1001
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Abstract
Auxin influences nearly every aspect of plant biology through a simple signaling pathway; however, it remains unclear how much of the diversity in auxin effects is explained by variation in the core signaling components and which properties of these components may contribute to diversification in response dynamics. Here, we recapitulated the entire Arabidopsis thaliana forward nuclear auxin signal transduction pathway in Saccharomyces cerevisiae to test whether signaling module composition enables tuning of the dynamic response. Sensitivity analysis guided by a small mathematical model revealed the centrality of auxin/indole-3-acetic acid (Aux/IAA) transcriptional corepressors in controlling response dynamics and highlighted the strong influence of natural variation in Aux/IAA degradation rates on circuit performance. When the basic auxin response circuit was expanded to include multiple Aux/IAAs, we found that dominance relationships between coexpressed Aux/IAAs were sufficient to generate distinct response modules similar to those seen during plant development. Our work provides a new method for dissecting auxin signaling and demonstrates the key role of Aux/IAAs in tuning auxin response dynamics.
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1002
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Nerusheva OO, Galander S, Fernius J, Kelly D, Marston AL. Tension-dependent removal of pericentromeric shugoshin is an indicator of sister chromosome biorientation. Genes Dev 2014; 28:1291-309. [PMID: 24939933 PMCID: PMC4066400 DOI: 10.1101/gad.240291.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/20/2014] [Indexed: 12/24/2022]
Abstract
During mitosis and meiosis, sister chromatid cohesion resists the pulling forces of microtubules, enabling the generation of tension at kinetochores upon chromosome biorientation. How tension is read to signal the bioriented state remains unclear. Shugoshins form a pericentromeric platform that integrates multiple functions to ensure proper chromosome biorientation. Here we show that budding yeast shugoshin Sgo1 dissociates from the pericentromere reversibly in response to tension. The antagonistic activities of the kinetochore-associated Bub1 kinase and the Sgo1-bound phosphatase protein phosphatase 2A (PP2A)-Rts1 underlie a tension-dependent circuitry that enables Sgo1 removal upon sister kinetochore biorientation. Sgo1 dissociation from the pericentromere triggers dissociation of condensin and Aurora B from the centromere, thereby stabilizing the bioriented state. Conversely, forcing sister kinetochores to be under tension during meiosis I leads to premature Sgo1 removal and precocious loss of pericentromeric cohesion. Overall, we show that the pivotal role of shugoshin is to build a platform at the pericentromere that attracts activities that respond to the absence of tension between sister kinetochores. Disassembly of this platform in response to intersister kinetochore tension signals the bioriented state. Therefore, tension sensing by shugoshin is a central mechanism by which the bioriented state is read.
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Affiliation(s)
- Olga O. Nerusheva
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Stefan Galander
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Josefin Fernius
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - David Kelly
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Adele L. Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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1003
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Shimizu-Mitao Y, Kakimoto T. Auxin Sensitivities of All Arabidopsis Aux/IAAs for Degradation in the Presence of Every TIR1/AFB. ACTA ACUST UNITED AC 2014; 55:1450-9. [DOI: 10.1093/pcp/pcu077] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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1004
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Nuclear pores protect genome integrity by assembling a premitotic and Mad1-dependent anaphase inhibitor. Cell 2014; 156:1017-31. [PMID: 24581499 DOI: 10.1016/j.cell.2014.01.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/21/2013] [Accepted: 01/03/2014] [Indexed: 11/23/2022]
Abstract
The spindle assembly checkpoint (SAC) delays anaphase until all chromosomes are bioriented on the mitotic spindle. Under current models, unattached kinetochores transduce the SAC by catalyzing the intramitotic production of a diffusible inhibitor of APC/C(Cdc20) (the anaphase-promoting complex/cyclosome and its coactivator Cdc20, a large ubiquitin ligase). Here we show that nuclear pore complexes (NPCs) in interphase cells also function as scaffolds for anaphase-inhibitory signaling. This role is mediated by Mad1-Mad2 complexes tethered to the nuclear basket, which activate soluble Mad2 as a binding partner and inhibitor of Cdc20 in the cytoplasm. Displacing Mad1-Mad2 from nuclear pores accelerated anaphase onset, prevented effective correction of merotelic errors, and increased the threshold of kinetochore-dependent signaling needed to halt mitosis in response to spindle poisons. A heterologous Mad1-NPC tether restored Cdc20 inhibitor production and normal M phase control. We conclude that nuclear pores and kinetochores both emit "wait anaphase" signals that preserve genome integrity.
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1005
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Park A, Won ST, Pentecost M, Bartkowski W, Lee B. CRISPR/Cas9 allows efficient and complete knock-in of a destabilization domain-tagged essential protein in a human cell line, allowing rapid knockdown of protein function. PLoS One 2014; 9:e95101. [PMID: 24743236 PMCID: PMC3990584 DOI: 10.1371/journal.pone.0095101] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/21/2014] [Indexed: 12/26/2022] Open
Abstract
Although modulation of protein levels is an important tool for study of protein function, it is difficult or impossible to knockdown or knockout genes that are critical for cell growth or viability. For such genes, a conditional knockdown approach would be valuable. The FKBP protein-based destabilization domain (DD)-tagging approach, which confers instability to the tagged protein in the absence of the compound Shield-1, has been shown to provide rapid control of protein levels determined by Shield-1 concentration. Although a strategy to knock-in DD-tagged protein at the endogenous loci has been employed in certain parasite studies, partly due to the relative ease of knock-in as a result of their mostly haploid lifecycles, this strategy has not been demonstrated in diploid or hyperploid mammalian cells due to the relative difficulty of achieving complete knock-in in all alleles. The recent advent of CRISPR/Cas9 homing endonuclease-mediated targeted genome cleavage has been shown to allow highly efficient homologous recombination at the targeted locus. We therefore assessed the feasibility of using CRISPR/Cas9 to achieve complete knock-in to DD-tag the essential gene Treacher Collins-Franceschetti syndrome 1 (TCOF1) in human 293T cells. Using a double antibiotic selection strategy to select clones with at least two knock-in alleles, we obtained numerous complete knock-in clones within three weeks of initial transfection. DD-TCOF1 expression in the knock-in cells was Shield-1 concentration-dependent, and removal of Shield-1 resulted in destabilization of DD-TCOF1 over the course of hours. We further confirmed that the tagged TCOF1 retained the nucleolar localization of the wild-type untagged protein, and that destabilization of DD-TCOF1 resulted in impaired cell growth, as expected for a gene implicated in ribosome biogenesis. CRISPR/Cas9-mediated homologous recombination to completely knock-in a DD tag likely represents a generalizable and efficient strategy to achieve rapid modulation of protein levels in mammalian cells.
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Affiliation(s)
- Arnold Park
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sohui T Won
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mickey Pentecost
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Wojciech Bartkowski
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benhur Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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1006
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Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP, Legube G. Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat Struct Mol Biol 2014; 21:366-74. [PMID: 24658350 PMCID: PMC4300393 DOI: 10.1038/nsmb.2796] [Citation(s) in RCA: 468] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 02/24/2014] [Indexed: 12/17/2022]
Abstract
Although both homologous recombination (HR) and nonhomologous end joining can repair DNA double-strand breaks (DSBs), the mechanisms by which one of these pathways is chosen over the other remain unclear. Here we show that transcriptionally active chromatin is preferentially repaired by HR. Using chromatin immunoprecipitation-sequencing (ChIP-seq) to analyze repair of multiple DSBs induced throughout the human genome, we identify an HR-prone subset of DSBs that recruit the HR protein RAD51, undergo resection and rely on RAD51 for efficient repair. These DSBs are located in actively transcribed genes and are targeted to HR repair via the transcription elongation-associated mark trimethylated histone H3 K36. Concordantly, depletion of SETD2, the main H3 K36 trimethyltransferase, severely impedes HR at such DSBs. Our study thereby demonstrates a primary role in DSB repair of the chromatin context in which a break occurs.
