1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
|
4
|
McQuaid ME, Polvi EJ, Dobson MJ. DNA sequence elements required for partitioning competence of the Saccharomyces cerevisiae 2-micron plasmid STB locus. Nucleic Acids Res 2019; 47:716-728. [PMID: 30445476 PMCID: PMC6344848 DOI: 10.1093/nar/gky1150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
Equal partitioning of the multi-copy yeast 2-micron plasmid requires association of plasmid proteins Rep1 and Rep2 with tandem repeats at the plasmid STB locus. To identify sequence elements required for these associations we generated synthetic versions of a 63-bp section of STB, encompassing one repeat. A single copy of this sequence was sufficient for Rep protein association in vivo, while two directly arrayed copies provided partitioning function to a plasmid lacking all other 2-micron sequences. Partitioning efficiency increased with increasing repeat number, reaching that conferred by the native STB repeat array. By altering sequences in synthetic repeats, we identified the TGCA component of a TGCATTTTT motif as critical for Rep protein recognition, with a second TGCA sequence in each repeat also contributing to association. Mutation of TGCATTTTT to TGTATTTT, as found in variant 2-micron STB repeats, also allowed Rep protein association, while mutation to TGCATTAAT impaired inheritance without abolishing Rep protein recognition, suggesting an alternate role for the T-tract. Our identification of sequence motifs required for Rep protein recognition provides the basis for understanding higher-order Rep protein arrangements at STB that enable the yeast 2-micron plasmid to be efficiently partitioned during host cell division.
Collapse
Affiliation(s)
- Mary E McQuaid
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Elizabeth J Polvi
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Melanie J Dobson
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
5
|
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.
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
A Rizvi SM, Prajapati HK, Nag P, Ghosh SK. The 2-μm plasmid encoded protein Raf1 regulates both stability and copy number of the plasmid by blocking the formation of the Rep1-Rep2 repressor complex. Nucleic Acids Res 2017; 45:7167-7179. [PMID: 28472368 PMCID: PMC5499539 DOI: 10.1093/nar/gkx316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/14/2017] [Indexed: 12/02/2022] Open
Abstract
The 2-μm plasmid of the budding yeast Saccharomyces cerevisiae achieves a high chromosome-like stability with the help of four plasmid-encoded (Rep1, Rep2, Raf1 and Flp) and several host-encoded proteins. Rep1 and Rep2 and the DNA locus STB form the partitioning system ensuring equal segregation of the plasmid. The Flp recombinase and its target sites FRTs form the amplification system which is responsible for the steady state plasmid copy number. In this work we show that the absence of Raf1 can affect both the plasmid stability and the steady sate copy number. We also show that the Rep proteins do bind to the promoter regions of the 2-μm encoded genes, as predicted by earlier models and Raf1 indeed blocks the formation of the Rep1–Rep2 repressor complex not by blocking the transcription of the REP1 and REP2 genes but by physically associating with the Rep proteins and negating their interactions. This explains the role of Raf1 in both the partitioning and the amplification systems as the Rep1–Rep2 complex is believed to modulate both these systems. Based on this study, we have provided, from a systems biology perspective, a model for the mechanism of the 2-μm plasmid maintenance.
Collapse
Affiliation(s)
- Syed M A Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Hemant K Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Purba Nag
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane Queensland 4006, Australia
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, Maharashtra, India
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Prajapati HK, Rizvi SMA, Rathore I, Ghosh SK. Microtubule-associated proteins, Bik1 and Bim1, are required for faithful partitioning of the endogenous 2 micron plasmids in budding yeast. Mol Microbiol 2017; 103:1046-1064. [PMID: 28004422 DOI: 10.1111/mmi.13608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 12/01/2022]
Abstract
The 2 μ plasmid of budding yeast shows high mitotic stability similar to that of chromosomes by using its self-encoded systems, namely partitioning and amplification. The partitioning system consists of the plasmid-borne proteins Rep1, Rep2 and a cis-acting locus STB that, along with several host factors, ensures efficient segregation of the plasmid. The plasmids show high stability as they presumably co-segregate with chromosomes through utilization of various host factors. To acquire these host factors, the plasmids are thought to localize to a certain sub-nuclear locale probably assisted by the motor protein, Kip1 and microtubules. Here, we show that the microtubule-associated proteins Bik1 and Bim1 are also important host factors in this process, perhaps by acting as an adapter between the plasmid and the motor and thus helping to anchor the plasmid to microtubules. Abrogation of Kip1 recruitment at STB in the absence of Bik1 argues for its function at STB upstream of Kip1. Consistent with this, both Bik1 and Bim1 associate with plasmids without any assistance from the Rep proteins. As observed earlier with other host factors, lack of Bik1 or Bim1 also causes a cohesion defect between sister plasmids leading to plasmid missegregation.
