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Ma CH, Kumar D, Jayaram M, Ghosh SK, Iyer VR. The selfish yeast plasmid exploits a SWI/SNF-type chromatin remodeling complex for hitchhiking on chromosomes and ensuring high-fidelity propagation. PLoS Genet 2023; 19:e1010986. [PMID: 37812641 PMCID: PMC10586699 DOI: 10.1371/journal.pgen.1010986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Extra-chromosomal selfish DNA elements can evade the risk of being lost at every generation by behaving as chromosome appendages, thereby ensuring high fidelity segregation and stable persistence in host cell populations. The yeast 2-micron plasmid and episomes of the mammalian gammaherpes and papilloma viruses that tether to chromosomes and segregate by hitchhiking on them exemplify this strategy. We document for the first time the utilization of a SWI/SNF-type chromatin remodeling complex as a conduit for chromosome association by a selfish element. One principal mechanism for chromosome tethering by the 2-micron plasmid is the bridging interaction of the plasmid partitioning proteins (Rep1 and Rep2) with the yeast RSC2 complex and the plasmid partitioning locus STB. We substantiate this model by multiple lines of evidence derived from genomics, cell biology and interaction analyses. We describe a Rep-STB bypass system in which a plasmid engineered to non-covalently associate with the RSC complex mimics segregation by chromosome hitchhiking. Given the ubiquitous prevalence of SWI/SNF family chromatin remodeling complexes among eukaryotes, it is likely that the 2-micron plasmid paradigm or analogous ones will be encountered among other eukaryotic selfish elements.
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Affiliation(s)
- Chien-Hui Ma
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Deepanshu Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Makkuni Jayaram
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Santanu K. Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vishwanath R. Iyer
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Livestrong Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas, United States of America
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2
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Mereshchuk A, Johnstone PS, Chew JSK, Dobson MJ. The yeast 2-micron plasmid Rep2 protein has Rep1-independent partitioning function. Nucleic Acids Res 2022; 50:10571-10585. [PMID: 36156142 PMCID: PMC9561267 DOI: 10.1093/nar/gkac810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/18/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Equal partitioning of the multi-copy 2-micron plasmid of the budding yeast Saccharomyces cerevisiae requires association of the plasmid Rep1 and Rep2 proteins with the plasmid STB partitioning locus. Determining how the Rep proteins contribute has been complicated by interactions between the components. Here, each Rep protein was expressed fused to the DNA-binding domain of the bacterial repressor protein LexA in yeast harboring a replication-competent plasmid that had LexA-binding sites but lacked STB. Plasmid transmission to daughter cells was increased only by Rep2 fusion expression. Neither Rep1 nor a functional RSC2 complex (a chromatin remodeler required for 2-micron plasmid partitioning) were needed for the improvement. Deletion analysis showed the carboxy-terminal 65 residues of Rep2 were required and sufficient for this Rep1-independent inheritance. Mutation of a conserved basic motif in this domain impaired Rep1-independent and Rep protein/STB-dependent plasmid partitioning. Our findings suggest Rep2, which requires Rep1 and the RSC2 complex for functional association with STB, directly participates in 2-micron plasmid partitioning by linking the plasmid to a host component that is efficiently partitioned during cell division. Further investigation is needed to reveal the host factor targeted by Rep2 that contributes to the survival of these plasmids in their budding yeast hosts.
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Affiliation(s)
- Anastasiia Mereshchuk
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Peter S Johnstone
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Joyce S K Chew
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Melanie J Dobson
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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The selfish yeast plasmid utilizes the condensin complex and condensed chromatin for faithful partitioning. PLoS Genet 2021; 17:e1009660. [PMID: 34270553 PMCID: PMC8318298 DOI: 10.1371/journal.pgen.1009660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/28/2021] [Accepted: 06/10/2021] [Indexed: 11/19/2022] Open
Abstract
Equipartitioning by chromosome association and copy number correction by DNA amplification are at the heart of the evolutionary success of the selfish yeast 2-micron plasmid. The present analysis reveals frequent plasmid presence near telomeres (TELs) and centromeres (CENs) in mitotic cells, with a preference towards the former. Inactivation of Cdc14 causes plasmid missegregation, which is correlated to the non-disjunction of TELs (and of rDNA) under this condition. Induced missegregation of chromosome XII, one of the largest yeast chromosomes which harbors the rDNA array and is highly dependent on the condensin complex for proper disjunction, increases 2-micron plasmid missegregation. This is not the case when chromosome III, one of the smallest chromosomes, is forced to missegregate. Plasmid stability decreases when the condensin subunit Brn1 is inactivated. Brn1 is recruited to the plasmid partitioning locus (STB) with the assistance of the plasmid-coded partitioning proteins Rep1 and Rep2. Furthermore, in a dihybrid assay, Brn1 interacts with Rep1-Rep2. Taken together, these findings support a role for condensin and/or condensed chromatin in 2-micron plasmid propagation. They suggest that condensed chromosome loci are among favored sites utilized by the plasmid for its chromosome-associated segregation. By homing to condensed/quiescent chromosome locales, and not over-perturbing genome homeostasis, the plasmid may minimize fitness conflicts with its host. Analogous persistence strategies may be utilized by other extrachromosomal selfish genomes, for example, episomes of mammalian viruses that hitchhike on host chromosomes for their stable maintenance.
