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Tenjo-Castaño F, Montoya G, Carabias A. Transposons and CRISPR: Rewiring Gene Editing. Biochemistry 2023; 62:3521-3532. [PMID: 36130724 PMCID: PMC10734217 DOI: 10.1021/acs.biochem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/11/2022] [Indexed: 11/30/2022]
Abstract
CRISPR-Cas is driving a gene editing revolution because of its simple reprogramming. However, off-target effects and dependence on the double-strand break repair pathways impose important limitations. Because homology-directed repair acts primarily in actively dividing cells, many of the current gene correction/replacement approaches are restricted to a minority of cell types. Furthermore, current approaches display low efficiency upon insertion of large DNA cargos (e.g., sequences containing multiple gene circuits with tunable functionalities). Recent research has revealed new links between CRISPR-Cas systems and transposons providing new scaffolds that might overcome some of these limitations. Here, we comment on two new transposon-associated RNA-guided mechanisms considering their potential as new gene editing solutions. Initially, we focus on a group of small RNA-guided endonucleases of the IS200/IS605 family of transposons, which likely evolved into class 2 CRISPR effector nucleases (Cas9s and Cas12s). We explore the diversity of these nucleases (named OMEGA, obligate mobile element-guided activity) and analyze their similarities with class 2 gene editors. OMEGA nucleases can perform gene editing in human cells and constitute promising candidates for the design of new compact RNA-guided platforms. Then, we address the co-option of the RNA-guided activity of different CRISPR effector nucleases by a specialized group of Tn7-like transposons to target transposon integration. We describe the various mechanisms used by these RNA-guided transposons for target site selection and integration. Finally, we assess the potential of these new systems to circumvent some of the current gene editing challenges.
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Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Arturo Carabias
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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2
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Stepchenkova EI, Zadorsky SP, Shumega AR, Aksenova AY. Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification. Int J Mol Sci 2023; 24:11960. [PMID: 37569333 PMCID: PMC10419131 DOI: 10.3390/ijms241511960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.
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Affiliation(s)
- Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Sergey P. Zadorsky
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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3
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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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4
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High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
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5
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Miravet-Verde S, Burgos R, Delgado J, Lluch-Senar M, Serrano L. FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies. Nucleic Acids Res 2020; 48:e102. [PMID: 32813015 PMCID: PMC7515713 DOI: 10.1093/nar/gkaa679] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/28/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
Transposon sequencing is commonly applied for identifying the minimal set of genes required for cellular life; a major challenge in fields such as evolutionary or synthetic biology. However, the scientific community has no standards at the level of processing, treatment, curation and analysis of this kind data. In addition, we lack knowledge about artifactual signals and the requirements a dataset has to satisfy to allow accurate prediction. Here, we have developed FASTQINS, a pipeline for the detection of transposon insertions, and ANUBIS, a library of functions to evaluate and correct deviating factors known and uncharacterized until now. ANUBIS implements previously defined essentiality estimate models in addition to new approaches with advantages like not requiring a training set of genes to predict general essentiality. To highlight the applicability of these tools, and provide a set of recommendations on how to analyze transposon sequencing data, we performed a comprehensive study on artifacts corrections and essentiality estimation at a 1.5-bp resolution, in the genome-reduced bacterium Mycoplasma pneumoniae. We envision FASTQINS and ANUBIS to aid in the analysis of Tn-seq procedures and lead to the development of accurate genome essentiality estimates to guide applications such as designing live vaccines or growth optimization.
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Affiliation(s)
- Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.,Pulmobiotics, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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6
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Malavia D, Gow NAR, Usher J. Advances in Molecular Tools and In Vivo Models for the Study of Human Fungal Pathogenesis. Microorganisms 2020; 8:E803. [PMID: 32466582 PMCID: PMC7356103 DOI: 10.3390/microorganisms8060803] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogenic fungi represent an increasing infectious disease threat to humans, especially with an increasing challenge of antifungal drug resistance. Over the decades, numerous tools have been developed to expedite the study of pathogenicity, initiation of disease, drug resistance and host-pathogen interactions. In this review, we highlight advances that have been made in the use of molecular tools using CRISPR technologies, RNA interference and transposon targeted mutagenesis. We also discuss the use of animal models in modelling disease of human fungal pathogens, focusing on zebrafish, the silkworm, Galleria mellonella and the murine model.
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Affiliation(s)
| | | | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (N.A.R.G.)
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7
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Abstract
Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both
in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
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8
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Johnson MS, Martsul A, Kryazhimskiy S, Desai MM. Higher-fitness yeast genotypes are less robust to deleterious mutations. Science 2019; 366:490-493. [PMID: 31649199 PMCID: PMC7204892 DOI: 10.1126/science.aay4199] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
Natural selection drives populations toward higher fitness, but second-order selection for adaptability and mutational robustness can also influence evolution. In many microbial systems, diminishing-returns epistasis contributes to a tendency for more-fit genotypes to be less adaptable, but no analogous patterns for robustness are known. To understand how robustness varies across genotypes, we measure the fitness effects of hundreds of individual insertion mutations in a panel of yeast strains. We find that more-fit strains are less robust: They have distributions of fitness effects with lower mean and higher variance. These differences arise because many mutations have more strongly deleterious effects in faster-growing strains. This negative correlation between fitness and robustness implies that second-order selection for robustness will tend to conflict with first-order selection for fitness.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alena Martsul
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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9
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Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ. Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes. Genome Res 2019; 29:396-406. [PMID: 30635343 PMCID: PMC6396416 DOI: 10.1101/gr.232330.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/03/2019] [Indexed: 12/22/2022]
Abstract
To understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene. These results are often ported to newly sequenced genomes by using sequence homology. However, sequence similarity does not always mean identical function or phenotype, suggesting that new methods are required to functionally annotate newly sequenced species. We have implemented comparative analysis by high-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent functions and/or different genetic interactions. Comprehensive gene dispensability comparisons with S. cerevisiae predicted diverged dispensability at 12% of conserved orthologs, and validation experiments confirmed 22 differentially essential genes. Despite their differences in essentiality, these genes were capable of cross-species complementation, demonstrating that trans-acting factors that are background-dependent contribute to differential gene essentiality. This study shows that direct experimental testing of gene disruption phenotypes across species can inform comparative genomic analyses and improve gene annotations. Our method can be widely applied in microorganisms to further our understanding of genome evolution.