Collapse
Affiliation(s)
- Hemant Kumar Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Syed Meraj Azhar Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| |
Collapse
|
10
|
Liu YT, Chang KM, Ma CH, Jayaram M. Replication-dependent and independent mechanisms for the chromosome-coupled persistence of a selfish genome. Nucleic Acids Res 2016; 44:8302-23. [PMID: 27492289 PMCID: PMC5041486 DOI: 10.1093/nar/gkw694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
The yeast 2-micron plasmid epitomizes the evolutionary optimization of selfish extra-chromosomal genomes for stable persistence without jeopardizing their hosts' fitness. Analyses of fluorescence-tagged single-copy reporter plasmids and/or the plasmid partitioning proteins in native and non-native hosts reveal chromosome-hitchhiking as the likely means for plasmid segregation. The contribution of the partitioning system to equal segregation is bipartite- replication-independent and replication-dependent. The former nearly eliminates 'mother bias' (preferential plasmid retention in the mother cell) according to binomial distribution, thus limiting equal segregation of a plasmid pair to 50%. The latter enhances equal segregation of plasmid sisters beyond this level, elevating the plasmid close to chromosome status. Host factors involved in plasmid partitioning can be functionally separated by their participation in the replication-independent and/or replication-dependent steps. In the hitchhiking model, random tethering of a pair of plasmids to chromosomes signifies the replication-independent component of segregation; the symmetric tethering of plasmid sisters to sister chromatids embodies the replication-dependent component. The 2-micron circle broadly resembles the episomes of certain mammalian viruses in its chromosome-associated propagation. This unifying feature among otherwise widely differing selfish genomes suggests their evolutionary convergence to the common logic of exploiting, albeit via distinct molecular mechanisms, host chromosome segregation machineries for self-preservation.
Collapse
Affiliation(s)
- Yen-Ting Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Keng-Ming Chang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
11
|
The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells. Microbiol Spectr 2016; 2. [PMID: 25541598 DOI: 10.1128/microbiolspec.plas-0003-2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.
Collapse
|
12
|
Sau S, Liu YT, Ma CH, Jayaram M. Stable persistence of the yeast plasmid by hitchhiking on chromosomes during vegetative and germ-line divisions of host cells. Mob Genet Elements 2015; 5:1-8. [PMID: 26442178 DOI: 10.1080/2159256x.2015.1031359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/02/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022] Open
Abstract
The chromosome-like stability of the Saccharomyces cerevisiae plasmid 2 micron circle likely stems from its ability to tether to chromosomes and segregate by a hitchhiking mechanism. The plasmid partitioning system, responsible for chromosome-coupled segregation, is comprised of 2 plasmid coded proteins Rep1 and Rep2 and a partitioning locus STB. The evidence for the hitchhiking model for mitotic plasmid segregation, although compelling, is almost entirely circumstantial. Direct tests for plasmid-chromosome association are hampered by the limited resolving power of current cell biological tools for analyzing yeast chromosomes. Recent investigations, exploiting the improved resolution of yeast meiotic chromosomes, have revealed the plasmid's propensity to be present at or near chromosome tips. This localization is consistent with the rapid plasmid movements during meiosis I prophase, closely resembling telomere dynamics driven by a meiosis-specific nuclear envelope motor. Current evidence is consistent with the plasmid utilizing the motor as a platform for gaining access to telomeres. Episomes of viruses of the papilloma family and the gammaherpes subfamily persist in latently infected cells by tethering to chromosomes. Selfish genetic elements from fungi to mammals appear to have, by convergent evolution, arrived at the common strategy of chromosome association as a means for stable propagation.
