151
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Conservation of miR-15a/16-1 and miR-15b/16-2 clusters. Mamm Genome 2009; 21:88-94. [PMID: 20013340 DOI: 10.1007/s00335-009-9240-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 11/11/2009] [Indexed: 02/07/2023]
Abstract
MiR-15a/16-1 and miR-15b/16-2 clusters have been shown to play very important roles in regulating cell proliferation and apoptosis by targeting cell cycle proteins and the antiapoptotic Bcl-2 gene. However, the physiological implications of those two clusters are largely elusive. By aligning the primary miR-15a/16-1 sequence among 44 vertebrates, we found that there was a gap in the homologous region of the rat genome. To verify that there was a similar miR-15a/16-1 cluster in rats, we amplified this region from rat genomic DNA using PCR and found that a 697-bp sequence was missing in the current rat genome database, which covers the miR-15a/16-1 cluster. Subsequently, we also investigated the expression pattern of individual miRNAs spliced from miR-15a/16-1 and miR-15b/16-2 clusters, including miR-15a, miR-15a*, miR-15b, miR-15b*, miR-16-1/2, and miR-16-1/2* from various rat tissues, and found that all of those miRNAs were expressed in the investigated tissues. MiR-16 was most expressed in the heart, followed by the brain, lung, kidney, and small intestine, which indicates tissue specificity for individual miRNA expression from both clusters. Our results demonstrated that both miR-15a/16-1 and miR-15b/16-2 clusters are highly conserved among mammalian species. The investigation of the biological functions of those two clusters using transgenic or knockout/knockdown models will provide new clues to understanding their implications in human diseases and finding a new approach for miRNA-based therapy.
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152
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Mönnich M, Banks S, Eccles M, Dickinson E, Horsfield J. Expression of cohesin and condensin genes during zebrafish development supports a non-proliferative role for cohesin. Gene Expr Patterns 2009; 9:586-94. [PMID: 19723591 DOI: 10.1016/j.gep.2009.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 08/25/2009] [Indexed: 12/27/2022]
Abstract
Cohesin and condensin are similar, but distinct multi-subunit protein complexes that have well-described roles in sister chromatid cohesion and chromosome condensation, respectively. Recently it has emerged that cohesin, and proteins that regulate cohesin function have additional developmental roles. To further understand the role of cohesin in development, we analyzed the expression of genes encoding cohesin and condensin subunits in developing zebrafish embryos and juvenile brain. We found that cohesin subunits are expressed in a pattern that is similar (but not quite identical) to the expression of condensin subunits. Cohesin genes smc1a, rad21, pds5b and smc3 were expressed in the forebrain ventricular zone, the tectum, the mid-hindbrain boundary, the fourth ventricle, branchial arches, the otic vesicle, the eye and faintly in the developing pectoral fins. Condensin genes smc2 and smc4 were expressed in the forebrain ventricular zone, the tectum, the mid-hindbrain boundary, the fourth ventricle, branchial arches, eye and pectoral fins. Condensin genes were additionally expressed in the hindbrain proliferative zone, an area in which cohesin genes were not detected. A comparison with pcna expression and BrdU incorporation revealed that the expression of cohesins and condensins closely overlap with zones of proliferation. Interestingly, cohesin genes were expressed in non-proliferating cells flanking rhombomere boundaries in the developing brain. In mature brain and eye, cohesin was expressed in both proliferating cells and in broad zones of post-mitotic cells. The distribution of cohesin and condensin mRNAs supports existing evidence for a non-cell cycle role for cohesin in the developing brain.
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Affiliation(s)
- Maren Mönnich
- Department of Pathology, The University of Otago, Dunedin, New Zealand
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153
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Ku B, Lim JH, Shin HC, Shin SY, Oh BH. Crystal structure of the MukB hinge domain with coiled-coil stretches and its functional implications. Proteins 2009; 78:1483-90. [DOI: 10.1002/prot.22664] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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154
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Jin H, Guacci V, Yu HG. Pds5 is required for homologue pairing and inhibits synapsis of sister chromatids during yeast meiosis. ACTA ACUST UNITED AC 2009; 186:713-25. [PMID: 19736318 PMCID: PMC2742186 DOI: 10.1083/jcb.200810107] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A meiosis-conditional pds5 allele in yeast provides a more detailed understanding of homologue pairing and synaptonemal complex formation. During meiosis, homologues become juxtaposed and synapsed along their entire length. Mutations in the cohesin complex disrupt not only sister chromatid cohesion but also homologue pairing and synaptonemal complex formation. In this study, we report that Pds5, a cohesin-associated protein known to regulate sister chromatid cohesion, is required for homologue pairing and synapsis in budding yeast. Pds5 colocalizes with cohesin along the length of meiotic chromosomes. In the absence of Pds5, the meiotic cohesin subunit Rec8 remains bound to chromosomes with only minor defects in sister chromatid cohesion, but sister chromatids synapse instead of homologues. Double-strand breaks (DSBs) are formed but are not repaired efficiently. In addition, meiotic chromosomes undergo hypercondensation. When the mitotic cohesin subunit Mcd1 is substituted for Rec8 in Pds5-depleted cells, chromosomes still hypercondense, but synapsis of sister chromatids is abolished. These data suggest that Pds5 modulates the Rec8 activity to facilitate chromosome morphological changes required for homologue synapsis, DSB repair, and meiotic chromosome segregation.
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Affiliation(s)
- Hui Jin
- Department of Biological Science, The Florida State University, Tallahassee, FL 32306, USA
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155
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Bernad R, Sánchez P, Losada A. Epigenetic specification of centromeres by CENP-A. Exp Cell Res 2009; 315:3233-41. [DOI: 10.1016/j.yexcr.2009.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 07/28/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
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156
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The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence. Curr Biol 2009; 19:1777-87. [PMID: 19853451 DOI: 10.1016/j.cub.2009.09.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 09/11/2009] [Accepted: 09/15/2009] [Indexed: 12/21/2022]
Abstract
BACKGROUND The C. elegans dosage compensation complex (DCC) associates with both X chromosomes of XX animals to reduce X-linked transcript levels. Five DCC members are homologous to subunits of the evolutionarily conserved condensin complex, and two noncondensin subunits are required for DCC recruitment to X. RESULTS We investigated the molecular mechanism of DCC recruitment and spreading along X by examining gene expression and the binding patterns of DCC subunits in different stages of development, and in strains harboring X;autosome (X;A) fusions. We show that DCC binding is dynamically specified according to gene activity during development and that the mechanism of DCC spreading is independent of X chromosome DNA sequence. Accordingly, in X;A fusion strains, DCC binding propagates from X-linked recruitment sites onto autosomal promoters as a function of distance. Quantitative analysis of spreading suggests that the condensin-like subunits spread from recruitment sites to promoters more readily than subunits involved in initial X targeting. CONCLUSIONS A highly conserved chromatin complex is appropriated to accomplish domain-scale transcriptional regulation during C. elegans development. Unlike X recognition, which is specified partly by DNA sequence, spreading is sequence independent and coupled to transcriptional activity. Similarities to the X recognition and spreading strategies used by the Drosophila DCC suggest mechanisms fundamental to chromosome-scale gene regulation.
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157
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Heaslip AT, Ems-McClung SC, Hu K. TgICMAP1 is a novel microtubule binding protein in Toxoplasma gondii. PLoS One 2009; 4:e7406. [PMID: 19823689 PMCID: PMC2758671 DOI: 10.1371/journal.pone.0007406] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/16/2009] [Indexed: 01/06/2023] Open
Abstract
The microtubule cytoskeleton provides essential structural support for all eukaryotic cells and can be assembled into various higher order structures that perform drastically different functions. Understanding how microtubule-containing assemblies are built in a spatially and temporally controlled manner is therefore fundamental to understanding cell physiology. Toxoplasma gondii, a protozoan parasite, contains at least five distinct tubulin-containing structures, the spindle pole, centrioles, cortical microtubules, the conoid, and the intra-conoid microtubules. How these five structurally and functionally distinct sets of tubulin containing structures are constructed and maintained in the same cell is an intriguing problem. Previously, we performed a proteomic analysis of the T. gondii apical complex, a cytoskeletal complex located at the apical end of the parasite that is composed of the conoid, three ring-like structures, and the two short intra-conoid microtubules. Here we report the characterization of one of the proteins identified in that analysis, TgICMAP1. We show that TgICMAP1 is a novel microtubule binding protein that can directly bind to microtubules in vitro and stabilizes microtubules when ectopically expressed in mammalian cells. Interestingly, in T. gondii, TgICMAP1 preferentially binds to the intra-conoid microtubules, providing us the first molecular tool to investigate the intra-conoid microtubule assembly process during daughter construction.
