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Murphy RO, Beckmann JF. Using Baker's Yeast to Determine Functions of Novel Wolbachia (and Other Prokaryotic) Effectors. Methods Mol Biol 2024; 2739:321-336. [PMID: 38006560 DOI: 10.1007/978-1-0716-3553-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Yeasts are single-celled eukaryotic organisms classified as fungi, mostly in the phylum Ascomycota. Of about 1500 named species, Saccharomyces cerevisiae, also known as baker's yeast, domesticated by humans in the context of cooking and brewing, is a profound genetic tool for exploring functions of novel effector proteins from Wolbachia and prokaryotes in general. Wolbachia is a Gram-negative alpha-proteobacterium that infects up to ~75% of all insects as an obligate intracellular microbe (Jeyaprakash A, Hoy MA, Insect Mol Biol 9:393-405, 2000). Wolbachia's lifestyle presents unique challenges for researchers. Wolbachia cannot be axenically cultured and has never been genetically manipulated. Furthermore, many Wolbachia genes have no known function or well-annotated orthologs in other genomes. Yet given the effects of Wolbachia on host phenotypes, which have considerable practical applications for pest control, they undoubtedly involve secreted effector proteins that interact with host gene products. Studying these effectors is challenging with Wolbachia's current genetic limitations. However, some of the constraints to working with Wolbachia can be overcome by expressing candidate proteins in S. cerevisiae. This approach capitalizes on yeast's small genome (~6500 genes), typical eukaryotic cellular organization, and the sophisticated suite of genetic tools available for its manipulation in culture. Thus, yeast can serve as a powerful mock eukaryotic host background to study Wolbachia effector function. Specifically, yeast is used for recombinant protein expression, drug discovery, protein localization studies, protein interaction mapping (yeast two-hybrid system), modeling chromosomal evolution, and examining interactions between proteins responsible for complex phenotypes in less tractable prokaryotic systems. As an example, the paired genes responsible for Wolbachia-mediated cytoplasmic incompatibility (CI) encode novel proteins with limited homology to other known proteins, and no obvious function. This article details how S. cerevisiae was used as an initial staging ground to explore the molecular basis of one of Wolbachia's trademark phenotypes (CI).
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Affiliation(s)
- Richard O Murphy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.
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2
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Wu P, Zhou J, Yu Y, Lu H. Characterization of essential elements for improved episomal expressions in
Kluyveromyces marxianus. Biotechnol J 2022; 17:e2100382. [DOI: 10.1002/biot.202100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/16/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Pingping Wu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
- National Technology Innovation Center of Synthetic Biology Tianjin China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China
- Shanghai Engineering Research Center of Industrial Microorganisms Shanghai China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology Shanghai China
- National Technology Innovation Center of Synthetic Biology Tianjin China
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4
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Parapouli M, Vasileiadis A, Afendra AS, Hatziloukas E. Saccharomyces cerevisiae and its industrial applications. AIMS Microbiol 2020; 6:1-31. [PMID: 32226912 PMCID: PMC7099199 DOI: 10.3934/microbiol.2020001] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/19/2020] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is the best studied eukaryote and a valuable tool for most aspects of basic research on eukaryotic organisms. This is due to its unicellular nature, which often simplifies matters, offering the combination of the facts that nearly all biological functions found in eukaryotes are also present and well conserved in S. cerevisiae. In addition, it is also easily amenable to genetic manipulation. Moreover, unlike other model organisms, S. cerevisiae is concomitantly of great importance for various biotechnological applications, some of which date back to several thousands of years. S. cerevisiae's biotechnological usefulness resides in its unique biological characteristics, i.e., its fermentation capacity, accompanied by the production of alcohol and CO2 and its resilience to adverse conditions of osmolarity and low pH. Among the most prominent applications involving the use of S. cerevisiae are the ones in food, beverage -especially wine- and biofuel production industries. This review focuses exactly on the function of S. cerevisiae in these applications, alone or in conjunction with other useful microorganisms involved in these processes. Furthermore, various aspects of the potential of the reservoir of wild, environmental, S. cerevisiae isolates are examined under the perspective of their use for such applications.
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Affiliation(s)
- Maria Parapouli
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
| | - Anastasios Vasileiadis
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
| | - Amalia-Sofia Afendra
- Genetics Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Efstathios Hatziloukas
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
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5
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Hohnholz R, Achstetter T. Recombinant multicopy plasmids in yeast – interactions with the endogenous 2 μm. FEMS Yeast Res 2019; 19:5425451. [DOI: 10.1093/femsyr/foz001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/09/2019] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT
Flp-mediated site specific intramolecular recombination in Saccharomyces cerevisiae is considered responsible for amplification of the endogenous 2 μm plasmid. For YEp-type vectors, a similar mechanism can be imagined by which such plasmids achieve high copy numbers, a trait desired for many research applications and necessary for industrial production. We have cultivated yeast carrying one of six isomeric YEp-type model expression plasmids under two different conditions and back transformed the shuttle vectors into Escherichia coli. Our analysis of 586 ampR clones represents a high-resolution snapshot of plasmid forms present in the transformed yeast cells with a detection limit of structural changes of <2%. Altered forms summed up to about 11%, constituting likely a lower limit. We have observed two categories of recombination events. One is Flp based, with products of intermolecular recombination with the 2 μm, likely intermediates that are prerequisites for YEp-type plasmid amplification. The other type is based on Flp-independent homologous recombination leading to oligomerization of such plasmids also in a 2μm-free [cir°] strain, i.e. in the absence of Flp. Beyond the general maintenance and its functional sequences, only the gene of interest and its expression might have an impact on the physiology of the host.
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Affiliation(s)
- Ruben Hohnholz
- Department of Industrial Microbiology, City University of Applied Sciences Bremen, Neustadtswall 30, D-28199 Bremen, Germany
| | - Tilman Achstetter
- Department of Industrial Microbiology, City University of Applied Sciences Bremen, Neustadtswall 30, D-28199 Bremen, Germany
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Lin A, Zeng C, Wang Q, Zhang W, Li M, Hanna M, Xiao W. Utilization of a Strongly Inducible DDI2 Promoter to Control Gene Expression in Saccharomyces cerevisiae. Front Microbiol 2018; 9:2736. [PMID: 30505295 PMCID: PMC6250804 DOI: 10.3389/fmicb.2018.02736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/25/2018] [Indexed: 11/15/2022] Open
Abstract
Regulating target gene expression is a common method in yeast research. In Saccharomyces cerevisiae, there are several widely used regulated expression systems, such as the GAL and Tet-off systems. However, all current expression systems possess some intrinsic deficiencies. We have previously reported that the DDI2 gene can be induced to very high levels upon cyanamide or methyl methanesulfonate treatment. Here we report the construction of gene expression systems based on the DDI2 promoter in both single- and multi-copy plasmids. Using GFP as a reporter gene, it was demonstrated that the target gene expression could be increased by up to 2,000-fold at the transcriptional level by utilizing the above systems. In addition, a DDI2-based construct was created for promoter shuffling in the budding yeast genome to control endogenous gene expression. Overall, this study offers a set of convenient and highly efficient experimental tools to control target gene expression in budding yeast.
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Affiliation(s)
- Aiyang Lin
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chuanwen Zeng
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Qian Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Wenqing Zhang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Mengyao Li
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michelle Hanna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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Phung HTT, Nguyen HLH, Nguyen DH. The possible function of Flp1 in homologous recombination repair in Saccharomyces cerevisiae. AIMS GENETICS 2018; 5:161-176. [PMID: 31435519 PMCID: PMC6698574 DOI: 10.3934/genet.2018.2.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/18/2018] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae Mus81 is a structure-selective endonuclease which constitutes an alternative pathway in parallel with the helicase-topoisomerase Sgs1-Top3-Rmi1 complex to resolve a number of DNA intermediates during DNA replication, repair, and homologous recombination. Previously, it was showed that the N-terminal region of Mus81 was required for its in vivo function in a redundant manner with Sgs1; mus81Δ120N mutant that lacks the first 120 amino acid residues at the N-terminus exhibited synthetic lethality in combination with the loss of SGS1. In this study, the physiologically important role of the N-terminal region of Mus81 in processing toxic intermediates was further investigated. We examined the cellular defect of sgs1Δmus81Δ100N cells and observed that although viable, the cells became very sensitive to DNA damaging agents. A single-copy suppressor screening to seek for a factor(s) that could rescue the drug sensitivity of sgs1Δmus81Δ100N cells was performed and revealed that Flp1, a site-specific recombinase 1 encoded on the 2-micron plasmid was a suppressor. Moreover, Flp1 overexpression could partially suppress the drug sensitivity of mus81Δ cells at 37 °C. Our findings suggest a possible function of Flp1 in coordination with Mus81 and Sgs1 to jointly resolve the branched-DNA structures generated in cells attempting to repair DNA damages.