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Affiliation(s)
- François Aymard
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Beatrix Bugler
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Christine K Schmidt
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2] Department of Biochemistry, University of Cambridge, Cambridge, UK. [3] Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Emmanuelle Guillou
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Pierre Caron
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Sébastien Briois
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM, University of Toulouse, Toulouse, France
| | - Virginie Daburon
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
| | - Kyle M Miller
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2]
| | - Stephen P Jackson
- 1] Gurdon Institute, University of Cambridge, Cambridge, UK. [2] Department of Biochemistry, University of Cambridge, Cambridge, UK. [3] Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Gaëlle Legube
- 1] Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Université de Toulouse, Université Paul Sabatier, Toulouse, France. [2] CNRS, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Toulouse, France
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1007
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Nuttall JM, Motley AM, Hettema EH. Deficiency of the exportomer components Pex1, Pex6, and Pex15 causes enhanced pexophagy in Saccharomyces cerevisiae. Autophagy 2014; 10:835-45. [PMID: 24657987 PMCID: PMC5119063 DOI: 10.4161/auto.28259] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Turnover of damaged, dysfunctional, or excess organelles is critical to cellular homeostasis. We screened mutants disturbed in peroxisomal protein import, and found that a deficiency in the exportomer subunits Pex1, Pex6, and Pex15 results in enhanced turnover of peroxisomal membrane structures compared with other mutants. Strikingly, almost all peroxisomal membranes were associated with phagophore assembly sites in pex1Δ atg1Δ cells. Degradation depended on Atg11 and the pexophagy receptor Atg36, which mediates degradation of superfluous peroxisomes. Mutants of PEX1, PEX6, and PEX15 accumulate ubiquitinated receptors at the peroxisomal membrane. This accumulation has been suggested to trigger pexophagy in mammalian cells. We show by genetic analysis that preventing this accumulation does not abolish pexophagy in Saccharomyces cerevisiae. We find Atg36 is modified in pex1Δ cells even when Atg11 binding is prevented, suggesting Atg36 modification is an early event in the degradation of dysfunctional peroxisomal structures in pex1Δ cells via pexophagy.
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Affiliation(s)
- James M Nuttall
- Department of Molecular Biology and Biotechnology; University of Sheffield, Western Bank; Sheffield, UK
| | - Alison M Motley
- Department of Molecular Biology and Biotechnology; University of Sheffield, Western Bank; Sheffield, UK
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology; University of Sheffield, Western Bank; Sheffield, UK
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1008
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Mehta GD, Agarwal M, Ghosh SK. Functional characterization of kinetochore protein, Ctf19 in meiosis I: an implication of differential impact of Ctf19 on the assembly of mitotic and meiotic kinetochores in Saccharomyces cerevisiae. Mol Microbiol 2014; 91:1179-99. [PMID: 24446862 DOI: 10.1111/mmi.12527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 11/29/2022]
Abstract
Meiosis is a specialized cell division process through which chromosome numbers are reduced by half for the generation of gametes. Kinetochore, a multiprotein complex that connects centromeres to microtubules, plays essential role in chromosome segregation. Ctf19 is the key central kinetochore protein that recruits all the other non-essential proteins of the Ctf19 complex in budding yeast. Earlier studies have shown the role of Ctf19 complex in enrichment of cohesin around the centromeres both during mitosis and meiosis, leading to sister chromatid cohesion and meiosis II disjunction. Here we show that Ctf19 is also essential for the proper execution of the meiosis I specific unique events, such as non-homologous centromere coupling, homologue pairing, chiasmata resolution and proper orientation of homologues and sister chromatids with respect to the spindle poles. Additionally, this investigation reveals that proper kinetochore function is required for faithful chromosome condensation in meiosis. Finally, this study suggests that absence of Ctf19 affects the integrity of meiotic kinetochore differently than that of the mitotic kinetochore. Consequently, absence of Ctf19 leads to gross chromosome missegregation during meiosis as compared with mitosis. Hence, this study reports for the first time the differential impact of a non-essential kinetochore protein on the mitotic and meiotic kinetochore ensembles and hence chromosome segregation.
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Affiliation(s)
- Gunjan D Mehta
- Department of Biosciences and Bioengineering, Wadhawani Research Centre of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 40076, India
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1009
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Verzijlbergen KF, Nerusheva OO, Kelly D, Kerr A, Clift D, de Lima Alves F, Rappsilber J, Marston AL. Shugoshin biases chromosomes for biorientation through condensin recruitment to the pericentromere. eLife 2014; 3:e01374. [PMID: 24497542 PMCID: PMC3910079 DOI: 10.7554/elife.01374] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To protect against aneuploidy, chromosomes must attach to microtubules from opposite poles (‘biorientation’) prior to their segregation during mitosis. Biorientation relies on the correction of erroneous attachments by the aurora B kinase, which destabilizes kinetochore-microtubule attachments that lack tension. Incorrect attachments are also avoided because sister kinetochores are intrinsically biased towards capture by microtubules from opposite poles. Here, we show that shugoshin acts as a pericentromeric adaptor that plays dual roles in biorientation in budding yeast. Shugoshin maintains the aurora B kinase at kinetochores that lack tension, thereby engaging the error correction machinery. Shugoshin also recruits the chromosome-organizing complex, condensin, to the pericentromere. Pericentromeric condensin biases sister kinetochores towards capture by microtubules from opposite poles. Our findings uncover the molecular basis of the bias to sister kinetochore capture and expose shugoshin as a pericentromeric hub controlling chromosome biorientation. DOI:http://dx.doi.org/10.7554/eLife.01374.001 When a cell divides to create two new daughter cells, it must produce a copy of each of its chromosomes. It is important that each daughter cell gets just one copy of each chromosome. If an error occurs and one cell gets two copies of a single chromosome, it can lead to cancer or birth defects. Fortunately, there are multiple checks to ensure that this does not happen. During cell division the chromosomes line up in a way that increases the likelihood that each daughter cell will have one copy of each chromosome. After this process—which is called biorientation—is completed, microtubules pull the chromosomes to opposite ends of the cell, which then divides. Proteins called shugoshin proteins are known to be involved in biorientation in many organisms. These proteins are found in a region called the pericentromere, which surrounds the area on the chromosomes that the microtubules attach to, but the details of their involvement in biorientation are not fully understood. Now Verzijlbergen et al. have exploited sophisticated genetic techniques in yeast to explore how shugoshin proteins work. These experiments showed that the shugoshin protein helps to recruit condensin—a protein that keeps the DNA organized within the chromosome—to the pericentromere to assist with biorientation. It also keeps aurora B kinase—one of the enzymes that helps to correct errors during cell division—in the pericentromere when a microtubule attaches to the wrong chromosome. These results help us understand how a ‘hub’ in the pericentromere ensures biorientation. The next challenge will be to understand how this hub is disassembled after biorientation to allow error-free cell division to proceed. As shugoshins have been found to be damaged in some cancers, understanding the workings of this hub could also shed new light on how they contribute to disease. DOI:http://dx.doi.org/10.7554/eLife.01374.002
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Affiliation(s)
- Kitty F Verzijlbergen
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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1010
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Farr CJ, Antoniou-Kourounioti M, Mimmack ML, Volkov A, Porter ACG. The α isoform of topoisomerase II is required for hypercompaction of mitotic chromosomes in human cells. Nucleic Acids Res 2014; 42:4414-26. [PMID: 24476913 PMCID: PMC3985649 DOI: 10.1093/nar/gku076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
As proliferating cells transit from interphase into M-phase, chromatin undergoes extensive reorganization, and topoisomerase (topo) IIα, the major isoform of this enzyme present in cycling vertebrate cells, plays a key role in this process. In this study, a human cell line conditional null mutant for topo IIα and a derivative expressing an auxin-inducible degron (AID)-tagged version of the protein have been used to distinguish real mitotic chromosome functions of topo IIα from its more general role in DNA metabolism and to investigate whether topo IIβ makes any contribution to mitotic chromosome formation. We show that topo IIβ does contribute, with endogenous levels being sufficient for the initial stages of axial shortening. However, a significant effect of topo IIα depletion, seen with or without the co-depletion of topo IIβ, is the failure of chromosomes to hypercompact when delayed in M-phase. This requires much higher levels of topo II protein and is impaired by drugs or mutations that affect enzyme activity. A prolonged delay at the G2/M border results in hyperefficient axial shortening, a process that is topo IIα-dependent. Rapid depletion of topo IIα has allowed us to show that its function during late G2 and M-phase is truly required for shaping mitotic chromosomes.