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Affiliation(s)
- Aoife T. Heaslip
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | | | - Ke Hu
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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158
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Uhlmann F. A matter of choice: the establishment of sister chromatid cohesion. EMBO Rep 2009; 10:1095-102. [PMID: 19745840 PMCID: PMC2744122 DOI: 10.1038/embor.2009.207] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 08/19/2009] [Indexed: 11/09/2022] Open
Abstract
Sister chromatid cohesion is the basis for the recognition of chromosomal DNA replication products for their bipolar segregation in mitosis. Fundamental to sister chromatid cohesion is the ring-shaped cohesin complex, which is loaded onto chromosomes long before the initiation of DNA replication and is thought to hold replicated sister chromatids together by topological embrace. What happens to cohesin when the replication fork approaches, and how cohesin recognizes newly synthesized sister chromatids, is poorly understood. The characterization of a number of cohesion establishment factors has begun to provide hints as to the reactions involved. Cohesin is a member of the evolutionarily conserved family of Smc subunit-based protein complexes that contribute to many aspects of chromosome biology by mediating long-range DNA interactions. I propose that the establishment of cohesion equates to the selective stabilization of those cohesin-mediated DNA interactions that link sister chromatids in the wake of replication forks.
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Affiliation(s)
- Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, UK.
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159
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Schubert V, Weissleder A, Ali H, Fuchs J, Lermontova I, Meister A, Schubert I. Cohesin gene defects may impair sister chromatid alignment and genome stability in Arabidopsis thaliana. Chromosoma 2009; 118:591-605. [PMID: 19533160 DOI: 10.1007/s00412-009-0220-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 05/22/2009] [Indexed: 12/19/2022]
Abstract
In contrast to yeast, plant interphase nuclei often display incomplete alignment (cohesion) along sister chromatid arms. Sister chromatid cohesion mediated by the multi-subunit cohesin complex is essential for correct chromosome segregation during nuclear divisions and for DNA recombination repair. The cohesin complex consists of the conserved proteins SMC1, SMC3, SCC3, and an alpha-kleisin subunit. Viable homozygous mutants could be selected for the Arabidopsis thaliana alpha-kleisins SYN1, SYN2, and SYN4, which can partially compensate each other. For the kleisin SYN3 and for the single-copy genes SMC1, SMC3, and SCC3, only heterozygous mutants were obtained that displayed between 77% and 97% of the wild-type transcript level. Compared to wild-type nuclei, sister chromatid alignment was significantly decreased along arms in 4C nuclei of the homozygous syn1 and syn4 and even of the heterozygous smc1, smc3, scc3, and syn3 mutants. Knocking out SYN1 and SYN4 additionally impaired sister centromere cohesion. Homozygous mutants of SWITCH1 (required for meiotic sister chromatid alignment) displayed sterility and decreased sister arm alignment. For the cohesin loading complex subunit SCC2, only heterozygous mutants affecting sister centromere alignment were obtained. Defects of the alpha-kleisin SYN4, which impair sister chromatid alignment in 4C differentiated nuclei, do apparently not disturb alignment during prometaphase nor cause aneuploidy in meristematic cells. The syn2, 3, 4 scc3 and swi1 mutants display a high frequency of anaphases with bridges (~10% to >20% compared to 2.6% in wild type). Our results suggest that (a) already a slight reduction of the average transcript level in heterozygous cohesin mutants may cause perturbation of cohesion, at least in some leaf cells at distinct loci; (b) the decreased sister chromatid alignment in cohesin mutants can obviously not fully be compensated by other cohesion mechanisms such as DNA concatenation; (c) some cohesin genes, in addition to cohesion, might have further essential functions (e.g., for genome stability, apparently by facilitating correct recombination repair of double-strand breaks).
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
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160
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Abstract
The six Saccharomyces cerevisiae SLX genes were identified in a screen for factors required for the viability of cells lacking Sgs1, a member of the RecQ helicase family involved in processing stalled replisomes and in the maintenance of genome stability. The six SLX gene products form three distinct heterodimeric complexes, and all three have catalytic activity. Slx3-Slx2 (also known as Mus81-Mms4) and Slx1-Slx4 are both heterodimeric endonucleases with a marked specificity for branched replication fork-like DNA species, whereas Slx5-Slx8 is a SUMO (small ubiquitin-related modifier)-targeted E3 ubiquitin ligase. All three complexes play important, but distinct, roles in different aspects of the cellular response to DNA damage and perturbed DNA replication. Slx4 interacts physically not only with Slx1, but also with Rad1-Rad10 [XPF (xeroderma pigmentosum complementation group F)-ERCC1 (excision repair cross-complementing 1) in humans], another structure-specific endonuclease that participates in the repair of UV-induced DNA damage and in a subpathway of recombinational DNA DSB (double-strand break) repair. Curiously, Slx4 is essential for repair of DSBs by Rad1-Rad10, but is not required for repair of UV damage. Slx4 also promotes cellular resistance to DNA-alkylating agents that block the progression of replisomes during DNA replication, by facilitating the error-free mode of lesion bypass. This does not require Slx1 or Rad1-Rad10, and so Slx4 has several distinct roles in protecting genome stability. In the present article, I provide an overview of our current understanding of the cellular roles of the Slx proteins, paying particular attention to the advances that have been made in understanding the cellular roles of Slx4. In particular, protein-protein interactions and underlying molecular mechanisms are discussed and I draw attention to the many questions that have yet to be answered.
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161
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Abstract
DNA chromosomal DSBs (double-strand breaks) are potentially hazardous DNA lesions, and their accurate repair is essential for the successful maintenance and propagation of genetic information. Two major pathways have evolved to repair DSBs: HR (homologous recombination) and NHEJ (non-homologous end-joining). Depending on the context in which the break is encountered, HR and NHEJ may either compete or co-operate to fix DSBs in eukaryotic cells. Defects in either pathway are strongly associated with human disease, including immunodeficiency and cancer predisposition. Here we review the current knowledge of how NHEJ and HR are controlled in somatic mammalian cells, and discuss the role of the chromatin context in regulating each pathway. We also review evidence for both co-operation and competition between the two pathways.
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162
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Mets DG, Meyer BJ. Condensins regulate meiotic DNA break distribution, thus crossover frequency, by controlling chromosome structure. Cell 2009; 139:73-86. [PMID: 19781752 DOI: 10.1016/j.cell.2009.07.035] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 05/17/2009] [Accepted: 07/08/2009] [Indexed: 12/27/2022]
Abstract
Meiotic crossover (CO) recombination facilitates evolution and accurate chromosome segregation. CO distribution is tightly regulated: homolog pairs receive at least one CO, CO spacing is nonrandom, and COs occur preferentially in short genomic intervals called hotspots. We show that CO number and distribution are controlled on a chromosome-wide basis at the level of DNA double-strand break (DSB) formation by a condensin complex composed of subunits from two known condensins: the C. elegans dosage compensation complex and mitotic condensin II. Disruption of any subunit of the CO-controlling condensin dominantly changes DSB distribution, and thereby COs, and extends meiotic chromosome axes. These phenotypes are cosuppressed by disruption of a chromosome axis element. Our data implicate higher-order chromosome structure in the regulation of CO recombination, provide a model for the rapid evolution of CO hotspots, and show that reshuffling of interchangeable molecular parts can create independent machines with similar architectures but distinct biological functions.