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Ma CH, Su BY, Maciaszek A, Fan HF, Guga P, Jayaram M. A Flp-SUMO hybrid recombinase reveals multi-layered copy number control of a selfish DNA element through post-translational modification. PLoS Genet 2019; 15:e1008193. [PMID: 31242181 PMCID: PMC6594588 DOI: 10.1371/journal.pgen.1008193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
Abstract
Mechanisms for highly efficient chromosome-associated equal segregation, and for maintenance of steady state copy number, are at the heart of the evolutionary success of the 2-micron plasmid as a stable multi-copy extra-chromosomal selfish DNA element present in the yeast nucleus. The Flp site-specific recombination system housed by the plasmid, which is central to plasmid copy number maintenance, is regulated at multiple levels. Transcription of the FLP gene is fine-tuned by the repressor function of the plasmid-coded partitioning proteins Rep1 and Rep2 and their antagonist Raf1, which is also plasmid-coded. In addition, the Flp protein is regulated by the host’s post-translational modification machinery. Utilizing a Flp-SUMO fusion protein, which functionally mimics naturally sumoylated Flp, we demonstrate that the modification signals ubiquitination of Flp, followed by its proteasome-mediated degradation. Furthermore, reduced binding affinity and cooperativity of the modified Flp decrease its association with the plasmid FRT (Flp recombination target) sites, and/or increase its dissociation from them. The resulting attenuation of strand cleavage and recombination events safeguards against runaway increase in plasmid copy number, which is deleterious to the host—and indirectly—to the plasmid. These results have broader relevance to potential mechanisms by which selfish genomes minimize fitness conflicts with host genomes by holding in check the extra genetic load they pose. Plasmids of budding yeasts, exemplified by the 2-micron plasmid of Saccharomyces cerevisiae, and mammalian papilloma and gammaherpes viruses typify eukaryotic extra-chromosomal selfish DNA elements. The plasmid and the viral episomes, despite the long evolutionary divergence of their hosts, share striking similarities in lifestyles. These include the ability to segregate to daughter cells by hitchhiking on chromosomes and to switch from cell cycle regulated replication to iterative replication for copy number maintenance. While selfish elements, including those integrated into chromosomes, rely on their hosts’ genetic potential for long-term survival, their genetic load is carefully regulated to minimize fitness conflicts with the hosts. Our study focuses on the Flp site-specific recombinase, which is central to the copy number control of the 2-micron plasmid and whose steady state levels are regulated through transcriptional control by plasmid coded proteins and through post-translational modification by the host’s sumoylation machinery. We demonstrate that sumoylation, in addition, attenuates the catalytic activity of Flp by diminishing its DNA binding affinity and inter-monomer cooperativity, providing another layer of protection against runaway increase in plasmid copy number. Population control by self-imposed and host-mediated mechanisms is likely a general strategy among selfish elements to ensure nearly conflict-free coexistence with host genomes.
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Affiliation(s)
- Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, Taipei City, Taiwan
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Lodz, Poland
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, Taipei City, Taiwan
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Lodz, Poland
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
- * E-mail:
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Insights into the DNA sequence elements required for partitioning and copy number control of the yeast 2-micron plasmid. Curr Genet 2019; 65:887-892. [PMID: 30915516 DOI: 10.1007/s00294-019-00958-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 10/27/2022]
Abstract
The yeast 2-micron plasmid is an almost perfect selfish DNA. The entire coding capacity of the plasmid is dedicated to ensuring its own inheritance, with no benefit to its host. Despite high copy number, the plasmid confers no phenotype. It manages this feat by possessing mechanisms for plasmid copy-number control and for partitioning. The former increases plasmid numbers when they fall, but is repressed at high copy number, while the latter ensures 2-micron copies are equally partitioned during host cell division. Although the plasmid amplification mechanism is well established, the partitioning system and the means by which the 2-micron plasmid partitioning proteins, Rep1 and Rep2, regulate plasmid copy number remain incompletely understood. This review focuses on recent efforts to determine the nature of Rep protein complexes formed at the plasmid stability locus (STB) and at plasmid gene promoters, the identity of DNA sequence elements required for Rep protein association, and the mechanism by which the Rep proteins manage their dual roles of plasmid partitioning and plasmid gene repression.