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Affiliation(s)
- Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam
| | | | - Dung Hoang Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam
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Lei J, Miao Y, Lan Y, Han X, Liu H, Gan Y, Niu L, Wang Y, Zheng Z. A Novel Complementation Assay for Quick and Specific Screen of Genes Encoding Glycerol-3-Phosphate Acyltransferases. FRONTIERS IN PLANT SCIENCE 2018; 9:353. [PMID: 29616064 PMCID: PMC5867339 DOI: 10.3389/fpls.2018.00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
The initial step in glycerolipid biosynthesis, especially in diverse allopolyploid crop species, is poorly understood, mainly due to the lack of an effective and convenient method for functional characterization of genes encoding glycerol-3-phosphate acyltransferases (GPATs) catalyzing this reaction. Here we present a novel complementation assay for quick and specific characterization of GPAT-encoding genes. Its key design involves rational construction of yeast conditional lethal gat1Δgat2Δ double mutant bearing the heterologous Arabidopsis AtGPAT1 gene whose leaky expression under repressed conditions does not support any non-specific growth, thereby circumventing the false positive problem encountered with the system based on the gat1Δgat2Δ mutant harboring the native episomal GAT1 gene whose leaky expression appears to be sufficient for generating enough GPAT activities for the non-specific restoration of the mutant growth. A complementation assay developed based on this novel mutant enables quick phenotypic screen of GPAT sequences. A high degree of specificity of our assay was exemplified by its ability to differentiate effectively GPAT-encoding genes from those of other fatty acyltransferases and lipid-related sequences. Using this assay, we show that Arabidopsis AtGPAT1, AtGPAT5, and AtGPAT7 can complement the phosphatidate biosynthetic defect in the double mutants. Collectively, our assay provides a powerful tool for rapid screening, validation and optimization of GPAT sequences, aiding future engineering of the initial step of the triacylglycerol biosynthesis in oilseeds.
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Affiliation(s)
- Jie Lei
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Yingchun Miao
- School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Yu Lan
- School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - Xiuxiu Han
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Hongbo Liu
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Yi Gan
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Leilei Niu
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Yanyan Wang
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Zhifu Zheng
- School of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
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9
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Xiao W, Rank GH. Curing IndustrialSaccharomycesYeasts of Parasitic 2μm Plasmid. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-48-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Wei Xiao
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W0
| | - Gerald H. Rank
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W0
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10
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Jalal D, Chalissery J, Hassan AH. Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases. Nucleic Acids Res 2017; 45:2242-2261. [PMID: 28115630 PMCID: PMC5389695 DOI: 10.1093/nar/gkw1369] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/02/2017] [Indexed: 01/08/2023] Open
Abstract
The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyces cerevisiae have advanced our understanding of the DNA damage response, as well as the mechanisms the cell employs to maintain genome stability and how these mechanisms are regulated. Eukaryotic cells utilize post-translational modifications as a means for fine-tuning protein functions. Ubiquitylation and SUMOylation involve the attachment of small protein molecules onto proteins to modulate function or protein–protein interactions. SUMO in particular, was shown to act as a molecular glue when DNA damage occurs, facilitating the assembly of large protein complexes in repair foci. In other instances, SUMOylation alters a protein's biochemical activities, and interactions. SUMO-targeted ubiquitin ligases (STUbLs) are enzymes that target SUMOylated proteins for ubiquitylation and subsequent degradation, providing a function for the SUMO modification in the regulation and disassembly of repair complexes. Here, we discuss the major contributions of SUMO and STUbLs in the regulation of DNA damage repair pathways as well as in the maintenance of critical regions of the genome, namely rDNA regions, telomeres and the 2 μm circle in budding yeast.
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Affiliation(s)
- Deena Jalal
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Jisha Chalissery
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Ahmed H Hassan
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
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Abstract
Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching?
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12
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Jensen IS, Inui K, Drakulic S, Jayaprakash S, Sander B, Golas MM. Expression of Flp Protein in a Baculovirus/Insect Cell System for Biotechnological Applications. Protein J 2017; 36:332-342. [PMID: 28660316 DOI: 10.1007/s10930-017-9724-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Saccharomyces cerevisiae Flp protein is a site-specific recombinase that recognizes and binds to the Flp recognition target (FRT) site, a specific sequence comprised of at least two inverted repeats separated by a spacer. Binding of four monomers of Flp is required to mediate recombination between two FRT sites. Because of its site-specific cleavage characteristics, Flp has been established as a genome engineering tool. Amongst others, Flp is used to direct insertion of genes of interest into eukaryotic cells based on single and double FRT sites. A Flp-encoding plasmid is thereby typically cotransfected with an FRT-harboring donor plasmid. Moreover, Flp can be used to excise DNA sequences that are flanked by FRT sites. Therefore, the aim of this study was to determine whether Flp protein and its step-arrest mutant, FlpH305L, recombinantly expressed in insect cells, can be used for biotechnological applications. Using a baculovirus system, the proteins were expressed as C-terminally 3 × FLAG-tagged proteins and were purified by anti-FLAG affinity selection. As demonstrated by electrophoretic mobility shift assays (EMSAs), purified Flp and FlpH305L bind to FRT-containing DNA. Furthermore, using a cell assay, purified Flp was shown to be active in recombination and to mediate efficient insertion of a donor plasmid into the genome of target cells. Thus, these proteins can be used for applications such as DNA-binding assays, in vitro recombination, or genome engineering.
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Affiliation(s)
- Ida S Jensen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Ken Inui
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Srdja Drakulic
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Sakthidasan Jayaprakash
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Bjoern Sander
- Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Monika M Golas
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark.
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Schwarzhans JP, Luttermann T, Wibberg D, Winkler A, Hübner W, Huser T, Kalinowski J, Friehs K. A Mitochondrial Autonomously Replicating Sequence from Pichia pastoris for Uniform High Level Recombinant Protein Production. Front Microbiol 2017; 8:780. [PMID: 28512458 PMCID: PMC5411459 DOI: 10.3389/fmicb.2017.00780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
Pichia pastoris is a non-conventional methylotrophic yeast that is widely used for recombinant protein production, typically by stably integrating the target gene into the genome as part of an expression cassette. However, the comparatively high clonal variability associated with this approach usually necessitates a time intense screening step in order to find strains with the desired productivity. Some of the factors causing this clonal variability can be overcome using episomal vectors containing an autonomously replicating sequence (ARS). Here, we report on the discovery, characterization, and application of a fragment of mitochondrial DNA from P. pastoris for use as an ARS. First encountered as an off-target event in an experiment aiming for genomic integration, the newly created circular plasmid named “pMito” consists of the expression cassette and a fragment of mitochondrial DNA. Multiple matches to known ARS consensus sequence motifs, but no exact match to known chromosomal ARS from P. pastoris were detected on the fragment, indicating the presence of a novel ARS element. Different variants of pMito were successfully used for transformation and their productivity characteristics were assayed. All analyzed clones displayed a highly uniform expression level, exceeding by up to fourfold that of a reference with a single copy integrated in its genome. Expressed GFP could be localized exclusively to the cytoplasm via super-resolution fluorescence microscopy, indicating that pMito is present in the nucleus. While expression levels were homogenous among pMito clones, an apparent upper limit of expression was visible that could not be explained based on the gene dosage. Further investigation is necessary to fully understand the bottle-neck hindering this and other ARS vectors in P. pastoris from reaching their full capability. Lastly, we could demonstrate that the mitochondrial ARS from P. pastoris is also suitable for episomal vector transformation in Saccharomyces cerevisiae, widening the potential for biotechnological application. pMito displayed strong potential to reduce clonal variability in experiments targeting recombinant protein production. These findings also showcase the as of yet largely untapped potential of mitochondrial ARS from different yeasts for biotechnological applications.