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Affiliation(s)
- David G Mets
- Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA 94720-3204, USA
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163
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Shintomi K, Hirano T. Releasing cohesin from chromosome arms in early mitosis: opposing actions of Wapl-Pds5 and Sgo1. Genes Dev 2009; 23:2224-36. [PMID: 19696148 PMCID: PMC2751989 DOI: 10.1101/gad.1844309] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 07/28/2009] [Indexed: 11/24/2022]
Abstract
The cohesin complex establishes sister chromatid cohesion during S phase. In metazoan cells, most if not all cohesin dissociates from chromatin during mitotic prophase, leading to the formation of metaphase chromosomes with two cytologically discernible chromatids. This process, known as sister chromatid resolution, is believed to be a prerequisite for synchronous separation of sister chromatids in subsequent anaphase. To dissect this process at a mechanistic level, we set up an in vitro system. Sister chromatid resolution is severely impaired upon depletion of Wapl from Xenopus egg extracts. Exogenously added human Wapl can rescue these defects and, remarkably, it can do so in a very short time window of early mitosis. A similar set of observations is made for Pds5, a factor implicated previously in the stabilization of interphase cohesion. Characteristic amino acid motifs (the FGF motifs) in Wapl coordinate its physical and functional interactions with Pds5 and cohesin subunits. We propose that Wapl and Pds5 directly modulate conformational changes of cohesin to make it competent for dissociation from chromatin during prophase. Evidence is also presented that Sgo1 plays a hitherto underappreciated role in stabilizing cohesin along chromosome arms, which is antagonized by the mitotic kinases polo-like kinsase (Plk1) and aurora B.
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Affiliation(s)
- Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan
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164
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Watanabe K, Pacher M, Dukowic S, Schubert V, Puchta H, Schubert I. The STRUCTURAL MAINTENANCE OF CHROMOSOMES 5/6 complex promotes sister chromatid alignment and homologous recombination after DNA damage in Arabidopsis thaliana. THE PLANT CELL 2009; 21:2688-99. [PMID: 19737979 PMCID: PMC2768936 DOI: 10.1105/tpc.108.060525] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/13/2009] [Accepted: 08/24/2009] [Indexed: 05/18/2023]
Abstract
Sister chromatids are often arranged as incompletely aligned entities in interphase nuclei of Arabidopsis thaliana. The STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC) 5/6 complex, together with cohesin, is involved in double-strand break (DSB) repair by sister chromatid recombination in yeasts and mammals. Here, we analyzed the function of genes in Arabidopsis. The wild-type allele of SMC5 is essential for seed development. Each of the two SMC6 homologs of Arabidopsis is required for efficient repair of DNA breakage via intermolecular homologous recombination in somatic cells. Alignment of sister chromatids is enhanced transiently after X-irradiation (and mitomycin C treatment) in wild-type nuclei. In the smc5/6 mutants, the x-ray-mediated increase in sister chromatid alignment is much lower and delayed. The reduced S phase-established cohesion caused by a knockout mutation in one of the alpha-kleisin genes, SYN1, also perturbed enhancement of sister chromatid alignment after irradiation, suggesting that the S phase-established cohesion is a prerequisite for correct DSB-dependent cohesion. The radiation-sensitive51 mutant, deficient in heteroduplex formation during DSB repair, showed wild-type frequencies of sister chromatid alignment after X-irradiation, implying that the irradiation-mediated increase in sister chromatid alignment is a prerequisite for, rather than a consequence of, DNA strand exchange between sister chromatids. Our results suggest that the SMC5/6 complex promotes sister chromatid cohesion after DNA breakage and facilitates homologous recombination between sister chromatids.
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Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Stefanie Dukowic
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Holger Puchta
- Botanical Institute II, University Karlsruhe, 76128 Karlsruhe, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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165
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Pai DA, Engelke DR. Spatial organization of genes as a component of regulated expression. Chromosoma 2009; 119:13-25. [PMID: 19727792 DOI: 10.1007/s00412-009-0236-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/05/2009] [Accepted: 08/06/2009] [Indexed: 12/15/2022]
Abstract
The DNA of living cells is highly compacted. Inherent in this spatial constraint is the need for cells to organize individual genetic loci so as to facilitate orderly retrieval of information. Complex genetic regulatory mechanisms are crucial to all organisms, and it is becoming increasingly evident that spatial organization of genes is one very important mode of regulation for many groups of genes. In eukaryotic nuclei, it appears not only that DNA is organized in three-dimensional space but also that this organization is dynamic and interactive with the transcriptional state of the genes. Spatial organization occurs throughout evolution and with genes transcribed by all classes of RNA polymerases in all eukaryotic nuclei, from yeast to human. There is an increasing body of work examining the ways in which this organization and consequent regulation are accomplished. In this review, we discuss the diverse strategies that cells use to preferentially localize various classes of genes.
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Affiliation(s)
- Dave A Pai
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-0606, USA
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166
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Shin HC, Lim JH, Woo JS, Oh BH. Focal localization of MukBEF condensin on the chromosome requires the flexible linker region of MukF. FEBS J 2009; 276:5101-10. [PMID: 19674109 DOI: 10.1111/j.1742-4658.2009.07206.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Condensin complexes are the key mediators of chromosome condensation. The MukB-MukE-MukF complex is a bacterial condensin, in which the MukB subunit forms a V-shaped dimeric structure with two ATPase head domains. MukE and MukF together form a tight complex, which binds to the MukB head via the C-terminal winged-helix domain (C-WHD) of MukF. One of the two bound C-WHDs of MukF is forced to detach from two ATP-bound, engaged MukB heads, and this detachment reaction depends on the MukF flexible linker preceding the C-WHD. Whereas MukB is known to focally localize at particular positions in cells by an unknown mechanism, mukE- or mukF-null mutation causes MukB to become dispersed in cells. Here, we report that mutations in MukF causing a defect in the detachment reaction interfere with the focal localization of MukB, and that the dispersed distribution of MukB in cells correlates directly with defects in cell growth and division. The data strongly suggest that the MukB-MukE-MukF condensin forms huge clusters through the ATP-dependent detachment reaction, and this cluster formation is critical for chromosome condensation by this machinery. We also show that the MukF flexible linker is involved in the dimerization and ATPase activity of the MukB head.
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Affiliation(s)
- Ho-Chul Shin
- Center for Biomolecular Recognition and Division of Molecular and Life Science, Pohang University of Science and Technology, Kyungbuk, Korea
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167
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Outwin EA, Irmisch A, Murray JM, O'Connell MJ. Smc5-Smc6-dependent removal of cohesin from mitotic chromosomes. Mol Cell Biol 2009; 29:4363-75. [PMID: 19528228 PMCID: PMC2725735 DOI: 10.1128/mcb.00377-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/14/2009] [Accepted: 06/03/2009] [Indexed: 11/20/2022] Open
Abstract
The function of the essential cohesin-related Smc5-Smc6 complex has remained elusive, though hypomorphic mutants have defects late in recombination, in checkpoint maintenance, and in chromosome segregation. Recombination and checkpoints are not essential for viability, and Smc5-Smc6-null mutants die in lethal mitoses. This suggests that the chromosome segregation defects may be the source of lethality in irradiated Smc5-Smc6 hypomorphs. We show that in smc6 mutants, following DNA damage in interphase, chromosome arm segregation fails due to an aberrant persistence of cohesin, which is normally removed by the Separase-independent pathway. This postanaphase persistence of cohesin is not dependent on DNA damage, since the synthetic lethality of smc6 hypomorphs with a topoisomerase II mutant, defective in mitotic chromosome structure, is also due to the retention of cohesin on undamaged chromosome arms. In both cases, Separase overexpression bypasses the defect and restores cell viability, showing that defective cohesin removal is a major determinant of the mitotic lethality of Smc5-Smc6 mutants.