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Affiliation(s)
- Christine J Farr
- Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UK and Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Rd, London W12 0NN, UK
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1011
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Gonzalez-Huici V, Szakal B, Urulangodi M, Psakhye I, Castellucci F, Menolfi D, Rajakumara E, Fumasoni M, Bermejo R, Jentsch S, Branzei D. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity. EMBO J 2014; 33:327-40. [PMID: 24473148 PMCID: PMC3983681 DOI: 10.1002/embj.201387425] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.
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1012
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Rapid and reversible knockdown of endogenous proteins by peptide-directed lysosomal degradation. Nat Neurosci 2014; 17:471-80. [PMID: 24464042 PMCID: PMC3937121 DOI: 10.1038/nn.3637] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/16/2013] [Indexed: 12/13/2022]
Abstract
Rapid and reversible methods for altering the level of endogenous proteins are critically important for studying biological systems and developing therapeutics. Here, we describe a membrane permeable targeting peptide-based method that rapidly and reversibly knocks down endogenous proteins through chaperone-mediated autophagy in vitro and in vivo. We demonstrated the specificity, efficacy and generalizability of the method by showing efficient knockdown of various proteins including death associated protein kinase 1 (160kDa), scaffolding protein PSD-95 (95kDa) and α-synuclein (18kDa) with their respective targeting peptides in a dose-, time- and lysosomal activity-dependent manner in neuronal cultures. More significantly, we showed that when given systemically, the peptide system efficiently knocked down the targeted protein in the brain of intact rats. Our study provides a robust and convenient research tool to manipulate endogenous protein levels, and may also lead to the development of protein knockdown-based novel therapeutics for treating various human diseases.
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1013
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Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol 2014; 15:95-107. [PMID: 24434884 DOI: 10.1038/nrm3738] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in DNA manipulation and gene circuit engineering has greatly improved our ability to programme and probe mammalian cell behaviour. These advances have led to a new generation of synthetic biology research tools and potential therapeutic applications. Programmable DNA-binding domains and RNA regulators are leading to unprecedented control of gene expression and elucidation of gene function. Rebuilding complex biological circuits such as T cell receptor signalling in isolation from their natural context has deepened our understanding of network motifs and signalling pathways. Synthetic biology is also leading to innovative therapeutic interventions based on cell-based therapies, protein drugs, vaccines and gene therapies.
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1014
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Sasabe M, Shintani S, Kintaka R, Kaizu K, Makanae K, Moriya H. Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW. BMC SYSTEMS BIOLOGY 2014; 8:2. [PMID: 24393197 PMCID: PMC3892067 DOI: 10.1186/1752-0509-8-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/27/2013] [Indexed: 12/19/2022]
Abstract
Background Identifying permissible limits of intracellular parameters such as protein expression provides important information for examining robustness. In this study, we used the TEV protease-mediated induction of protein instability (TIPI) in combination with the genetic Tug-of-War (gTOW) to develop a method to measure the lower limit of protein level. We first tested the feasibility of this method using ADE2 as a marker and then analyzed some cell cycle regulators to reveal genetic interactions. Results Using TIPI-gTOW, we successfully constructed a strain in which GFP-TDegFAde2 was expressed at the lower limit, just sufficient to support cellular growth under the -Ade condition by accelerating degradation by TEV protease. We also succeeded in constructing a strain in which the minimal level of GFP-TDegFCdc20 was expressed by TIPI-gTOW. Using this strain, we studied genetic interactions between cell cycle regulators and CDC20, and the result was highly consistent with the previously identified interactions. Comparison of the experimental data with predictions of a mathematical model revealed some interactions that were not implemented into the current model. Conclusions TIPI-gTOW is useful for estimating changes in the lower limit of a protein under different conditions, such as different genetic backgrounds and environments. TIPI-gTOW is also useful for analyzing genetic interactions of essential genes whose deletion mutants cannot be obtained.
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Affiliation(s)
| | | | | | | | | | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan.
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1015
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Germann SM, Schramke V, Pedersen RT, Gallina I, Eckert-Boulet N, Oestergaard VH, Lisby M. TopBP1/Dpb11 binds DNA anaphase bridges to prevent genome instability. ACTA ACUST UNITED AC 2013; 204:45-59. [PMID: 24379413 PMCID: PMC3882784 DOI: 10.1083/jcb.201305157] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
TopBP1/Dpb11 prevents accumulation of anaphase chromatin bridges by stimulating the Mec1/ATR kinase and suppressing homologous recombination. DNA anaphase bridges are a potential source of genome instability that may lead to chromosome breakage or nondisjunction during mitosis. Two classes of anaphase bridges can be distinguished: DAPI-positive chromatin bridges and DAPI-negative ultrafine DNA bridges (UFBs). Here, we establish budding yeast Saccharomyces cerevisiae and the avian DT40 cell line as model systems for studying DNA anaphase bridges and show that TopBP1/Dpb11 plays an evolutionarily conserved role in their metabolism. Together with the single-stranded DNA binding protein RPA, TopBP1/Dpb11 binds to UFBs, and depletion of TopBP1/Dpb11 led to an accumulation of chromatin bridges. Importantly, the NoCut checkpoint that delays progression from anaphase to abscission in yeast was activated by both UFBs and chromatin bridges independently of Dpb11, and disruption of the NoCut checkpoint in Dpb11-depleted cells led to genome instability. In conclusion, we propose that TopBP1/Dpb11 prevents accumulation of anaphase bridges via stimulation of the Mec1/ATR kinase and suppression of homologous recombination.
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Affiliation(s)
- Susanne M Germann
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, DK-2200 Copenhagen N, Denmark
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1016
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Copsey A, Tang S, Jordan PW, Blitzblau HG, Newcombe S, Chan ACH, Newnham L, Li Z, Gray S, Herbert AD, Arumugam P, Hochwagen A, Hunter N, Hoffmann E. Smc5/6 coordinates formation and resolution of joint molecules with chromosome morphology to ensure meiotic divisions. PLoS Genet 2013; 9:e1004071. [PMID: 24385939 PMCID: PMC3873251 DOI: 10.1371/journal.pgen.1004071] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
Abstract
During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and the regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of a subset of joint-molecule intermediates. In this regard, Smc5/6 functions independently of the major crossover pathway defined by the MutLγ complex. Furthermore, we show that Smc5/6 is required for stable chromosomal localization of the XPF-family endonuclease, Mus81-Mms4(Eme1). Our data suggest that the Smc5/6 complex is required for specific recombination and chromosomal processes throughout meiosis and that in its absence, attempts at cell division with unresolved joint molecules and residual cohesin lead to severe recombination-induced meiotic catastrophe.
