1
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Chow EWL, Song Y, Wang H, Xu X, Gao J, Wang Y. Genome-wide profiling of piggyBac transposon insertion mutants reveals loss of the F 1F 0 ATPase complex causes fluconazole resistance in Candida glabrata. Mol Microbiol 2024; 121:781-797. [PMID: 38242855 DOI: 10.1111/mmi.15229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/21/2024]
Abstract
Invasive candidiasis caused by non-albicans species has been on the rise, with Candida glabrata emerging as the second most common etiological agent. Candida glabrata possesses an intrinsically lower susceptibility to azoles and an alarming propensity to rapidly develop high-level azole resistance during treatment. In this study, we have developed an efficient piggyBac (PB) transposon-mediated mutagenesis system in C. glabrata to conduct genome-wide genetic screens and applied it to profile genes that contribute to azole resistance. When challenged with the antifungal drug fluconazole, PB insertion into 270 genes led to significant resistance. A large subset of these genes has a role in the mitochondria, including almost all genes encoding the subunits of the F1F0 ATPase complex. We show that deleting ATP3 or ATP22 results in increased azole resistance but does not affect susceptibility to polyenes and echinocandins. The increased azole resistance is due to increased expression of PDR1 that encodes a transcription factor known to promote drug efflux pump expression. Deleting PDR1 in the atp3Δ or atp22Δ mutant resulted in hypersensitivity to fluconazole. Our results shed light on the mechanisms contributing to azole resistance in C. glabrata. This PB transposon-mediated mutagenesis system can significantly facilitate future genome-wide genetic screens.
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Affiliation(s)
- Eve W L Chow
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Yabing Song
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haitao Wang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Xiaoli Xu
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Wang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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2
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Bosch-Guiteras N, van Leeuwen J. Exploring conditional gene essentiality through systems genetics approaches in yeast. Curr Opin Genet Dev 2022; 76:101963. [PMID: 35939967 DOI: 10.1016/j.gde.2022.101963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/25/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022]
Abstract
An essential gene encodes for a cellular function that is required for viability. Although viability is a straightforward phenotype to analyze in yeast, defining a gene as essential is not always trivial. Gene essentiality has generally been studied in specific laboratory strains and under standard growth conditions, however, essentiality can vary across species, strains, and environments. Recent systematic studies of gene essentiality revealed that two sets of essential genes exist: core essential genes that are always required for viability and conditional essential genes that vary in essentiality in different genetic and environmental contexts. Here, we review recent advances made in the systematic analysis of gene essentiality in yeast and discuss the properties that distinguish core from context-dependent essential genes.
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Affiliation(s)
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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3
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Wagner JM, Palmer CM, Venkataraman MV, Lauffer LH, Wiggers JM, Williams EV, Yi X, Alper HS. Genome Engineering of Yarrowia lipolytica with the PiggyBac Transposon System. Methods Mol Biol 2021; 2307:1-24. [PMID: 33847979 DOI: 10.1007/978-1-0716-1414-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A mutant excision+/integration- piggyBac transposase can be used to seamlessly excise a chromosomally integrated, piggyBac-compatible selection marker cassette from the Yarrowia lipolytica genome. This piggyBac transposase-based genome engineering process allows for both positive selection of targeted homologous recombination events and scarless or footprint-free genome modifications after precise marker recovery. Residual non-native sequences left in the genome after marker excision can be minimized (0-4 nucleotides) or customized (user-defined except for a TTAA tetranucleotide). Both of these options reduce the risk of unintended homologous recombination events in strains with multiple genomic edits. A suite of dual positive/negative selection marker pairs flanked by piggyBac inverted terminal repeats (ITRs) have been constructed and are available for precise genome engineering in Y. lipolytica using this method. This protocol specifically describes the split marker homologous recombination-based disruption of Y. lipolytica ADE2 with a piggyBac ITR-flanked URA3 cassette, followed by piggyBac transposase-mediated excision of the URA3 marker to leave a 50 nucleotide synthetic barcode at the ADE2 locus. The resulting ade2 strain is auxotrophic for adenine, which enables the use of ADE2 as a selectable marker for further strain engineering.