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Affiliation(s)
- Emily A Outwin
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
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168
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The Deinococcus radiodurans SMC protein is dispensable for cell viability yet plays a role in DNA folding. Extremophiles 2009; 13:827-37. [DOI: 10.1007/s00792-009-0270-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
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169
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Seipold S, Priller FC, Goldsmith P, Harris WA, Baier H, Abdelilah-Seyfried S. Non-SMC condensin I complex proteins control chromosome segregation and survival of proliferating cells in the zebrafish neural retina. BMC DEVELOPMENTAL BIOLOGY 2009; 9:40. [PMID: 19586528 PMCID: PMC2727499 DOI: 10.1186/1471-213x-9-40] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 07/08/2009] [Indexed: 12/18/2022]
Abstract
Background The condensation of chromosomes and correct sister chromatid segregation during cell division is an essential feature of all proliferative cells. Structural maintenance of chromosomes (SMC) and non-SMC proteins form the condensin I complex and regulate chromosome condensation and segregation during mitosis. However, due to the lack of appropriate mutants, the function of the condensin I complex during vertebrate development has not been described. Results Here, we report the positional cloning and detailed characterization of retinal phenotypes of a zebrafish mutation at the cap-g locus. High resolution live imaging reveals that the progression of mitosis between prometa- to telophase is delayed and that sister chromatid segregation is impaired upon loss of CAP-G. CAP-G associates with chromosomes between prometa- and telophase of the cell cycle. Loss of the interaction partners CAP-H and CAP-D2 causes cytoplasmic mislocalization of CAP-G throughout mitosis. DNA content analysis reveals increased genomic imbalances upon loss of non-SMC condensin I subunits. Within the retina, loss of condensin I function causes increased rates of apoptosis among cells within the proliferative ciliary marginal zone (CMZ) whereas postmitotic retinal cells are viable. Inhibition of p53-mediated apoptosis partially rescues cell numbers in cap-g mutant retinae and allows normal layering of retinal cell types without alleviating their aberrant nuclear sizes. Conclusion Our findings indicate that the condensin I complex is particularly important within rapidly amplifying progenitor cell populations to ensure faithful chromosome segregation. In contrast, differentiation of postmitotic retinal cells is not impaired upon polyploidization.
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Affiliation(s)
- Sabine Seipold
- Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany.
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170
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C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation. Chromosome Res 2009; 17:215-27. [PMID: 19308702 DOI: 10.1007/s10577-008-9011-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The C. elegans dosage compensation complex (DCC) reduces transcript levels from each of the two hermaphrodite X chromosomes to equalize X-linked gene expression to that of XO males. Several of the proteins that comprise the DCC are homologous to subunits of the evolutionarily conserved condensin complexes, which in most organisms function in mitotic and meiotic chromosome condensation. These include the DCC subunits MIX-1 and DPY-27, which belong to the structural maintenance of chromosomes (SMC) family of proteins. Several of the C. elegans DCC subunits also perform double duty as members of the canonical meiotic and mitotic condensin complexes. Here, we review what is known about the C. elegans DCC and how study of this model might shed light on general mechanisms of domain-scale transcriptional regulation. We discuss how condensin-like complexes may be targeted to specific chromosomal locations for performance of their functions.
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171
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Lim JH, Oh BH. Structural and functional similarities between two bacterial chromosome compacting machineries. Biochem Biophys Res Commun 2009; 386:415-9. [PMID: 19523447 DOI: 10.1016/j.bbrc.2009.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/05/2009] [Indexed: 12/25/2022]
Abstract
Chromosomes are condensed in all forms of life. SMC-based condensins are the key mediators in this process, but their molecular mechanisms remain elusive. Two different condensin complexes have been identified in prokaryotic organisms: MukB-MukE-MukF and SMC-ScpA-ScpB. This review focuses on comparison between the two machineries based on structural, biochemical and other related information in the light of their structure and function.
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Affiliation(s)
- Jae-Hong Lim
- Beamline division, Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Republic of Korea
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172
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Replication stress induces sister-chromatid bridging at fragile site loci in mitosis. Nat Cell Biol 2009; 11:753-60. [PMID: 19465922 DOI: 10.1038/ncb1882] [Citation(s) in RCA: 470] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 02/09/2009] [Indexed: 12/11/2022]
Abstract
Several inherited syndromes in humans are associated with cancer predisposition. The gene products defective in two of these disorders, BLM (a helicase defective in Bloom's syndrome) and FANC A-N (defective in Fanconi anaemia), associate in a multienzyme complex called BRAFT. How these proteins suppress tumorigenesis remains unclear, although both conditions are associated with chromosome instability. Here we show that the Fanconi anaemia proteins FANCD2 and FANCI specifically associate with common fragile site loci irrespective of whether the chromosome is broken. Unexpectedly, these loci are frequently interlinked through BLM-associated ultra-fine DNA bridges (UFBs) even as cells traverse mitosis. Similarly to fragile site expression, fragile site bridging is induced after partial inhibition of DNA replication. We propose that, after replication stress, sister chromatids are interlinked by replication intermediates primarily at genetic loci with intrinsic replication difficulties, such as fragile sites. In Bloom's syndrome cells, inefficient resolution of DNA linkages at fragile sites gives rise to increased numbers of anaphase UFBs and micronuclei containing fragile site DNA. Our data have general implications concerning the contribution of fragile site loci to chromosomal instability and tumorigenesis.
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173
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Abstract
DNA topoisomerases are enzymes that disentangle the topological problems that arise in double-stranded DNA. Many of these can be solved by the generation of either single or double strand breaks. However, where there is a clear requirement to alter DNA topology by introducing transient double strand breaks, only DNA topoisomerase II (TOP2) can carry out this reaction. Extensive biochemical and structural studies have provided detailed models of how TOP2 alters DNA structure, and recent molecular studies have greatly expanded knowledge of the biological contexts in which TOP2 functions, such as DNA replication, transcription and chromosome segregation -- processes that are essential for preventing tumorigenesis.
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Affiliation(s)
- John L Nitiss
- Molecular Pharmacology Department, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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174
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Schurko AM, Logsdon JM, Eads BD. Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution. BMC Evol Biol 2009; 9:78. [PMID: 19383157 PMCID: PMC2680839 DOI: 10.1186/1471-2148-9-78] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Accepted: 04/21/2009] [Indexed: 11/21/2022] Open
Abstract
Background Thousands of parthenogenetic animal species have been described and cytogenetic manifestations of this reproductive mode are well known. However, little is understood about the molecular determinants of parthenogenesis. The Daphnia pulex genome must contain the molecular machinery for different reproductive modes: sexual (both male and female meiosis) and parthenogenetic (which is either cyclical or obligate). This feature makes D. pulex an ideal model to investigate the genetic basis of parthenogenesis and its consequences for gene and genome evolution. Here we describe the inventory of meiotic genes and their expression patterns during meiotic and parthenogenetic reproduction to help address whether parthenogenesis uses existing meiotic and mitotic machinery, or whether novel processes may be involved. Results We report an inventory of 130 homologs representing over 40 genes encoding proteins with diverse roles in meiotic processes in the genome of D. pulex. Many genes involved in cell cycle regulation and sister chromatid cohesion are characterized by expansions in copy number. In contrast, most genes involved in DNA replication and homologous recombination are present as single copies. Notably, RECQ2 (which suppresses homologous recombination) is present in multiple copies while DMC1 is the only gene in our inventory that is absent in the Daphnia genome. Expression patterns for 44 gene copies were similar during meiosis versus parthenogenesis, although several genes displayed marked differences in expression level in germline and somatic tissues. Conclusion We propose that expansions in meiotic gene families in D. pulex may be associated with parthenogenesis. Taking into account our findings, we provide a mechanistic model of parthenogenesis, highlighting steps that must differ from meiosis including sister chromatid cohesion and kinetochore attachment.
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Affiliation(s)
- Andrew M Schurko
- Roy J Carver Center for Comparative Genomics and Department of Biology, The University of Iowa, Iowa City, IA 52242, USA.
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175
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Rivera T, Losada A. Shugoshin regulates cohesion by driving relocalization of PP2A in Xenopus extracts. Chromosoma 2009; 118:223-33. [PMID: 18987869 DOI: 10.1007/s00412-008-0190-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/13/2008] [Accepted: 10/15/2008] [Indexed: 01/20/2023]
Abstract
Sister chromatid cohesion is mediated by cohesin. At the onset of mitosis, most cohesin dissociates from chromatin with the exception of a small population, present along chromosome arms and enriched at centromeres. A protein known as shugoshin (Sgo) is essential to maintain arm and centromeric cohesion until the onset of anaphase in transformed human cells, but not in other organisms like Drosophila or mouse. We have used Xenopus egg extracts to further explore this issue. Chromosomes assembled in extracts depleted of Sgo have little or no cohesin at centromeres and display centromeric cohesion defects. Unlike transformed human cells, however, arm cohesion is maintained in the absence of Sgo. Furthermore, Sgo depletion impairs the prophase dissociation of cohesin. This phenotype can be rescued by inhibition of PP2A. The protein phosphatase interacts with Sgo and accumulates at centromeres in mitosis in a Sgo-dependent manner. We propose that Sgo drives relocalization of PP2A from arms to centromeres and, in this way, coordinates release of arm cohesin with protection of centromeric cohesin in mitosis.