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Affiliation(s)
- Alice Copsey
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Shangming Tang
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, United States of America
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, United States of America
| | - Philip W. Jordan
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Hannah G. Blitzblau
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Sonya Newcombe
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Andrew Chi-ho Chan
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Louise Newnham
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Zhaobo Li
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Stephen Gray
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Alex D. Herbert
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Prakash Arumugam
- Department of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Andreas Hochwagen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, United States of America
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, United States of America
- Department of Biology, New York University, New York, New York, United States of America
- Department of Molecular & Cellular Biology, University of California, Davis, Davis, California, United States of America
- Department of Cell Biology & Human Anatomy, University of California, Davis, Davis, California, United States of America
| | - Eva Hoffmann
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
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1017
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Abe K, Ohno Y, Sassa T, Taguchi R, Çalışkan M, Ober C, Kihara A. Mutation for nonsyndromic mental retardation in the trans-2-enoyl-CoA reductase TER gene involved in fatty acid elongation impairs the enzyme activity and stability, leading to change in sphingolipid profile. J Biol Chem 2013; 288:36741-9. [PMID: 24220030 PMCID: PMC3868783 DOI: 10.1074/jbc.m113.493221] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 11/07/2013] [Indexed: 11/06/2022] Open
Abstract
Very long-chain fatty acids (VLCFAs, chain length >C20) exist in tissues throughout the body and are synthesized by repetition of the fatty acid (FA) elongation cycle composed of four successive enzymatic reactions. In mammals, the TER gene is the only gene encoding trans-2-enoyl-CoA reductase, which catalyzes the fourth reaction in the FA elongation cycle. The TER P182L mutation is the pathogenic mutation for nonsyndromic mental retardation. This mutation substitutes a leucine for a proline residue at amino acid 182 in the TER enzyme. Currently, the mechanism by which the TER P182L mutation causes nonsyndromic mental retardation is unknown. To understand the effect of this mutation on the TER enzyme and VLCFA synthesis, we have biochemically characterized the TER P182L mutant enzyme using yeast and mammalian cells transfected with the TER P182L mutant gene and analyzed the FA elongation cycle in the B-lymphoblastoid cell line with the homozygous TER P182L mutation (TER(P182L/P182L) B-lymphoblastoid cell line). We have found that TER P182L mutant enzyme exhibits reduced trans-2-enoyl-CoA reductase activity and protein stability, thereby impairing VLCFA synthesis and, in turn, altering the sphingolipid profile (i.e. decreased level of C24 sphingomyelin and C24 ceramide) in the TER(P182L/P182L) B-lymphoblastoid cell line. We have also found that in addition to the TER enzyme-catalyzed fourth reaction, the third reaction in the FA elongation cycle is affected by the TER P182L mutation. These findings provide new insight into the biochemical defects associated with this genetic mutation.
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Affiliation(s)
- Kensuke Abe
- From the Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Yusuke Ohno
- From the Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Takayuki Sassa
- From the Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ryo Taguchi
- the Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan, and
| | - Minal Çalışkan
- the Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
| | - Carole Ober
- the Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
| | - Akio Kihara
- From the Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
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1018
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Watson AT, Daigaku Y, Mohebi S, Etheridge TJ, Chahwan C, Murray JM, Carr AM. Optimisation of the Schizosaccharomyces pombe urg1 expression system. PLoS One 2013; 8:e83800. [PMID: 24376751 PMCID: PMC3869809 DOI: 10.1371/journal.pone.0083800] [Citation(s) in RCA: 21] [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: 10/02/2013] [Accepted: 11/17/2013] [Indexed: 01/04/2023] Open
Abstract
The ability to study protein function in vivo often relies on systems that regulate the presence and absence of the protein of interest. Two limitations for previously described transcriptional control systems that are used to regulate protein expression in fission yeast are: the time taken for inducing conditions to initiate transcription and the ability to achieve very low basal transcription in the "OFF-state". In previous work, we described a Cre recombination-mediated system that allows the rapid and efficient regulation of any gene of interest by the urg1 promoter, which has a dynamic range of approximately 75-fold and which is induced within 30-60 minutes of uracil addition. In this report we describe easy-to-use and versatile modules that can be exploited to significantly tune down Purg1 "OFF-levels" while maintaining an equivalent dynamic range. We also provide plasmids and tools for combining Purg1 transcriptional control with the auxin degron tag to help maintain a null-like phenotype. We demonstrate the utility of this system by improved regulation of HO-dependent site-specific DSB formation, by the regulation Rtf1-dependent replication fork arrest and by controlling Rhp18(Rad18)-dependent post replication repair.
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Affiliation(s)
- Adam T. Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Yasukazu Daigaku
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Saed Mohebi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Thomas J. Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Charly Chahwan
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex, United Kingdom
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1019
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Phosphatidic acid and phosphoinositides facilitate liposome association of Yas3p and potentiate derepression of ARE1 (alkane-responsive element one)-mediated transcription control. Fungal Genet Biol 2013; 61:100-10. [DOI: 10.1016/j.fgb.2013.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/18/2013] [Accepted: 09/28/2013] [Indexed: 11/18/2022]
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1020
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McIsaac RS, Oakes BL, Botstein D, Noyes MB. Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters. J Vis Exp 2013:e51153. [PMID: 24300440 PMCID: PMC3992113 DOI: 10.3791/51153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Synthetic biology aims to rationally design and build synthetic circuits with desired quantitative properties, as well as provide tools to interrogate the structure of native control circuits. In both cases, the ability to program gene expression in a rapid and tunable fashion, with no off-target effects, can be useful. We have constructed yeast strains containing the ACT1 promoter upstream of a URA3 cassette followed by the ligand-binding domain of the human estrogen receptor and VP16. By transforming this strain with a linear PCR product containing a DNA binding domain and selecting against the presence of URA3, a constitutively expressed artificial transcription factor (ATF) can be generated by homologous recombination. ATFs engineered in this fashion can activate a unique target gene in the presence of inducer, thereby eliminating both the off-target activation and nonphysiological growth conditions found with commonly used conditional gene expression systems. A simple method for the rapid construction of GFP reporter plasmids that respond specifically to a native or artificial transcription factor of interest is also provided.
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Affiliation(s)
- R Scott McIsaac
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University
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1021
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Eykelenboom JK, Harte EC, Canavan L, Pastor-Peidro A, Calvo-Asensio I, Llorens-Agost M, Lowndes NF. ATR activates the S-M checkpoint during unperturbed growth to ensure sufficient replication prior to mitotic onset. Cell Rep 2013; 5:1095-107. [PMID: 24268773 DOI: 10.1016/j.celrep.2013.10.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/19/2013] [Accepted: 10/17/2013] [Indexed: 01/23/2023] Open
Abstract
Cells must accurately replicate and segregate their DNA once per cell cycle in order to successfully transmit genetic information. During S phase in the presence of agents that cause replication stress, ATR-dependent checkpoints regulate origin firing and the replication machinery as well as prevent untimely mitosis. Here, we investigate the role of ATR during unperturbed growth in vertebrate cells. In the absence of ATR, individual replication forks progress more slowly, and an increased number of replication origins are activated. These cells also enter mitosis early and divide more rapidly, culminating in chromosome bridges and laggards at anaphase, failed cytokinesis, and cell death. Interestingly, cell death can be rescued by prolonging mitosis with partial inhibition of the mitotic cyclin-dependent kinase 1. Our data indicate that one of the essential roles of ATR during normal growth is to minimize the level of unreplicated DNA before the onset of mitosis.