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Affiliation(s)
- James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Maya V Venkataraman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lars H Lauffer
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Joshua M Wiggers
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Eden V Williams
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Xiunan Yi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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4
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Schrevens S, Sanglard D. Hijacking Transposable Elements for Saturation Mutagenesis in Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:633876. [PMID: 37744130 PMCID: PMC10512250 DOI: 10.3389/ffunb.2021.633876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 09/26/2023]
Abstract
Transposable elements are present in almost all known genomes, these endogenous transposons have recently been referred to as the mobilome. They are now increasingly used in research in order to make extensive mutant libraries in different organisms. Fungi are an essential part of our lives on earth, they influence the availability of our food and they live inside our own bodies both as commensals and pathogenic organisms. Only few fungal species have been studied extensively, mainly due to the lack of appropriate molecular genetic tools. The use of transposon insertion libraries can however help to rapidly advance our knowledge of (conditional) essential genes, compensatory mutations and drug target identification in fungi. Here we give an overview of some recent developments in the use of different transposons for saturation mutagenesis in different fungi.
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Affiliation(s)
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
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5
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Legon L, Rallis C. Genome-wide screens in yeast models towards understanding chronological lifespan regulation. Brief Funct Genomics 2021; 21:4-12. [PMID: 33728458 PMCID: PMC8834652 DOI: 10.1093/bfgp/elab011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular models such as yeasts are a driving force in biogerontology studies. Their simpler genome, short lifespans and vast genetic and genomics resources make them ideal to characterise pro-ageing and anti-ageing genes and signalling pathways. Over the last three decades, yeasts have contributed to the understanding of fundamental aspects of lifespan regulation including the roles of nutrient response, global protein translation rates and quality, DNA damage, oxidative stress, mitochondrial function and dysfunction as well as autophagy. In this short review, we focus on approaches used for competitive and non-competitive cell-based screens using the budding yeast Saccharomyces cerevisiae, and the fission yeast Schizosaccharomyces pombe, for deciphering the molecular mechanisms underlying chronological ageing. Automation accompanied with appropriate computational tools allowed manipulation of hundreds of thousands of colonies, generation, processing and analysis of genome-wide lifespan data. Together with barcoding and modern mutagenesis technologies, these approaches have allowed to take decisive steps towards a global, comprehensive view of cellular ageing.
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Affiliation(s)
- Luc Legon
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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6
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Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions. G3-GENES GENOMES GENETICS 2020; 10:3859-3870. [PMID: 32819971 PMCID: PMC7534453 DOI: 10.1534/g3.120.401595] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from C. albicans and C. auris. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and sequenced more than 500,000 different semi-random insertions throughout the genome. With machine learning, we identified 1278 protein-encoding genes (25% of total) that could not tolerate transposon insertions and are likely essential for C. glabrata fitness in vitro. Interestingly, genes involved in mRNA splicing were less likely to be essential in C. glabrata than their orthologs in S. cerevisiae, whereas the opposite is true for genes involved in kinetochore function and chromosome segregation. When a pool of insertion mutants was challenged with the first-line antifungal fluconazole, insertions in several known resistance genes (e.g., PDR1, CDR1, PDR16, PDR17, UPC2A, DAP1, STV1) and 15 additional genes (including KGD1, KGD2, YHR045W) became hypersensitive to fluconazole. Insertions in 200 other genes conferred significant resistance to fluconazole, two-thirds of which function in mitochondria and likely down-regulate Pdr1 expression or function. Knockout mutants of KGD2 and IDH2, which consume and generate alpha-ketoglutarate in mitochondria, exhibited increased and decreased resistance to fluconazole through a process that depended on Pdr1. These findings establish the utility of transposon insertion profiling in forward genetic investigations of this important pathogen of humans.
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7
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Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality. Curr Genet 2020; 66:1117-1134. [PMID: 32681306 PMCID: PMC7599172 DOI: 10.1007/s00294-020-01096-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023]
Abstract
In vivo transposon mutagenesis, coupled with deep sequencing, enables large-scale genome-wide mutant screens for genes essential in different growth conditions. We analyzed six large-scale studies performed on haploid strains of three yeast species (Saccharomyces cerevisiae, Schizosaccaromyces pombe, and Candida albicans), each mutagenized with two of three different heterologous transposons (AcDs, Hermes, and PiggyBac). Using a machine-learning approach, we evaluated the ability of the data to predict gene essentiality. Important data features included sufficient numbers and distribution of independent insertion events. All transposons showed some bias in insertion site preference because of jackpot events, and preferences for specific insertion sequences and short-distance vs long-distance insertions. For PiggyBac, a stringent target sequence limited the ability to predict essentiality in genes with few or no target sequences. The machine learning approach also robustly predicted gene function in less well-studied species by leveraging cross-species orthologs. Finally, comparisons of isogenic diploid versus haploid S. cerevisiae isolates identified several genes that are haplo-insufficient, while most essential genes, as expected, were recessive. We provide recommendations for the choice of transposons and the inference of gene essentiality in genome-wide studies of eukaryotic haploid microbes such as yeasts, including species that have been less amenable to classical genetic studies.