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Affiliation(s)
- Monica R Sanchez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Frances Cheong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Blake T Hovde
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Sarah Bissonnette
- Department of Biological Sciences, California State University, Turlock, California 95382, USA
| | - Adam P Arkin
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Jeffrey M Skerker
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, California 94945, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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10
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A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: Riboflavin overproduction in Yarrowia lipolytica. Metab Eng 2018; 47:346-356. [DOI: 10.1016/j.ymben.2018.04.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/02/2018] [Accepted: 04/20/2018] [Indexed: 12/15/2022]
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11
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Mielich K, Shtifman-Segal E, Golz JC, Zeng G, Wang Y, Berman J, Kunze R. Maize Transposable Elements Ac/ Ds as Insertion Mutagenesis Tools in Candida albicans. G3 (BETHESDA, MD.) 2018; 8:1139-1145. [PMID: 29378819 PMCID: PMC5873905 DOI: 10.1534/g3.117.300388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
In nonmodel systems, genetic research is often limited by the lack of techniques for the generation and identification of gene mutations. One approach to overcome this bottleneck is the application of transposons for gene tagging. We have established a two-element transposon tagging system, based on the transposable elements Activator (Ac)/Dissociation (Ds) from maize, for in vivo insertion mutagenesis in the fungal human pathogen Candida albicans A nonautonomous Ds transposon carrying a selectable marker was constructed into the ADE2 promoter on chromosome 3 and a codon usage-adapted Ac transposase gene was inserted into the neutral NEUT5L locus on chromosome 5. In C. albicans cells expressing the transposase, the Ds element efficiently excised and reintegrated elsewhere in the genome, which makes the Ac/Ds transposons promising tools for saturating insertion mutagenesis in clinical strains of C. albicans.
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Affiliation(s)
- Kevin Mielich
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Ella Shtifman-Segal
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Julia C Golz
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
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12
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de Ruijter JC, Jurgens G, Frey AD. Screening for novel genes of Saccharomyces cerevisiae involved in recombinant antibody production. FEMS Yeast Res 2016; 17:fow104. [PMID: 27956492 DOI: 10.1093/femsyr/fow104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Cost-effective manufacturing of biopharmaceuticals in non-mammalian hosts still requires tremendous efforts in strain development. In order to expedite identification of novel leads for strain engineering, we used a transposon-mutagenized yeast genomic DNA library to create a collection of Saccharomyces cerevisiae deletion strains expressing a full-length IgG antibody. Using a high-throughput screening, transformants with either significantly higher or lower IgG expression were selected. The integration site of the transposon in three of the selected strains was located by DNA sequencing. The inserted DNA lay within the VPS30 and TAR1 open reading frame, and upstream of the HEM13 open reading frame. The complete coding sequence of these genes was deleted in the wild-type strain background to confirm the IgG expression phenotypes. Production of recombinant antibody was increased 2-fold in the Δvps30 strain, but only mildly affected secretion levels in the Δtar1 strain. Remarkably, expression of endogenous yeast acid phosphatase was increased 1.7- and 2.4-fold in Δvps30 and Δtar1 strains. The study confirmed the power of genome-wide high-throughput screens for strain development and highlights the importance of using the target molecule during the screening process.
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Affiliation(s)
- Jorg C de Ruijter
- Department of Biotechnology and Chemical Technology, Aalto University, 02150 Espoo, Finland
| | | | - Alexander D Frey
- Department of Biotechnology and Chemical Technology, Aalto University, 02150 Espoo, Finland
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13
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Mutlu N, Kumar A. Mapping paths: new approaches to dissect eukaryotic signaling circuitry. F1000Res 2016; 5. [PMID: 27540473 PMCID: PMC4965690 DOI: 10.12688/f1000research.8818.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic cells are precisely “wired” to coordinate changes in external and intracellular signals with corresponding adjustments in the output of complex and often interconnected signaling pathways. These pathways are critical in understanding cellular growth and function, and several experimental trends are emerging with applicability toward more fully describing the composition and topology of eukaryotic signaling networks. In particular, recent studies have implemented CRISPR/Cas-based screens in mouse and human cell lines for genes involved in various cell growth and disease phenotypes. Proteomic methods using mass spectrometry have enabled quantitative and dynamic profiling of protein interactions, revealing previously undiscovered complexes and allele-specific protein interactions. Methods for the single-cell study of protein localization and gene expression have been integrated with computational analyses to provide insight into cell signaling in yeast and metazoans. In this review, we present an overview of exemplary studies using the above approaches, relevant for the analysis of cell signaling and indeed, more broadly, for many modern biological applications.