Collapse
Affiliation(s)
- Soumitra Sau
- Department of Molecular Biosciences; University of Texas at Austin ; Austin, TX USA
| | - Yen-Ting Liu
- Department of Molecular Biosciences; University of Texas at Austin ; Austin, TX USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences; University of Texas at Austin ; Austin, TX USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences; University of Texas at Austin ; Austin, TX USA
| |
Collapse
|
13
|
Sau S, Conrad MN, Lee CY, Kaback DB, Dresser ME, Jayaram M. A selfish DNA element engages a meiosis-specific motor and telomeres for germ-line propagation. ACTA ACUST UNITED AC 2014; 205:643-61. [PMID: 24914236 PMCID: PMC4050733 DOI: 10.1083/jcb.201312002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The yeast 2 micron plasmid engages a meiosis-specific motor that orchestrates telomere-led chromosome movements for its telomere-associated segregation during meiosis I. The chromosome-like mitotic stability of the yeast 2 micron plasmid is conferred by the plasmid proteins Rep1-Rep2 and the cis-acting locus STB, likely by promoting plasmid-chromosome association and segregation by hitchhiking. Our analysis reveals that stable plasmid segregation during meiosis requires the bouquet proteins Ndj1 and Csm4. Plasmid relocalization from the nuclear interior in mitotic cells to the periphery at or proximal to telomeres rises from early meiosis to pachytene. Analogous to chromosomes, the plasmid undergoes Csm4- and Ndj1-dependent rapid prophase movements with speeds comparable to those of telomeres. Lack of Ndj1 partially disrupts plasmid–telomere association without affecting plasmid colocalization with the telomere-binding protein Rap1. The plasmid appears to engage a meiosis-specific motor that orchestrates telomere-led chromosome movements for its telomere-associated segregation during meiosis I. This hitherto uncharacterized mode of germ-line transmission by a selfish genetic element signifies a mechanistic variation within the shared theme of chromosome-coupled plasmid segregation during mitosis and meiosis.
Collapse
Affiliation(s)
- Soumitra Sau
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Michael N Conrad
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Chih-Ying Lee
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - David B Kaback
- Department of Microbiology and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07101
| | - Michael E Dresser
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| |
Collapse
|
14
|
Liu YT, Ma CH, Jayaram M. Co-segregation of yeast plasmid sisters under monopolin-directed mitosis suggests association of plasmid sisters with sister chromatids. Nucleic Acids Res 2013; 41:4144-58. [PMID: 23423352 PMCID: PMC3627588 DOI: 10.1093/nar/gkt096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 11/13/2022] Open
Abstract
The 2-micron plasmid, a high copy extrachromosomal element in Saccharomyces cerevisiae, propagates itself with nearly the same stability as the chromosomes of its host. Plasmid stability is conferred by a partitioning system consisting of the plasmid-coded proteins Rep1 and Rep2 and a cis-acting locus STB. Circumstantial evidence suggests that the partitioning system couples plasmid segregation to chromosome segregation during mitosis. However, the coupling mechanism has not been elucidated. In order to probe into this question more incisively, we have characterized the segregation of a single-copy STB reporter plasmid by manipulating mitosis to force sister chromatids to co-segregate either without mother-daughter bias or with a finite daughter bias. We find that the STB plasmid sisters are tightly correlated to sister chromatids in the extents of co-segregation as well as the bias in co-segregation under these conditions. Furthermore, this correlation is abolished by delaying spindle organization or preventing cohesin assembly during a cell cycle. Normal segregation of the 2-micron plasmid has been shown to require spindle integrity and the cohesin complex. Our results are accommodated by a model in which spindle- and cohesin-dependent association of plasmid sisters with sister chromatids promotes their segregation by a hitchhiking mechanism.
Collapse
Affiliation(s)
| | | | - Makkuni Jayaram
- Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Ma CH, Cui H, Hajra S, Rowley PA, Fekete C, Sarkeshik A, Ghosh SK, Yates JR, Jayaram M. Temporal sequence and cell cycle cues in the assembly of host factors at the yeast 2 micron plasmid partitioning locus. Nucleic Acids Res 2012; 41:2340-53. [PMID: 23275556 PMCID: PMC3575823 DOI: 10.1093/nar/gks1338] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces cerevisiae 2 micron plasmid exemplifies a benign but selfish genome, whose stability approaches that of the chromosomes of its host. The plasmid partitioning locus STB (stability locus) displays certain functional analogies with centromeres along with critical distinctions, a significant one being the absence of the kinetochore complex at STB. The remodels the structure of chromatin (RSC) chromatin remodeling complex, the nuclear motor Kip1, the histone H3 variant Cse4 and the cohesin complex associate with both loci. These factors appear to contribute to plasmid segregation either directly or indirectly through their roles in chromosome segregation. Assembly and disassembly of the plasmid-coded partitioning proteins Rep1 and Rep2 and host factors at STB follow a temporal hierarchy during the cell cycle. Assembly is initiated by STB association of [Rsc8-Rsc58], followed by [Rep1-Rep2-Kip1] and [Cse4-Rsc2-Sth1] recruitment, and culminates in cohesin assembly. Disassembly starts with dissociation of RSC components, is followed by cohesin disassembly and Cse4 exit during anaphase and late telophase, respectively. [Rep1-Rep2-Kip1] persists through G1 of the ensuing cell cycle. The de novo assembly of the 'partitioning complex' is cued by the innate cell cycle clock and is dependent on DNA replication. Shared functional attributes of STB and centromere (CEN) are consistent with a potential evolutionary link between them.
