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Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [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] [Received: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
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Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
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2
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Lopez C, Cao M, Yao Z, Shao Z. Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering. Appl Microbiol Biotechnol 2021; 105:5959-5972. [PMID: 34357429 DOI: 10.1007/s00253-021-11399-4] [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] [Received: 12/17/2020] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.
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Affiliation(s)
- Carmen Lopez
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, University of Illinois, Urbana, IL, 60801, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
| | - Zhanyi Yao
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011, USA.
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
- The Ames Laboratory, Ames, IA, 50011, USA.
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3
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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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Cui Z, Zheng H, Jiang Z, Wang Z, Hou J, Wang Q, Liang Q, Qi Q. Identification and Characterization of the Mitochondrial Replication Origin for Stable and Episomal Expression in Yarrowia lipolytica. ACS Synth Biol 2021; 10:826-835. [PMID: 33739103 DOI: 10.1021/acssynbio.0c00619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Episomal plasmids are crucial expression tools for recombinant protein production and genome editing. In Saccharomyces cerevisiae, 2-μm artificial plasmids with a high copy number have been developed and used in metabolic engineering and synthetic biology. However, in unconventional yeasts such as Yarrowia lipolytica, episomal expression relies on a chromosome replication system; this system has the disadvantages of genetic instability and low copy numbers. In this study, we identified and characterized replication origins from the mitochondrial DNA (mtDNA) of Y. lipolytica. A 516-bp mtDNA sequence, mtORI, was confirmed to mediate the autonomous replication of circular plasmids with high protein expression levels and hereditary stability. However, the nonhomologous end-joining pathway could interfere with mtORI plasmid replication and engender genetic heterogeneity. In the Po 1f ΔKu70 strain, the homogeneity of the mtORI plasmid was significantly improved, and the highest copy number reached 5.0 per cell. Overall, mitochondrial-origin sequences can be used to establish highly stable and autonomously replicating plasmids, which can be a powerful supplement to the current synthetic biology tool library and promote the development of Y. lipolytica as a microbial cell factory.
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Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Huihui Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhennan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhaoxuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, PR China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
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5
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Hsu TM, Chang YR. High-Copy-Number Plasmid Segregation-Single-Molecule Dynamics in Single Cells. Biophys J 2019; 116:772-780. [PMID: 30773297 DOI: 10.1016/j.bpj.2019.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial high-copy-number (hcn) plasmids provide an excellent model to study the underlying physical mechanisms of DNA segment segregation in an intracellular context. Using two-color fluorescent repressor-operator systems and a synthetic repressible replication origin, we tracked the motion and segregation of single hcn plasmid molecules in individual cells. The plasmid diffusion dynamics revealed between-plasmid temporal associations (clustering) as well as entropic and elastic recoiling forces in the confined intracellular spaces outside of nucleoids. These two effects could be effectively used in models to predict the heterogeneity of segregation. Additionally, the motile behaviors of hcn plasmids provide quantitative estimates of entropic exclusion strength and dynamic associations between DNA segments. Overall, this study utilizes a, to our knowledge, novel approach to predict the polymer dynamics of DNA segments in spatially confined, crowded cellular compartments as well as during bacterial chromosome segregation.
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Affiliation(s)
- Tai-Ming Hsu
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Yi-Ren Chang
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan.
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Miermans CA, Broedersz CP. Bacterial chromosome organization by collective dynamics of SMC condensins. J R Soc Interface 2018; 15:rsif.2018.0495. [PMID: 30333247 DOI: 10.1098/rsif.2018.0495] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various nucleoid-associated proteins, including the ATPase Structural Maintenance of Chromosomes (SMC) condensin. Although the molecular structure of these ATPases has been mapped in detail, it still remains unclear by which physical mechanisms they collectively generate long-range chromosomal contacts. Here, we develop a computational model that captures the subtle interplay between molecular-scale activity of slip-links and large-scale chromosome organization. We first consider a scenario in which the ATPase activity of slip-links regulates their DNA-recruitment near the origin of replication, while the slip-link dynamics is assumed to be diffusive. We find that such diffusive slip-links can collectively organize the entire chromosome into a state with aligned arms, but not within physiological constraints. However, slip-links that include motor activity are far more effective at organizing the entire chromosome over all length-scales. The persistence of motor slip-links at physiological densities can generate large, nested loops and drive them into the bulk of the DNA. Finally, our model with motor slip-links can quantitatively account for the rapid arm-arm alignment of chromosomal arms observed in vivo.