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Affiliation(s)
- Nebibe Mutlu
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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14
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Abstract
Libraries of transposon-insertion alleles constitute powerful and versatile tools for large-scale analysis of yeast gene function. Transposon-insertion libraries are constructed most simply through mutagenesis of a plasmid-based genomic DNA library; modification of the mutagenizing transposon by incorporation of yeast selectable markers, recombination sites, and an epitope tag enables the application of insertion alleles for phenotypic screening and protein localization. In particular, yeast genomic DNA libraries have been mutagenized with modified bacterial transposons carrying the URA3 marker, lox recombination sites, and sequence encoding multiple copies of the hemagglutinin (HA) epitope. Mutagenesis with these transposons has yielded a large resource of insertion alleles affecting nearly 4000 yeast genes in total. Through well-established protocols, these insertion libraries can be introduced into the desired strain backgrounds and the resulting insertional mutants can be screened or systematically analyzed. Relative to alternative methods of UV irradiation or chemical mutagenesis, transposon-insertion alleles can be easily identified by PCR-based approaches or high-throughput sequencing. Transposon-insertion libraries also provide a cost-effective alternative to targeted deletion approaches, although, in contrast to start-codon to stop-codon deletions, insertion alleles might not represent true null-mutants. For protein-localization studies, transposon-insertion alleles can provide encoded epitope tags in-frame with internal codons; in many cases, these transposon-encoded epitope tags can provide a more accurate localization for proteins in which terminal sequences are crucial for intracellular targeting. Thus, overall, transposon-insertion libraries can be used quickly and economically and have a particular utility in screening for desired phenotypes and localization patterns in nonstandard genetic backgrounds.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048
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15
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Kumar A. Using Yeast Transposon-Insertion Libraries for Phenotypic Screening and Protein Localization. Cold Spring Harb Protoc 2016; 2016:2016/6/pdb.prot085217. [PMID: 27250939 DOI: 10.1101/pdb.prot085217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This protocol details how to use a transposon-insertion library for phenotypic screening and protein localization. The insertion library was generated by mutagenesis of a plasmid-based yeast genomic DNA library by using a multipurpose transposon; the transposon produces gene disruptions, and, by Cre-mediated recombination at lox sites incorporated within the transposon, alleles with an in-frame insertion can be truncated to a residual transposon encoding multiple copies of the hemagglutinin epitope. Insertions are generated in yeast by shuttle mutagenesis. Yeast genomic DNA containing a transposon insertion is released from the library, and the mutagenized DNA sequences are introduced into a desired strain of yeast, where the insertion alleles replace native loci by homologous recombination. The insertion mutants can be screened for phenotypes, and the site of transposon insertion can subsequently be identified in selected mutants by inverse polymerase chain reaction (PCR). In-frame insertions within genes of interest can be truncated to an epitope-tagged allele by Cre-lox recombination, and the subcellular localization of the encoded protein product can be identified by standard methods of indirect immunofluorescence. In summary, the transposon-insertion libraries represent an informative resource for large-scale mutagenesis, presenting a straightforward alternative to labor-intensive targeted approaches for the construction of deletion alleles and fluorescent protein fusions.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048
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16
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Abstract
Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.
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17
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Norman KL, Kumar A. Mutant power: using mutant allele collections for yeast functional genomics. Brief Funct Genomics 2016; 15:75-84. [PMID: 26453908 PMCID: PMC5065357 DOI: 10.1093/bfgp/elv042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology.
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Zordan RE, Beliveau BJ, Trow JA, Craig NL, Cormack BP. Avoiding the ends: internal epitope tagging of proteins using transposon Tn7. Genetics 2015; 200:47-58. [PMID: 25745023 PMCID: PMC4423380 DOI: 10.1534/genetics.114.169482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
Peptide tags fused to proteins are used in a variety of applications, including as affinity tags for purification, epitope tags for immunodetection, or fluorescent protein tags for visualization. However, the peptide tags can disrupt the target protein function. When function is disrupted by fusing a peptide to either the N or C terminus of the protein of interest, identifying alternative ways to create functional tagged fusion proteins can be difficult. Here, we describe a method to introduce protein tags internal to the coding sequence of a target protein. The method employs in vitro Tn7-transposon mutagenesis of plasmids for random introduction of the tag, followed by subsequent Gateway cloning steps to isolate alleles with mutations in the coding sequence of the target gene. The Tn7-epitope cassette is designed such that essentially all of the transposon is removed through restriction enzyme digestion, leaving only the protein tag at diverse sites internal to the ORF. We describe the use of this system to generate a panel of internally epitope-tagged versions of the Saccharomyces cerevisiae GPI-linked membrane protein Dcw1 and the Candida glabrata transcriptional regulator Sir3. This internal protein tagging system is, in principle, adaptable to tag proteins in any organism for which Gateway-adapted expression vectors exist.
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Affiliation(s)
- Rebecca E Zordan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
| | - Brian J Beliveau
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
| | - Jonathan A Trow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
| | - Nancy L Craig
- Department of Molecular Biology and Genetics, The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
| | - Brendan P Cormack
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
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19
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Horton BN, Kumar A. Genome-wide synthetic genetic screening by transposon mutagenesis in Candida albicans. Methods Mol Biol 2015; 1279:125-35. [PMID: 25636616 DOI: 10.1007/978-1-4939-2398-4_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transposon-based mutagenesis is an effective method for genetic screening on a genome-wide scale, with particular applicability in organisms possessing compact genomes where transforming DNA tends to integrate by homologous recombination. Methods for transposon mutagenesis have been applied with great success in the budding yeast Saccharomyces cerevisiae and in the related pathogenic yeast Candida albicans. In C. albicans, we have implemented transposon mutagenesis to generate heterozygous mutations for the analysis of complex haploinsufficiency, a type of synthetic genetic interaction wherein a pair of non-complementing heterozygous mutations results in a stronger phenotype then either individual mutation in isolation. Genes exhibiting complex haploinsufficiency typically function within a regulatory pathway, in parallel pathways, or in parallel branches within a single pathway. Here, we present protocols to implement transposon mutagenesis for complex haploinsufficiency screening in C. albicans, indicating methods for transposon construction, mutagenesis, phenotypic screening, and identification of insertion sites in strains of interest. In total, the approach is a useful means to implement large-scale synthetic genetic screening in the diploid C. albicans.