Collapse
Affiliation(s)
- Chien-Hui Ma
- Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Coffman VC, Wu P, Parthun MR, Wu JQ. CENP-A exceeds microtubule attachment sites in centromere clusters of both budding and fission yeast. ACTA ACUST UNITED AC 2012; 195:563-72. [PMID: 22084306 PMCID: PMC3257534 DOI: 10.1083/jcb.201106078] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The stoichiometries of kinetochores and their constituent proteins in yeast and vertebrate cells were determined using the histone H3 variant CENP-A, known as Cse4 in budding yeast, as a counting standard. One Cse4-containing nucleosome exists in the centromere (CEN) of each chromosome, so it has been assumed that each anaphase CEN/kinetochore cluster contains 32 Cse4 molecules. We report that anaphase CEN clusters instead contained approximately fourfold more Cse4 in Saccharomyces cerevisiae and ~40-fold more CENP-A (Cnp1) in Schizosaccharomyces pombe than predicted. These results suggest that the number of CENP-A molecules exceeds the number of kinetochore-microtubule (MT) attachment sites on each chromosome and that CENP-A is not the sole determinant of kinetochore assembly sites in either yeast. In addition, we show that fission yeast has enough Dam1-DASH complex for ring formation around attached MTs. The results of this study suggest the need for significant revision of existing CEN/kinetochore architectural models.
Collapse
Affiliation(s)
- Valerie C Coffman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
18
|
Histone H3-variant Cse4-induced positive DNA supercoiling in the yeast plasmid has implications for a plasmid origin of a chromosome centromere. Proc Natl Acad Sci U S A 2011; 108:13671-6. [PMID: 21807992 DOI: 10.1073/pnas.1101944108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces cerevisiae 2-μm plasmid is a multicopy selfish genome that resides in the nucleus. The genetic organization of the plasmid is optimized for stable, high-copy propagation in host-cell populations. The plasmid's partitioning system poaches host factors, including the centromere-specific histone H3-variant Cse4 and the cohesin complex, enabling replicated plasmid copies to segregate equally in a chromosome-coupled fashion. We have characterized the in vivo chromatin topology of the plasmid partitioning locus STB in its Cse4-associated and Cse4-nonassociated states. We find that the occupancy of Cse4 at STB induces positive DNA supercoiling, with a linking difference (ΔLk) contribution estimated between +1 and +2 units. One plausible explanation for this contrary topology is the presence of a specialized Cse4-containing nucleosome with a right-handed DNA writhe at a functional STB, contrasted by a standard histone H3-containing nucleosome with a left-handed DNA writhe at a nonfunctional STB. The similarities between STB and centromere in their nucleosome signature and DNA topology would be consistent with the potential origin of the unusual point centromere of budding yeast chromosomes from the partitioning locus of an ancestral plasmid.
Collapse
|
19
|
Huang CC, Hajra S, Ghosh SK, Jayaram M. Cse4 (CenH3) association with the Saccharomyces cerevisiae plasmid partitioning locus in its native and chromosomally integrated states: implications in centromere evolution. Mol Cell Biol 2011; 31:1030-40. [PMID: 21173161 PMCID: PMC3067819 DOI: 10.1128/mcb.01191-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/29/2010] [Accepted: 12/10/2010] [Indexed: 11/20/2022] Open
Abstract
The histone H3 variant Cse4 specifies centromere identity in Saccharomyces cerevisiae by its incorporation into a special nucleosome positioned at CEN DNA and promotes the assembly of the kinetochore complex, which is required for faithful chromosome segregation. Our previous work showed that Cse4 is also associated with the partitioning locus STB of the 2μm circle--a multicopy plasmid that resides in the yeast nucleus and propagates itself stably. Cse4 is essential for the functional assembly of the plasmid partitioning complex, including the recruitment of the yeast cohesin complex at STB. We have located Cse4 association strictly at the origin-proximal subregion of STB. Three of the five directly repeated tandem copies of a 62-bp consensus sequence element constituting this region are necessary and sufficient for the recruitment of Cse4. The association of Cse4 with STB is dependent on Scm3, the loading factor responsible for the incorporation of Cse4 into the CEN nucleosome. A chromosomally integrated copy of STB confers on the integration site the capacity for Cse4 association as well as cohesin assembly. The localization of Cse4 in chromatin digested by micrococcal nuclease is consistent with the potential assembly of one Cse4-containing nucleosome, but not more than two, at STB. The remarkable ability of STB to acquire a very specialized, and strictly regulated, chromosome segregation factor suggests its plausible evolutionary kinship with CEN.