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Affiliation(s)
- Christiaan A Miermans
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Chase P Broedersz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80333 München, Germany
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7
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Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance. Plasmid 2018; 99:82-88. [PMID: 30240700 DOI: 10.1016/j.plasmid.2018.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 01/03/2023]
Abstract
Naturally occurring plasmids have medical importance given that they frequently code for virulence or antibiotic resistance. In many cases, plasmids impose a fitness cost to their hosts, meaning that the growth rate of plasmid-bearing cells is lower than that of plasmid-free cells. However, this does not fit with the fact that plasmids are ubiquitous in nature nor that plasmids and their hosts adapt to each other very fast - as has been shown in laboratory evolutionary assays. Even when plasmids are costly, they seem to largely interact in such a way that the cost of two plasmids is lower than the cost of one of them alone. Moreover, it has been argued that transfer rates are too low to compensate for plasmid costs and segregation. Several mechanisms involving interactions between plasmids and other replicons could overcome this limitation, hence contributing to the maintenance of plasmids in bacterial populations. We examine the importance of these mechanisms from a clinical point of view, particularly the spread of antibiotic resistance genes.
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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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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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.
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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
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11
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Coray DS, Kurenbach B, Heinemann JA. Exploring the parameters of post-segregational killing using heterologous expression of secreted toxin barnase and antitoxin barstar in an Escherichia coli case study. MICROBIOLOGY-SGM 2017; 163:122-130. [PMID: 28270261 DOI: 10.1099/mic.0.000395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Post-segregational killing (PSK) is a phenotype determined by plasmids using a toxin and an antitoxin gene pair. Loss of the genes depletes the cell's reserve of antitoxin and allows the toxin to act upon the cell. PSK benefits mobile elements when it increases reproductive success relative to other mobile competitors. A side effect of PSK is that plasmids become refractory to displacement from the cell during growth as a monoculture. Most PSK systems use a cytoplasmic toxin, but the external toxins of bacteriocins also have a PSK-like effect. It may be that any toxin and antitoxin gene pair can demonstrate PSK when it is on a plasmid. The secreted ribonuclease barnase and its protein inhibitor barstar have features in common with PSK modules, though their native context is chromosomal. We hypothesized that their recruitment to a plasmid could produce an emergent PSK phenotype. Others had shown that secreted barnase could exert a lethal effect on susceptible bacteria similarly to bacteriocins. However, barnase toxicity did not occur under the conditions tested, suggesting that barnase is toxic to neighbouring cells only under very specific conditions. Bacteriocins are only produced under some conditions, and some conditionality on toxin function or release may be advantageous in general to PSKs with external toxins because it would prevent killing of potential plasmid-naive hosts. Too much conditionality, however, would limit how advantageous the gene pair was to mobile elements, making the genes unlikely to be recruited as a PSK system.
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Affiliation(s)
- Dorien S Coray
- Centre for Integrative Ecology and Centre for Integrated Research in Biosafety, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Brigitta Kurenbach
- Centre for Integrative Ecology and Centre for Integrated Research in Biosafety, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Jack A Heinemann
- Centre for Integrative Ecology and Centre for Integrated Research in Biosafety, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
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12
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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.
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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
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Filtration and Normalization of Sequencing Read Data in Whole-Metagenome Shotgun Samples. PLoS One 2016; 11:e0165015. [PMID: 27760173 PMCID: PMC5070866 DOI: 10.1371/journal.pone.0165015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/05/2016] [Indexed: 01/31/2023] Open
Abstract
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes. On the other hand, next-generation sequencing suffers from biases resulting in non-uniform coverage of the sequenced genomes. To overcome this difficulty, we present a model of GC-bias in sequencing metagenomic samples as well as filtration and normalization techniques necessary for accurate quantification of microbial organisms. While there has been substantial research in normalization and filtration of read-count data in such techniques as RNA-seq or Chip-seq, to our knowledge, this has not been the case for the field of whole-metagenome shotgun sequencing. The presented methods assume that complete genome references are available for most microorganisms of interest present in metagenomic samples. This is often a valid assumption in such fields as medical diagnostics of patient microbiota. Testing the model on two validation datasets showed four-fold reduction in root-mean-square error compared to non-normalized data in both cases. The presented methods can be applied to any pipeline for whole metagenome sequencing analysis relying on complete microbial genome references. We demonstrate that such pre-processing reduces the number of false positive hits and increases accuracy of abundance estimates.
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Abstract
Agrobacterium tumefaciens is a plant pathogen with the capacity to deliver a segment of oncogenic DNA carried on a large plasmid called the tumor-inducing or Ti plasmid to susceptible plant cells. A. tumefaciens belongs to the class Alphaproteobacteria, whose members include other plant pathogens (Agrobacterium rhizogenes), plant and insect symbionts (Rhizobium spp. and Wolbachia spp., respectively), human pathogens (Brucella spp., Bartonella spp., Rickettsia spp.), and nonpathogens (Caulobacter crescentus, Rhodobacter sphaeroides). Many species of Alphaproteobacteria carry large plasmids ranging in size from ∼100 kb to nearly 2 Mb. These large replicons typically code for functions essential for cell physiology, pathogenesis, or symbiosis. Most of these elements rely on a conserved gene cassette termed repABC for replication and partitioning, and maintenance at only one or a few copies per cell. The subject of this review is the ∼200-kb Ti plasmids carried by infectious strains of A. tumefaciens. We will summarize the features of this plasmid as a representative of the repABC family of megaplasmids. We will also describe novel features of this plasmid that enable A. tumefaciens cells to incite tumor formation in plants, sense and respond to an array of plant host and bacterial signal molecules, and maintain and disseminate the plasmid among populations of agrobacteria. At the end of this review, we will describe how this natural genetic engineer has been adapted to spawn an entire industry of plant biotechnology and review its potential for use in future therapeutic applications of plant and nonplant species.