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Affiliation(s)
- Brooke N Horton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
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20
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Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H. Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery. BMC Biol 2014; 12:103. [PMID: 25488358 PMCID: PMC4300041 DOI: 10.1186/s12915-014-0103-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/26/2014] [Indexed: 12/04/2022] Open
Abstract
Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0103-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
| | - Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland. .,Current address: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kieran Dilks
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Stefanie Storf
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | | | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
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21
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Parts L. Genome-wide mapping of cellular traits using yeast. Yeast 2014; 31:197-205. [PMID: 24700360 DOI: 10.1002/yea.3010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 11/09/2022] Open
Abstract
Yeast has long enjoyed superiority as a genetic model because of its short generation time and ease of generating alleles for genetic analysis. However, recent developments of guided nucleases for genome editing in higher eukaryotes, and funding pressures for translational findings, force all model organism communities to reaffirm and rearticulate the advantages of their chosen creature. Here I examine the utility of budding yeast for understanding the genetic basis of cellular traits, using natural variation as well as classical genetic perturbations, and its future prospects compared to undertaking the work in human cell lines. Will yeast remain central, or will it join the likes of phage as an early model that is no longer widely used to answer the pressing questions?
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Affiliation(s)
- Leopold Parts
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
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22
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Abstract
Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.
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23
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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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24
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Bharucha N, Chabrier-Roselló Y, Xu T, Johnson C, Sobczynski S, Song Q, Dobry CJ, Eckwahl MJ, Anderson CP, Benjamin AJ, Kumar A, Krysan DJ. A large-scale complex haploinsufficiency-based genetic interaction screen in Candida albicans: analysis of the RAM network during morphogenesis. PLoS Genet 2011; 7:e1002058. [PMID: 22103005 PMCID: PMC3084211 DOI: 10.1371/journal.pgen.1002058] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The morphogenetic transition between yeast and filamentous forms of the human
fungal pathogen Candida albicans is regulated by a variety of
signaling pathways. How these pathways interact to orchestrate morphogenesis,
however, has not been as well characterized. To address this question and to
identify genes that interact with the Regulation of Ace2 and Morphogenesis (RAM)
pathway during filamentation, we report the first large-scale genetic
interaction screen in C. albicans. Our strategy for this screen
was based on the concept of complex haploinsufficiency (CHI). A heterozygous
mutant of CBK1
(cbk1Δ/CBK1), a key RAM pathway
protein kinase, was subjected to transposon-mediated, insertional mutagenesis.
The resulting double heterozygous mutants (6,528 independent strains) were
screened for decreased filamentation on Spider Medium (SM). From the 441 mutants
showing altered filamentation, 139 transposon insertion sites were sequenced,
yielding 41 unique CBK1-interacting genes. This gene set was
enriched in transcriptional targets of Ace2 and, strikingly, the cAMP-dependent
protein kinase A (PKA) pathway, suggesting an interaction between these two
pathways. Further analysis indicates that the RAM and PKA pathways co-regulate a
common set of genes during morphogenesis and that hyper-activation of the PKA
pathway may compensate for loss of RAM pathway function. Our data also indicate
that the PKA–regulated transcription factor Efg1 primarily localizes to
yeast phase cells while the RAM–pathway regulated transcription factor
Ace2 localizes to daughter nuclei of filamentous cells, suggesting that Efg1 and
Ace2 regulate a common set of genes at separate stages of morphogenesis. Taken
together, our observations indicate that CHI–based screening is a useful
approach to genetic interaction analysis in C. albicans and
support a model in which these two pathways regulate a common set of genes at
different stages of filamentation. Candida albicans is the most common cause of fungal infections
in humans. As a diploid yeast without a classical sexual cycle, many genetic
approaches developed for large-scale genetic interaction studies in the model
yeast Saccharomyces cerevisiae cannot be applied to C.
albicans. Genetic interaction studies have proven to be powerful
genetic tools for the analysis of complex biological processes. Here, we
demonstrate that libraries of C. albicans strains containing
heterozygous mutations in two different genes can be generated and used to study
genetic interactions in C. albicans on a large scale. Double
heterozygous mutants that show more severe phenotypes than strains with single
heterozygous mutations are indicative of genetic interactions through a
phenomenon referred to as complex haploinsufficiency (CHI). We applied this
approach to the study of the RAM (Regulation of Ace2 and Morphogenesis)
signaling network during the morphogenetic transition of C.
albicans from yeast to filamentous growth. Among the genes that
interacted with CBK1, the key signaling kinase of the RAM
pathway, were transcriptional targets of the RAM pathway and the protein kinase
A pathway. Further analysis supports a model in which these two pathways
co-regulate a common set of genes at different stages of filamentation.