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8
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Yu ZQ, Sun LL, Jiang ZD, Liu XM, Zhao D, Wang HT, He WZ, Dong MQ, Du LL. Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy. Autophagy 2020; 16:2036-2051. [PMID: 31941401 PMCID: PMC7595586 DOI: 10.1080/15548627.2020.1713644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However, the extent, functional consequence, and evolutionary conservation of such interactions remain inadequately understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg38, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex I, interacts with Atg8 via an AIM, which is highly conserved in Atg38 proteins of fission yeast species, but not conserved in Atg38 proteins of other species. This interaction recruits Atg38 to Atg8 on the phagophore assembly site (PAS) and consequently enhances PAS accumulation of the PtdIns3K complex I and Atg proteins acting downstream of the PtdIns3K complex I, including Atg8. The disruption of the Atg38-Atg8 interaction leads to the reduction of autophagosome size and autophagic flux. Remarkably, the loss of this interaction can be compensated by an artificial Atg14-Atg8 interaction. Our findings demonstrate that the Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop between Atg8 and the PtdIns3K complex I to promote efficient autophagosome formation, underscore the prevalence and diversity of AIM-mediated connections within the autophagic machinery, and reveal unforeseen flexibility of such connections. Abbreviations: AIM: Atg8-family-interacting motif; AP-MS: affinity purification coupled with mass spectrometry; Atg: autophagy-related; FLIP: fluorescence loss in photobleaching; PAS: phagophore assembly site; PB: piggyBac; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate.
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Affiliation(s)
- Zhong-Qiu Yu
- National Institute of Biological Sciences , Beijing, China.,PTN Graduate Program, School of Life Sciences, Peking University , Beijing, China
| | - Ling-Ling Sun
- National Institute of Biological Sciences , Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences , Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences , Beijing, China
| | - Dan Zhao
- National Institute of Biological Sciences , Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences , Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences , Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
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9
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Potential for Isolation of Immortalized Hepatocyte Cell Lines by Liver-Directed In Vivo Gene Delivery of Transposons in Mice. Stem Cells Int 2019; 2019:5129526. [PMID: 31281376 PMCID: PMC6589260 DOI: 10.1155/2019/5129526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/06/2019] [Indexed: 12/14/2022] Open
Abstract
Isolation of hepatocytes and their culture in vitro represent important avenues to explore the function of such cells. However, these studies are often difficult to perform because of the inability of hepatocytes to proliferate in vitro. Immortalization of isolated hepatocytes is thus an important step toward continuous in vitro culture. For cellular immortalization, integration of relevant genes into the host chromosomes is a prerequisite. Transposons, which are mobile genetic elements, are known to facilitate integration of genes of interest (GOI) into chromosomes in vitro and in vivo. Here, we proposed that a combination of transposon- and liver-directed introduction of nucleic acids may confer acquisition of unlimited cellular proliferative potential on hepatocytes, enabling the possible isolation of immortalized hepatocyte cell lines, which has often failed using more traditional immortalization methods.
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10
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Basal transcription profiles of the rhamnose-inducible promoter P LRA3 and the development of efficient P LRA3-based systems for markerless gene deletion and a mutant library in Pichia pastoris. Curr Genet 2019; 65:785-798. [PMID: 30680438 DOI: 10.1007/s00294-019-00934-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/17/2018] [Accepted: 01/08/2019] [Indexed: 10/27/2022]
Abstract
An ideal inducible promoter presents inducibility with an inducer and no basal transcription without inducer. Previous studies have shown that PLRA3 in Pichia pastoris is a strong rhamnose-inducible promoter for driving the industrial production of recombinant proteins. However, another important profile of PLRA3, the basal transcription, was not investigated yet. In this study, the basal transcription of PLRA3 was assessed according to the profiles of two test strains grown in media lacking rhamnose: (1) the production of secretory β-galactosidase in P. pastoris GS115/PLRA3-LacB, in which lacB expression was regulated by PLRA3, and (2) growth in P. pastoris GS115/PLRA3-MazF, in which the expression of mazF, which encodes an intracellular toxic protein, was controlled by PLRA3. Analyses revealed low β-galactosidase production and non-obviously inhibited growth of the test strains, which suggests that there was a low basal transcription level of PLRA3 when rhamnose was absent. Thus, PLRA3 was an excellent candidate for genetic manipulation in P. pastoris due to its strict regulation, a strong and a low transcriptional activity with and without rhamnose, respectively. Subsequently, two systems were developed based on PLRA3 in P. pastoris: (1) an efficient markerless gene deletion system for single or multiple genes and (2) a high efficient piggyBac transposase-mediated mutation system for investigating the functions of unknown genes, as well as for the screening of expected mutants.