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15
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Donovan C, Heyer A, Pfeifer E, Polen T, Wittmann A, Krämer R, Frunzke J, Bramkamp M. A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria. Nucleic Acids Res 2015; 43:5002-16. [PMID: 25916847 PMCID: PMC4446434 DOI: 10.1093/nar/gkv374] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022] Open
Abstract
In host cells, viral replication is localized at specific subcellular sites. Viruses that infect eukaryotic and prokaryotic cells often use host-derived cytoskeletal structures, such as the actin skeleton, for intracellular positioning. Here, we describe that a prophage, CGP3, integrated into the genome of Corynebacterium glutamicum encodes an actin-like protein, AlpC. Biochemical characterization confirms that AlpC is a bona fide actin-like protein and cell biological analysis shows that AlpC forms filamentous structures upon prophage induction. The co-transcribed adaptor protein, AlpA, binds to a consensus sequence in the upstream promoter region of the alpAC operon and also interacts with AlpC, thus connecting circular phage DNA to the actin-like filaments. Transcriptome analysis revealed that alpA and alpC are among the early induced genes upon excision of the CGP3 prophage. Furthermore, qPCR analysis of mutant strains revealed that both AlpA and AlpC are required for efficient phage replication. Altogether, these data emphasize that AlpAC are crucial for the spatio-temporal organization of efficient viral replication. This is remarkably similar to actin-assisted membrane localization of eukaryotic viruses that use the actin cytoskeleton to concentrate virus particles at the egress sites and provides a link of evolutionary conserved interactions between intracellular virus transport and actin.
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Affiliation(s)
- Catriona Donovan
- Department of Biology I, Ludwig-Maximilians-University Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany Institute for Biochemistry, University of Cologne, Zülpicherstr. 47, 50674 Cologne, Germany
| | - Antonia Heyer
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Eugen Pfeifer
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Tino Polen
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anja Wittmann
- Institute for Biochemistry, University of Cologne, Zülpicherstr. 47, 50674 Cologne, Germany
| | - Reinhard Krämer
- Institute for Biochemistry, University of Cologne, Zülpicherstr. 47, 50674 Cologne, Germany
| | - Julia Frunzke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany Institute for Biochemistry, University of Cologne, Zülpicherstr. 47, 50674 Cologne, Germany
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16
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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.
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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
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17
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A novel transcriptional activator, tubX, is required for the stability of Bacillus sphaericus mosquitocidal plasmid pBsph. J Bacteriol 2014; 196:4304-14. [PMID: 25266379 DOI: 10.1128/jb.01855-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stable maintenance of the low-copy-number plasmid pBsph in Bacillus sphaericus requires a partitioning (par) system that consists of a filament-forming protein, B. sphaericus TubZ (TubZ-Bs); a centromere-binding protein, TubR-Bs; and a centromere-like DNA site, tubC, composed of three blocks (I, II, and III) of 12-bp degenerate repeats. Previous studies have shown that mini-pBsph replicons encoding the TubZ system are segregationally highly unstable, whereas the native pBsph is stably maintained. However, the mechanism underlying the stability discrepancy between pBsph and its minireplicon is poorly understood. Here orf187 (encoding TubX), a gene downstream of tubZ-Bs, was found to play a role in plasmid stabilization. Null mutation or overexpression of tubX resulted in a defect in pBsph stability and a significant decrease in the level of tubRZ-Bs expression, and the TubX-null phenotype was suppressed by ectopic expression of a wild-type copy of tubX and additional tubRZ-Bs. An electrophoresis mobility shift assay (EMSA) and a DNase I footprinting assay revealed that the TubX protein bound directly to five 8-bp degenerate repeats located in the par promoter region and that TubX competed with TubR-Bs for binding to the par promoter. Further studies demonstrated that TubX significantly stimulated the transcription of the par operon in the absence of tubR-Bs, and a higher level of gene activation was observed when tubR-Bs was present. These results suggested that TubX positively regulates tubRZ-Bs transcription by interfering with TubR-Bs-mediated repression and binding directly to the tubRZ-Bs promoter region.
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18
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Liu L, Otoupal P, Pan A, Alper HS. Increasing expression level and copy number of aYarrowia lipolyticaplasmid through regulated centromere function. FEMS Yeast Res 2014; 14:1124-7. [DOI: 10.1111/1567-1364.12201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Leqian Liu
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Peter Otoupal
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Anny Pan
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
- Institute for Cellular and Molecular Biology; The University of Texas at Austin; Austin TX USA
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19
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Dorman CJ. H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria. Plasmid 2014; 75:1-11. [DOI: 10.1016/j.plasmid.2014.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
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20
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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.