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Affiliation(s)
- Jan-Philipp Schwarzhans
- Fermentation Engineering, Faculty of Technology, Bielefeld UniversityBielefeld, Germany.,Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Tobias Luttermann
- Fermentation Engineering, Faculty of Technology, Bielefeld UniversityBielefeld, Germany.,Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld UniversityBielefeld, Germany
| | - Thomas Huser
- Biomolecular Photonics, Faculty of Physics, Bielefeld UniversityBielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Karl Friehs
- Fermentation Engineering, Faculty of Technology, Bielefeld UniversityBielefeld, Germany
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Pindyurin AV. Genomic mapping of chromatin proteins by using Dam inv modification of an FLP-dependent DamID approach. DOKL BIOCHEM BIOPHYS 2017; 472:15-18. [PMID: 28421443 DOI: 10.1134/s1607672917010057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Indexed: 11/22/2022]
Abstract
To identify interactions of chromatin proteins with the genome of the cell type of interest that is a part of heterologous tissues and organs of Drosophila, an FLP-dependent DamID approach was recently developed [4], which does not require sorting of cells or nuclei. Here, a modification of this approach, Daminv, is described. The modified approach was validated by generating the binding pattern of the LAM protein, a component of the inner membrane of the nuclear envelope, with the genome of glial cells of the Drosophila larval central brains.
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Affiliation(s)
- A V Pindyurin
- Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands. .,Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia.
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15
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Møller TSB, Hay J, Saxton MJ, Bunting K, Petersen EI, Kjærulff S, Finnis CJA. Human β-defensin-2 production from S. cerevisiae using the repressible MET17 promoter. Microb Cell Fact 2017; 16:11. [PMID: 28100236 PMCID: PMC5241953 DOI: 10.1186/s12934-017-0627-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background Baker’s yeast Saccharomyces cerevisiae is a proven host for the commercial production of recombinant biopharmaceutical proteins. For the manufacture of heterologous proteins with activities deleterious to the host it can be desirable to minimise production during the growth phase and induce production late in the exponential phase. Protein expression by regulated promoter systems offers the possibility of improving productivity in this way by separating the recombinant protein production phase from the yeast growth phase. Commonly used inducible promoters do not always offer convenient solutions for industrial scale biopharmaceutical production with engineered yeast systems. Results Here we show improved secretion of the antimicrobial protein, human β-defensin-2, (hBD2), using the S. cerevisiae MET17 promoter by repressing expression during the growth phase. In shake flask culture, a higher final concentration of human β-defensin-2 was obtained using the repressible MET17 promoter system than when using the strong constitutive promoter from proteinase B (PRB1) in a yeast strain developed for high-level commercial production of recombinant proteins. Furthermore, this was achieved in under half the time using the MET17 promoter compared to the PRB1 promoter. Cell density, plasmid copy-number, transcript level and protein concentration in the culture supernatant were used to study the effects of different initial methionine concentrations in the culture media for the production of human β-defensin-2 secreted from S. cerevisiae. Conclusions The repressible S. cerevisiae MET17 promoter was more efficient than a strong constitutive promoter for the production of human β-defensin-2 from S. cerevisiae in small-scale culture and offers advantages for the commercial production of this and other heterologous proteins which are deleterious to the host organism. Furthermore, the MET17 promoter activity can be modulated by methionine alone, which has a safety profile applicable to biopharmaceutical manufacturing.
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Affiliation(s)
- Thea S B Møller
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.,Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Joanna Hay
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Malcolm J Saxton
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Karen Bunting
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Evamaria I Petersen
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Søren Kjærulff
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Christopher J A Finnis
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.
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16
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Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res 2015; 26:36-49. [PMID: 26566658 PMCID: PMC4691749 DOI: 10.1101/gr.193433.115] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 11/12/2015] [Indexed: 01/08/2023]
Abstract
Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 synIXR SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed loxPsym sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3′ UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.
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Affiliation(s)
- Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China; Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, United Kingdom
| | - Giovanni Stracquadanio
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kun Yang
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Leslie A Mitchell
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Biochemistry and Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Medical Center, New York, New York 10016, USA
| | - Yaxin Xue
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yizhi Cai
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, United Kingdom
| | - Tai Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jessica S Dymond
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Kang Kang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | | | | | | | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Science, Hangzhou 310058, China
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Medical Center, New York, New York 10016, USA
| | - Joel S Bader
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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17
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Strope PK, Kozmin SG, Skelly DA, Magwene PM, Dietrich FS, McCusker JH. 2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae. FEMS Yeast Res 2015; 15:fov090. [PMID: 26463005 DOI: 10.1093/femsyr/fov090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/27/2022] Open
Abstract
We determined that extrachromosomal 2μ plasmid was present in 67 of the Saccharomyces cerevisiae 100-genome strains; in addition to variation in the size and copy number of 2μ, we identified three distinct classes of 2μ. We identified 2μ presence/absence and class associations with populations, clinical origin and nuclear genotypes. We also screened genome sequences of S. paradoxus, S. kudriavzevii, S. uvarum, S. eubayanus, S. mikatae, S. arboricolus and S. bayanus strains for both integrated and extrachromosomal 2μ. Similar to S. cerevisiae, we found no integrated 2μ sequences in any S. paradoxus strains. However, we identified part of 2μ integrated into the genomes of some S. uvarum, S. kudriavzevii, S. mikatae and S. bayanus strains, which were distinct from each other and from all extrachromosomal 2μ. We identified extrachromosomal 2μ in one S. paradoxus, one S. eubayanus, two S. bayanus and 13 S. uvarum strains. The extrachromosomal 2μ in S. paradoxus, S. eubayanus and S. cerevisiae were distinct from each other. In contrast, the extrachromosomal 2μ in S. bayanus and S. uvarum strains were identical with each other and with one of the three classes of S. cerevisiae 2μ, consistent with interspecific transfer.
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Affiliation(s)
- Pooja K Strope
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Stanislav G Kozmin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Daniel A Skelly
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Paul M Magwene
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Fred S Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - John H McCusker
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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18
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Deficient sumoylation of yeast 2-micron plasmid proteins Rep1 and Rep2 associated with their loss from the plasmid-partitioning locus and impaired plasmid inheritance. PLoS One 2013; 8:e60384. [PMID: 23555963 PMCID: PMC3610928 DOI: 10.1371/journal.pone.0060384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 02/26/2013] [Indexed: 11/19/2022] Open
Abstract
The 2-micron plasmid of the budding yeast Saccharomyces cerevisiae encodes copy-number amplification and partitioning systems that enable the plasmid to persist despite conferring no advantage to its host. Plasmid partitioning requires interaction of the plasmid Rep1 and Rep2 proteins with each other and with the plasmid-partitioning locus STB. Here we demonstrate that Rep1 stability is reduced in the absence of Rep2, and that both Rep proteins are sumoylated. Lysine-to-arginine substitutions in Rep1 and Rep2 that inhibited their sumoylation perturbed plasmid inheritance without affecting Rep protein stability or two-hybrid interaction between Rep1 and Rep2. One-hybrid and chromatin immunoprecipitation assays revealed that Rep1 was required for efficient retention of Rep2 at STB and that sumoylation-deficient mutants of Rep1 and Rep2 were impaired for association with STB. The normal co-localization of both Rep proteins with the punctate nuclear plasmid foci was also lost when Rep1 was sumoylation-deficient. The correlation of Rep protein sumoylation status with plasmid-partitioning locus association suggests a theme common to eukaryotic chromosome segregation proteins, sumoylated forms of which are found enriched at centromeres, and between the yeast 2-micron plasmid and viral episomes that depend on sumoylation of their maintenance proteins for persistence in their hosts.