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11
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Candida albicans gains azole resistance by altering sphingolipid composition. Nat Commun 2018; 9:4495. [PMID: 30374049 PMCID: PMC6206040 DOI: 10.1038/s41467-018-06944-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
Fungal infections by drug-resistant Candida albicans pose a global public health threat. However, the pathogen’s diploid genome greatly hinders genome-wide investigations of resistance mechanisms. Here, we develop an efficient piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans to conduct genome-wide genetic screens. We find that null mutants in either gene FEN1 or FEN12 (encoding enzymes for the synthesis of very-long-chain fatty acids as precursors of sphingolipids) exhibit resistance to fluconazole, a first-line antifungal drug. Mass-spectrometry analyses demonstrate changes in cellular sphingolipid composition in both mutants, including substantially increased levels of several mannosylinositolphosphoceramides with shorter fatty-acid chains. Treatment with fluconazole induces similar changes in wild-type cells, suggesting a natural response mechanism. Furthermore, the resistance relies on a robust upregulation of sphingolipid biosynthesis genes. Our results shed light into the mechanisms underlying azole resistance, and the new transposon-mediated mutagenesis system should facilitate future genome-wide studies of C. albicans. The fungal pathogen Candida albicans is diploid, which hinders genome-wide studies. Here, Gao et al. present a piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans strains, and use it to identify genes and mechanisms underlying azole resistance.
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12
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Zhu J, Zhu Q, Gong R, Xu Q, Cai M, Jiang T, Zhou X, Zhou M, Zhang Y. PiggyBac transposon-mediated mutagenesis and application in yeast Komagataella phaffii. Biotechnol Lett 2018; 40:1365-1376. [PMID: 30003383 DOI: 10.1007/s10529-018-2592-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/10/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Around one-fourth of the Komagataella phaffii genes encode hypothetical proteins with unknown functions. However, lack of powerful tools for genetic screening in K. phaffii significantly limits the functional analysis of these unknown genes. Transposon mutagenesis has been utilized as an insertional mutagenesis tool in many other organisms and would be extremely valuable if it could be applied in K. phaffii. RESULTS In this study, we investigated in K. phaffii the transposition activity and efficiency of piggyBac (PB) transposon, a DNA transposon from the cabbage looper moth Trichoplusia ni through the integrated-plasmid system. We also designed a binary-plasmid system which could generate stable mutants. Finally we evaluated the quality of this mutagenesis system by a simple screening for functional genes involved in K. phaffii carbon catabolite repression. CONCLUSIONS Our results demonstrate that PB-mediated mutagenesis could be a feasible and useful tool for functional gene screening in K. phaffii.
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Affiliation(s)
- Jinxiang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ruiqing Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Tianyi Jiang
- Roche R&D Center (China) Ltd., Shanghai, People's Republic of China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China
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13
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Mutumwinka D, Zhao SB, Liu YS, Mensah EO, Gao XD, Fujita M. PiggyBac-based screening identified BEM4 as a suppressor to rescue growth defects in och1-disrupted yeast cells. Biosci Biotechnol Biochem 2018; 82:1497-1507. [PMID: 29882469 DOI: 10.1080/09168451.2018.1482193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycoengineered yeast cells, which express human-compatible glycan structures, are particularly attractive host cells to produce therapeutic glycoproteins. Disruption of OCH1 gene, which encodes an α-1,6-mannosyltransferase required for mannan-type N-glycan formation, is essential for the elimination of yeast-specific N-glycan structures. However, the gene disruption causes cell wall defects leading to growth defects. Here, we tried to identify factors to rescue the growth defects of och1Δ cells by in vivo mutagenesis using piggyBac (PB)-based transposon. We isolated a mutant strain, named 121, which could grow faster than parental och1Δ cells. The PB element was introduced into the promoter region of BEM4 gene and upregulated the BEM4 expression. Overexpression of BEM4 suppressed growth defects in och1Δ cells. The slow grow phenotypes were partially rescued by expression of Rho1p, whose function is regulated by Bem4p. Our results indicate that BEM4 would be useful to produce therapeutic proteins in glycoengineered yeast without the growth defects.