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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
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21
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Abstract
Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other "precarious" features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.
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22
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Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R. The transcription factor titration effect dictates level of gene expression. Cell 2014; 156:1312-1323. [PMID: 24612990 DOI: 10.1016/j.cell.2014.02.022] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 11/15/2013] [Accepted: 02/03/2014] [Indexed: 02/01/2023]
Abstract
Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.
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Affiliation(s)
- Robert C Brewster
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Franz M Weinert
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Dan Song
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Biophysics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Mattias Rydenfelt
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
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23
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Topological similarity between the 2μm plasmid partitioning locus and the budding yeast centromere: evidence for a common evolutionary origin? Biochem Soc Trans 2013; 41:501-7. [PMID: 23514143 DOI: 10.1042/bst20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The partitioning locus STB of the selfish plasmid, the 2μm circle, of Saccharomyces cerevisiae is essential for the propagation of this multi-copy extra-chromosomal DNA element with nearly chromosome-like stability. The functional competence of STB requires the plasmid-coded partitioning proteins Rep1 and Rep2 as well as host-coded proteins. Host factors that associate with STB in a Rep1- and Rep2-dependent manner also interact with centromeres, and play important roles in chromosome segregation. They include the cohesin complex and the centromere-specific histone H3 variant Cse4. The genetically defined point centromere of S. cerevisiae differs starkly from the much more widespread epigenetically specified regional centromeres of eukaryotes. The particularly small size of the S. cerevisiae centromere and the association of chromosome segregation factors with STB raise the possibility of an evolutionary link between these two partitioning loci. The unusual positive supercoiling harboured by the S. cerevisiae centromere and STB in vivo in their functional states, unveiled by recent experiments, bolsters the notion of their potential descent from an ancestral plasmid partitioning locus.
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24
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Chen Y, Yang L, Ding Y, Zhang S, He T, Mao F, Zhang C, Zhang H, Huo C, Liu P. Tracing evolutionary footprints to identify novel gene functional linkages. PLoS One 2013; 8:e66817. [PMID: 23825567 PMCID: PMC3692504 DOI: 10.1371/journal.pone.0066817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
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Affiliation(s)
- Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
| | - Li Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tong He
- School of Applied Mathematics, Central University of Finance and Economics, Beijing, China
| | - Fenglou Mao
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Congyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huina Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chaoxing Huo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
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25
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Okibe N, Suzuki N, Inui M, Yukawa H. pCGR2 copy number depends on the par
locus that forms a ParC-ParB-DNA partition complex in Corynebacterium glutamicum. J Appl Microbiol 2013; 115:495-508. [DOI: 10.1111/jam.12257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/12/2013] [Accepted: 04/29/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Naoko Okibe
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Nobuaki Suzuki
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
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26
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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.
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Affiliation(s)
| | | | - Makkuni Jayaram
- Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
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27
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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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28
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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.
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Affiliation(s)
- Chien-Hui Ma
- Section of Molecular Genetics & Microbiology, University of Texas at Austin, Austin, TX 78712, USA
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29
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Functional characterization of the role of the chromosome I partitioning system in genome segregation in Deinococcus radiodurans. J Bacteriol 2012; 194:5739-48. [PMID: 22843847 DOI: 10.1128/jb.00610-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deinococcus radiodurans, a radiation-resistant bacterium, harbors a multipartite genome. Chromosome I contains three putative centromeres (segS1, segS2, and segS3), and ParA (ParA1) and ParB (ParB1) homologues. The ParB1 interaction with segS was sequence specific, and ParA1 was shown to be a DNA binding ATPase. The ATPase activity of ParA1 was stimulated when segS elements were coincubated with ParB1, but the greatest increase was observed with segS3. ParA1 incubated with the segS-ParB1 complex showed increased light scattering in the absence of ATP. In the presence of ATP, this increase was continued with segS1-ParA1B1 and segS2-ParA1B1 complexes, while it decreased rapidly after an initial increase for 30 min in the case of segS3. D. radiodurans cells expressing green fluorescent protein (GFP)-ParB1 produced foci on nucleoids, and the ΔparB1 mutant showed growth retardation and ∼13%-higher anucleation than the wild type. Unstable mini-F plasmids carrying segS1 and segS2 showed inheritance in Escherichia coli without ParA1B1, while segS3-mediated plasmid stability required the in trans expression of ParA1B1. Unlike untransformed E. coli cells, cells harboring pDAGS3, a plasmid carrying segS3 and also expressing ParB1-GFP, produced discrete GFP foci on nucleoids. These findings suggested that both segS elements and the ParA1B1 proteins of D. radiodurans are functionally active and have a role in genome segregation.