Collapse
Affiliation(s)
- Chu-Chun Huang
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Sujata Hajra
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Santanu Kumar Ghosh
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Makkuni Jayaram
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
20
|
Ghosh SK, Huang CC, Hajra S, Jayaram M. Yeast cohesin complex embraces 2 micron plasmid sisters in a tri-linked catenane complex. Nucleic Acids Res 2010; 38:570-84. [PMID: 19920123 PMCID: PMC2811031 DOI: 10.1093/nar/gkp993] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Revised: 10/15/2009] [Accepted: 10/16/2009] [Indexed: 11/30/2022] Open
Abstract
Sister chromatid cohesion, crucial for faithful segregation of replicated chromosomes in eukaryotes, is mediated by the multi-subunit protein complex cohesin. The Saccharomyces cerevisiae plasmid 2 micron circle mimics chromosomes in assembling cohesin at its partitioning locus. The plasmid is a multi-copy selfish DNA element that resides in the nucleus and propagates itself stably, presumably with assistance from cohesin. In metaphase cell lysates, or fractions enriched for their cohesed state by sedimentation, plasmid molecules are trapped topologically by the protein ring formed by cohesin. They can be released from cohesin's embrace either by linearizing the DNA or by cleaving a cohesin subunit. Assays using two distinctly tagged cohesin molecules argue against the hand-cuff (an associated pair of monomeric cohesin rings) or the bracelet (a dimeric cohesin ring) model as responsible for establishing plasmid cohesion. Our cumulative results most easily fit a model in which a single monomeric cohesin ring, rather than a series of such rings, conjoins a pair of sister plasmids. These features of plasmid cohesion account for its sister-to-sister mode of segregation by cohesin disassembly during anaphase. The mechanistic similarities of cohesion between mini-chromosome sisters and 2 micron plasmid sisters suggest a potential kinship between the plasmid partitioning locus and centromeres.
Collapse
Affiliation(s)
- Santanu K. Ghosh
- School of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India and Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | - Chu-Chun Huang
- School of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India and Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | - Sujata Hajra
- School of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India and Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- School of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India and Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
21
|
Rodley CDM, Bertels F, Jones B, O'Sullivan JM. Global identification of yeast chromosome interactions using Genome conformation capture. Fungal Genet Biol 2009; 46:879-86. [PMID: 19628047 DOI: 10.1016/j.fgb.2009.07.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/15/2009] [Accepted: 07/16/2009] [Indexed: 12/17/2022]
Abstract
The association of chromosomes with each other and other nuclear components plays a critical role in nuclear organization and Genome function. Here, using a novel and generally applicable methodology (Genome conformation capture [GCC]), we reveal the network of chromosome interactions for the yeast Saccharomyces cerevisiae. Inter- and intra-chromosomal interactions are non-random and the number of interactions per open reading frame depends upon the dispensability of the gene product. Chromosomal interfaces are organized and provide evidence of folding within chromosomes. Interestingly, the genomic connections also involve the 2 microm plasmid and the mitochondrial genome. Mitochondrial interaction partners include genes of alpha-proteobacterial origin and the ribosomal DNA. Organization of the 2 microm plasmid aligns two inverted repeats (IR1 and IR2) and displays the stability locus on a prominent loop thus making it available for plasmid clustering. Our results form the first global map of chromosomal interactions in a eukaryotic nucleus and demonstrate the highly connected nature of the yeast genome. These results have significant implications for understanding eukaryotic genome organization.