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Affiliation(s)
- John Kenneth Eykelenboom
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Emma Christina Harte
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Lynn Canavan
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Ana Pastor-Peidro
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Irene Calvo-Asensio
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Marta Llorens-Agost
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Noel Francis Lowndes
- Genome Stability Laboratory, Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
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1022
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Matsuo Y, Granneman S, Thoms M, Manikas RG, Tollervey D, Hurt E. Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export. Nature 2013; 505:112-116. [PMID: 24240281 PMCID: PMC3880858 DOI: 10.1038/nature12731] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/03/2013] [Indexed: 01/05/2023]
Abstract
Eukaryotic ribosomes are assembled by a complex pathway that extends from the nucleolus to the cytoplasm and is powered by many energy-consuming enzymes 1-3. Nuclear export is a key, irreversible step in pre-ribosome maturation4-8, but mechanisms underlying the timely acquisition of export competence remain poorly understood. Here we show that a conserved GTPase Nug2/Nog2 (called NGP-1, Gnl2 or nucleostemin 2 in human9) plays a key role in the timing of export competence. Nug2 binds the inter-subunit face of maturing, nucleoplasmic pre-60S particles, and the location clashes with the position of Nmd3, a key pre-60S export adaptor10. Nug2 and Nmd3 are not present on the same pre-60S particles, with Nug2 binding prior to Nmd3. Depletion of Nug2 causes premature Nmd3 binding to the pre-60S particles, whereas mutations in the G-domain of Nug2 block Nmd3 recruitment, resulting in severe 60S export defects. Two pre-60S remodeling factors, the Rea1 ATPase and its co-substrate Rsa4, are present on Nug2-associated particles, and both show synthetic lethal interactions with nug2 mutants. Release of Nug2 from pre-60S particles requires both its K+-dependent GTPase activity and the remodeling ATPase activity of Rea1. We conclude that Nug2 is a regulatory GTPase that monitors pre-60S maturation, with release from its placeholder site linked to recruitment of the nuclear export machinery.
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Affiliation(s)
- Yoshitaka Matsuo
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany
| | - Sander Granneman
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh UK.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, UK
| | - Matthias Thoms
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany
| | - Rizos-Georgios Manikas
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh UK
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany
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1023
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Kreidenweiss A, Hopkins AV, Mordmüller B. 2A and the auxin-based degron system facilitate control of protein levels in Plasmodium falciparum. PLoS One 2013; 8:e78661. [PMID: 24236031 PMCID: PMC3827281 DOI: 10.1371/journal.pone.0078661] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/23/2013] [Indexed: 11/19/2022] Open
Abstract
Analysis of gene function in Plasmodium falciparum, the most important human malaria parasite, is restricted by the lack of robust and simple reverse genetic tools. Approaches to manipulate protein levels post-translationally are powerful tools to study protein-off effects especially in the haploid malaria parasite where genetic knockouts of essential genes are lethal. We investigated if the auxin-inducible degron system is functional in P. falciparum and found that degron-tagged yellow fluorescent protein levels were efficiently reduced upon addition of auxin which otherwise had no effect on parasite viability. The genetic components required in this conditional approach were co-expressed in P. falciparum by applying the small peptide 2A. 2A is a self-processing peptide from Foot-And-Mouth Disease virus that allows the whole conditional system to be accommodated on a single plasmid vector and ensures stoichiometric expression levels.
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Affiliation(s)
- Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- * E-mail:
| | - Annika V. Hopkins
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
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1024
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Tay YD, Patel A, Kaemena DF, Hagan IM. Mutation of a conserved residue enhances the sensitivity of analogue-sensitised kinases to generate a novel approach to the study of mitosis in fission yeast. J Cell Sci 2013; 126:5052-61. [PMID: 23986474 DOI: 10.1242/jcs.135301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chemical genetic strategy in which mutational enlargement of the ATP-binding site sensitises of a protein kinase to bulky ATP analogues has proved to be an elegant tool for the generation of conditional analogue-sensitive kinase alleles in a variety of model organisms. Here, we describe a novel substitution mutation in the kinase domain that can enhance the sensitivity of analogue-sensitive kinases. Substitution of a methionine residue to phenylalanine in the +2 position after HRDLKxxN motif of the subdomain VIb within the kinase domain markedly increased the sensitivities of the analogue-sensitive kinases to ATP analogues in three out of five S. pombe kinases (i.e. Plo1, Orb5 and Wee1) that harbor this conserved methionine residue. Kinome alignment established that a methionine residue is found at this site in 5-9% of kinases in key model organisms, suggesting that a broader application of this structural modification may enhance ATP analogue sensitivity of analogue-sensitive kinases in future studies. We also show that the enhanced sensitivity of the wee1.as8 allele in a cdc25.22 background can be exploited to generate highly synchronised mitotic and S phase progression at 36°C. Proof-of-principle experiments show how this novel synchronisation technique will prove of great use in the interrogation of the mitotic or S-phase functions through temperature sensitivity mutation of molecules of interest in fission yeast.
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Affiliation(s)
- Ye-Dee Tay
- CRUK Cell Division Group, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
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1025
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Gombos L, Neuner A, Berynskyy M, Fava LL, Wade RC, Sachse C, Schiebel E. GTP regulates the microtubule nucleation activity of γ-tubulin. Nat Cell Biol 2013; 15:1317-27. [PMID: 24161932 DOI: 10.1038/ncb2863] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/19/2013] [Indexed: 12/25/2022]
Abstract
Both subunits of αβ-tubulin that comprise the core components of microtubules bind GTP. GTP binding to α-tubulin has a structural role, whereas β-tubulin binds and hydrolyses GTP to regulate microtubule dynamics. γ-tubulin, another member of the tubulin superfamily that seeds microtubule nucleation at microtubule-organizing centres, also binds GTP; however, the importance of this association remains elusive. To address the role of GTP binding to γ-tubulin, we systematically mutagenized the GTP contact residues in the yeast γ-tubulin Tub4. Tub4(GTP)-mutant proteins that exhibited greatly reduced GTP affinity still assembled into the small γ-tubulin complex. However, tub4(GTP) mutants were no longer viable, and had defects in interaction between γ-tubulin and αβ-tubulin, decreased microtubule nucleation and defects in microtubule organization. In vitro and in vivo data show that only γ-tubulin loaded with GTP nucleates microtubules. Our results suggest that GTP recruitment to γ-tubulin enhances its interaction with αβ-tubulin similarly to GTP recruitment to β-tubulin.
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Affiliation(s)
- Linda Gombos
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), ZMBH-DKFZ Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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1026
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Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
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Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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1027
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A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics. Sci Rep 2013; 3:2052. [PMID: 23787479 PMCID: PMC3689175 DOI: 10.1038/srep02052] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/06/2013] [Indexed: 12/23/2022] Open
Abstract
Time-resolved quantitative analysis of auxin-mediated processes in plant cells is as of yet limited. By applying a synergistic mammalian and plant synthetic biology approach, we have developed a novel ratiometric luminescent biosensor with wide applicability in the study of auxin metabolism, transport, and signalling. The sensitivity and kinetic properties of our genetically encoded biosensor open new perspectives for the analysis of highly complex auxin dynamics in plant growth and development.
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1028
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Caussinus E, Kanca O, Affolter M. Protein knockouts in living eukaryotes using deGradFP and green fluorescent protein fusion targets. ACTA ACUST UNITED AC 2013; 73:30.2.1-30.2.13. [PMID: 24510595 DOI: 10.1002/0471140864.ps3002s73] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This unit describes deGradFP (degrade Green Fluorescent Protein), an easy-to-implement protein knockout method applicable in any eukaryotic genetic system. Depleting a protein in order to study its function in a living organism is usually achieved at the gene level (genetic mutations) or at the RNA level (RNA interference and morpholinos). However, any system that acts upstream of the proteic level depends on the turnover rate of the existing target protein, which can be extremely slow. In contrast, deGradFP is a fast method that directly depletes GFP fusion proteins. In particular, deGradFP is able to counteract maternal effects in embryos and causes early and fast onset loss-of-function phenotypes of maternally contributed proteins.