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Affiliation(s)
- Teresa Rivera
- Spanish National Cancer Research Centre, Madrid, Spain
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176
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Irmisch A, Ampatzidou E, Mizuno K, O'Connell MJ, Murray JM. Smc5/6 maintains stalled replication forks in a recombination-competent conformation. EMBO J 2009; 28:144-55. [PMID: 19158664 DOI: 10.1038/emboj.2008.273] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/02/2008] [Indexed: 01/01/2023] Open
Abstract
The Smc5/6 structural maintenance of chromosomes complex is required for efficient homologous recombination (HR). Defects in Smc5/6 result in chromosome mis-segregation and fragmentation. By characterising two Schizosaccharomyces pombe smc6 mutants, we define two separate functions for Smc5/6 in HR. The first represents the previously described defect in processing recombination-dependent DNA intermediates when replication forks collapse, which leads to increased rDNA recombination. The second novel function defines Smc5/6 as a positive regulator of recombination in the rDNA and correlates mechanistically with a requirement to load RPA and Rad52 onto chromatin genome-wide when replication forks are stably stalled by nucleotide depletion. Rad52 is required for all HR repair, but Rad52 loading in response to replication fork stalling is unexpected and does not correlate with damage-induced foci. We propose that Smc5/6 is required to maintain stalled forks in a stable recombination-competent conformation primed for replication restart.
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Affiliation(s)
- Anja Irmisch
- Genome Damage and Stability Centre, University of Sussex, Brighton, E. Sussex, UK
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177
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Hsiao SJ, Smith S. Sister telomeres rendered dysfunctional by persistent cohesion are fused by NHEJ. ACTA ACUST UNITED AC 2009; 184:515-26. [PMID: 19221198 PMCID: PMC2654126 DOI: 10.1083/jcb.200810132] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Telomeres protect chromosome ends from being viewed as double-strand breaks and from eliciting a DNA damage response. Deprotection of chromosome ends occurs when telomeres become critically short because of replicative attrition or inhibition of TRF2. In this study, we report a novel form of deprotection that occurs exclusively after DNA replication in S/G2 phase of the cell cycle. In cells deficient in the telomeric poly(adenosine diphosphate ribose) polymerase tankyrase 1, sister telomere resolution is blocked. Unexpectedly, cohered sister telomeres become deprotected and are inappropriately fused. In contrast to telomeres rendered dysfunctional by TRF2, which engage in chromatid fusions predominantly between chromatids from different chromosomes (Bailey, S.M., M.N. Cornforth, A. Kurimasa, D.J. Chen, and E.H. Goodwin. 2001. Science. 293:2462–2465; Smogorzewska, A., J. Karlseder, H. Holtgreve-Grez, A. Jauch, and T. de Lange. 2002. Curr. Biol. 12:1635–1644), telomeres rendered dysfunctional by tankyrase 1 engage in chromatid fusions almost exclusively between sister chromatids. We show that cohered sister telomeres are fused by DNA ligase IV–mediated nonhomologous end joining. These results demonstrate that the timely removal of sister telomere cohesion is essential for the formation of a protective structure at chromosome ends after DNA replication in S/G2 phase of the cell cycle.
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Affiliation(s)
- Susan J Hsiao
- Molecular Pathogenesis Program, The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
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178
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Abstract
High fidelity chromosome transmission requires the pairing of sister chromatids by a group of conserved proteins called cohesins during S-phase. Sister chromatid cohesion is maintained until anaphase onset. Presently, there are two sets of models of cohesin complex popular in the cohesin biology field: one model predicts that single cohesin rings entrap both sister chromatids, and the other model proposes that cohesin complexes associate with each sister chromatid and become paired during DNA replication. It is the first model that currently predominate the field--in part because prior efforts failed to detect higher order cohesin-cohesin interactions. However, the static configuration and size limitation of the one ring embrace model are the major limitations of the embrace model, and cannot explain various functions of cohesin in DNA replication, DNA repair and gene expression. In a recent study published by Zhang et al. in the Journal of Cell Biology describes a two-ring handcuff model for the cohesin complex, and provides new information regarding how sister chromatid cohesion and separation are achieved in vertebrate cell systems.
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Affiliation(s)
- Nenggang Zhang
- Texas Children’s Cancer Center; Department of Pediatric Hematology/Oncology; Baylor College of Medicine; Houston, Texas USA
| | - Debananda Pati
- Texas Children’s Cancer Center; Department of Pediatric Hematology/Oncology; Baylor College of Medicine; Houston, Texas USA
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179
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Sollier J, Driscoll R, Castellucci F, Foiani M, Jackson SP, Branzei D. The Saccharomyces cerevisiae Esc2 and Smc5-6 proteins promote sister chromatid junction-mediated intra-S repair. Mol Biol Cell 2009; 20:1671-82. [PMID: 19158389 DOI: 10.1091/mbc.e08-08-0875] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recombination is important for DNA repair, but it can also contribute to genome rearrangements. RecQ helicases, including yeast Sgs1 and human BLM, safeguard genome integrity through their functions in DNA recombination. Sgs1 prevents the accumulation of Rad51-dependent sister chromatid junctions at damaged replication forks, and its functionality seems to be regulated by Ubc9- and Mms21-dependent sumoylation. We show that mutations in Smc5-6 and Esc2 also lead to an accumulation of recombinogenic structures at damaged replication forks. Because Smc5-6 is sumoylated in an Mms21-dependent manner, this finding suggests that Smc5-6 may be a crucial target of Mms21 implicated in this process. Our data reveal that Smc5-6 and Esc2 are required to tolerate DNA damage and that their functionality is critical in genotoxic conditions in the absence of Sgs1. As reported previously for Sgs1 and Smc5-6, we find that Esc2 physically interacts with Ubc9 and SUMO. This interaction is correlated with the ability of Esc2 to promote DNA damage tolerance. Collectively, these data suggest that Esc2 and Smc5-6 act in concert with Sgs1 to prevent the accumulation of recombinogenic structures at damaged replication forks, likely by integrating sumoylation activities to regulate the repair pathways in response to damaged DNA.
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Affiliation(s)
- Julie Sollier
- IFOM, The FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, 20139 Milan, Italy
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180
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Ho CY, Wong CH, Li HY. Perturbation of the chromosomal binding of RCC1, Mad2 and survivin causes spindle assembly defects and mitotic catastrophe. J Cell Biochem 2008; 105:835-46. [PMID: 18712773 DOI: 10.1002/jcb.21879] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mitotic catastrophe is a form of cell death that results from aberrant mitosis. Currently, the mechanisms involved in this form of cell death remain poorly understood. We found that actinomycin D induces mitotic catastrophe with severe spindle assembly defects. We have studied the nature of three groups of chromosome binding proteins in mitotic cells treated with actinomycin D. We found that actinomycin D reduced the binding affinity of RCC1 to the mitotic chromosome, which led to a reduction of RanGTP level. In addition, Mad2 was not concentrated at the kinetochores, indicating that the mitotic spindle checkpoint was affected. Furthermore, the localization of survivin was altered in cells. These data suggested that chromosomal binding of the mitotic regulators such as RCC1, Mad2 and survivin is essential for mitotic progression. Mitotic chromosomes not only carry the genetic material needed for the newly synthesized daughter cells, but also serve as docking sites for some of the mitotic regulators. Perturbation of their binding to the mitotic chromosome by actinomycin D could affect their functions in regulating mitotic progression thus leading to severe spindle defects and mitotic catastrophe.
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Affiliation(s)
- Chin-Yee Ho
- Division of Molecular and Cell Biology, School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Singapore
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181
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Zhang N, Kuznetsov SG, Sharan SK, Li K, Rao PH, Pati D. A handcuff model for the cohesin complex. J Cell Biol 2008; 183:1019-31. [PMID: 19075111 PMCID: PMC2600748 DOI: 10.1083/jcb.200801157] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 11/14/2008] [Indexed: 12/30/2022] Open
Abstract
The cohesin complex is responsible for the accurate separation of sister chromatids into two daughter cells. Several models for the cohesin complex have been proposed, but the one-ring embrace model currently predominates the field. However, the static configuration of the embrace model is not flexible enough for cohesins to perform their functions during DNA replication, transcription, and DNA repair. We used coimmunoprecipitation, a protein fragment complement assay, and a yeast two-hybrid assay to analyze the protein-protein interactions among cohesin subunits. The results show that three of the four human cohesin core subunits (Smc1, Smc3, and Rad21) interact with themselves in an Scc3 (SA1/SA2)-dependent manner. These data support a two-ring handcuff model for the cohesin complex, which is flexible enough to establish and maintain sister chromatid cohesion as well as ensure the fidelity of chromosome segregation in higher eukaryotes.