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19
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Cell lineage tracing techniques for the study of brain development and regeneration. Int J Dev Neurosci 2012; 30:560-9. [PMID: 22944528 DOI: 10.1016/j.ijdevneu.2012.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/12/2012] [Accepted: 08/12/2012] [Indexed: 11/22/2022] Open
Abstract
Characterization of the means by which cells are generated and organized to make an organ as complex as the brain is a formidable task. Understanding how adult stem cells give rise to progeny that integrate into the existing structures during regeneration or in response to injury is equally challenging. Lineage tracing techniques are essential to studying cell behaviors such as proliferation, migration and differentiation, since they allow stem or precursor cells to be marked and their descendants followed and characterized over time. Here, we describe some of the key lineage tracing techniques available to date, highlighting advantages and drawbacks and focusing on their application in neural fate mapping. The more traditional methods are now joined by exciting new approaches to provide a vast array of tools at the disposal of neurobiologists.
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20
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Satwika D, Klassen R, Meinhardt F. Anticodon nuclease encoding virus-like elements in yeast. Appl Microbiol Biotechnol 2012; 96:345-56. [PMID: 22899498 DOI: 10.1007/s00253-012-4349-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/29/2022]
Abstract
A variety of yeast species are known to host systems of cytoplasmic linear dsDNA molecules that establish replication and transcription independent of the nucleus via self-encoded enzymes that are phylogenetically related to those encoded by true infective viruses. Such yeast virus-like elements (VLE) fall into two categories: autonomous VLEs encode all the essential functions for their inheritance, and additional, dependent VLEs, which may encode a toxin-antitoxin system, generally referred to as killer toxin and immunity. In the two cases studied in depth, killer toxin action relies on chitin binding and hydrophobic domains, together allowing a separate toxic subunit to sneak into the target cell. Mechanistically, the latter sabotages codon-anticodon interaction by endonucleolytic cleavage of specific tRNAs 3' of the wobble nucleotide. This primary action provokes a number of downstream effects, including DNA damage accumulation, which contribute to the cell-killing efficiency and highlight the importance of proper transcript decoding capacity for other cellular processes than translation itself. Since wobble uridine modifications are crucial for efficient anticodon nuclease (ACNase) action of yeast killer toxins, the latter are valuable tools for the characterization of a surprisingly complex network regulating the addition of wobble base modifications in tRNA.
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Affiliation(s)
- Dhira Satwika
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstr. 3, 48149, Münster, Germany
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21
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Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res 2012; 22:908-24. [PMID: 22369888 PMCID: PMC3337436 DOI: 10.1101/gr.130310.111] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this species--i.e., its "pan-genome"--has been less explored. We created a multispecies microarray platform containing probes covering the genomes of several Saccharomyces species: S. cerevisiae, including regions not found in the standard laboratory S288c strain, as well as the mitochondrial and 2-μm circle genomes-plus S. paradoxus, S. mikatae, S. kudriavzevii, S. uvarum, S. kluyveri, and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) on 83 different S. cerevisiae strains collected across a wide range of habitats; of these, 69 were commercial wine strains, while the remaining 14 were from a diverse set of other industrial and natural environments. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole-genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.
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Affiliation(s)
- Barbara Dunn
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
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22
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23
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Dato L, Branduardi P, Passolunghi S, Cattaneo D, Riboldi L, Frascotti G, Valli M, Porro D. Advances in molecular tools for the use of Zygosaccharomyces bailii as host for biotechnological productions and construction of the first auxotrophic mutant. FEMS Yeast Res 2010; 10:894-908. [DOI: 10.1111/j.1567-1364.2010.00668.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
Centromeres are chromosomal elements that are both necessary and sufficient for chromosome segregation. However, the puzzlingly broad range in centromere complexity, from simple "point" centromeres to multi-megabase arrays of DNA satellites, has defied explanation. We posit that ancestral centromeres were epigenetically defined and that point centromeres, such as those of budding yeast, have derived from the partitioning elements of selfish plasmids. We further propose that the larger centromere sizes in plants and animals and the rapid evolution of their centromeric proteins is the result of an intense battle for evolutionary dominance due to the asymmetric retention of only one product of female meiosis.
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Affiliation(s)
- Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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25
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Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. EUKARYOTIC CELL 2009; 8:1521-31. [PMID: 19666779 DOI: 10.1128/ec.00110-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A 10-kb region of the nuclear genome of the yeast Vanderwaltozyma polyspora contains an unusual cluster of five pseudogenes homologous to five different genes from yeast killer viruses, killer plasmids, the 2microm plasmid, and a Penicillium virus. By further database searches, we show that this phenomenon is not unique to V. polyspora but that about 40% of the sequenced genomes of Saccharomycotina species contain integrated copies of genes from DNA plasmids or RNA viruses. We propose the name NUPAVs (nuclear sequences of plasmid and viral origin) for these objects, by analogy to NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) of organellar origin. Although most of the NUPAVs are pseudogenes, one intact and active gene that was formed in this way is the KHS1 chromosomal killer locus of Saccharomyces cerevisiae. We show that KHS1 is a NUPAV related to M2 killer virus double-stranded RNA. Many NUPAVs are located beside tRNA genes, and some contain sequences from a mixture of different extrachromosomal sources. We propose that NUPAVs are sequences that were captured by the nuclear genome during the repair of double-strand breaks that occurred during evolution and that some of their properties may be explained by repeated breakage at fragile chromosomal sites.
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26
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Abstract
The rate of spontaneous change from psi(-) to the psi(+) condition, determined in yeast by states of the Sup35p protein, is briefly discussed together with the conditions necessary for such change to occur. Conditions that promote and which affect the rate of induction of psi(+) in Sup35p and of other prion-forming proteins to their respective prion forms are also discussed. These include the influence of the amount of non-prion protein, the presence of other prions, the activity of chaperones, and brief descriptions of the role of native sequences in the proteins and how alteration of sequences in prion-forming proteins influences the rate of induction of [prion(+)] and amyloid forms. The second part of this article discusses the conditions which affect the reversion of psi(+) to psi-, including factors which affect the copy-number of prion "seeds" or propagons and their partition. The principal factor discussed is the activity of the chaperone Hsp104, but the existence of other factors, such protein sequence and of other, less well-studied agents is touched upon and comparisons are made, as appropriate, with studies with other yeast prions. We conclude with a discussion of models of maintenance, in particular that of Tanaka et al. published in Nature (2006), which provides much insight into the phenotypic and genetic parameters of the numerous "variants" of prions increasingly being described in the literature.
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Affiliation(s)
- Brian S Cox
- Department of Biosciences, University of Kent, Canterbury, Kent, UK
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Whiteson KL, Chen Y, Chopra N, Raymond AC, Rice PA. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. ACTA ACUST UNITED AC 2007; 14:121-9. [PMID: 17317566 PMCID: PMC1857323 DOI: 10.1016/j.chembiol.2007.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 01/30/2007] [Indexed: 11/23/2022]
Abstract
Flp provides a unique opportunity to apply the tools of chemical biology to phosphoryl transfer reactions. Flp and other tyrosine recombinases catalyze site-specific DNA rearrangements via a phosphotyrosine intermediate. Unlike most related enzymes, Flp's nucleophilic tyrosine derives from a different protomer than the remainder of its active site. Because the tyrosine can be supplied exogenously, nonnatural synthetic analogs can be used. Here we examine the catalytic role of Flp's conserved H305. DNA cleavage was studied using a peptide containing either tyrosine (pKa congruent with 10) or 3-fluoro-tyrosine (pKa congruent with 8.4). Religation was studied using DNA substrates with 3'-phospho-cresol (pKa congruent with 10) or 3'-para-nitro-phenol (pKa congruent with 7.1). In both cases, the tyrosine analog with the lower pKa specifically restored the activity of an H305 mutant. These results provide experimental evidence that this conserved histidine functions as a general acid/base catalyst in tyrosine recombinases.