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Affiliation(s)
- Nike Bharucha
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Yeissa Chabrier-Roselló
- Department of Pediatrics, University of
Rochester School of Medicine and Dentistry, Rochester, New York, United States
of America
| | - Tao Xu
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Cole Johnson
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Sarah Sobczynski
- Department of Microbiology/Immunology,
University of Rochester School of Medicine and Dentistry, Rochester, New York,
United States of America
| | - Qingxuan Song
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Craig J. Dobry
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Matthew J. Eckwahl
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Christopher P. Anderson
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Andrew J. Benjamin
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
| | - Anuj Kumar
- Department of Molecular, Cellular, and
Developmental Biology, University of Michigan, Ann Arbor, Michigan, United
States of America
- * E-mail: (DJK); (AK)
| | - Damian J. Krysan
- Department of Pediatrics, University of
Rochester School of Medicine and Dentistry, Rochester, New York, United States
of America
- Department of Microbiology/Immunology,
University of Rochester School of Medicine and Dentistry, Rochester, New York,
United States of America
- * E-mail: (DJK); (AK)
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25
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Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae. EUKARYOTIC CELL 2011; 10:1705-13. [PMID: 22037179 DOI: 10.1128/ec.05215-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The integrity of mitosis is dependent upon strict regulation of microtubule stability and dynamics. Although much information has been accumulated on regulators of the microtubule cytoskeleton, our knowledge of the specific pathways involved is still limited. Here we designed genetic screens to identify regulators of microtubule stability that are dispensable in the wild type yet become essential under microtubule-disrupting conditions. We found that the transcriptional cofactor Swi6p and activator Swi4p, as well as the G(2)/M-specific cyclin Clb2p, are required in a microtubule-destabilizing environment. Swi6p and Swi4p can combine as a transcriptional complex, called the SBF complex (SBF for Swi4/6 cell cycle box [SCB]-binding factor) that is functionally homologous to the metazoan DP1/2-E2F complex and that controls the G(1)/S transition through the genes it regulates. We show that Swi6p's contribution to microtubule stability can be either dependent or independent of the SBF complex. The SBF-dependent pathway requires downregulation of SBF complex levels and may thereby reroute the transcriptional program in favor of greater microtubule stability. This pathway can be triggered by overexpression of Fcp1p, a phosphatase in the general transcription machinery, or by expression of an allele of SWI6 that is associated with reduced transcription from SBF-controlled promoters. The SBF-independent pathway is activated by a constitutively nuclear allele of Swi6p. Our results introduce novel roles in microtubule stability for genes whose participation in the process may be masked under normal conditions yet nonetheless acquire a dominant role when microtubule stability is compromised.
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26
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Xu T, Bharucha N, Kumar A. Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans. Methods Mol Biol 2011; 765:207-24. [PMID: 21815095 DOI: 10.1007/978-1-61779-197-0_13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transposon mutagenesis is an effective method for generating large sets of random mutations in target DNA, with applicability toward numerous types of genetic screens in prokaryotes, single-celled eukaryotes, and metazoans alike. Relative to methods of random mutagenesis by chemical/UV treatment, transposon insertions can be easily identified in mutants with phenotypes of interest. The construction of transposon insertion mutants is also less labor-intensive on a genome-wide scale than methods for targeted gene replacement, although transposon insertions are not precisely targeted to a specific residue, and thus coverage of the target DNA can be problematic. The collective advantages of transposon mutagenesis have been well demonstrated in studies of the budding yeast Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans, as transposon mutagenesis has been used extensively for phenotypic screens in both yeasts. Consequently, we present here protocols for the generation and utilization of transposon-insertion DNA libraries in S. cerevisiae and C. albicans. Specifically, we present methods for the large-scale introduction of transposon insertion alleles in a desired strain of S. cerevisiae. Methods are also presented for transposon mutagenesis of C. albicans, encompassing both the construction of the plasmid-based transposon-mutagenized DNA library and its introduction into a desired strain of Candida. In total, these methods provide the necessary information to implement transposon mutagenesis in yeast, enabling the construction of large sets of identifiable gene disruption mutations, with particular utility for phenotypic screening in nonstandard genetic backgrounds.
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Affiliation(s)
- Tao Xu
- Department of Molecular, Cellular, and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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27
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Granek JA, Magwene PM. Environmental and genetic determinants of colony morphology in yeast. PLoS Genet 2010; 6:e1000823. [PMID: 20107600 PMCID: PMC2809765 DOI: 10.1371/journal.pgen.1000823] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 12/21/2009] [Indexed: 12/30/2022] Open
Abstract
Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs.
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Affiliation(s)
- Joshua A. Granek
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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28
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Snyder M, Gallagher JEG. Systems biology from a yeast omics perspective. FEBS Lett 2009; 583:3895-9. [PMID: 19903479 PMCID: PMC3262145 DOI: 10.1016/j.febslet.2009.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 11/05/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in Saccharomyces cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled the elucidation of global regulatory networks. These studies have helped provide an understanding of cellular pathways and processes at a global and systems level.
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Affiliation(s)
- Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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29
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30
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Nonklang S, Abdel-Banat BMA, Cha-aim K, Moonjai N, Hoshida H, Limtong S, Yamada M, Akada R. High-temperature ethanol fermentation and transformation with linear DNA in the thermotolerant yeast Kluyveromyces marxianus DMKU3-1042. Appl Environ Microbiol 2008; 74:7514-21. [PMID: 18931291 PMCID: PMC2607150 DOI: 10.1128/aem.01854-08] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/13/2008] [Indexed: 11/20/2022] Open
Abstract
We demonstrate herein the ability of Kluyveromyces marxianus to be an efficient ethanol producer and host for expressing heterologous proteins as an alternative to Saccharomyces cerevisiae. Growth and ethanol production by strains of K. marxianus and S. cerevisiae were compared under the same conditions. K. marxianus DMKU3-1042 was found to be the most suitable strain for high-temperature growth and ethanol production at 45 degrees C. This strain, but not S. cerevisiae, utilized cellobiose, xylose, xylitol, arabinose, glycerol, and lactose. To develop a K. marxianus DMKU3-1042 derivative strain suitable for genetic engineering, a uracil auxotroph was isolated and transformed with a linear DNA of the S. cerevisiae ScURA3 gene. Surprisingly, Ura(+) transformants were easily obtained. By Southern blot hybridization, the linear ScURA3 DNA was found to have inserted randomly into the K. marxianus genome. Sequencing of one Lys(-) transformant confirmed the disruption of the KmLYS1 gene by the ScURA3 insertion. A PCR-amplified linear DNA lacking K. marxianus sequences but containing an Aspergillus alpha-amylase gene under the control of the ScTDH3 promoter together with an ScURA3 marker was subsequently used to transform K. marxianus DMKU3-1042 in order to obtain transformants expressing Aspergillus alpha-amylase. Our results demonstrate that K. marxianus DMKU3-1042 can be an alternative cost-effective bioethanol producer and a host for transformation with linear DNA by use of S. cerevisiae-based molecular genetic tools.