Collapse
Affiliation(s)
- C D M Rodley
- Institute of Molecular Biosciences, Massey University, Private Bag 102 904, Albany, NSMC, Auckland, New Zealand
| | | | | | | |
Collapse
|
22
|
Cui H, Ghosh SK, Jayaram M. The selfish yeast plasmid uses the nuclear motor Kip1p but not Cin8p for its localization and equal segregation. J Cell Biol 2009; 185:251-64. [PMID: 19364922 PMCID: PMC2700366 DOI: 10.1083/jcb.200810130] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 03/23/2009] [Indexed: 01/31/2023] Open
Abstract
The 2 micron plasmid of Saccharomyces cerevisiae uses the Kip1 motor, but not the functionally redundant Cin8 motor, for its precise nuclear localization and equal segregation. The timing and lifetime of Kip1p association with the plasmid partitioning locus STB are consistent with Kip1p being an authentic component of the plasmid partitioning complex. Kip1-STB association is not blocked by disassembling the mitotic spindle. Lack of Kip1p disrupts recruitment of the cohesin complex at STB and cohesion of replicated plasmid molecules. Colocalization of a 2 micron reporter plasmid with Kip1p in close proximity to the spindle pole body is reminiscent of that of a CEN reporter plasmid. Absence of Kip1p displaces the plasmid from this nuclear address, where it has the potential to tether to a chromosome or poach chromosome segregation factors. Exploiting Kip1p, which is subsidiary to Cin8p for chromosome segregation, to direct itself to a "partitioning center" represents yet another facet of the benign parasitism of the yeast plasmid.
Collapse
Affiliation(s)
- Hong Cui
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | |
Collapse
|
23
|
Carlson SR, Rudgers GW, Zieler H, Mach JM, Luo S, Grunden E, Krol C, Copenhaver GP, Preuss D. Meiotic transmission of an in vitro-assembled autonomous maize minichromosome. PLoS Genet 2007; 3:1965-74. [PMID: 17953486 PMCID: PMC2041994 DOI: 10.1371/journal.pgen.0030179] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 09/05/2007] [Indexed: 12/13/2022] Open
Abstract
Autonomous chromosomes are generated in yeast (yeast artificial chromosomes) and human fibrosarcoma cells (human artificial chromosomes) by introducing purified DNA fragments that nucleate a kinetochore, replicate, and segregate to daughter cells. These autonomous minichromosomes are convenient for manipulating and delivering DNA segments containing multiple genes. In contrast, commercial production of transgenic crops relies on methods that integrate one or a few genes into host chromosomes; extensive screening to identify insertions with the desired expression level, copy number, structure, and genomic location; and long breeding programs to produce varieties that carry multiple transgenes. As a step toward improving transgenic crop production, we report the development of autonomous maize minichromosomes (MMCs). We constructed circular MMCs by combining DsRed and nptII marker genes with 7-190 kb of genomic maize DNA fragments containing satellites, retroelements, and/or other repeats commonly found in centromeres and using particle bombardment to deliver these constructs into embryogenic maize tissue. We selected transformed cells, regenerated plants, and propagated their progeny for multiple generations in the absence of selection. Fluorescent in situ hybridization and segregation analysis demonstrated that autonomous MMCs can be mitotically and meiotically maintained. The MMC described here showed meiotic segregation ratios approaching Mendelian inheritance: 93% transmission as a disome (100% expected), 39% transmission as a monosome crossed to wild type (50% expected), and 59% transmission in self crosses (75% expected). The fluorescent DsRed reporter gene on the MMC was expressed through four generations, and Southern blot analysis indicated the encoded genes were intact. This novel approach for plant transformation can facilitate crop biotechnology by (i) combining several trait genes on a single DNA fragment, (ii) arranging genes in a defined sequence context for more consistent gene expression, and (iii) providing an independent linkage group that can be rapidly introgressed into various germplasms.
Collapse
Affiliation(s)
| | | | - Helge Zieler
- Chromatin, Chicago, Illinois, United States of America
| | | | - Song Luo
- Chromatin, Chicago, Illinois, United States of America
| | - Eric Grunden
- Chromatin, Chicago, Illinois, United States of America
| | - Cheryl Krol
- Chromatin, Chicago, Illinois, United States of America
| | - Gregory P Copenhaver
- Chromatin, Chicago, Illinois, United States of America
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daphne Preuss
- Chromatin, Chicago, Illinois, United States of America
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
24
|
Abstract
Autonomous chromosomes are generated in yeast (yeast artificial chromosomes) and human fibrosarcoma cells (human artificial chromosomes) by introducing purified DNA fragments that nucleate a kinetochore, replicate, and segregate to daughter cells. These autonomous minichromosomes are convenient for manipulating and delivering DNA segments containing multiple genes. In contrast, commercial production of transgenic crops relies on methods that integrate one or a few genes into host chromosomes; extensive screening to identify insertions with the desired expression level, copy number, structure, and genomic location; and long breeding programs to produce varieties that carry multiple transgenes. As a step toward improving transgenic crop production, we report the development of autonomous maize minichromosomes (MMCs). We constructed circular MMCs by combining DsRed and nptII marker genes with 7-190 kb of genomic maize DNA fragments containing satellites, retroelements, and/or other repeats commonly found in centromeres and using particle bombardment to deliver these constructs into embryogenic maize tissue. We selected transformed cells, regenerated plants, and propagated their progeny for multiple generations in the absence of selection. Fluorescent in situ hybridization and segregation analysis demonstrated that autonomous MMCs can be mitotically and meiotically maintained. The MMC described here showed meiotic segregation ratios approaching Mendelian inheritance: 93% transmission as a disome (100% expected), 39% transmission as a monosome crossed to wild type (50% expected), and 59% transmission in self crosses (75% expected). The fluorescent DsRed reporter gene on the MMC was expressed through four generations, and Southern blot analysis indicated the encoded genes were intact. This novel approach for plant transformation can facilitate crop biotechnology by (i) combining several trait genes on a single DNA fragment, (ii) arranging genes in a defined sequence context for more consistent gene expression, and (iii) providing an independent linkage group that can be rapidly introgressed into various germplasms.