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Affiliation(s)
| | | | - Neeraj Chopra
- Biochemistry and Molecular Biology Department, University of Chicago, 929 E. 57 St. CIS W125, Current: Department of Pathology, The University of Chicago, N344, 5841 South Maryland Avenue, Chicago, Illinois 60637,
| | - Amy C. Raymond
- deCODE biostructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, Current: Sloan-Kettering Institute 1275 York Ave., Box 73, New York, NY 10021,
| | - Phoebe A. Rice
- Biochemistry and Molecular Biology Department, The University of Chicago, 929 E. 57 St. CIS W125, Chicago, IL 60637, , phone: 773 834 1723, fax: 773 702 0439
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28
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Falcon AA, Rios N, Aris JP. 2-micron circle plasmids do not reduce yeast life span. FEMS Microbiol Lett 2006; 250:245-51. [PMID: 16085372 PMCID: PMC3586270 DOI: 10.1016/j.femsle.2005.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 06/22/2005] [Accepted: 07/12/2005] [Indexed: 10/25/2022] Open
Abstract
Extrachromosomal rDNA circles (ERCs) and recombinant origin-containing plasmids (ARS-plasmids) are thought to reduce replicative life span in the budding yeast Saccharomyces cerevisiae due to their accumulation in yeast cells by an asymmetric inheritance process known as mother cell bias. Most commonly used laboratory yeast strains contain the naturally occurring, high copy number 2-micron circle plasmid. 2-micron plasmids are known to exhibit stable mitotic inheritance, unlike ARS-plasmids and ERCs, but the fidelity of inheritance during replicative aging and cell senescence has not been studied. This raises the question: do 2-micron circles reduce replicative life span? To address this question we have used a convenient method to cure laboratory yeast strains of the 2-micron plasmid. We find no difference in the replicative life spans of otherwise isogenic cir+ and cir0 strains, with and without the 2-micron plasmid. Consistent with this, we find that 2-micron circles do not accumulate in old yeast cells. These findings indicate that naturally occurring levels of 2-micron plasmids do not adversely affect life span, and that accumulation due to asymmetric inheritance is required for reduction of replicative life span by DNA episomes.
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Affiliation(s)
- Alaric A Falcon
- Department of Anatomy and Cell Biology, Health Science Center, 1600 SW Archer Road, University of Florida, Gainesville, FL 32610-0235, USA.
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29
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Dobson MJ, Pickett AJ, Velmurugan S, Pinder JB, Barrett LA, Jayaram M, Chew JSK. The 2 microm plasmid causes cell death in Saccharomyces cerevisiae with a mutation in Ulp1 protease. Mol Cell Biol 2005; 25:4299-310. [PMID: 15870298 PMCID: PMC1087720 DOI: 10.1128/mcb.25.10.4299-4310.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 11/20/2004] [Accepted: 02/13/2005] [Indexed: 11/20/2022] Open
Abstract
The 2 microm circle plasmid confers no phenotype in wild-type Saccharomyces cerevisiae but in a nib1 mutant, an elevated plasmid copy number is associated with cell death. Complementation was used to identify nib1 as a mutant allele of the ULP1 gene that encodes a protease required for removal of a ubiquitin-like protein, Smt3/SUMO, from protein substrates. The nib1 mutation replaces conserved tryptophan 490 with leucine in the protease domain of Ulp1. Complete deletion of ULP1 is lethal, even in a strain that lacks the 2 microm circle. Partial deletion of ULP1, like the nib1 mutation, results in clonal variations in plasmid copy number. In addition, a subset of these mutant cells produces lineages in which all cells have reduced proliferative capacity, and this phenotype is dependent upon the presence of the 2 microm circle. Segregation of the 2 microm circle requires two plasmid-encoded proteins, Rep1 and Rep2, which were found to colocalize with Ulp1 protein in the nucleus and interact with Smt3 in a two-hybrid assay. These associations and the observation of missegregation of a fluorescently tagged 2 microm circle reporter plasmid in a subset of ulp1 mutant cells suggest that Smt3 modification plays a role in both plasmid copy number control and segregation.
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Affiliation(s)
- Melanie J Dobson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, Nova Scotia, Canada B3H 1X5.
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Welte MA, Tetrault JM, Dellavalle RP, Lindquist SL. A new method for manipulating transgenes: engineering heat tolerance in a complex, multicellular organism. Curr Biol 2005; 3:842-53. [PMID: 15335817 DOI: 10.1016/0960-9822(93)90218-d] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/1993] [Revised: 11/03/1993] [Accepted: 11/08/1993] [Indexed: 11/27/2022]
Abstract
BACKGROUND Heat-shock proteins (hsps) are thought to protect cells against stresses, especially due to elevated temperatures. But while genetic manipulation of hsp gene expression can protect microorganisms and cultured metazoan cells against lethal stress, this has so far not been demonstrated in multicellular organisms. Testing whether expression of an hsp transgene contributes to increased stress tolerance is complicated by a general problem of transgene analysis: if the transgene cannot be targeted to a precise site in the genome, newly observed phenotypes may be due to either the action of the transgene or mutations caused by the transgene insertion. RESULTS To study the relationship between heat tolerance and hsp expression in Drosophila melanogaster, we have developed a novel method for transgene analysis, based upon the site-specific FLP recombinase. The method employs site-specific sister chromatid exchange to create an allelic series of transgene insertions that share the same integration site, but differ in transgene copy number. Phenotypic differences between members of this series can be confidently attributed to the transgenes. Using such an allelic series and a novel thermotolerance assay for Drosophila embryos, we investigated the role of the 70 kD heat-shock protein, Hsp 70, in thermotolerance. At early embryonic stages, Hsp70 accumulation was rate-limiting for thermotolerance, and elevated Hsp70 expression increased survival at extreme temperatures. CONCLUSION Our results provide an improved method for analyzing transgenes and demonstrate that, in Drosophila, Hsp70 is a critical thermotolerance factor. They show, moreover, that manipulating the expression of a single hsp can be sufficient to improve the stress tolerance of a complex multicellular organism.
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Affiliation(s)
- M A Welte
- Howard Hughes Medical Institute and Department of Molecular Genetics and Cell Biology, The University of Chicago, 5841 South Maryland, MC 1028 Chicago, Illinois 60637, USA
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Boucher N, McNicoll F, Laverdière M, Rochette A, Chou MN, Papadopoulou B. The ribosomal RNA gene promoter and adjacent cis-acting DNA sequences govern plasmid DNA partitioning and stable inheritance in the parasitic protozoan Leishmania. Nucleic Acids Res 2004; 32:2925-36. [PMID: 15161957 PMCID: PMC419617 DOI: 10.1093/nar/gkh617] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Detailed analysis of the Leishmania donovani ribosomal RNA (rRNA) gene promoter region has allowed the identification of cis-acting sequences involved in plasmid DNA partitioning and stable plasmid inheritance. We report that plasmids bearing the 350 bp rRNA promoter along with the 200 bp region immediately 3' to the promoter exhibited a 6.5-fold increase in transformation frequency and were transmitted to daughter cells as single-copy molecules. This is in contrast to what has been observed for plasmid molecules in this organism so far. Moreover, we show that these low-copy-number plasmids displayed a remarkable mitotic stability in the absence of selective pressure. The region in the vicinity of the RNA pol I transcription initiation site, and also in the adjacent 200 nt, displays a complex structural organization and shares sequence similarity to the yeast autonomously replicating consensus sequence and centromere DNA elements. Deletion analyses indicated that these elements were necessary but not sufficient for plasmid DNA partitioning and stable inheritance, and that the rRNA promoter region was required for optimal function. These results suggest an interplay between RNA pol I transcription, DNA replication, DNA partitioning and mitotic stability in trypanosomatids. This is the first example of defined DNA elements for plasmid partitioning and stable inheritance in the protozoan parasite Leishmania.
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Affiliation(s)
- Nathalie Boucher
- Infectious Disease Research Center, CHUL Research Center, Faculty of Medicine, Laval University, Quebec, Canada
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32
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Sengupta A, Blomqvist K, Pickett AJ, Zhang Y, Chew JS, Dobson MJ. Functional domains of yeast plasmid-encoded Rep proteins. J Bacteriol 2001; 183:2306-15. [PMID: 11244071 PMCID: PMC95138 DOI: 10.1128/jb.183.7.2306-2315.2001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both of the Saccharomyces cerevisiae 2 microm circle-encoded Rep1 and Rep2 proteins are required for efficient distribution of the plasmid to daughter cells during cellular division. In this study two-hybrid and in vitro protein interaction assays demonstrate that the first 129 amino acids of Rep1 are sufficient for self-association and for interaction with Rep2. Deletion of the first 76 amino acids of Rep1 abolished the Rep1-Rep2 interaction but still allowed some self-association, suggesting that different but overlapping domains specify these interactions. Amino- or carboxy-terminally truncated Rep1 fusion proteins were unable to complement defective segregation of a 2 microm-based stability vector with rep1 deleted, supporting the idea of the requirement of Rep protein interaction for plasmid segregation but indicating a separate required function for the carboxy-terminal portion of Rep1. The results of in vitro baiting assays suggest that Rep2 contains two nonoverlapping domains, both of which are capable of mediating Rep2 self-association. The amino-terminal domain interacts with Rep1, while the carboxy-terminal domain was shown by Southwestern analysis to have DNA-binding activity. The overlapping Rep1 and Rep2 interaction domains in Rep1, and the ability of Rep2 to interact with Rep1, Rep2, and DNA, suggest a model in which the Rep proteins polymerize along the 2 microm circle plasmid stability locus, forming a structure that mediates plasmid segregation. In this model, competition between Rep1 and Rep2 for association with Rep1 determines the formation or disassembly of the segregation complex.