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30
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Abstract
Genomic analyses increasingly make use of sophisticated statistical and computational approaches in investigations of genomic function and evolution. Scientists implementing and developing these approaches are often computational scientists, physicists, or mathematicians. This article aims to provide a compact overview of genome biology for these scientists. Thus, the article focuses on providing biological context to the genomic features, processes, and structures analysed by these approaches. Topics covered include (1) differences between eukaryotic and prokaryotic cells; (2) the physical structure of genomes and chromatin; (3) different categories of genomic regions, including those serving as templates for RNA and protein synthesis, regulatory regions, repetitive regions, and "architectural" or "organisational" regions, such as centromeres and telomeres; (4) the cell cycle; (5) an overview of transcription, translation, and protein structure; and (6) a glossary of relevant terms.
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31
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Abstract
Chromosome aberration assays are employed to detect the induction of chromosome breakage (clastogenesis) in somatic and germ cells by direct observation of the chromosomal damage during metaphase analysis, or by indirect observation of chromosomal fragments. Thus, various types of cytogenetic change can be detected such as structural chromosome aberrations (CA), sister chromatid exchanges (SCE), ploidy changes, and micronuclei. Following the induction of the chromosomal damage, most of the aberrations and abnormalities detected by these assays can be detrimental or even lethal to the cell. Their presence, however, indicates a potential to also induce more subtle and therefore transmissible chromosomal damage which survives cell division to produce heritable cytogenetic changes. Usually, induced cytogenetic damage is accompanied by other genotoxic damage such as gene mutations.
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32
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Gartenberg MR. Generation of DNA circles in yeast by inducible site-specific recombination. Methods Mol Biol 2011; 833:103-13. [PMID: 22183590 DOI: 10.1007/978-1-61779-477-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Site-specific recombinases have been harnessed for a variety of genetic manipulations involving the gain, loss, or rearrangement of genomic DNA in a variety of organisms. The enzymes have been further exploited in the model eukaryote Saccharomyces cerevisiae for mechanistic studies involving chromosomal context. In these cases, a chromosomal element of interest is converted into a DNA circle within living cells, thereby uncoupling the element from neighboring regulatory sequences, obligatory chromosomal events, and other context-dependent effects that could alter or mask intrinsic functions of the element. In this chapter, I discuss general considerations in using site-specific recombination to create DNA circles in yeast and the specific application of the R recombinase.
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Affiliation(s)
- Marc R Gartenberg
- Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA.
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33
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Laha S, Das SP, Hajra S, Sanyal K, Sinha P. Functional characterization of the Saccharomyces cerevisiae protein Chl1 reveals the role of sister chromatid cohesion in the maintenance of spindle length during S-phase arrest. BMC Genet 2011; 12:83. [PMID: 21943249 PMCID: PMC3190345 DOI: 10.1186/1471-2156-12-83] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 09/23/2011] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Metaphase cells have short spindles for efficient bi-orientation of chromosomes. The cohesin proteins hold sister chromatids together, creating Sister Chromatid Cohesion (SCC) that helps in the maintenance of short spindle lengths in metaphase. The budding yeast protein Chl1p, which has human homologs, is required for DNA damage repair, recombination, transcriptional silencing and aging. This protein is also needed to establish SCC between sister chromatids in S-phase. RESULTS In the present study we have further characterized Chl1p for its role in the yeast Saccharomyces cerevisiae when cells are under replication stress. We show that when DNA replication is arrested by hydroxyurea (HU), the chl1 mutation causes growth deficiency and a mild loss in cell viability. Although both mutant and wild-type cells remained arrested with undivided nuclei, mutant cells had mitotic spindles, which were about 60-80% longer than wild-type spindles. Spindle extension occurred in S-phase in the presence of an active S-phase checkpoint pathway. Further, the chl1 mutant did not show any kinetochore-related defect that could have caused spindle extension. These cells were affected in the retention of SCC in that they had only about one-fourth of the normal levels of the cohesin subunit Scc1p at centromeres, which was sufficient to bi-orient the chromosomes. The mutant cells showed defects in SCC, both during its establishment in S-phase and in its maintenance in G2. Mutants with partial and pericentromeric cohesion defects also showed spindle elongation when arrested in S-phase by HU. CONCLUSIONS Our work shows that Chl1p is required for normal growth and cell viability in the presence of the replication block caused by HU. The absence of this protein does not, however, compromize the replication checkpoint pathway. Even though the chl1 mutation gives synthetic lethal interactions with kinetochore mutations, its absence does not affect kinetochore function; kinetochore-microtubule interactions remain unperturbed. Further, chl1 cells were found to lose SCC at centromeres in both S- and G2 phases, showing the requirement of Chl1p for the maintenance of cohesion in G2 phase of these cells. This work documents for the first time that SCC is an important determinant of spindle size in the yeast Saccharomyces cerevisiae when genotoxic agents cause S-phase arrest of cells.