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Affiliation(s)
- Nenggang Zhang
- Department of Pediatric Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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182
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McNairn AJ, Gerton JL. Cohesinopathies: One ring, many obligations. Mutat Res 2008; 647:103-11. [PMID: 18786550 DOI: 10.1016/j.mrfmmm.2008.08.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/31/2008] [Accepted: 08/07/2008] [Indexed: 12/24/2022]
Abstract
Over 75 years ago, two human genetic disorders were initially described and named for their founding physicians: Cornelia de Lange (CdLS) and Roberts syndrome (RBS)/SC Phocomelia (SC). In the past 4 years, genetic studies of patients have revealed the primary genes involved in these disorders are the essential, evolutionarily conserved components of the cohesin pathway. This pathway serves to facilitate cohesion between replicated sister chromatids, thereby enabling proper chromosome segregation. As a result of these findings, these disorders now represent a novel class of human genetic disorders known as cohesinopathies. Over 60% of CdLS patients examined have de novo mutations in either: SCC2/NIPBL, SMC1, or SMC3, whereas the causative gene in Roberts syndrome and SC Phocomelia has been identified as ESCO2. Now modern genetic, biochemical, and cell biological approaches may be applied to determine the underlying mechanism of these genetic disorders.
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Affiliation(s)
- Adrian J McNairn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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183
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Takagi M, Bunai K, Yanagi KI, Imamoto N. Cloning of Xenopus orthologs of Ctf7/Eco1 acetyltransferase and initial characterization of XEco2. FEBS J 2008; 275:6109-22. [PMID: 19016859 DOI: 10.1111/j.1742-4658.2008.06736.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sister chromatid cohesion is important for the correct alignment and segregation of chromosomes during cell division. Although the cohesin complex has been shown to play a physical role in holding sister chromatids together, its loading onto chromatin is not sufficient for the establishment of sister chromatid cohesion. The activity of the cohesin complex must be turned on by Ctf7/Eco1 acetyltransferase at the replication forks as the result of a specific mechanism. To dissect this mechanism in the well established in vitro system based on the use of Xenopus egg extracts, we cloned two Xenopus orthologs of Ctf7/Eco1 acetyltransferase, XEco1 and XEco2. Both proteins share a domain structure with known members of Ctf7/Eco1 family proteins. Moreover, biochemical analysis showed that XEco2 exhibited acetyltransferase activity. We raised a specific antibody against XEco2 and used it to further characterize XEco2. In tissue culture cells, XEco2 gradually accumulated in nuclei through the S phase. In nuclei formed in egg extract, XEco2 was loaded into the chromatin at a constant level in a manner sensitive to geminin, an inhibitor of the pre-replication complex assembly, but insensitive to aphidicolin, an inhibitor of DNA polymerases. In both systems, no specific localization was observed during mitosis. In XEco2-depleted egg extracts, DNA replication occurred with normal kinetics and efficiency, and the condensation and sister chromatid cohesion of subsequently formed mitotic chromosomes was unaffected. These observations will serve as a platform for elucidating the molecular function of Ctf7/Eco1 acetyltransferase in the establishment of sister chromatid cohesion in future studies, in which XEco1 and XEco2 should be dissected in parallel.
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Affiliation(s)
- Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Advanced Science Institute, Saitama, Japan
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184
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Bermejo R, Branzei D, Foiani M. Cohesion by topology: sister chromatids interlocked by DNA. Genes Dev 2008; 22:2297-301. [PMID: 18765785 DOI: 10.1101/gad.1719308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sister chromatid cohesion is coupled with chromosome replication and influences chromosome segregation and intra-S repair. Specialized proteins, the cohesins, together with other pathways contribute to tether sister chromatids. In this issue of Genes & Development, Wang and colleagues (pp. 2426-2433 demonstrate that TopoIV, a type II DNA topoisomerase, modulates cohesion in Escherichia coli, by removing interlocked DNA junctions between sister chromatids. They propose that DNA precatenanes, arising during replication fork progression, hold sister chromatids together.
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Affiliation(s)
- Rodrigo Bermejo
- Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute of Molecular Oncology Foundation, 20139 Milan, Italy
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185
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Coprinus cinereus rad50 mutants reveal an essential structural role for Rad50 in axial element and synaptonemal complex formation, homolog pairing and meiotic recombination. Genetics 2008; 180:1889-907. [PMID: 18940790 DOI: 10.1534/genetics.108.092775] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mre11/Rad50/Nbs1 (MRN) complex is required for eukaryotic DNA double-strand break (DSB) repair and meiotic recombination. We cloned the Coprinus cinereus rad50 gene and showed that it corresponds to the complementation group previously named rad12, identified mutations in 15 rad50 alleles, and mapped two of the mutations onto molecular models of Rad50 structure. We found that C. cinereus rad50 and mre11 mutants arrest in meiosis and that this arrest is Spo11 dependent. In addition, some rad50 alleles form inducible, Spo11-dependent Rad51 foci and therefore must be forming meiotic DSBs. Thus, we think it likely that arrest in both mre11-1 and the collection of rad50 mutants is the result of unrepaired or improperly processed DSBs in the genome and that Rad50 and Mre11 are dispensable in C. cinereus for DSB formation, but required for appropriate DSB processing. We found that the ability of rad50 mutant strains to form Rad51 foci correlates with their ability to promote synaptonemal complex formation and with levels of stable meiotic pairing and that partial pairing, recombination initiation, and synapsis occur in the absence of wild-type Rad50 catalytic domains. Examination of single- and double-mutant strains showed that a spo11 mutation that prevents DSB formation enhances axial element (AE) formation for rad50-4, an allele predicted to encode a protein with intact hook region and hook-proximal coiled coils, but not for rad50-1, an allele predicted to encode a severely truncated protein, or for rad50-5, which encodes a protein whose hook-proximal coiled-coil region is disrupted. Therefore, Rad50 has an essential structural role in the formation of AEs, separate from the DSB-processing activity of the MRN complex.
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186
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Pebernard S, Schaffer L, Campbell D, Head SR, Boddy MN. Localization of Smc5/6 to centromeres and telomeres requires heterochromatin and SUMO, respectively. EMBO J 2008; 27:3011-23. [PMID: 18923417 DOI: 10.1038/emboj.2008.220] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/22/2008] [Indexed: 01/19/2023] Open
Abstract
The Smc5/6 holocomplex executes key functions in genome maintenance that include ensuring the faithful segregation of chromosomes at mitosis and facilitating critical DNA repair pathways. Smc5/6 is essential for viability and therefore, dissecting its chromosome segregation and DNA repair roles has been challenging. We have identified distinct epigenetic and post-translational modifications that delineate roles for fission yeast Smc5/6 in centromere function, versus replication fork-associated DNA repair. We monitored Smc5/6 subnuclear and genomic localization in response to different replicative stresses, using fluorescence microscopy and chromatin immunoprecipitation (ChIP)-on-chip methods. Following hydroxyurea treatment, and during an unperturbed S phase, Smc5/6 is transiently enriched at the heterochromatic outer repeats of centromeres in an H3-K9 methylation-dependent manner. In contrast, methyl methanesulphonate treatment induces the accumulation of Smc5/6 at subtelomeres, in an Nse2 SUMO ligase-dependent, but H3-K9 methylation-independent manner. Finally, we determine that Smc5/6 loads at all genomic tDNAs, a phenomenon that requires intact consensus TFIIIC-binding sites in the tDNAs.