Collapse
|
25
|
Ghosh SK, Hajra S, Jayaram M. Faithful segregation of the multicopy yeast plasmid through cohesin-mediated recognition of sisters. Proc Natl Acad Sci U S A 2007; 104:13034-9. [PMID: 17670945 PMCID: PMC1941829 DOI: 10.1073/pnas.0702996104] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Indexed: 11/18/2022] Open
Abstract
The 2-microm yeast plasmid, a benign high-copy nuclear parasite, propagates itself with nearly the same fidelity as the chromosomes of its host. Equal plasmid segregation is absolutely dependent on the cohesin complex assembled at the plasmid partitioning locus STB. However, the mechanism of cohesin action in the context of multiple plasmid copies, resident within two separate clusters after DNA replication, is unknown. By using "single-copy" derivatives of the 2-microm plasmid, we demonstrate that recruitment of cohesin at STB during S phase indeed translates into cohesion between plasmid molecules. Through binary fluorescence tagging, we reveal that segregation of replicated plasmids occurs in a sister-to-sister fashion. Thus, cohesin serves the same fundamental purpose in plasmid and chromosome segregation.
Collapse
Affiliation(s)
- Santanu K. Ghosh
- Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
| | - Sujata Hajra
- Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
| | - Makkuni Jayaram
- Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
| |
Collapse
|
26
|
Maruyama S, Nozaki H. Sequence and Intranuclear Location of the Extrachromosomal rDNA Plasmid of the Amoebo-Flagellate Naegleria gruberi. J Eukaryot Microbiol 2007; 54:333-7. [PMID: 17669158 DOI: 10.1111/j.1550-7408.2007.00273.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several lower eukaryotic genomes have distinctive organization of rDNA on extrachromosomal molecules: the rDNAs of the amoebo-flagellate Naegleria gruberi (Heterolobosea) are encoded on an extrachromosomal circular plasmid. Although the presence of a circular rDNA plasmid in N. gruberi has now been accepted, its sequence and intracellular location are still unclear. We have now sequenced the entire 14,128 bp of the extrachromosomal circular rDNA plasmid. It contains a single rRNA gene unit composed of 18S, 5.8S, and 28S rRNA genes, but no tRNA or 5S RNA genes. We predict that there are two open reading frames. The region that flanks the rRNA gene unit is A/T-rich, except for a highly G/C-rich region that is approximately 900 bp upstream of the rRNA genes. Fluorescence in situ hybridization of N. gruberi cells revealed that the rDNA plasmids cluster within the nucleolus, suggesting that they are highly organized for the efficient transcription of rRNAs. The N. gruberi rDNA plasmid has a unique high-order cluster structure that provides both a molecular basis for understanding chromosomal organization in basal eukaryotes, and a vehicle for constructing stable transgenic vectors.