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Affiliation(s)
| | - Shankar P Das
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA-01604, USA
| | - Sujata Hajra
- R&D Manager (Molecular Biology), HiMedia Laboratories Pvt. Ltd., Mumbai, India
| | - Kaustuv Sanyal
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560 064, India
| | - Pratima Sinha
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VII M, Kolkata
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Jayaram M. Association of a centromere specific nucleosome with the yeast plasmid partitioning locus: Implications beyond plasmid partitioning. Mob Genet Elements 2011; 1:203-207. [PMID: 22479687 DOI: 10.4161/mge.1.3.17431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/14/2011] [Accepted: 07/15/2011] [Indexed: 11/19/2022] Open
Abstract
The genetically defined point centromeres of budding yeasts and the epigenetically specified regional centromeres of all other eukaryotes harbor a common epigenetic mark in the form of a non-standard nucleosome. Although, the composition of the protein core of the centromere specific nucleosome and the nature of the DNA wrap around it are at present controversial, there is no doubt that this specialized nucleosome harbors a variant of the standard histone H3 (cenH3). The association of cenH3, called Cse4 in Saccharomyces cerevisiae, with the partitioning locus (STB) of the high copy selfish plasmid 2 micron circle that resides in the yeast nucleus and propagates itself stably is intriguing. Recent observations are consistent with Cse4 being a nucleosome component at STB. A common nucleosome identity for the partitioning loci of the chromosomes and the plasmid of yeast support arguments based on evolutionary considerations that the origin of the unusual point centromere of budding yeasts may be traced to the STB locus of an ancestral plasmid.
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Affiliation(s)
- Makkuni Jayaram
- Section of Molecular Genetics and Microbiology; University of Texas at Austin; Austin, TX USA
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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.
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Hu B, Itoh T, Mishra A, Katoh Y, Chan KL, Upcher W, Godlee C, Roig MB, Shirahige K, Nasmyth K. ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4 loading complex. Curr Biol 2011; 21:12-24. [PMID: 21185190 PMCID: PMC4763544 DOI: 10.1016/j.cub.2010.12.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/23/2010] [Accepted: 12/02/2010] [Indexed: 01/05/2023]
Abstract
BACKGROUND The Cohesin complex that holds sister chromatins together until anaphase is comprised of three core subunits: Smc1 and Smc3, two long-rod-shaped proteins with an ABC-like ATPase head (nucleotide-binding domain [NBD]) and a dimerization domain linked by a 50 nm long intramolecular antiparallel coiled-coil, and Scc1, an α-kleisin subunit interconnecting the NBD domains of Smc1 and Smc3. Cohesin's stable association with chromosomes is thought to involve entrapment of chromatin fibers by its tripartite Smc1-Smc3-Scc1 ring via a poorly understood mechanism dependent on a separate Scc2/4 loading complex. A key issue concerns where entrapment initially takes place: at sites where cohesin is found stably associated or at distinct "loading" sites from which it translocates. RESULTS In this study, we find transition state mutant versions (Smc1E1158Q and SmcE1155Q) defective in disengagement of their nucleotide binding domains (NBDs), unlike functional cohesin, colocalize with Scc2/4 at core centromeres, sites that catalyze wild-type cohesin's recruitment to sequences 20 kb or more away. In addition to Scc2/4, the unstable association of transition state complexes with core centromeres requires Scc1's association with Smc1 and Smc3 NBDs, ATP-driven NBD engagement, cohesin's Scc3 subunit, and its hinge domain. CONCLUSION We propose that cohesin's association with chromosomes is driven by two key events. NBD engagement driven by ATP binding produces an unstable association with specific loading sites like core centromeres, whereas subsequent ATP hydrolysis triggers DNA entrapment, which permits translocation along chromatin fibers.
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Affiliation(s)
- Bin Hu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Takehiko Itoh
- Laboratory of In Silico Functional Genomics, Graduate School of Bioscience, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Ajay Mishra
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Yuki Katoh
- Laboratory of In Silico Functional Genomics, Graduate School of Bioscience, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Kok-Lung Chan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - William Upcher
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Camilla Godlee
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maurici B. Roig
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Katsuhiko Shirahige
- Laboratory of In Silico Functional Genomics, Graduate School of Bioscience, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Huang L, Yin P, Zhu X, Zhang Y, Ye K. Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100. Nucleic Acids Res 2010; 39:2954-68. [PMID: 21123191 PMCID: PMC3074162 DOI: 10.1093/nar/gkq915] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plasmid pCXC100 from the Gram-positive bacterium Leifsonia xyli subsp. cynodontis uses a type Ib partition system that includes a centromere region, a Walker-type ATPase ParA and a centromere-binding protein ParB for stable segregation. However, ParB shows no detectable sequence homology to any DNA-binding motif. Here, we study the ParB centromere interaction by structural and biochemical approaches. The crystal structure of the C-terminal DNA-binding domain of ParB at 1.4 Å resolution reveals a dimeric ribbon-helix-helix (RHH) motif, supporting the prevalence of RHH motif in centromere binding. Using hydroxyl radical footprinting and quantitative binding assays, we show that the centromere core comprises nine uninterrupted 9-nt direct repeats that can be successively bound by ParB dimers in a cooperative manner. However, the interaction of ParB with a single subsite requires 18 base pairs covering one immediate repeat as well as two halves of flanking repeats. Through mutagenesis, sequence specificity was determined for each position of an 18-bp subsite. These data suggest an unique centromere recognition mechanism by which the repeat sequence is jointly specified by adjacent ParB dimers bound to an overlapped region.