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Affiliation(s)
- Stephanie Pebernard
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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187
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Haeusler RA, Pratt-Hyatt M, Good PD, Gipson TA, Engelke DR. Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes. Genes Dev 2008; 22:2204-14. [PMID: 18708579 DOI: 10.1101/gad.1675908] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The 274 tRNA genes in Saccharomyces cerevisiae are scattered throughout the linear maps of the 16 chromosomes, but the genes are clustered at the nucleolus when compacted in the nucleus. This clustering is dependent on intact nucleolar organization and contributes to tRNA gene-mediated (tgm) silencing of RNA polymerase II transcription near tRNA genes. After examination of the localization mechanism, we find that the chromosome-condensing complex, condensin, is involved in the clustering of tRNA genes. Conditionally defective mutations in all five subunits of condensin, which we confirm is bound to active tRNA genes in the yeast genome, lead to loss of both pol II transcriptional silencing near tRNA genes and nucleolar clustering of the genes. Furthermore, we show that condensin physically associates with a subcomplex of RNA polymerase III transcription factors on the tRNA genes. Clustering of tRNA genes by condensin appears to be a separate mechanism from their nucleolar localization, as microtubule disruption releases tRNA gene clusters from the nucleolus, but does not disperse the clusters. These observations suggest a widespread role for condensin in gene organization and packaging of the interphase yeast nucleus.
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Affiliation(s)
- Rebecca A Haeusler
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
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188
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Llano E, Gómez R, Gutiérrez-Caballero C, Herrán Y, Sánchez-Martín M, Vázquez-Quiñones L, Hernández T, de Álava E, Cuadrado A, Barbero JL, Suja JA, Pendás AM. Shugoshin-2 is essential for the completion of meiosis but not for mitotic cell division in mice. Genes Dev 2008; 22:2400-13. [PMID: 18765791 PMCID: PMC2532928 DOI: 10.1101/gad.475308] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 07/04/2008] [Indexed: 01/09/2023]
Abstract
Shugoshin-2 (SGOL2) is one of the two mammalian orthologs of the Shugoshin/Mei-S322 family of proteins that regulate sister chromatid cohesion by protecting the integrity of the multiprotein cohesin complexes. This protective system is essential for faithful chromosome segregation during mitosis and meiosis, which is the physical basis of Mendelian inheritance. Regardless of its evolutionary conservation from yeast to mammals, little is known about the in vivo relevance and specific role that SGOL2 plays in mammals. Here we show that disruption of the gene encoding mouse SGOL2 does not cause any alteration in sister chromatid cohesion in embryonic cultured fibroblasts and adult somatic tissues. Moreover, mutant mice develop normally and survive to adulthood without any apparent alteration. However, both male and female Sgol2-deficient mice are infertile. We demonstrate that SGOL2 is necessary for protecting centromeric cohesion during mammalian meiosis I. In vivo, the loss of SGOL2 promotes a premature release of the meiosis-specific REC8 cohesin complexes from anaphase I centromeres. This molecular alteration is manifested cytologically by the complete loss of centromere cohesion at metaphase II leading to single chromatids and physiologically with the formation of aneuploid gametes that give rise to infertility.
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Affiliation(s)
- Elena Llano
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Departamento de Fisiología, Campus Miguel de Unamuno S/N, 37007 Salamanca, Spain
| | - Rocío Gómez
- Unidad de Biología Celular, Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Cristina Gutiérrez-Caballero
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Yurema Herrán
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | | | - Luis Vázquez-Quiñones
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Teresa Hernández
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Enrique de Álava
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Ana Cuadrado
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José Luis Barbero
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José A. Suja
- Unidad de Biología Celular, Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alberto M. Pendás
- Instituto de Biología Molecular y Celular del Cáncer (CSIC-USAL), Campus Miguel de Unamuno, 37007 Salamanca, Spain
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189
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Losada A. The regulation of sister chromatid cohesion. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1786:41-8. [PMID: 18474253 DOI: 10.1016/j.bbcan.2008.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/06/2008] [Accepted: 04/08/2008] [Indexed: 01/20/2023]
Abstract
Sister chromatid cohesion is a major feature of the eukaryotic chromosome. It entails the formation of a physical linkage between the two copies of a chromosome that result from the duplication process. This linkage must be maintained until chromosome segregation takes place in order to ensure the accurate distribution of the genomic information. Cohesin, a multiprotein complex conserved from yeast to humans, is largely responsible for sister chromatid cohesion. Other cohesion factors regulate the interaction of cohesin with chromatin as well as the establishment and dissolution of cohesion. In addition, the presence of cohesin throughout the genome appears to influence processes other than chromosome segregation, such as transcription and DNA repair. In this review I summarize recent advances in our understanding of cohesin function and regulation in mitosis, and discuss the consequences of impairing the cohesion process at the level of the whole organism.
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Affiliation(s)
- Ana Losada
- Chromosome Dynamics Group, Spanish National Cancer Research Centre, Melchor Fernández Almagro 3, Madrid E-28029, Spain.
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190
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Inoue A, Hyle J, Lechner MS, Lahti JM. Perturbation of HP1 localization and chromatin binding ability causes defects in sister-chromatid cohesion. Mutat Res 2008; 657:48-55. [PMID: 18790078 DOI: 10.1016/j.mrgentox.2008.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 08/11/2008] [Indexed: 01/06/2023]
Abstract
Sister-chromatid cohesion, the machinery used in eukaryote organisms to prevent aneuploidy, tethers sister chromatids together after their replication in S phase until mitosis. Previous studies in fission yeast, Drosophila and mammals have demonstrated the requirement for the heterochromatin formation pathway for proper centromeric cohesion. However, the exact role of heterochromatin protein 1 (HP1) in sister-chromatid cohesion in mammals is still unknown. In this study, we disrupted endogenous HP1 expression in HeLa cells using a dominant-negative mutant of HP1beta and wild-type or mutant forms of HP1alpha. We then examined their effects on chromosome alignment, segregation and cohesion. Enforced expression of these constructs leads to frequent chromosome misalignment and missegregation. Mitotic chromosomes from these cells also exhibit a loosened primary constriction and separated sister chromatids. We further demonstrate that alignment of the cohesin proteins around kinetochores was also aberrant and that cohesin complexes bound less tightly in these cells. Unexpectedly, we observed a "wavy" chromosome morphology resembling that seen upon depletion of condensin proteins in cells with over-expression of HP1alpha, but not in cells expressing the HP1beta mutant. These results indicate that proper HP1 status is required for sister-chromatid cohesion in mammalian cells, and suggest that HP1alpha might be required for chromosome condensation.
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Affiliation(s)
- Akira Inoue
- Department of Genetics and Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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191
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Zhang J, Shi X, Li Y, Kim BJ, Jia J, Huang Z, Yang T, Fu X, Jung SY, Wang Y, Zhang P, Kim ST, Pan X, Qin J. Acetylation of Smc3 by Eco1 is required for S phase sister chromatid cohesion in both human and yeast. Mol Cell 2008; 31:143-51. [PMID: 18614053 DOI: 10.1016/j.molcel.2008.06.006] [Citation(s) in RCA: 329] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/11/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
Abstract
Sister chromatid cohesion is normally established in S phase in a process that depends on the cohesion establishment factor Eco1, a conserved acetyltransferase. However, due to the lack of known in vivo substrates, how Eco1 regulates cohesion is not understood. Here we report that yeast Eco1 and its human ortholog, ESCO1, both acetylate Smc3, a component of the cohesin complex that physically holds the sister chromatid together, at two conserved lysine residues. Mutating these lysine residues to a nonacetylatable form leads to increased loss of sister chromatid cohesion and genome instability in both yeast and human. In addition, we clarified that the acetyltransferase activity of Eco1 is essential for its function. Our study thus identified a molecular target for the acetyltransferase Eco1 and revealed that Smc3 acetylation is a conserved mechanism in regulating sister chromatid cohesion.
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Affiliation(s)
- Jinglan Zhang
- Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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192
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Blasius M, Sommer S, Hübscher U. Deinococcus radiodurans: what belongs to the survival kit? Crit Rev Biochem Mol Biol 2008; 43:221-38. [PMID: 18568848 DOI: 10.1080/10409230802122274] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Deinococcus radiodurans, one of the most radioresistant organisms known to date, is able to repair efficiently hundreds of DNA double- and single-strand breaks as well as other types of DNA damages promoted by ionizing or ultraviolet radiation. We review recent discoveries concerning several aspects of radioresistance and survival under high genotoxic stress. We discuss different hypotheses and possibilities that have been suggested to contribute to radioresistance and propose that D. radiodurans combines a variety of physiological tools that are tightly coordinated. A complex network of regulatory proteins may be discovered in the near future that might allow further understanding of radioresistance.