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Affiliation(s)
- Sanom Nonklang
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Tokiwadai, Ube 755-8611, Japan
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31
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Linheiro RS, Bergman CM. Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Res 2008; 36:6199-208. [PMID: 18829720 PMCID: PMC2577343 DOI: 10.1093/nar/gkn563] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the molecular mechanisms that influence transposable element target site preferences is a fundamental challenge in functional and evolutionary genomics. Large-scale transposon insertion projects provide excellent material to study target site preferences in the absence of confounding effects of post-insertion evolutionary change. Growing evidence from a wide variety of prokaryotes and eukaryotes indicates that DNA transposons recognize staggered-cut palindromic target site motifs (TSMs). Here, we use over 10 000 accurately mapped P-element insertions in the Drosophila melanogaster genome to test predictions of the staggered-cut palindromic target site model for DNA transposon insertion. We provide evidence that the P-element targets a 14-bp palindromic motif that can be identified at the primary sequence level, which predicts the local spacing, hotspots and strand orientation of P-element insertions. Intriguingly, we find that the although P-element destroys the complete 14-bp target site upon insertion, the terminal three nucleotides of the P-element inverted repeats complement and restore the original TSM, suggesting a mechanistic link between transposon target sites and their terminal inverted repeats. Finally, we discuss how the staggered-cut palindromic target site model can be used to assess the accuracy of genome mappings for annotated P-element insertions.
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Affiliation(s)
- Raquel S Linheiro
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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32
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Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast. Methods Mol Biol 2008; 416:117-29. [PMID: 18392964 DOI: 10.1007/978-1-59745-321-9_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Transposons have long been recognized as useful laboratory tools facilitating genome-scale studies of gene function. Relative to traditional methods, transposon mutagenesis offers a rapid and economical means of generating large numbers of independent insertions in target DNA through minimal experimental manipulation. In particular, the transposon insertion library described here is an excellent tool for the analysis of gene function on a large scale in the budding yeast Saccharomyces cerevisiae. The transposon utilized in this library is multifunctional, such that the library can be used to screen for disruption phenotypes while also providing a means to generate epitope-tagged alleles and, in many cases, conditional alleles. Provided here are complete protocols by which the transposon insertion library may be used to screen for mutant phenotypes in yeast as well as accompanying protocols describing a means of identifying transposon insertion sites within strains of interest. In total, this insertion library is a singularly useful tool for genome-wide functional analysis, and the general approach is applicable to other organisms in which transforming DNA tends to integrate by homologous recombination.
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33
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In vitro mutagenesis of Bacillus subtilis by using a modified Tn7 transposon with an outward-facing inducible promoter. Appl Environ Microbiol 2008; 74:3419-25. [PMID: 18408063 DOI: 10.1128/aem.00476-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A Tn7 donor plasmid, pTn7SX, was constructed for use with the model gram-positive bacterium Bacillus subtilis. This new mini-Tn7, mTn7SX, contains a spectinomycin resistance cassette and an outward-facing, xylose-inducible promoter, thereby allowing for the regulated expression of genes downstream of the transposon. We demonstrate that mTn7SX inserts are obtained at a high frequency and occur randomly throughout the B. subtilis genome. The utility of this system was demonstrated by the selection of mutants with increased resistance to the antibiotic fosfomycin or duramycin.
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Kines KJ, Morales ME, Mann VH, Gobert GN, Brindley PJ. Integration of reporter transgenes into Schistosoma mansoni chromosomes mediated by pseudotyped murine leukemia virus. FASEB J 2008; 22:2936-48. [PMID: 18403630 DOI: 10.1096/fj.08-108308] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The recent release of draft genome sequences of two of the major human schistosomes has underscored the pressing need to develop functional genomics approaches for these significant pathogens. The sequence information also makes feasible genome-scale investigation of transgene integration into schistosome chromosomes. Retrovirus-mediated transduction offers a means to establish transgenic lines of schistosomes, to elucidate schistosome gene function and expression, and to advance functional genomics approaches for these parasites. We investigated the utility of the Moloney murine leukemia retrovirus (MLV) pseudotyped with vesicular stomatitis virus glycoprotein (VSVG) for the transduction of Schistosoma mansoni and delivery of reporter transgenes into schistosome chromosomes. Schistosomula were exposed to virions of VSVG-pseudotyped MLV, after which genomic DNA was extracted from the transduced schistosomes. Southern hybridization analysis indicated the presence of proviral MLV retrovirus in the transduced schistosomes. Fragments of the MLV transgene and flanking schistosome sequences recovered using an anchored PCR-based approach demonstrated definitively that somatic transgenesis of schistosome chromosomes had taken place and, moreover, revealed widespread retrovirus integration into schistosome chromosomes. More specifically, MLV transgenes had inserted in the vicinity of genes encoding immunophilin, zinc finger protein Sma-Zic, and others, as well as near the endogenous schistosome retrotransposons, the fugitive and SR1. Proviral integration of the MLV transgene appeared to exhibit primary sequence site specificity, targeting a gGATcc-like motif. Reporter luciferase transgene activity driven by the schistosome actin gene promoter was expressed in the tissues of transduced schistosomula and adult schistosomes. Luciferase activity appeared to be developmentally expressed in schistosomula with increased activity observed after 1 to 2 wk in culture. These findings indicate the utility of VSVG-pseudotyped MLV for transgenesis of S. mansoni, herald a tractable pathway forward toward germline transgenesis and functional genomics of parasitic helminths, and provide the basis for comparative molecular pathogenesis studies of chromosomal lesions arising from retroviral integration into human compared with schistosome chromosomes.