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Affiliation(s)
- Diane Mutumwinka
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Shen-Bao Zhao
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Yi-Shi Liu
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Emmanuel Osei Mensah
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Xiao-Dong Gao
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Morihisa Fujita
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
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14
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Wagner JM, Williams EV, Alper HS. Developing a piggyBac Transposon System and Compatible Selection Markers for Insertional Mutagenesis and Genome Engineering in Yarrowia lipolytica. Biotechnol J 2018; 13:e1800022. [PMID: 29493878 DOI: 10.1002/biot.201800022] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/17/2018] [Indexed: 12/30/2022]
Abstract
Yarrowia lipolytica is a non-conventional yeast of interest to the biotechnology industry. However, the physiology, metabolism, and genetic regulation of Y. lipolytica diverge significantly from more well-studied and characterized yeasts such as Saccharomyces cerevisiae. To develop additional genetic tools for this industrially relevant host, the piggyBac transposon system to enable efficient generation of genome-wide insertional mutagenesis libraries and introduction of scarless, footprint-free genomic modifications in Y. lipolytica. Specifically, we demonstrate piggyBac transposition in Y. lipolytica, and then use the approach to screen transposon insertion libraries for rapid isolation of mutations that confer altered canavanine resistance, pigment formation, and neutral lipid accumulation. We also develop a variety of piggyBac compatible selection markers for footprint-free genome engineering, including a novel dominant marker cassette (Escherichia coli guaB) for effective Y. lipolytica selection using mycophenolic acid. We utilize these marker cassettes to construct a piggyBac vector set that allows for auxotrophic selection (uracil or tryptophan biosynthesis) or dominant selection (hygromycin, nourseothricin, chlorimuron ethyl, or mycophenolic acid resistance) and subsequent marker excision. These new genetic tools and techniques will help to facilitate and accelerate the engineering of Y. lipolytica strains for efficient and sustainable production of a wide variety of small molecules and proteins.
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Affiliation(s)
- James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Eden V Williams
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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15
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Laptev IA, Raevskaya NM, Filimonova NA, Sineoky SP. The piggyBac Transposon as a Tool in Genetic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s000368381709006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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16
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Kasai Y, Matsuzaki K, Ikeda F, Yoshimitsu Y, Harayama S. Precise excision of a selectable marker gene in transgenic Coccomyxa strains by the piggyBac transposase. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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17
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Johnson ET, Owens JB, Moisyadi S. Vast potential for using the piggyBac transposon to engineer transgenic plants at specific genomic locations. Bioengineered 2016; 7:3-6. [PMID: 26930269 DOI: 10.1080/21655979.2015.1131367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The acceptance of bioengineered plants by some nations is hampered by a number of factors, including the random insertion of a transgene into the host genome. Emerging technologies, such as site-specific nucleases, are enabling plant scientists to promote recombination or mutations at specific plant loci. Off target activity of these nucleases may limit widespread use. Insertion of transgenes by transposases engineered with a specific DNA binding domain has been accomplished in a number of organisms, but not in plants. The piggyBac transposon system, originally isolated from an insect, has been utilized to transform a variety of organisms. The piggyBac transposase is amendable to structural modifications, and was able to insert a transgene at a specific human locus through fusion of a DNA binding domain to its N-terminus. Recent developments demonstrating the activity of piggyBac transposase in plants is an important first step toward the potential use of engineered versions of piggyBac transposase for site-specific transgene insertion in plants.
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Affiliation(s)
- Eric T Johnson
- a Crop Bioprotection Research, USDA ARS , Peoria , Illinois
| | - Jesse B Owens
- b Institute for Biogenesis Research, University of Hawaii at Manoa , Honolulu , Hawaii
| | - Stefan Moisyadi
- b Institute for Biogenesis Research, University of Hawaii at Manoa , Honolulu , Hawaii
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Kuan CS, Cham CY, Singh G, Yew SM, Tan YC, Chong PS, Toh YF, Atiya N, Na SL, Lee KW, Hoh CC, Yee WY, Ng KP. Genomic Analyses of Cladophialophora bantiana, a Major Cause of Cerebral Phaeohyphomycosis Provides Insight into Its Lifestyle, Virulence and Adaption in Host. PLoS One 2016; 11:e0161008. [PMID: 27570972 PMCID: PMC5003357 DOI: 10.1371/journal.pone.0161008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022] Open
Abstract
Cladophialophora bantiana is a dematiaceous fungus with a predilection for causing central nervous system (CNS) infection manifesting as brain abscess in both immunocompetent and immunocompromised patients. In this paper, we report comprehensive genomic analyses of C. bantiana isolated from the brain abscess of an immunocompetent man, the first reported case in Malaysia and Southeast Asia. The identity of the fungus was determined using combined morphological analysis and multilocus phylogeny. The draft genome sequence of a neurotrophic fungus, C. bantiana UM 956 was generated using Illumina sequencing technology to dissect its genetic fundamental and basic biology. The assembled 37.1 Mb genome encodes 12,155 putative coding genes, of which, 1.01% are predicted transposable elements. Its genomic features support its saprophytic lifestyle, renowned for its versatility in decomposing hemicellulose and pectin components. The C. bantiana UM 956 was also found to carry some important putative genes that engaged in pathogenicity, iron uptake and homeostasis as well as adaptation to various stresses to enable the organism to survive in hostile microenvironment. This wealth of resource will further catalyse more downstream functional studies to provide better understanding on how this fungus can be a successful and persistent pathogen in human.