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Affiliation(s)
- A Sengupta
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7
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33
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Sleep D, Finnis C, Turner A, Evans L. Yeast 2 microm plasmid copy number is elevated by a mutation in the nuclear gene UBC4. Yeast 2001; 18:403-21. [PMID: 11255249 DOI: 10.1002/yea.679] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The copy number of the Saccharomyces cerevisiae endogenous 2 microm plasmid is under strict control to ensure efficient propagation to the daughter cell without significantly reducing the growth rate of the mother or the daughter cell. A recessive mutation has been identified that resulted in an elevated but stable 2 microm plasmid copy number, which could be complemented by a genomic DNA clone containing the UBC4 gene, encoding an E2 ubiquitin-conjugating enzyme. A ubc4::URA3 deletion resulted in the same elevated 2 microm plasmid copy number. An analysis of the endogenous 2 microm transcripts revealed that the steady-state abundance of REP1, REP2, FLP and RAF were all increased 4-5-fold in the mutant. Analysis of the mutant ubc4 allele identified a single base pair mutation within the UBC4 coding region, which would generate a glutamic acid to lysine amino acid substitution within a region of conserved tertiary structure located within the first alpha-helix of Ubc4p. These investigations represent the first molecular characterization of a mutation within a Saccharomyces cerevisiae nuclear gene shown to affect 2 microm steady-state plasmid copy number and implicate the ubiquitin-dependent proteolytic pathway in host control of 2 microm plasmid copy number.
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Affiliation(s)
- D Sleep
- Delta Biotechnology Ltd, Castle Court, 59 Castle Boulevard, Nottingham NG7 1FD, UK.
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34
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Mönch J, Stahl U. Polymorphisms of industrial strains ofsaccharomycesyeasts: Genotypic and phenotypic features. FOOD BIOTECHNOL 2000. [DOI: 10.1080/08905430009549984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Affiliation(s)
- J E Hughes
- Department of Biology, Utah State University, Logan 84322-5305, USA
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36
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Velmurugan S, Yang XM, Chan CSM, Dobson M, Jayaram M. Partitioning of the 2-microm circle plasmid of Saccharomyces cerevisiae. Functional coordination with chromosome segregation and plasmid-encoded rep protein distribution. J Cell Biol 2000; 149:553-66. [PMID: 10791970 PMCID: PMC2174858 DOI: 10.1083/jcb.149.3.553] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The efficient partitioning of the 2-microm plasmid of Saccharomyces cerevisiae at cell division is dependent on two plasmid-encoded proteins (Rep1p and Rep2p), together with the cis-acting locus REP3 (STB). In addition, host encoded factors are likely to contribute to plasmid segregation. Direct observation of a 2-microm-derived plasmid in live yeast cells indicates that the multiple plasmid copies are located in the nucleus, predominantly in clusters with characteristic shapes. Comparison to a single-tagged chromosome or to a yeast centromeric plasmid shows that the segregation kinetics of the 2-microm plasmid and the chromosome are quite similar during the yeast cell cycle. Immunofluorescence analysis reveals that the plasmid is colocalized with the Rep1 and Rep2 proteins within the yeast nucleus. Furthermore, the Rep proteins (and therefore the plasmid) tend to concentrate near the poles of the yeast mitotic spindle. Depolymerization of the spindle results in partial dispersion of the Rep proteins in the nucleus concomitant with a loosening in the association between plasmid molecules. In an ipl1-2 yeast strain, shifted to the nonpermissive temperature, the chromosomes and plasmid almost always missegregate in tandem. Our results suggest that, after DNA replication, plasmid distribution to the daughter cells occurs in the form of specific DNA-protein aggregates. They further indicate that the plasmid partitioning mechanism may exploit at least some of the components of the cellular machinery required for chromosomal segregation.
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Affiliation(s)
- Soundarapandian Velmurugan
- Section of Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Xian-Mei Yang
- Section of Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Clarence S.-M. Chan
- Section of Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Melanie Dobson
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7
| | - Makkuni Jayaram
- Section of Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
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37
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Morlino GB, Tizzani L, Fleer R, Frontali L, Bianchi MM. Inducible amplification of gene copy number and heterologous protein production in the yeast Kluyveromyces lactis. Appl Environ Microbiol 1999; 65:4808-13. [PMID: 10543790 PMCID: PMC91648 DOI: 10.1128/aem.65.11.4808-4813.1999] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterologous protein production can be doubled by increasing the copy number of the corresponding heterologous gene. We constructed a host-vector system in the yeast Kluyveromyces lactis that was able to induce copy number amplification of pKD1 plasmid-based vectors upon expression of an integrated copy of the plasmid recombinase gene. We increased the production and secretion of two heterologous proteins, glucoamylase from the yeast Arxula adeninivorans and mammalian interleukin-1beta, following gene dosage amplification when the heterologous genes were carried by pKD1-based vectors. The choice of the promoters for expression of the integrated recombinase gene and of the episomal heterologous genes are critical for the mitotic stability of the host-vector system.
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Affiliation(s)
- G B Morlino
- Department of Cell and Developmental Biology, University of Rome "La Sapienza," Rome 00185, Italy
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38
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O'Kennedy RD, Patching JW. The isolation of strains of Saccharomyces cerevisiae showing altered plasmid stability characteristics by means of selective continuous culture. J Biotechnol 1999; 69:203-14. [PMID: 10361727 DOI: 10.1016/s0168-1656(99)00047-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A recombinant strain of Saccharomyces cerevisiae containing a plasmid-encoded lacZ gene from Escherichia coli was grown for 420 generations under selective conditions in glucose-limited continuous culture. A ura3-based auxotrophic system was used to apply selection in favour of plasmid-containing organisms. A similar strategy had previously proved successful at evolving clones of Bacillus subtilis, showing improved plasmid stability characteristics. In this study a series of clones were isolated which exhibited large variation in their ability to retain the recombinant plasmid. Clones showed both significantly increased and reduced capacity to maintain the recombinant plasmid. The probabilities of obtaining clones in either category were essentially equal so that selection was not seen to enrich for more stable clones. Periodic selection events appeared to exert a greater influence on the distribution of stability characteristics amongst clones than did the applied selective pressure. Alterations in plasmid retention characteristics could be associated with host or plasmid. The most stable clone isolated exhibited a approximately 30% improvement of its overall stability (sigma(N+)) and an 80% improvement in productivity, when compared to the parental strain CGpLG. This improved stability was associated with alterations in the plasmid genome.