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Affiliation(s)
- Kristine J Kines
- Department of Tropical Medicine, and Biomedical Sciences Program, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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Mobini-Dehkordi M, Nahvi I, Zarkesh-Esfahani H, Ghaedi K, Tavassoli M, Akada R. Isolation of a novel mutant strain of Saccharomyces cerevisiae by an ethyl methane sulfonate-induced mutagenesis approach as a high producer of bioethanol. J Biosci Bioeng 2008; 105:403-8. [DOI: 10.1263/jbb.105.403] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 01/23/2008] [Indexed: 11/17/2022]
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Abstract
The rapid accumulation of complete genomic sequences offers the opportunity to carry out an analysis of inter- and intra-individual genome variation within a species on a routine basis. Sequencing whole genomes requires resources that are currently beyond those of a single laboratory and therefore it is not a practical approach for resequencing hundreds of individual genomes. DNA microarrays present an alternative way to study differences between closely related genomes. Advances in microarray-based approaches have enabled the main forms of genomic variation (amplifications, deletions, insertions, rearrangements and base-pair changes) to be detected using techniques that are readily performed in individual laboratories using simple experimental approaches.
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Jin R, Dobry CJ, McCown PJ, Kumar A. Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression. Mol Biol Cell 2007; 19:284-96. [PMID: 17989363 DOI: 10.1091/mbc.e07-05-0519] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Under certain conditions of nutrient stress, the budding yeast Saccharomyces cerevisiae initiates a striking developmental transition to a filamentous form of growth, resembling developmental transitions required for virulence in closely related pathogenic fungi. In yeast, filamentous growth involves known mitogen-activated protein kinase and protein kinase A signaling modules, but the full scope of this extensive filamentous response has not been delineated. Accordingly, we have undertaken the first systematic gene disruption and overexpression analysis of yeast filamentous growth. Standard laboratory strains of yeast are nonfilamentous; thus, we constructed a unique set of reagents in the filamentous Sigma1278b strain, encompassing 3627 integrated transposon insertion alleles and 2043 overexpression constructs. Collectively, we analyzed 4528 yeast genes with these reagents and identified 487 genes conferring mutant filamentous phenotypes upon transposon insertion and/or gene overexpression. Using a fluorescent protein reporter integrated at the MUC1 locus, we further assayed each filamentous growth mutant for aberrant protein levels of the key flocculence factor Muc1p. Our results indicate a variety of genes and pathways affecting filamentous growth. In total, this filamentous growth gene set represents a wealth of yeast biology, highlighting 84 genes of uncharacterized function and an underappreciated role for the mitochondrial retrograde signaling pathway as an inhibitor of filamentous growth.
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Affiliation(s)
- Rui Jin
- Department of Molecular, Cellular, and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
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Laurentino EC, Ruiz JC, Brito LO, Fiandt M, Nicoletti LM, Jamur MC, Oliver C, Tosi LRO, Cruz AK. The use of Tn5 transposable elements in a gene trapping strategy for the protozoan Leishmania. Int J Parasitol 2007; 37:735-42. [PMID: 17362967 DOI: 10.1016/j.ijpara.2006.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 12/17/2006] [Accepted: 12/22/2006] [Indexed: 11/28/2022]
Abstract
The use of transposable elements as a gene-trapping strategy is a powerful tool for gene discovery. Herein we describe the development of a transposable system, based on the bacterial Tn5 transposon, which has been used successfully in Leishmania braziliensis. The transposon carries the neomycin phosphotransferase gene, which is expressed only when inserted in-frame with a Leishmania gene present in the target DNA. Four cosmid clones from a L. braziliensis genomic library were used as targets in transposition reactions and four insertional libraries were constructed and transfected in L. braziliensis. Clones resistant to G418 were selected and analysed by immunofluorescence in order to identify the subcellular localisation of the protein coded by the trapped gene. A definitive subcellular localisation for neomycin phosphotransferase/targeted protein fusion was not obtained in any of the four Leishmania clones investigated. However, the constructed transposable element is highly efficient considering the frequency of insertion in large targets and is therefore a useful tool for functional genetic studies in Leishmania. Our data confirm the utility of the Tn5 transposon system for insertion of sequencing priming sites into target DNA. Furthermore, the high frequency of insertion and even distribution are important in studying genomic regions bearing long and polymorphic repetitive sequences.
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Affiliation(s)
- Eliane C Laurentino
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av Bandeirantes, Ribeirão Preto, São Paulo, Brazil
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Kivistik PA, Kivisaar M, Hõrak R. Target site selection of Pseudomonas putida transposon Tn4652. J Bacteriol 2007; 189:3918-21. [PMID: 17351034 PMCID: PMC1913344 DOI: 10.1128/jb.01863-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the target preferences of a Tn3 family transposon Tn4652. Alignment of 93 different insertion sites revealed a consensus sequence which resembles that of Tn3, indicating that despite a low similarity between Tn4652 and Tn3 transposases, their target site recognition is conserved.