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Affiliation(s)
- Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chun Yoong Cham
- Department of Neurosurgery, Hospital Pulau Pinang, Jalan Residensi, Georgetown, Pulau Pinang, Malaysia
- Department of Surgery, Neurosurgical Division, University of Malaya, Kuala Lumpur, Malaysia
| | - Gurmit Singh
- Department of Neurosurgery, Hospital Pulau Pinang, Jalan Residensi, Georgetown, Pulau Pinang, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nadia Atiya
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Wei Lee
- Codon Genomics SB, Selangor Darul Ehsan, Malaysia
| | | | - Wai-Yan Yee
- Codon Genomics SB, Selangor Darul Ehsan, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Abstract
The piggyBac transposon was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, the piggyBac transposon was not recognized as a member of a large transposon superfamily for a long time. Initially, the piggyBac transposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence of piggyBac-like repetitive elements. The isolation of active copies of the piggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, the piggyBac transposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of the piggyBac superfamily use TTAA as their integration target sites. In addition, the piggyBac transposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed that piggyBac does not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and the piggyBac transposon is currently the most widely used transposon system for genetic manipulations.
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Abstract
Next-generation sequencing approaches have considerably advanced our understanding of genome function and regulation. However, the knowledge of gene function and complex cellular processes remains a challenge and bottleneck in biological research. Phenomics is a rapidly emerging area, which seeks to rigorously characterize all phenotypes associated with genes or gene variants. Such high-throughput phenotyping under different conditions can be a potent approach toward gene function. The fission yeast Schizosaccharomyces pombe (S. pombe) is a proven eukaryotic model organism that is increasingly used for genomewide screens and phenomic assays. In this review, we highlight current large-scale, cell-based approaches used with S. pombe, including computational colony-growth measurements, genetic interaction screens, parallel profiling using barcodes, microscopy-based cell profiling, metabolomic methods and transposon mutagenesis. These diverse methods are starting to offer rich insights into the relationship between genotypes and phenotypes.
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Affiliation(s)
- Charalampos Rallis
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
| | - Jürg Bähler
- a Research Department of Genetics , Evolution and Environment and UCL Institute of Healthy Ageing, University College London , London , UK
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21
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Johnson ET, Dowd PF. A non-autonomous insect piggyBac transposable element is mobile in tobacco. Mol Genet Genomics 2014; 289:895-902. [PMID: 24858840 DOI: 10.1007/s00438-014-0860-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid only requires expression of piggyBac transposase. To determine if piggyBac could function in dicotyledonous plants, a two-element system was developed in tobacco (Nicotiana tabacum) to test for transposable element excision and insertion. The first transgenic line constitutively expressed piggyBac transposase, while the second transgenic line contained at least two non-autonomous piggyBac transposable elements. Progeny from crosses of the two transgenic lines was analyzed for piggyBac excision and transposition. Several progeny displayed excision events, and all the sequenced excision sites exhibited evidence of the precise excision mechanism characteristic of piggyBac transposase. Two unique transposition insertion events were identified that each included diagnostic duplication of the target site. These data indicate that piggyBac transposase is active in a dicotyledonous plant, although at a low frequency.