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Affiliation(s)
- R D O'Kennedy
- Department of Microbiology, National University of Ireland, Galway, Ireland
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39
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Compagno C, Porro D, Radice S, Martegani E, Ranzi BM. Selection of yeast cells with a higher plasmid copy number in a Saccharomyces cerevisiae autoselection system. Yeast 1998. [DOI: 10.1002/(sici)1097-0061(19960315)12:3<199::aid-yea895>3.0.co;2-u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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40
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Velmurugan S, Ahn YT, Yang XM, Wu XL, Jayaram M. The 2 micrometer plasmid stability system: analyses of the interactions among plasmid- and host-encoded components. Mol Cell Biol 1998; 18:7466-77. [PMID: 9819432 PMCID: PMC109327 DOI: 10.1128/mcb.18.12.7466] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stable inheritance of the 2 micrometer plasmid in a growing population of Saccharomyces cerevisiae is dependent on two plasmid-encoded proteins (Rep1p and Rep2p), together with the cis-acting locus REP3 (STB). In this study we demonstrate that short carboxy-terminal deletions of Rep1p and Rep2p severely diminish their normal capacity to localize to the yeast nucleus. The nuclear targeting, as well as their functional role in plasmid partitioning, can be restored by the addition of a nuclear localization sequence to the amino or the carboxy terminus of the shortened Rep proteins. Analyses of deletion derivatives of the Rep proteins by using the in vivo dihybrid genetic test in yeast, as well as by glutathione S-transferase fusion trapping assays in vitro demonstrate that the amino-terminal portion of Rep1p (ca. 150 amino acids long) is responsible for its interactions with Rep2p. In a monohybrid in vivo assay, we have identified Rep1p, Rep2p, and a host-encoded protein, Shf1p, as being capable of interacting with the STB locus. The Shf1 protein expressed in Escherichia coli can bind with high specificity to the STB sequence in vitro. In a yeast strain deleted for the SHF1 locus, a 2 micrometer circle-derived plasmid shows relatively poor stability.
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Affiliation(s)
- S Velmurugan
- Department of Microbiology and Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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41
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Scott-Drew S, Murray JA. Localisation and interaction of the protein components of the yeast 2 mu circle plasmid partitioning system suggest a mechanism for plasmid inheritance. J Cell Sci 1998; 111 ( Pt 13):1779-89. [PMID: 9625741 DOI: 10.1242/jcs.111.13.1779] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replicating plasmids are highly unstable in yeast, because they are retained in mother cells. The 2 mu circle plasmid overcomes this maternal inheritance bias by using a partitioning system that involves the plasmid encoded proteins Rep1p and Rep2p, and the cis-acting locus STB. It is thus widely exploited as a cloning vehicle in yeast. However, little is known about the cellular or molecular mechanisms by which effective partitioning is achieved, and models of both free diffusion and plasmid localisation have been proposed. Here we show that Rep1p and Rep2p proteins interact to form homo- and hetero-complexes in vitro. In vivo, Rep1p and Rep2p are shown to be nuclear proteins, exhibiting sub-nuclear concentration in distinct foci. The number of foci appears constant regardless of plasmid copy number and cell ploidy level. Before cell division, the number of foci increases, and we observe approximately equal allocation of foci to mother and daughter cell nuclei. We show that whereas Rep2p expressed alone is found exclusively in the nucleus, Rep1p requires the presence of Rep2p for effective nuclear localisation. High levels of 2 mu plasmid induce a multiple-budded elongated cell phenotype, which we show can be phenocopied by overexpression of both REP1 and REP2 together but not alone. Taken together, these results suggest that Rep1p and Rep2p interact in vivo, and occupy defined nuclear sites that are allocated to both mother and daughter nuclei during division. We propose a model for 2 mum plasmid partitioning based on these results, involving the association of plasmid DNA with specific, segregated subnuclear sites.
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Affiliation(s)
- S Scott-Drew
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, UK
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42
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Galli A, Schiestl RH. Effects of DNA double-strand and single-strand breaks on intrachromosomal recombination events in cell-cycle-arrested yeast cells. Genetics 1998; 149:1235-50. [PMID: 9649517 PMCID: PMC1460227 DOI: 10.1093/genetics/149.3.1235] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intrachromosomal recombination between repeated elements can result in deletion (DEL recombination) events. We investigated the inducibility of such intrachromosomal recombination events at different stages of the cell cycle and the nature of the primary DNA lesions capable of initiating these events. Two genetic systems were constructed in Saccharomyces cerevisiae that select for DEL recombination events between duplicated alleles of CDC28 and TUB2. We determined effects of double-strand breaks (DSBs) and single-strand breaks (SSBs) between the duplicated alleles on DEL recombination when induced in dividing cells or cells arrested in G1 or G2. Site-specific DSBs and SSBs were produced by overexpression of the I-Sce I endonuclease and the gene II protein (gIIp), respectively. I-Sce I-induced DSBs caused an increase in DEL recombination frequencies in both dividing and cell-cycle-arrested cells, indicating that G1- and G2-arrested cells are capable of completing DSB repair. In contrast, gIIp-induced SSBs caused an increase in DEL recombination frequency only in dividing cells. To further examine these phenomena we used both gamma-irradiation, inducing DSBs as its most relevant lesion, and UV, inducing other forms of DNA damage. UV irradiation did not increase DEL recombination frequencies in G1 or G2, whereas gamma-rays increased DEL recombination frequencies in both phases. Both forms of radiation, however, induced DEL recombination in dividing cells. The results suggest that DSBs but not SSBs induce DEL recombination, probably via the single-strand annealing pathway. Further, DSBs in dividing cells may result from the replication of a UV or SSB-damaged template. Alternatively, UV induced events may occur by replication slippage after DNA polymerase pausing in front of the damage.
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Affiliation(s)
- A Galli
- Department of Molecular and Cellular Toxicology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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43
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Sektas M, Szybalski W. Tightly controlled two-stage expression vectors employing the Flp/FRT-mediated inversion of cloned genes. Mol Biotechnol 1998; 9:17-24. [PMID: 9592765 DOI: 10.1007/bf02752694] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have developed a tightly controlled, two-stage expression system. It is based on a single plasmid that carries the TetR repressor/Ptet promoter/Otet operator for the first-stage control, and the Flp recombinase/ FRT sites for the second-stage control. The gene to be expressed (GENE) is cloned in an inverted orientation (with respect to the stationary promoter) into a multiple-cloning site (MCS) located between two convergent FRT1 and FRT2 sites. In the OFF stage, no inadvertent transcription can enter the 5' end of cloned GENE because of four rrnBT1 terminators, located just outside the FRT1-MCS-FRT2 cassette and because the FRT2 construct was deprived of any promoter function. When using the lacZ reporter, it was shown that in their OFF stage our two-stage expression plasmids exhibit a significantly lower basal expression than the repressed single-stage tetR/PtetOtet-lacZ vectors. To enter the ON stage, the tetR/PtetOtet module is induced by adding autoclaved chlortetracycline (cTc), leading to synthesis of the Flp recombinase, which in turn, inverts the FRT1-MCS-FRT2 module together with the cloned GENE. This results in the massive GENE expression from one (pInvMS) or two (pImpMS) stationary promoters.
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Affiliation(s)
- M Sektas
- Department of Microbiology, University of Gdańsk, Poland.
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44
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Blaisonneau J, Sor F, Cheret G, Yarrow D, Fukuhara H. A circular plasmid from the yeast Torulaspora delbrueckii. Plasmid 1998; 38:202-9. [PMID: 9435022 DOI: 10.1006/plas.1997.1315] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A new member of the 2-micron family of plasmids, named pTD1, was found in the yeast Torulaspora delbrueckii, a widespread yeast associated with food. Nucleotide sequences revealed the presence of a pair of inverted repeats and three open reading frames, one of which is a homologue of the FLP recombinase gene of 2-micron plasmid. An ARS region was identified, by replication in Saccharomyces cerevisiae and T. delbrueckii, near one of the inverted repeats. By the use of pTD1 derivatives and auxotrophic mutant hosts an efficient host-vector system was established for T. delbrueckii. So far, the 2-micron family of plasmids is restricted to four closely related genera (Q6 group): Saccharomyces, Zygosaccharomyces, Kluyveromyces, and Torulaspora. After a survey of 2500 strains belonging to about 500 species (80 genera) of yeast, no circular plasmids were found in other genera.
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Affiliation(s)
- J Blaisonneau
- Institut Curie Section de Recherche, UMR 216, Centre Universitaire Paris XI, Orsay, France
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45
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Bogdanova AI, Kustikova OS, Agaphonov MO, Ter-Avanesyan MD. Sequences of Saccharomyces cerevisiae 2 microns DNA improving plasmid partitioning in Hansenula polymorpha. Yeast 1998; 14:1-9. [PMID: 9483791 DOI: 10.1002/(sici)1097-0061(19980115)14:1<1::aid-yea195>3.0.co;2-d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Insertion of the HindIII-PstI fragment of Saccharomyces cerevisiae 2 microns DNA into the Hansenula polymorpha replicative plasmids decreases plasmid copy number and ensures their distribution to daughter cells at both mitotic and meiotic cell divisions. This suggests that the stabilization effect is caused by the improvement of plasmid partitioning. Deletion analysis revealed that the region of 2 microns DNA sequence responsible for the increase of mitotic stability of H. polymorpha plasmids involves the 2 microns STB locus and adjoining region. Further analysis demonstrated that the stabilization effect may depend on the number of 24-28 bp imperfect repeats which were found in several copies in the STB locus and adjoining region.