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Affiliation(s)
| | - Oguz Kanca
- Biozentrum, University of Basel, Basel, Switzerland
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1029
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Abstract
Membrane trafficking and mitosis are two essential processes in eukaryotic cells. Surprisingly, many proteins best known for their role in membrane trafficking have additional 'moonlighting' functions in mitosis. Despite having proteins in common, there is insufficient evidence for a specific connection between these two processes. Instead, these phenomena demonstrate the adaptability of the membrane trafficking machinery that allows its repurposing for different cellular functions.
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Affiliation(s)
- Stephen J Royle
- Division of Biomedical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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1030
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Chan KL, Gligoris T, Upcher W, Kato Y, Shirahige K, Nasmyth K, Beckouët F. Pds5 promotes and protects cohesin acetylation. Proc Natl Acad Sci U S A 2013; 110:13020-5. [PMID: 23878248 PMCID: PMC3740900 DOI: 10.1073/pnas.1306900110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cohesin's Smc1 and Smc3 subunits form V-shaped heterodimers, the nucleotide binding domains (NBDs) of which bind the C- and N-terminal domains, respectively, of the α-kleisin subunit, forming a large tripartite ring within in which sister DNAs are entrapped, and thereby held together (sister chromatid cohesion). During replication, establishment of stable cohesion is dependent on Eco1-mediated acetylation of Smc3's NBD, which is thought to prevent dissociation of α-kleisin from Smc3, thereby locking shut a "DNA exit gate." How Scc3 and Pds5, regulatory subunits bound to α-kleisin, regulate cohesion establishment and maintenance is poorly understood. We show here that by binding to α-kleisin adjacent to its Smc3 nucleotide binding N-terminal domain, Pds5 not only promotes cohesin's release from chromatin but also mediates de novo acetylation of Smc3 by Eco1 during S phase and subsequently prevents de-acetylation by the deacetylase Hos1/HDAC8. By first promoting cohesin's release from chromosomes and subsequently creating and guarding the chemical modification responsible for blocking release, Pds5 enables chromosomal cohesin to switch during S phase from a state of high turnover to one capable of tenaciously holding sister chromatids together for extended periods of time, a duality that has hitherto complicated analysis of this versatile cohesin subunit.
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Affiliation(s)
- Kok-Lung Chan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Thomas Gligoris
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - William Upcher
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Yuki Kato
- Department for Epigenetic Disease, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Department for Epigenetic Disease, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
| | - Frédéric Beckouët
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and
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1031
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Morawska M, Ulrich HD. An expanded tool kit for the auxin-inducible degron system in budding yeast. Yeast 2013; 30:341-51. [PMID: 23836714 PMCID: PMC4171812 DOI: 10.1002/yea.2967] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 11/11/2022] Open
Abstract
Fusion of inducible degradation signals, so-called degrons, to cellular proteins is an elegant method of controlling protein levels in vivo. Recently, a degron system relying on the plant hormone auxin has been described for use in yeast and vertebrate cells. We now report the construction of a series of vectors that significantly enhance the versatility of this auxin-inducible degron (AID) system in Saccharomyces cerevisiae. We have minimized the size of the degron and appended a series of additional epitope tags, allowing detection by commercial antibodies or fluorescence microscopy. The vectors are compatible with PCR-based genomic tagging strategies, allow for C- or N-terminal fusion of the degron, and provide a range of selection markers. Application to a series of yeast proteins, including essential replication factors, provides evidence for a general usefulness of the system.
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Affiliation(s)
- Magdalena Morawska
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
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1032
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Han JS, Holland AJ, Fachinetti D, Kulukian A, Cetin B, Cleveland DW. Catalytic assembly of the mitotic checkpoint inhibitor BubR1-Cdc20 by a Mad2-induced functional switch in Cdc20. Mol Cell 2013; 51:92-104. [PMID: 23791783 DOI: 10.1016/j.molcel.2013.05.019] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 11/09/2012] [Accepted: 05/16/2013] [Indexed: 01/29/2023]
Abstract
The mitotic checkpoint acts to maintain chromosome content by generation of a diffusible anaphase inhibitor. Unattached kinetochores catalyze a conformational shift in Mad2, converting an inactive open form into a closed form that can capture Cdc20, the mitotic activator of the APC/C ubiquitin ligase. Mad2 binding is now shown to promote a functional switch in Cdc20, exposing a previously inaccessible site for binding to BubR1's conserved Mad3 homology domain. BubR1, but not Mad2, binding to APC/C(Cdc20) is demonstrated to inhibit ubiquitination of cyclin B. Closed Mad2 is further shown to catalytically amplify production of BubR1-Cdc20 without necessarily being part of the complex. Thus, the mitotic checkpoint is produced by a cascade of two catalytic steps: an initial step acting at unattached kinetochores to produce a diffusible Mad2-Cdc20 intermediate and a diffusible step in which that intermediate amplifies production of BubR1-Cdc20, the inhibitor of cyclin B ubiquitination, by APC/C(Cdc20).
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Affiliation(s)
- Joo Seok Han
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA
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1033
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Adkins NL, Niu H, Sung P, Peterson CL. Nucleosome dynamics regulates DNA processing. Nat Struct Mol Biol 2013; 20:836-42. [PMID: 23728291 PMCID: PMC3711194 DOI: 10.1038/nsmb.2585] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 04/12/2013] [Indexed: 11/18/2022]
Abstract
The repair of DNA double strand breaks (DSBs) is critical for the maintenance of genome integrity. The first step in DSB repair by homologous recombination is processing of the ends by one of two resection pathways, exemplified by Saccharomyces cerevisiae Exo1 and Sgs1–Dna2. Here we report in vitro and in vivo studies that characterize the impact of chromatin on each resection pathway. We find that efficient resection by the Sgs1-Dna2 -dependent machinery requires a nucleosome-free gap adjacent to the DSB. Resection by Exo1 is blocked by nucleosomes, and processing activity can be partially restored by removal of the H2A-H2B dimers. Our study also supports a role for the dynamic incorporation of the H2A.Z histone variant in Exo1 processing, and it further suggests that the two resection pathways require distinct chromatin remodeling events in order to navigate chromatin structure.
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Affiliation(s)
- Nicholas L Adkins
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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1034
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Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae. PLoS One 2013; 8:e64419. [PMID: 23675537 PMCID: PMC3651225 DOI: 10.1371/journal.pone.0064419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene's functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology.
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1035
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Skaar JR, Pagan JK, Pagano M. Mechanisms and function of substrate recruitment by F-box proteins. Nat Rev Mol Cell Biol 2013; 14:369-81. [PMID: 23657496 DOI: 10.1038/nrm3582] [Citation(s) in RCA: 505] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
S phase kinase-associated protein 1 (SKP1)-cullin 1 (CUL1)-F-box protein (SCF) ubiquitin ligase complexes use a family of F-box proteins as substrate adaptors to mediate the degradation of a large number of regulatory proteins involved in diverse processes. The dysregulation of SCF complexes and their substrates contributes to multiple pathologies. In the 14 years since the identification and annotation of the F-box protein family, the continued identification and characterization of novel substrates has greatly expanded our knowledge of the regulation of substrate targeting and the roles of F-box proteins in biological processes. Here, we focus on the evolution of our understanding of substrate recruitment by F-box proteins, the dysregulation of substrate recruitment in disease and potential avenues for F-box protein-directed disease therapies.
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Affiliation(s)
- Jeffrey R Skaar
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, New York 10016, USA.