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Affiliation(s)
- Eric T Johnson
- Crop Bioprotection Research, USDA ARS, 1815 N. University St, Peoria, IL, 61604, USA,
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Wei Y, Wang HT, Zhai Y, Russell P, Du LL. Mdb1, a fission yeast homolog of human MDC1, modulates DNA damage response and mitotic spindle function. PLoS One 2014; 9:e97028. [PMID: 24806815 PMCID: PMC4013092 DOI: 10.1371/journal.pone.0097028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
During eukaryotic DNA damage response (DDR), one of the earliest events is the phosphorylation of the C-terminal SQ motif of histone H2AX (H2A in yeasts). In human cells, phosphorylated H2AX (γH2AX) is recognized by MDC1, which serves as a binding platform for the accumulation of a myriad of DDR factors on chromatin regions surrounding DNA lesions. Despite its important role in DDR, no homolog of MDC1 outside of metazoans has been described. Here, we report the characterization of Mdb1, a protein from the fission yeast Schizosaccharomyces pombe, which shares significant sequence homology with human MDC1 in their C-terminal tandem BRCT (tBRCT) domains. We show that in vitro, recombinant Mdb1 protein binds a phosphorylated H2A (γH2A) peptide, and the phospho-specific binding requires two conserved phospho-binding residues in the tBRCT domain of Mdb1. In vivo, Mdb1 forms nuclear foci at DNA double strand breaks (DSBs) induced by the HO endonuclease and ionizing radiation (IR). IR-induced Mdb1 focus formation depends on γH2A and the phospho-binding residues of Mdb1. Deleting the mdb1 gene does not overtly affect DNA damage sensitivity in a wild type background, but alters the DNA damage sensitivity of cells lacking another γH2A binder Crb2. Overexpression of Mdb1 causes severe DNA damage sensitivity in a manner that requires the interaction between Mdb1 and γH2A. During mitosis, Mdb1 localizes to spindles and concentrates at spindle midzones at late mitosis. The spindle midzone localization of Mdb1 requires its phospho-binding residues, but is independent of γH2A. Loss of Mdb1 or mutating its phospho-binding residues makes cells more resistant to the microtubule depolymerizing drug thiabendazole. We propose that Mdb1 performs dual roles in DDR and mitotic spindle regulation.
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Affiliation(s)
- Yi Wei
- College of Life Sciences, Beijing Normal University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences, Beijing, China
| | - Yonggong Zhai
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Paul Russell
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (PR); (LLD)
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- * E-mail: (PR); (LLD)
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Hong JB, Chou FJ, Ku AT, Fan HH, Lee TL, Huang YH, Yang TL, Su IC, Yu IS, Lin SW, Chien CL, Ho HN, Chen YT. A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells. PLoS One 2014; 9:e89396. [PMID: 24586748 PMCID: PMC3933532 DOI: 10.1371/journal.pone.0089396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 01/20/2014] [Indexed: 11/25/2022] Open
Abstract
PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3–4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.
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Affiliation(s)
- Jin-Bon Hong
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Fu-Ju Chou
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Amy T. Ku
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsiang-Hsuan Fan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tung-Lung Lee
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yung-Hsin Huang
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Tsung-Lin Yang
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Chang Su
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - I-Shing Yu
- Transgenic Mouse Model Core Facility of the National Research Program for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Laboratory Animal Center, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Liang Chien
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hong-Nerng Ho
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - You-Tzung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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24
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Li J, Du LL. piggyBac transposon-based insertional mutagenesis for the fission yeast Schizosaccharomyces pombe. Methods Mol Biol 2014; 1163:213-222. [PMID: 24841310 DOI: 10.1007/978-1-4939-0799-1_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Transposon-mediated insertional mutagenesis is a powerful tool for genetic screens. We have developed a piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe. Here, we describe in detail the procedure for inducing and selecting transpositions, and two protocols for identifying the transposon insertion sites, one using inverse PCR to identify the insertion sites in individual mutants, and the other using high-throughput sequencing to reveal the insertion sites in a mutant pool containing hundreds to thousands of mutants.
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Affiliation(s)
- Jun Li
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, People's Republic of China
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25
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Ding S, Xu T, Wu X. Generation of genetically engineered mice by the piggyBac transposon system. Methods Mol Biol 2014; 1194:171-85. [PMID: 25064103 DOI: 10.1007/978-1-4939-1215-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genetically engineered mice (GEM) are invaluable tools not only for understanding mammalian biology but also for modeling human diseases. Here we present protocols to generate GEM with the piggyBac (PB) transposon system. In the first part, we describe a transgenic procedure that co-injects the transgene carried by a PB donor plasmid and a PB transposase (PBase)-expressing helper plasmid into the pronuclei of fertilized eggs. In the second part, we provide a large-scale, cost-effective insertional mutagenesis strategy that remobilizes single-copy PB transposons in the male germ line. Given that PB can transpose in a broad spectrum of eukaryotic hosts, the protocols described here could be adapted for other species in the future.