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Affiliation(s)
- A I Bogdanova
- Institute of Experimental Cardiology, Cardiology Research Center, Moscow, Russia
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46
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Ahn YT, Wu XL, Biswal S, Velmurugan S, Volkert FC, Jayaram M. The 2microm-plasmid-encoded Rep1 and Rep2 proteins interact with each other and colocalize to the Saccharomyces cerevisiae nucleus. J Bacteriol 1997; 179:7497-506. [PMID: 9393716 PMCID: PMC179702 DOI: 10.1128/jb.179.23.7497-7506.1997] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The efficient partitioning of the 2microm plasmid of Saccharomyces cerevisiae at cell division requires two plasmid-encoded proteins (Rep1p and Rep2p) and a cis-acting locus, REP3 (STB). By using protein hybrids containing fusions of the Rep proteins to green fluorescent protein (GFP), we show here that fluorescence from GFP-Rep1p or GFP-Rep2p is almost exclusively localized in the nucleus in a cir+ strain. Nuclear localization of GFP-Rep1p and GFP-Rep2p, though discernible, is less efficient in a cir(0) host. GFP-Rep2p or GFP-Rep1p is able to promote the stability of a 2microm circle-derived plasmid harboring REP1 or REP2, respectively, in a cir(0) background. Under these conditions, fluorescence from GFP-Rep2p or GFP-Rep1p is concentrated within the nucleus, as is the case in cir+ cells. This characteristic nuclear accumulation is not dependent on the expression of the FLP or RAF1 gene of the 2microm circle. Nuclear colocalization of Rep1p and Rep2p is consistent with the hypothesis that the two proteins directly or indirectly interact to form a functional bipartite or high-order protein complex. Immunoprecipitation experiments as well as baiting assays using GST-Rep hybrid proteins suggest a direct interaction between Rep1p and Rep2p which, in principle, may be modulated by other yeast proteins. Furthermore, these assays provide evidence for Rep1p-Rep1p and Rep2p-Rep2p associations as well. The sum of these interactions may be important in controlling the effective cellular concentration of the Rep1p-Rep2p complex.
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Affiliation(s)
- Y T Ahn
- Department of Microbiology, University of Texas at Austin, 78712, USA
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47
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Ludwig DL, Stringer JR, Wight DC, Doetschman HC, Duffy JJ. FLP-mediated site-specific recombination in microinjected murine zygotes. Transgenic Res 1996; 5:385-95. [PMID: 8840521 DOI: 10.1007/bf01980203] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The FLP recombinase of yeast catalyses site-specific recombination between repeated FLP recombinase target (FRT) elements in yeast and in heterologous systems (Escherichia coli, Drosophila, mosquito and cultured mammalian cells). In this report, it is shown that transient FLP recombinase expression can recombine and activate an extrachromosomal silent reporter gene following coinjection into fertilized one-cell mouse eggs. Furthermore, it is demonstrated that introduction of a FLP-recombinase expression vector into transgenic one-cell fertilized mouse eggs induces a recombination event at a chromosomal FRT target locus. The resulting event occurred at the one-cell stage and deleted a chromosomal tandem array of a FRT containing lacZ expression cassette down to one or two copies. These results demonstrate that the FLP recombinase can be utilized to manipulate the genome of transgenic animals and suggest that FLP recombinase-mediated plasmid-to-chromosome targeting is feasible in microinjected eggs.
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Affiliation(s)
- D L Ludwig
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati Medical Center, OH 45267-0524, USA
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48
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Abstract
Industrial yeast strains carry one of two homeologous 2 microns plasmids designated as type-1 or type-2. The 2 microns plasmid, Scp1, found in common laboratory strains of Saccharomyces cerevisiae is considered a type-2 plasmid, since the ori, STB, RAF and REP1 loci and intergenic sequences of the right-unique region of Scp1 are homologous to the corresponding loci in industrial strain type-2 plasmids. However, within both its 599 bp inverted repeats Scp1 has 142-bp sequences homologous to the bakers' yeast type-1 plasmid. DNA sequence analyses and oligonucleotide hybridizations indicate that the 142-bp insertion in Scp1 was probably due to homeologous recombination between type-1 and type-2 plasmids. These results suggest that some of the plasmid and chromosomal sequence polymorphisms seen in laboratory yeast strains result from homeologous recombination in their ancestral breeding stock.
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Affiliation(s)
- W Xiao
- Department of Microbiology, University of Saskatchewan, Saskatoon, Canada
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49
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Compagno C, Porro D, Radice S, Martegani E, Ranzi BM. Selection of yeast cells with a higher plasmid copy number in a Saccharomyces cerevisiae autoselection system. Yeast 1996; 12:199-205. [PMID: 8904331 DOI: 10.1002/(sici)1097-0061(19960315)12:3%3c199::aid-yea895%3e3.0.co;2-u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Autoselection systems allow the selection of a genetically engineered population independently of the growth medium composition. The structure of a Saccharomyces cerevisiae population transformed with an autoselection plasmid, in which a carbon-source-dependent modulation of the plasmid copy number occurs, was analysed. By means of flow cytometric procedures we tested the cell viability, dynamics of growth and heterologous protein production at single cell level. Such analyses allow the identification and the tracking of a specific cellular sub-population with a higher plasmid copy number which arises after the carbon source shift. The effects of the cellular plasmid distribution on the dynamics of growth are also discussed.
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Affiliation(s)
- C Compagno
- Dipartimento di Fisiologia e Biochimica Generali, Sez. Biochimica Comparata, Universita di Milano, Italy
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50
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Hensing MC, Rouwenhorst RJ, Heijnen JJ, van Dijken JP, Pronk JT. Physiological and technological aspects of large-scale heterologous-protein production with yeasts. Antonie Van Leeuwenhoek 1995; 67:261-79. [PMID: 7778895 DOI: 10.1007/bf00873690] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Commercial production of heterologous proteins by yeasts has gained considerable interest. Expression systems have been developed for Saccharomyces cerevisiae and a number of other yeasts. Generally, much attention is paid to the molecular aspects of heterologous-gene expression. The success of this approach is indicated by the high expression levels that have been obtained in shake-flask cultures. For large-scale production however, possibilities and restrictions related to host-strain physiology and fermentation technology also have to be considered. In this review, these physiological and technological aspects have been evaluated with the aid of numerical simulations. Factors that affect the choice of a carbon substrate for large-scale production involve price, purity and solubility. Since oxygen demand and heat production (which are closely linked) limit the attainable growth rate in large-scale processes, the biomass yield on oxygen is also a key parameter. Large-scale processes impose restrictions on the expression system. Many promoter systems that work well in small-scale systems cannot be implemented in industrial environments. Furthermore, large-scale fed-batch fermentations involve a substantial number of generations. Therefore, even low expression-cassette instability has a profound effect on the overall productivity of the system. Multicopy-integration systems may provide highly stable expression systems for industrial processes. Large-scale fed-batch processes are typically performed at a low growth rate. Therefore, effects of a low growth rate on the physiology and product formation rates of yeasts are of key importance. Due to the low growth rates in the industrial process, a substantial part of the substrate carbon is expended to meet maintenance-energy requirements. Factors that reduce maintenance-energy requirements will therefore have a positive effect on product yield. The relationship between specific growth rate and specific product formation rate (kg product.[kg biomass]-1.h-1) is the main factor influencing production levels in large-scale production processes. Expression systems characterized by a high specific rate of product formation at low specific growth rates are highly favourable for large-scale heterologous-protein production.
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Affiliation(s)
- M C Hensing
- Department of Microbiology and Enzymology, Kluyver Laboratory of Biotechnology, Delft University of Technology, The Netherlands
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