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Sau S, Ghosh SK, Liu YT, Ma CH, Jayaram M. Hitchhiking on chromosomes: A persistence strategy shared by diverse selfish DNA elements. Plasmid 2019; 102:19-28. [PMID: 30726706 DOI: 10.1016/j.plasmid.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
An underlying theme in the segregation of low-copy bacterial plasmids is the assembly of a 'segrosome' by DNA-protein and protein-protein interactions, followed by energy-driven directed movement. Analogous partitioning mechanisms drive the segregation of host chromosomes as well. Eukaryotic extra-chromosomal elements, exemplified by budding yeast plasmids and episomes of certain mammalian viruses, harbor partitioning systems that promote their physical association with chromosomes. In doing so, they indirectly take advantage of the spindle force that directs chromosome movement to opposite cell poles. Molecular-genetic, biochemical and cell biological studies have revealed several unsuspected aspects of 'chromosome hitchhiking' by the yeast 2-micron plasmid, including the ability of plasmid sisters to associate symmetrically with sister chromatids. As a result, the plasmid overcomes the 'mother bias' experienced by plasmids lacking a partitioning system, and elevates itself to near chromosome status in equal segregation. Chromosome association for stable propagation, without direct energy expenditure, may also be utilized by a small minority of bacterial plasmids-at least one case has been reported. Given the near perfect accuracy of chromosome segregation, it is not surprising that elements residing in evolutionarily distant host organisms have converged upon the common strategy of gaining passage to daughter cells as passengers on chromosomes.
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Affiliation(s)
- Soumitra Sau
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Yen-Ting Liu
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA.
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Abstract
Herpesvirus genomes exist and replicate as episomes inside the host cell nucleus during latent infection. Chiu et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201702013) find that unlike Epstein-Barr virus, which partitions viral genomes faithfully during cell division, Kaposi's Sarcoma-associated herpesvirus clusters viral genomes into loci that are distributed unequally to daughter cells.
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Chiu YF, Sugden AU, Fox K, Hayes M, Sugden B. Kaposi's sarcoma-associated herpesvirus stably clusters its genomes across generations to maintain itself extrachromosomally. J Cell Biol 2017; 216:2745-2758. [PMID: 28696226 PMCID: PMC5584176 DOI: 10.1083/jcb.201702013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 02/08/2023] Open
Abstract
Several human tumor viruses, including Kaposi’s sarcoma–associated herpesvirus (KSHV), maintain their plasmid genomes by tethering them to cellular chromosomes. Chiu et al. identify a viral segregation mechanism: KSHV stably clusters some of its genomes, which are inherited as units. Clustering, as predicted computationally and observed in live cells, rapidly establishes high viral copy numbers in cells. Genetic elements that replicate extrachromosomally are rare in mammals; however, several human tumor viruses, including the papillomaviruses and the gammaherpesviruses, maintain their plasmid genomes by tethering them to cellular chromosomes. We have uncovered an unprecedented mechanism of viral replication: Kaposi’s sarcoma–associated herpesvirus (KSHV) stably clusters its genomes across generations to maintain itself extrachromosomally. To identify and characterize this mechanism, we developed two complementary, independent approaches: live-cell imaging and a predictive computational model. The clustering of KSHV requires the viral protein, LANA1, to bind viral genomes to nucleosomes arrayed on both cellular and viral DNA. Clustering affects both viral partitioning and viral genome numbers of KSHV. The clustering of KSHV plasmids provides it with an effective evolutionary strategy to rapidly increase copy numbers of genomes per cell at the expense of the total numbers of cells infected.
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Affiliation(s)
- Ya-Fang Chiu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI.,Research Center for Emerging Viral Infections, Chang-Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang-Gung University, Taoyuan, Taiwan.,Department of Medical Laboratory, Chang-Gung Memorial Hospital, Taoyuan, Taiwan
| | - Arthur U Sugden
- Department of Neuroscience, Brown University, Providence, RI.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Kathryn Fox
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI.,Flow Cytometry Laboratory, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Mitchell Hayes
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
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Rizvi SMA, Prajapati HK, Ghosh SK. The 2 micron plasmid: a selfish genetic element with an optimized survival strategy within Saccharomyces cerevisiae. Curr Genet 2017; 64:25-42. [PMID: 28597305 DOI: 10.1007/s00294-017-0719-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 11/27/2022]
Abstract
Since its discovery in the early 70s, the 2 micron plasmid of Saccharomyces cerevisiae continues to intrigue researchers with its high protein-coding capacity and a selfish nature yet high stability, earning it the title of a 'miniaturized selfish genetic element'. It codes for four proteins (Rep1, Rep2, Raf1, and Flp) vital for its own survival and recruits several host factors (RSC2, Cohesin, Cse4, Kip1, Bik1, Bim1, and microtubules) for its faithful segregation during cell division. The plasmid maintains a high-copy number with the help of Flp-mediated recombination. The plasmids organize in the form of clusters that hitch-hike the host chromosomes presumably with the help of the plasmid-encoded Rep proteins and host factors such as microtubules, Kip1 motor, and microtubule-associated proteins Bik1 and Bim1. Although there is no known yeast cell phenotype associated with the 2 micron plasmid, excessive copies of the plasmid are lethal for the cells, warranting a tight control over the plasmid copy number. This control is achieved through a combination of feedback loops involving the 2 micron encoded proteins. Thus, faithful segregation and a concomitant tightly controlled plasmid copy number ensure an optimized benign parasitism of the 2 micron plasmid within budding yeast.
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Affiliation(s)
- Syed Meraj Azhar Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Hemant Kumar Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India.
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