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Affiliation(s)
- Paula Ann Kivistik
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, 51010 Tartu, Estonia
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Bisson LF, Karpel JE, Ramakrishnan V, Joseph L. Functional genomics of wine yeast Saccharomyces cerevisiae. ADVANCES IN FOOD AND NUTRITION RESEARCH 2007; 53:65-121. [PMID: 17900497 DOI: 10.1016/s1043-4526(07)53003-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The application of genomic technologies to the analysis of wine strains of Saccharomyces cerevisiae has greatly enhanced our understanding of both native and laboratory strains of this important model eukaryote. Not only are differences in transcript, protein, and metabolite profiles being uncovered, but the heritable basis of these differences is also being elucidated. Although some challenges remain in the application of functional genomic technologies to commercial and native strains of S. cerevisiae, recent improvements, particularly in data analysis, have greatly extended the utility of these tools. Comparative analysis of laboratory and wine isolates is refining our understanding of the mechanisms of genome evolution. Genomic analysis of Saccharomyces in native environments is providing evidence of gene function to previously uncharacterized open reading frames and delineating the physiological parameters of ecological niche specialization and stress adaptation. The wealth of information being generated will soon be utilized to construct commercial stains with more desirable phenotypes, traits that will be designed to be genetically stable under commercial production conditions.
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Affiliation(s)
- Linda F Bisson
- Department of Viticulture and Enology, University of California, Davis, California 95616, USA
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Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, Dunham MJ. Global mapping of transposon location. PLoS Genet 2006; 2:e212. [PMID: 17173485 PMCID: PMC1698948 DOI: 10.1371/journal.pgen.0020212] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 11/01/2006] [Indexed: 12/17/2022] Open
Abstract
Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.
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Affiliation(s)
- Abram Gabriel
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- * To whom correspondence should be addressed. E-mail: (AG); (MJD)
| | - Johannes Dapprich
- Generation Biotech, Lawrenceville, New Jersey, United States of America
| | - Mark Kunkel
- Generation Biotech, Lawrenceville, New Jersey, United States of America
| | - David Gresham
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Stephen C Pratt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Maitreya J Dunham
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, United States of America
- * To whom correspondence should be addressed. E-mail: (AG); (MJD)
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N/A, 张 万. N/A. Shijie Huaren Xiaohua Zazhi 2006; 14:1714-1720. [DOI: 10.11569/wcjd.v14.i17.1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Res 2006; 34:e57. [PMID: 16648358 PMCID: PMC1450332 DOI: 10.1093/nar/gkl184] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed. However, many transposons preferentially insert at specific nucleotide sequences. It is unclear to what extent such bias affects their usefulness as mutagenesis tools. Here, we examine insertion site specificity and global insertion behavior of two mini-transposons previously used for large-scale gene disruption in Saccharomyces cerevisiae: Tn3 and Tn7. Using an expanded set of insertion data, we confirm that Tn3 displays marked preference for the AT-rich 5 bp consensus site TA[A/T]TA, whereas Tn7 displays negligible target site preference. On a genome level, both transposons display marked non-uniform insertion behavior: certain sites are targeted far more often than expected, and both distributions depart drastically from Poisson. Thus, to compare their insertion behavior on a genome level, we developed a windowed Kolmogorov–Smirnov (K–S) test to analyze transposon insertion distributions in sequence windows of various sizes. We find that when scored in large windows (>300 bp), both Tn3 and Tn7 distributions appear uniform, whereas in smaller windows, Tn7 appears uniform while Tn3 does not. Thus, both transposons are effective tools for gene disruption, but Tn7 does so with less duplication and a more uniform distribution, better approximating the behavior of the ideal transposon.
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Affiliation(s)
- Michael Seringhaus
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology and Life Sciences Institute, University of MichiganAnn Arbor, MI 48109-2216, USA
| | - John Hartigan
- Department of Statistics, Yale UniversityNew Haven, CT 06520, USA
| | - Michael Snyder
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew Haven, CT 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale UniversityNew Haven, CT 06520, USA
- To whom correspondence should be addressed: Tel: 203 432 6105; Fax: 203 432 6946;
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Current awareness on yeast. Yeast 2005; 22:593-600. [PMID: 16003861 DOI: 10.1002/yea.1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Zhang C, Kitsberg D, Chy H, Zhou Q, Morrison JR. Transposon-mediated generation of targeting vectors for the production of gene knockouts. Nucleic Acids Res 2005; 33:e24. [PMID: 15699181 PMCID: PMC549422 DOI: 10.1093/nar/gni014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vectors used for gene targeting experiments usually consist of a selectable marker flanked by two regions of homology to the targeted gene. In a homologous recombination event, the selectable marker replaces an essential element of the target gene rendering it inactive. Other applications of gene targeting technology include gene replacement (knockins) and conditional vectors which allow for the generation of inducible or tissue-specific gene-targeting events. The assembly of gene-targeting vectors is generally a laborious process requiring considerable technical skill. The procedures presented here report the application of transposons as tools for the construction of targeting vectors. Two mini-Mu transposons were sequentially inserted by in vitro transposition at each side of the region targeted for deletion. One such transposon carries an antibiotic resistance marker suitable for selection in mammalian cells. A deletion is then generated between the two transposons either by LoxP-induced recombination or by restriction digestion followed by ligation. This deletion removes part of both transposons plus the targeted region in between, leaving a transposon carrying the selectable marker flanked by two arms which are homologous to the targeted gene. Targeting vectors constructed using these transposons were electroporated into embryonic stem cells and shown to be effective in gene-targeting events.
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Affiliation(s)
- Chunfang Zhang
- CopyRat Pty Ltd 27-31 Wright Street, Clayton, Victoria 3168, Australia.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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