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Affiliation(s)
- Sheng Ding
- State Key Laboratory of Genetic Engineering and Institute of Developmental Biology and Molecular Medicine, Fudan-Yale Biomedical Research Center, School of Life Sciences, Fudan University, Shanghai, 200433, China
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26
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Fattash I, Bhardwaj P, Hui C, Yang G. A rice Stowaway MITE for gene transfer in yeast. PLoS One 2013; 8:e64135. [PMID: 23704977 PMCID: PMC3660474 DOI: 10.1371/journal.pone.0064135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 04/11/2013] [Indexed: 02/06/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) lack protein coding capacity and often share very limited sequence similarity with potential autonomous elements. Their capability of efficient transposition and dramatic amplification led to the proposition that MITEs are an untapped rich source of materials for transposable element (TE) based genetic tools. To test the concept of using MITE sequence in gene transfer, a rice Stowaway MITE previously shown to excise efficiently in yeast was engineered to carry cargo genes (neo and gfp) for delivery into the budding yeast genome. Efficient excision of the cargo gene cassettes was observed even though the excision frequency generally decreases with the increase of the cargo sizes. Excised elements insert into new genomic loci efficiently, with about 65% of the obtained insertion sites located in genes. Elements at the primary insertion sites can be remobilized, frequently resulting in copy number increase of the element. Surprisingly, the orientation of a cargo gene (neo) on a construct bearing dual reporter genes (gfp and neo) was found to have a dramatic effect on transposition frequency. These results demonstrated the concept that MITE sequences can be useful in engineering genetic tools to deliver cargo genes into eukaryotic genomes.
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Affiliation(s)
- Isam Fattash
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Priyanka Bhardwaj
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Caleb Hui
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Guojun Yang
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
- * E-mail:
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27
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Sun Z, Sun Y, Zhou Y, Wan Y. Yeast Genomics Technique for High-Throughput Drug Target Discovery. Drug Dev Res 2012. [DOI: 10.1002/ddr.21030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zijun Sun
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yanyan Sun
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yaxian Zhou
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
| | - Yakun Wan
- The Key Laboratory of Developmental Genes and Human Disease; Ministry of Education; Institute of Life Sciences; Southeast University; Nanjing; 210096; China
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28
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Genome walking by next generation sequencing approaches. BIOLOGY 2012; 1:495-507. [PMID: 24832505 PMCID: PMC4009806 DOI: 10.3390/biology1030495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/31/2012] [Accepted: 09/25/2012] [Indexed: 01/07/2023]
Abstract
Genome Walking (GW) comprises a number of PCR-based methods for the identification of nucleotide sequences flanking known regions. The different methods have been used for several purposes: from de novo sequencing, useful for the identification of unknown regions, to the characterization of insertion sites for viruses and transposons. In the latter cases Genome Walking methods have been recently boosted by coupling to Next Generation Sequencing technologies. This review will focus on the development of several protocols for the application of Next Generation Sequencing (NGS) technologies to GW, which have been developed in the course of analysis of insertional libraries. These analyses find broad application in protocols for functional genomics and gene therapy. Thanks to the application of NGS technologies, the original vision of GW as a procedure for walking along an unknown genome is now changing into the possibility of observing the parallel marching of hundreds of thousands of primers across the borders of inserted DNA molecules in host genomes.
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29
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Chen BR, Hale DC, Ciolek PJ, Runge KW. Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe. BMC Genomics 2012; 13:161. [PMID: 22554201 PMCID: PMC3418178 DOI: 10.1186/1471-2164-13-161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Genetics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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30
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Wu J, Du H, Liao X, Zhao Y, Li L, Yang L. Tn5 transposase-assisted transformation of indica rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:186-200. [PMID: 21635585 DOI: 10.1111/j.1365-313x.2011.04663.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Here, we describe experiments on Tn5 transposase-assisted transformation of indica rice. Transposomes were formed in vitro as a result of hyperactive Tn5 transposase complexing with a transposon that contained a 19-bp tetracycline operator (tetO) sequence. To form modified projectiles for transformation, the Tn10-derived prokaryotic tetracycline repressor (TetR) proteins, which can bind transposomes via the high affinity of TetR for tetO, were immobilized onto the surface of bare gold microscopic particles. These projectiles were introduced into cells of the indica rice cultivar Zhuxian B by particle bombardment. Once projectiles were inside the cell, tetracycline induced an allosteric conformational change in TetR that resulted in the dissociation of TetR from tetO, and thus generated free transposomes. Molecular evidence of transposition was obtained by the cloning of insertion sites from many transgenic plants. We also demonstrated that the introduced foreign DNA was inherited stably over several generations. This technique is a promising transformation method for other plant species as it is species independent.
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Affiliation(s)
- Jun Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
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