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1036
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Cheeseman LP, Harry EF, McAinsh AD, Prior IA, Royle SJ. Specific removal of TACC3-ch-TOG-clathrin at metaphase deregulates kinetochore fiber tension. J Cell Sci 2013; 126:2102-13. [PMID: 23532825 PMCID: PMC3666260 DOI: 10.1242/jcs.124834] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2013] [Indexed: 12/19/2022] Open
Abstract
Microtubule-associated proteins of the mitotic spindle are thought to be important for the initial assembly and the maintenance of spindle structure and function. However, distinguishing assembly and maintenance roles for a given protein is difficult. Most experimental methods for protein inactivation are slow and therefore affect both assembly and maintenance. Here, we have used 'knocksideways' to rapidly (∼5 minutes) and specifically remove TACC3-ch-TOG-clathrin non-motor complexes from kinetochore fibers (K-fibers). This method allows the complex to be inactivated at defined stages of mitosis. Removal of TACC3-ch-TOG-clathrin after nuclear envelope breakdown caused severe delays in chromosome alignment. Inactivation at metaphase, following a normal prometaphase, significantly delayed progression to anaphase. In these cells, K-fiber tension was reduced and the spindle checkpoint was not satisfied. Surprisingly, there was no significant loss of K-fiber microtubules, even after prolonged removal. TACC3-ch-TOG-clathrin removal during metaphase also resulted in a decrease in spindle length and significant alteration in kinetochore dynamics. Our results indicate that TACC3-ch-TOG-clathrin complexes are important for the maintenance of spindle structure and function as well as for initial spindle assembly.
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Affiliation(s)
- Liam P. Cheeseman
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Edward F. Harry
- Centre for Mechanochemical Cell Biology, Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Molecular Organization and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology, Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Ian A. Prior
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Stephen J. Royle
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
- Centre for Mechanochemical Cell Biology, Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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1037
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Yu H, Moss BL, Jang SS, Prigge M, Klavins E, Nemhauser JL, Estelle M. Mutations in the TIR1 auxin receptor that increase affinity for auxin/indole-3-acetic acid proteins result in auxin hypersensitivity. PLANT PHYSIOLOGY 2013; 162:295-303. [PMID: 23539280 PMCID: PMC3641209 DOI: 10.1104/pp.113.215582] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The phytohormone auxin regulates virtually every aspect of plant development. The hormone directly mediates the interaction between the two members of the auxin coreceptor complex, a TRANSPORT INHIBITOR RESPONSE (TIR1)/AUXIN SIGNALING F-BOX protein and an AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressor. To learn more about the interaction between these proteins, a mutant screen was performed using the yeast (Saccharomyces cerevisiae) two-hybrid system in Arabidopsis (Arabidopsis thaliana). Two tir1 mutations were identified that increased interaction with Aux/IAAs. The D170E and M473L mutations increase affinity between TIR1 and the degron motif of Aux/IAAs and enhance the activity of the SCF(TIR1) complex. This resulted in faster degradation of Aux/IAAs and increased transcription of auxin-responsive genes in the plant. Plants carrying the pTIR1:tir1 D170E/M473L-Myc transgene exhibit diverse developmental defects during plant growth and display an auxin-hypersensitive phenotype. This work demonstrates that changes in the leucine-rich repeat domain of the TIR1 auxin coreceptor can alter the properties of SCF(TIR1).
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1038
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Fernius J, Nerusheva O, Galander S, Alves F, Rappsilber J, Marston A. Cohesin-dependent association of scc2/4 with the centromere initiates pericentromeric cohesion establishment. Curr Biol 2013; 23:599-606. [PMID: 23499533 PMCID: PMC3627958 DOI: 10.1016/j.cub.2013.02.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/14/2013] [Accepted: 02/08/2013] [Indexed: 12/29/2022]
Abstract
Cohesin is a conserved ring-shaped multiprotein complex that participates in chromosome segregation, DNA repair, and transcriptional regulation [1, 2]. Cohesin loading onto chromosomes universally requires the Scc2/4 "loader" complex (also called NippedBL/Mau2), mutations in which cause the developmental disorder Cornelia de Lange syndrome in humans [1-9]. Cohesin is most concentrated in the pericentromere, the region surrounding the centromere [10-15]. Enriched pericentromeric cohesin requires the Ctf19 kinetochore subcomplex in budding yeast [16-18]. Here, we uncover the spatial and temporal determinants for Scc2/4 centromere association. We demonstrate that the critical role of the Ctf19 complex is to enable Scc2/4 association with centromeres, through which cohesin loads and spreads onto the adjacent pericentromere. We show that, unexpectedly, Scc2 association with centromeres depends on cohesin itself. The absence of the Scc1/Mcd1/Rad21 cohesin subunit precludes Scc2 association with centromeres from anaphase until late G1. Expression of SCC1 is both necessary and sufficient for the binding of cohesin to its loader, the association of Scc2 with centromeres, and cohesin loading. We propose that cohesin triggers its own loading by enabling Scc2/4 to connect with chromosomal landmarks, which at centromeres are specified by the Ctf19 complex. Overall, our findings provide a paradigm for the spatial and temporal control of cohesin loading.
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Affiliation(s)
- Josefin Fernius
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Olga O. Nerusheva
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Stefan Galander
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Flavia de Lima Alves
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Juri Rappsilber
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Adele L. Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
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1039
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A LOV2 Domain-Based Optogenetic Tool to Control Protein Degradation and Cellular Function. ACTA ACUST UNITED AC 2013; 20:619-26. [DOI: 10.1016/j.chembiol.2013.03.005] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/26/2013] [Accepted: 03/04/2013] [Indexed: 11/23/2022]
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1040
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Sengupta S, van Deursen F, de Piccoli G, Labib K. Dpb2 Integrates the Leading-Strand DNA Polymerase into the Eukaryotic Replisome. Curr Biol 2013; 23:543-52. [DOI: 10.1016/j.cub.2013.02.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 01/14/2013] [Accepted: 02/04/2013] [Indexed: 01/27/2023]
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1041
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Szakal B, Branzei D. Premature Cdk1/Cdc5/Mus81 pathway activation induces aberrant replication and deleterious crossover. EMBO J 2013; 32:1155-67. [PMID: 23531881 PMCID: PMC3630363 DOI: 10.1038/emboj.2013.67] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/04/2013] [Indexed: 12/31/2022] Open
Abstract
The error-free DNA damage tolerance (DDT) pathway is crucial for replication completion and genome integrity. Mechanistically, this process is driven by a switch of templates accompanied by sister chromatid junction (SCJ) formation. Here, we asked if DDT intermediate processing is temporarily regulated, and what impact such regulation may have on genome stability. We find that persistent DDT recombination intermediates are largely resolved before anaphase through a G2/M damage checkpoint-independent, but Cdk1/Cdc5-dependent pathway that proceeds via a previously described Mus81-Mms4-activating phosphorylation. The Sgs1-Top3- and Mus81-Mms4-dependent resolution pathways occupy different temporal windows in relation to replication, with the Mus81-Mms4 pathway being restricted to late G2/M. Premature activation of the Cdk1/Cdc5/Mus81 pathway, achieved here with phosphomimetic Mms4 variants as well as in S-phase checkpoint-deficient genetic backgrounds, induces crossover-associated chromosome translocations and precocious processing of damage-bypass SCJ intermediates. Taken together, our results underscore the importance of uncoupling error-free versus erroneous recombination intermediate processing pathways during replication, and establish a new paradigm for the role of the DNA damage response in regulating genome integrity by controlling crossover timing.
