some patients with hereditary spastic paraplegia (HSP). We showed that SPG48 physically interacts with other HSP proteins and that patient cells are sensitive to DNA damaging drugs. Our data suggest a link between HSP and DNA repair and we propose that HSP patients should be screened for KIAA0415/SPG48 mutations in the future.
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Affiliation(s)
- Mikołaj Słabicki
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mirko Theis
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Dragomir B. Krastev
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Emeline Mundwiller
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
| | - Magno Junqueira
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Joan Teyra
- Structural Bioinformatics, BIOTEC TU, Dresden, Germany
| | | | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Jérémy Truchetto
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
| | | | - Cécilia Marelli
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
- APHP, Pitié-Salpêtrière Hospital, Department of Genetics and Cytogenetics, Paris, France
| | - Alexandra Durr
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
- APHP, Pitié-Salpêtrière Hospital, Department of Genetics and Cytogenetics, Paris, France
| | | | - Alexis Brice
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
- APHP, Pitié-Salpêtrière Hospital, Department of Genetics and Cytogenetics, Paris, France
| | - Andrej Shevchenko
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Giovanni Stevanin
- INSERM, Unit 975 Paris, France
- Université Pierre et Marie Curie-Paris6, Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinière, Paris, France
- CNRS, Unité Mixte de Recherche 7225 Paris, France
- APHP, Pitié-Salpêtrière Hospital, Department of Genetics and Cytogenetics, Paris, France
| | - Frank Buchholz
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail:
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1714] [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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