Collapse
MESH Headings
- Animals
- DNA, Ribosomal/analysis
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA/genetics
- Naegleria/chemistry
- Naegleria/genetics
- Plasmids/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/analysis
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5S/analysis
- RNA, Ribosomal, 5S/genetics
- Sequence Analysis
Collapse
Affiliation(s)
- Shinichiro Maruyama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | | |
Collapse
|
27
|
Affiliation(s)
- Elaine Yeh
- Elaine Yeh & Kerry Bloom are in the Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, North Carolina 27599-3280, USA
| | - Kerry Bloom
- Elaine Yeh & Kerry Bloom are in the Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, North Carolina 27599-3280, USA
- Tel: +1 919 962 1182; Fax: +1 919 962 8461;
| |
Collapse
|
28
|
Hajra S, Ghosh SK, Jayaram M. The centromere-specific histone variant Cse4p (CENP-A) is essential for functional chromatin architecture at the yeast 2-microm circle partitioning locus and promotes equal plasmid segregation. J Cell Biol 2006; 174:779-90. [PMID: 16966420 PMCID: PMC2064333 DOI: 10.1083/jcb.200603042] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 08/04/2006] [Indexed: 01/19/2023] Open
Abstract
The centromere protein A homologue Cse4p is required for kinetochore assembly and faithful chromosome segregation in Saccharomyces cerevisiae. It has been regarded as the exquisite hallmark of centromeric chromatin. We demonstrate that Cse4 resides at the partitioning locus STB of the 2-microm plasmid. Cse4p-STB association is absolutely dependent on the plasmid partitioning proteins Rep1p and Rep2p and the integrity of the mitotic spindle. The kinetochore mutation ndc10-1 excludes Cse4p from centromeres without dislodging it from STB. Cse4p-STB association lasts from G1/S through late telophase during the cell cycle. The release of Cse4p from STB chromatin is likely mediated through spindle disassembly. A lack of functional Cse4p disrupts the remodeling of STB chromatin by the RSC2 complex, negates Rep2p binding and cohesin assembly at STB, and causes plasmid missegregation. Poaching of a specific histone variant by the plasmid to mark its partitioning locus with a centromere tag reveals yet another one of the molecular trickeries it performs for achieving chromosome- like fidelity in segregation.
Collapse
Affiliation(s)
- Sujata Hajra
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | |
Collapse
|
29
|
Miyazaki T, Tsai HF, Bennett JE. Kre29p is a novel nuclear protein involved in DNA repair and mitotic fidelity in Candida glabrata. Curr Genet 2006; 50:11-22. [PMID: 16775745 DOI: 10.1007/s00294-006-0072-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 03/09/2006] [Accepted: 03/10/2006] [Indexed: 01/27/2023]
Abstract
Candida glabrata KRE29 is an ortholog of Saccharomyces cerevisiae KRE29. S. cerevisiae Kre29p has been identified by affinity purification as a subunit of the Smc5-Smc6 complex, which is required for DNA repair and chromosome segregation. However, mutant phenotypes of S. cerevisiae KRE29 have not been well characterized and none of its orthologs' functions has been reported. Here we report phenotypic characteristics of a C. glabrata kre29 deletant. The absence of C. glabrata Kre29p resulted in decreased viability, exhibiting cell cycle arrest between late S-phase and metaphase even under normal growth conditions, and also caused an increase of plasmid loss rate, implying that Kre29p is required for mitotic chromosome transmission fidelity. The deletant showed increased sensitivity to high temperature as well as to DNA damaging agents including UV, gamma ray, 4-nitroquinoline-1-oxide and methyl methanesulfonate, and the phenotypes were restored in the KRE29 reintegrant. Consistent with the Deltakre29 phenotypes, a Kre29p-GFP fusion protein was located in the nucleus. Furthermore, Kre29p-GFP became concentrated and formed distinct foci after exposure to 4-nitroquinoline-1-oxide. These results suggest the involvement of C. glabrata Kre29p in DNA repair. To our knowledge, this is the first report addressing a cellular protein involved in DNA repair in C. glabrata.
Collapse
Affiliation(s)
- Taiga Miyazaki
- Clinical Mycology Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | |
Collapse
|
30
|
Abstract
The fundamental problems in duplicating and transmitting genetic information posed by the geometric and topological features of DNA, combined with its large size, are qualitatively similar for prokaryotic and eukaryotic chromosomes. The evolutionary solutions to these problems reveal common themes. However, depending on differences in their organization, ploidy, and copy number, chromosomes and plasmids display distinct segregation strategies as well. In bacteria, chromosome duplication, likely mediated by a stationary replication factory, is accompanied by rapid, directed migration of the daughter duplexes with assistance from DNA-compacting and perhaps translocating proteins. The segregation of unit-copy or low-copy bacterial plasmids is also regulated spatially and temporally by their respective partitioning systems. Eukaryotic chromosomes utilize variations of a basic pairing and unpairing mechanism for faithful segregation during mitosis and meiosis. Rather surprisingly, the yeast plasmid 2-micron circle also resorts to a similar scheme for equal partitioning during mitosis.
Collapse
Affiliation(s)
- Santanu Kumar Ghosh
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712-0612, USA.
| | | | | | | |
Collapse
|
31
|
Current awareness on yeast. Yeast 2005; 22:1249-56. [PMID: 16320446 DOI: 10.1002/yea.1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|