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Affiliation(s)
- Lin Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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Pawlowski WP. Chromosome organization and dynamics in plants. CURRENT OPINION IN PLANT BIOLOGY 2010; 13:640-645. [PMID: 20970369 DOI: 10.1016/j.pbi.2010.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/02/2010] [Accepted: 09/23/2010] [Indexed: 05/28/2023]
Abstract
The past few years have brought renewed interest in understanding the dynamics of chromosomes in interphase cells as well as during cell division, particularly meiosis. This research has been fueled by new imaging methods, particularly three-dimensional, high-resolution, and live microscopy. Major contributors are also new genetic tools that allow elucidation of mechanisms controlling chromosome behavior. Recent studies in plants have explored chromatin arrangement in interphase nuclei, chromosome interactions and movement during meiotic prophase I, and mechanisms that ensure correct segregation of chromosomes during anaphase. These studies shed light on chromosome dynamics in a small-genome plant Arabidopsis thaliana, as well as in plants with large and complex genomes of polyploid origin, such as wheat and maize.
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Affiliation(s)
- Wojciech P Pawlowski
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, United States.
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Salje J, Gayathri P, Löwe J. The ParMRC system: molecular mechanisms of plasmid segregation by actin-like filaments. Nat Rev Microbiol 2010; 8:683-92. [PMID: 20844556 DOI: 10.1038/nrmicro2425] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ParMRC plasmid partitioning apparatus is one of the best characterized systems for bacterial DNA segregation. Bundles of actin-like filaments are used to push plasmids to opposite poles of the cell, whereupon they are stably inherited on cell division. This plasmid-encoded system comprises just three components: an actin-like protein, ParM, a DNA-binding adaptor protein, ParR, and a centromere-like region, parC. The properties and interactions of these components have been finely tuned to enable ParM filaments to search the cell space for plasmids and then move ParR-parC-bound DNA molecules apart. In this Review, we look at some of the most exciting questions in the field concerning the exact molecular mechanisms by which the components of this self-contained system modulate one another's activity to achieve bipolar DNA segregation.
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Affiliation(s)
- Jeanne Salje
- Medical Research Centre Laboratory of Molecular Biology, Cambridge, UK
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Abstract
Non-essential extra-chromosomal DNA elements such as plasmids are responsible for their own propagation in dividing host cells, and one means to ensure this is to carry a miniature active segregation system reminiscent of the mitotic spindle. Plasmids that are maintained at low numbers in prokaryotic cells have developed a range of such active partitioning systems, which are characterized by an impressive simplicity and efficiency and which are united by the use of dynamic, nucleotide-driven filaments to separate and position DNA molecules. A comparison of different plasmid segregation systems reveals (i) how unrelated filament-forming and DNA-binding proteins have been adopted and modified to create a range of simple DNA segregating complexes and (ii) how subtle changes in the few components of these DNA segregation machines has led to a remarkable diversity in the molecular mechanisms of closely related segregation systems. Here, our current understanding of plasmid segregation systems is reviewed and compared with other DNA segregation systems, and this is extended by a discussion of basic principles of plasmid segregation systems, evolutionary implications and the relationship between an autonomous DNA element and its host cell.
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Affiliation(s)
- Jeanne Salje
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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Mehta GD, Agarwal MP, Ghosh SK. Centromere identity: a challenge to be faced. Mol Genet Genomics 2010; 284:75-94. [PMID: 20585957 DOI: 10.1007/s00438-010-0553-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 06/16/2010] [Indexed: 11/26/2022]
Abstract
The centromere is a genetic locus, required for faithful chromosome segregation, where spindle fibers attach to the chromosome through kinetochore. Loss of centromere or formation of multiple centromeres on a single chromosome leads to chromosome missegregation or chromosome breakage, respectively, which are detrimental for fitness and survival of a cell. Therefore, understanding the mechanism of centromere locus determination on the chromosome and perpetuation of such a locus in subsequent generation (known as centromere identity) is very fundamental to combat conditions like aneuploidy, spontaneous abortion, developmental defects, cell lethality and cancer. Recent studies have come up with different models to explain centromere identity. However, the exact mechanism still remains elusive. It has been observed that most eukaryotic centromeres are determined epigenetically rather than by a DNA sequence. The epigenetic marks that are instrumental in determining centromere identity are the histone H3 variant, CENP-A and the specialized posttranslational modification of the core histones. Here we will review the recent studies on the factors responsible for generating unique centromeric chromatin and how it perpetuates during cell division giving the present-day models. We will further focus on the probable mechanism of de novo centromere formation with an example of neocentromere. As a matter of similitude, this review will include marking extrachromosomal chromatin to be served as a partitioning locus by deposition of CENP-A homolog in budding yeast.