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Affiliation(s)
- Barnabas Szakal
- Department of Molecular Oncology, Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, Milan 20139, Italy
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1042
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Kubota T, Nishimura K, Kanemaki MT, Donaldson AD. The Elg1 replication factor C-like complex functions in PCNA unloading during DNA replication. Mol Cell 2013; 50:273-80. [PMID: 23499004 DOI: 10.1016/j.molcel.2013.02.012] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 01/02/2013] [Accepted: 02/06/2013] [Indexed: 12/15/2022]
Abstract
The ring-shaped complex PCNA coordinates DNA replication, encircling DNA to act as a polymerase clamp and a sliding platform to recruit other replication proteins. PCNA is loaded onto DNA by replication factor C, but it has been unknown how PCNA is removed from DNA when Okazaki fragments are completed or the replication fork terminates. Here we show that the Elg1 replication factor C-like complex (Elg1-RLC) functions in PCNA unloading. Using an improved degron system we show that without Elg1, PCNA accumulates on Saccharomyces cerevisiae chromatin during replication. The accumulated PCNA can be removed from chromatin in vivo by switching on Elg1 expression. We find moreover that treating chromatin with purified Elg1-RLC causes PCNA unloading in vitro. Our results demonstrate that Elg1-RLC functions in unloading of both unmodified and SUMOylated PCNA during DNA replication, while the genome instability of an elg1Δ mutant suggests timely PCNA unloading is critical for chromosome maintenance.
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Affiliation(s)
- Takashi Kubota
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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1043
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Furukawa K, Hohmann S. Synthetic biology: lessons from engineering yeast MAPK signalling pathways. Mol Microbiol 2013; 88:5-19. [PMID: 23461595 DOI: 10.1111/mmi.12174] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2013] [Indexed: 02/04/2023]
Abstract
All living cells respond to external stimuli and execute specific physiological responses through signal transduction pathways. Understanding the mechanisms controlling signalling pathways is important for diagnosing and treating diseases and for reprogramming cells with desired functions. Although many of the signalling components in the budding yeast Saccharomyces cerevisiae have been identified by genetic studies, many features concerning the dynamic control of pathway activity, cross-talk, cell-to-cell variability or robustness against perturbation are still incompletely understood. Comparing the behaviour of engineered and natural signalling pathways offers insight complementary to that achievable with standard genetic and molecular studies. Here, we review studies that aim at a deeper understanding of signalling design principles and generation of novel signalling properties by engineering the yeast mitogen-activated protein kinase (MAPK) pathways. The underlying approaches can be applied to other organisms including mammalian cells and offer opportunities for building synthetic pathways and functionalities useful in medicine and biotechnology.
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Affiliation(s)
- Kentaro Furukawa
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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1044
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Borges V, Smith DJ, Whitehouse I, Uhlmann F. An Eco1-independent sister chromatid cohesion establishment pathway in S. cerevisiae. Chromosoma 2013; 122:121-34. [PMID: 23334284 PMCID: PMC3608886 DOI: 10.1007/s00412-013-0396-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 10/28/2022]
Abstract
Cohesion between sister chromatids, mediated by the chromosomal cohesin complex, is a prerequisite for their alignment on the spindle apparatus and segregation in mitosis. Budding yeast cohesin first associates with chromosomes in G1. Then, during DNA replication in S-phase, the replication fork-associated acetyltransferase Eco1 acetylates the cohesin subunit Smc3 to make cohesin's DNA binding resistant to destabilization by the Wapl protein. Whether stabilization of cohesin molecules that happen to link sister chromatids is sufficient to build sister chromatid cohesion, or whether additional reactions are required to establish these links, is not known. In addition to Eco1, several other factors contribute to cohesion establishment, including Ctf4, Ctf18, Tof1, Csm3, Chl1 and Mrc1, but little is known about their roles. Here, we show that each of these factors facilitates cohesin acetylation. Moreover, the absence of Ctf4 and Chl1, but not of the other factors, causes a synthetic growth defect in cells lacking Eco1. Distinct from acetylation defects, sister chromatid cohesion in ctf4Δ and chl1Δ cells is not improved by removing Wapl. Unlike previously thought, we do not find evidence for a role of Ctf4 and Chl1 in Okazaki fragment processing, or of Okazaki fragment processing in sister chromatid cohesion. Thus, Ctf4 and Chl1 delineate an additional acetylation-independent pathway that might hold important clues as to the mechanism of sister chromatid cohesion establishment.
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Affiliation(s)
- Vanessa Borges
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
| | - Duncan J. Smith
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London, WC2A 3LY UK
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1045
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Ausländer S, Fussenegger M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol 2013; 31:155-68. [DOI: 10.1016/j.tibtech.2012.11.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
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1046
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Abstract
One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.
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Affiliation(s)
- Takafumi Miyamoto
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
| | - Shiva Razavi
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205
| | - Robert DeRose
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD, 21205
- PRESTO Investigator, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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1047
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Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69-102. [PMID: 23413816 DOI: 10.1146/annurev-chembioeng-061312-103351] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems.
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Affiliation(s)
- Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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1048
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Oliva M, Farcot E, Vernoux T. Plant hormone signaling during development: insights from computational models. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:19-24. [PMID: 23219863 DOI: 10.1016/j.pbi.2012.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 05/23/2023]
Abstract
Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms of hormone perception and of regulation of cellular responses such as transcription in response to hormones. In addition, modeling approaches have contributed significantly to exploring how spatio-temporal regulation of hormone signaling contributes to plant growth and patterning. New tools have also been developed to obtain quantitative information on hormone distribution during development and to test model predictions, opening the way for quantitative understanding of the developmental roles of hormones.
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Affiliation(s)
- Marina Oliva
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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1049
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CENP-T provides a structural platform for outer kinetochore assembly. EMBO J 2013; 32:424-36. [PMID: 23334297 DOI: 10.1038/emboj.2012.348] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/14/2012] [Indexed: 11/09/2022] Open
Abstract
The kinetochore forms a dynamic interface with microtubules from the mitotic spindle during mitosis. The Ndc80 complex acts as the key microtubule-binding complex at kinetochores. However, it is unclear how the Ndc80 complex associates with the inner kinetochore proteins that assemble upon centromeric chromatin. Here, based on a high-resolution structural analysis, we demonstrate that the N-terminal region of vertebrate CENP-T interacts with the 'RWD' domain in the Spc24/25 portion of the Ndc80 complex. Phosphorylation of CENP-T strengthens a cryptic hydrophobic interaction between CENP-T and Spc25 resulting in a phospho-regulated interaction that occurs without direct recognition of the phosphorylated residue. The Ndc80 complex interacts with both CENP-T and the Mis12 complex, but we find that these interactions are mutually exclusive, supporting a model in which two distinct pathways target the Ndc80 complex to kinetochores. Our results provide a model for how the multiple protein complexes at kinetochores associate in a phospho-regulated manner.
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1050
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Lopez-Serra L, Lengronne A, Borges V, Kelly G, Uhlmann F. Budding yeast Wapl controls sister chromatid cohesion maintenance and chromosome condensation. Curr Biol 2013; 23:64-9. [PMID: 23219725 DOI: 10.1016/j.cub.2012.11.030] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/21/2012] [Accepted: 11/13/2012] [Indexed: 12/11/2022]
Abstract
The establishment of stable sister chromatid cohesion during DNA replication requires acetylation of the chromosomal cohesin complex by the replication fork-associated acetyltransferase Eco1. Cohesin acetylation is thought to facilitate replication fork progression by counteracting an as yet ill-defined cohesion "antiestablishment" activity imposed by the Wapl protein. Here, using budding yeast, we find no evidence that cohesin acetylation must overcome Wapl during replication fork progression. Instead, Wapl emerges as a negative regulator of cohesion maintenance in G2, a function that it likely exerts through its role as destabilizer of unacetylated, chromosome-bound cohesin. Our results suggest that acetylation renders cohesin Wapl-resistant from S phase onward until mitosis. In the absence of Wapl, sister chromatid cohesion functions well, suggesting that Wapl partakes in a cohesin function outside of sister chromatid cohesion. We find that Wapl is not required for cohesin's known role in transcriptional regulation. Rather, cells lacking Wapl display increased chromosome condensation in both interphase and mitosis. Thus, as a conserved regulator of cohesin dynamics on chromosomes, Wapl controls cohesion maintenance after its establishment in S phase and adjusts the chromosome condensation status.
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Affiliation(s)
- Lidia Lopez-Serra
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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