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Affiliation(s)
- Gunjan D Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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Abstract
Maintenance of genomic stability is needed for cells to survive many rounds of division throughout their lifetime. Key to the proper inheritance of intact genome is the tight temporal and spatial coordination of cell cycle events. Moreover, checkpoints are present that function to monitor the proper execution of cell cycle processes. For instance, the DNA damage and spindle assembly checkpoints ensure genomic integrity by delaying cell cycle progression in the presence of DNA or spindle damage, respectively. A checkpoint that has recently been gaining attention is the antephase checkpoint that acts to prevent cells from entering mitosis in response to a range of stress agents. We review here what is known about the pathway that monitors the status of the cells at the brink of entry into mitosis when cells are exposed to insults that threaten the proper inheritance of chromosomes. We highlight issues which are unresolved in terms of our understanding of the antephase checkpoint and provide some perspectives on what lies ahead in the understanding of how the checkpoint functions.
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Linear plasmid SLP2 is maintained by partitioning, intrahyphal spread, and conjugal transfer in Streptomyces. J Bacteriol 2010; 192:307-15. [PMID: 19880600 DOI: 10.1128/jb.01192-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Low-copy-number plasmids generally encode a partitioning system to ensure proper segregation after replication. Little is known about partitioning of linear plasmids in Streptomyces. SLP2 is a 50-kb low-copy-number linear plasmid in Streptomyces lividans, which contains a typical parAB partitioning operon. In S. lividans and Streptomyces coelicolor, a parAB deletion resulted in moderate plasmid loss and growth retardation of colonies. The latter was caused by conjugal transfer from plasmid-containing hyphae to plasmidless hyphae. Deletion of the transfer (traB) gene eliminated conjugal transfer, lessened the growth retardation of colonies, and increased plasmid loss through sporulation cycles. The additional deletion of an intrahyphal spread gene (spd1) caused almost complete plasmid loss in a sporulation cycle and eliminated all growth retardation. Moreover, deletion of spd1 alone severely reduced conjugal transfer and stability of SLP2 in S. coelicolor M145 but had no effect on S. lividans TK64. These results revealed the following three systems for SLP2 maintenance: partitioning and spread for moving the plasmid DNA along the hyphae and into spores and conjugal transfer for rescuing plasmidless hyphae. In S. lividans, both spread and partitioning appear to overlap functionally, but in S. coelicolor, spread appears to play the main role.
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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.
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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
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Scanlon TC, Gray EC, Griswold KE. Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries. BMC Biotechnol 2009; 9:95. [PMID: 19930565 PMCID: PMC2784458 DOI: 10.1186/1472-6750-9-95] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 11/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. RESULTS It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. CONCLUSION These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply transformed yeast cells have important implications for yeast library screens. The quantitative information described herein should increase awareness of this issue, and the rapid sequencing approach developed for these studies should be widely useful for identifying multiple vector transformants and avoiding complications associated with cells that have acquired more than one unique plasmid.
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Leslie M. A plasmid goes motoring. J Biophys Biochem Cytol 2009. [PMCID: PMC2673550 DOI: 10.1083/jcb.1852if] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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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.
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Affiliation(s)
- Hong Cui
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
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49
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Classification of plasmid vectors using replication origin, selection marker and promoter as criteria. Plasmid 2009; 61:47-51. [DOI: 10.1016/j.plasmid.2008.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 08/22/2008] [Accepted: 09/10/2008] [Indexed: 11/23/2022]
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50
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Löwe J, Ellonen A, Allen MD, Atkinson C, Sherratt DJ, Grainge I. Molecular mechanism of sequence-directed DNA loading and translocation by FtsK. Mol Cell 2008; 31:498-509. [PMID: 18722176 DOI: 10.1016/j.molcel.2008.05.027] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 03/10/2008] [Accepted: 05/29/2008] [Indexed: 11/17/2022]
Abstract
Dimeric circular chromosomes, formed by recombination between monomer sisters, cannot be segregated to daughter cells at cell division. XerCD site-specific recombination at the Escherichia coli dif site converts these dimers to monomers in a reaction that requires the DNA translocase FtsK. Short DNA sequences, KOPS (GGGNAGGG), which are polarized toward dif in the chromosome, direct FtsK translocation. FtsK interacts with KOPS through a C-terminal winged helix domain gamma. The crystal structure of three FtsKgamma domains bound to 8 bp KOPS DNA demonstrates how three gamma domains recognize KOPS. Using covalently linked dimers of FtsK, we infer that three gamma domains per hexamer are sufficient to recognize KOPS and load FtsK and subsequently activate recombination at dif. During translocation, FtsK fails to recognize an inverted KOPS sequence. Therefore, we propose that KOPS act solely as a loading site for FtsK, resulting in a unidirectionally oriented hexameric motor upon DNA.
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Affiliation(s)
- Jan Löwe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
| | - Antti Ellonen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark D Allen
- Centre for Protein Engineering, MRC, Hills Road, Cambridge CB2 0QH, UK
| | - Claire Atkinson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Ian Grainge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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