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Affiliation(s)
- Melanie Blasius
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich-Irchel, Zurich, Switzerland
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193
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Gluenz E, Sharma R, Carrington M, Gull K. Functional characterization of cohesin subunit SCC1 in Trypanosoma brucei and dissection of mutant phenotypes in two life cycle stages. Mol Microbiol 2008; 69:666-80. [PMID: 18554326 PMCID: PMC2610385 DOI: 10.1111/j.1365-2958.2008.06320.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2008] [Indexed: 11/30/2022]
Abstract
In yeast and metazoa, structural maintenance of chromosome (SMC) complexes play key roles in chromosome segregation, architecture and DNA repair. The main function of the cohesin complex is to hold replicated sister chromatids together until segregation at anaphase, which is dependent on proteolytic cleavage of the cohesin subunit SCC1. Analysis of trypanosomatid genomes showed that the core cohesin and condensin complexes are conserved, but SMC5/6 is absent. To investigate the functional conservation of cohesin in eukaryotes distantly related to yeast and metazoa, we characterized the Trypanosoma brucei SCC1 orthologue. TbSCC1 is expressed prior to DNA synthesis at late G1, remains in the nucleus throughout S- and G2-phases of the cell cycle and disappears at anaphase. Depletion of SCC1 by RNAi or expression of a non-cleavable SCC1 resulted in karyokinesis failure. Using the dominant negative phenotype of non-cleavable SCC1 we investigated checkpoint regulation of cytokinesis in response to mitosis failure at anaphase. In the absence of chromosome segregation, procyclic trypanosomes progressed through cytokinesis to produce one nucleated and one anucleate cell (zoid). In contrast, cytokinesis was incomplete in bloodstream forms, where cleavage was initiated but cells failed to progress to abscission. Kinetoplast duplication was uninterrupted resulting in cells with multiple kinetoplasts and flagella.
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Affiliation(s)
- Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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194
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McNairn AJ, Gerton JL. The chromosome glue gets a little stickier. Trends Genet 2008; 24:382-9. [PMID: 18602182 DOI: 10.1016/j.tig.2008.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 12/25/2022]
Abstract
Since their discovery, the cohesin proteins have been intensely studied in multiple model systems to determine the mechanism of chromosome cohesion. Recent studies have demonstrated that cohesin is much more than a molecular glue that holds chromosomes together in mitosis. Indeed, cohesin performs critical roles in gene regulation, possibly through the formation of higher-order chromatin structure. Moreover, this newly appreciated role is necessary for proper development in metazoan species, with mutations in the cohesin pathway resulting in human developmental disorders.
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Affiliation(s)
- Adrian J McNairn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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195
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Pebernard S, Perry JJP, Tainer JA, Boddy MN. Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability. Mol Biol Cell 2008; 19:4099-109. [PMID: 18667531 DOI: 10.1091/mbc.e08-02-0226] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Smc5-Smc6 holocomplex plays essential but largely enigmatic roles in chromosome segregation, and facilitates DNA repair. The Smc5-Smc6 complex contains six conserved non-SMC subunits. One of these, Nse1, contains a RING-like motif that often confers ubiquitin E3 ligase activity. We have functionally characterized the Nse1 RING-like motif, to determine its contribution to the chromosome segregation and DNA repair roles of Smc5-Smc6. Strikingly, whereas a full deletion of nse1 is lethal, the Nse1 RING-like motif is not essential for cellular viability. However, Nse1 RING mutant cells are hypersensitive to a broad spectrum of genotoxic stresses, indicating that the Nse1 RING motif promotes DNA repair functions of Smc5-Smc6. We tested the ability of both human and yeast Nse1 to mediate ubiquitin E3 ligase activity in vitro and found no detectable activity associated with full-length Nse1 or the isolated RING domains. Interestingly, however, the Nse1 RING-like domain is required for normal Nse1-Nse3-Nse4 trimer formation in vitro and for damage-induced recruitment of Nse4 and Smc5 to subnuclear foci in vivo. Thus, we propose that the Nse1 RING-like motif is a protein-protein interaction domain required for Smc5-Smc6 holocomplex integrity and recruitment to, or retention at, DNA lesions.
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Affiliation(s)
- Stephanie Pebernard
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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196
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Decaux O, Lodé L, Magrangeas F, Charbonnel C, Gouraud W, Jézéquel P, Attal M, Harousseau JL, Moreau P, Bataille R, Campion L, Avet-Loiseau H, Minvielle S. Prediction of survival in multiple myeloma based on gene expression profiles reveals cell cycle and chromosomal instability signatures in high-risk patients and hyperdiploid signatures in low-risk patients: a study of the Intergroupe Francophone du Myélome. J Clin Oncol 2008; 26:4798-805. [PMID: 18591550 DOI: 10.1200/jco.2007.13.8545] [Citation(s) in RCA: 284] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Survival of patients with multiple myeloma is highly heterogeneous, from periods of a few weeks to more than 10 years. We used gene expression profiles of myeloma cells obtained at diagnosis to identify broadly applicable prognostic markers. PATIENTS AND METHODS In a training set of 182 patients, we used supervised methods to identify individual genes associated with length of survival. A survival model was built from these genes. The validity of our model was assessed in our test set of 68 patients and in three independent cohorts comprising 853 patients with multiple myeloma. RESULTS The 15 strongest genes associated with the length of survival were used to calculate a risk score and to stratify patients into low-risk and high-risk groups. The survival-predictor score was significantly associated with survival in both the training and test sets and in the external validation cohorts. The Kaplan-Meier estimates of rates of survival at 3 years were 90.5% (95% CI, 85.6% to 95.3%) and 47.4% (95% CI, 33.5% to 60.1%), respectively, in our patients having a low risk or high risk independently of traditional prognostic factors. High-risk patients constituted a homogeneous biologic entity characterized by the overexpression of genes involved in cell cycle progression and its surveillance, whereas low-risk patients were heterogeneous and displayed hyperdiploid signatures. CONCLUSION Gene expression-based survival prediction and molecular features associated with high-risk patients may be useful for developing prognostic markers and may provide basis to treat these patients with new targeted antimitotics.
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Affiliation(s)
- Olivier Decaux
- L'Institut National de la Santé et de la Recherche Médicale, U892, University of Nantes, University, Hospital, Hematology Laboratory, Nantes, France
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197
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Hwang JY, Smith S, Ceschia A, Torres-Rosell J, Aragon L, Myung K. Smc5-Smc6 complex suppresses gross chromosomal rearrangements mediated by break-induced replications. DNA Repair (Amst) 2008; 7:1426-36. [PMID: 18585101 DOI: 10.1016/j.dnarep.2008.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 04/30/2008] [Accepted: 05/08/2008] [Indexed: 11/30/2022]
Abstract
Translocations in chromosomes alter genetic information. Although the frequent translocations observed in many tumors suggest the altered genetic information by translocation could promote tumorigenesis, the mechanisms for how translocations are suppressed and produced are poorly understood. The smc6-9 mutation increased the translocation class gross chromosomal rearrangement (GCR). Translocations produced in the smc6-9 strain are unique because they are non-reciprocal and dependent on break-induced replication (BIR) and independent of non-homologous end joining. The high incidence of translocations near repetitive sequences such as delta sequences, ARS, tRNA genes, and telomeres in the smc6-9 strain indicates that Smc5-Smc6 suppresses translocations by reducing DNA damage at repetitive sequences. Synergistic enhancements of translocations in strains defective in DNA damage checkpoints by the smc6-9 mutation without affecting de novo telomere addition class GCR suggest that Smc5-Smc6 defines a new pathway to suppress GCR formation.
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Affiliation(s)
- Ji-Young Hwang
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Drive, Bethesda, MD 20892 USA
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198
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Hegermann J, Halbedel S, Dumke R, Regula J, Gabdoulline RR, Mayer F, Stülke J, Herrmann R. The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell. MICROBIOLOGY-SGM 2008; 154:1185-1192. [PMID: 18375811 DOI: 10.1099/mic.0.2007/013342-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The protein Mpn474 encoded by the mpn474 gene of the human-pathogenic Mycoplasma pneumoniae contains 1033 amino acids and has an isoelectric point of 4.79, which is caused by the large excess of glutamic acid residues (11 %). Although the protein lacks recognizable export signals we showed by immuno-electron microscopy that Mpn474 is surface exposed, covering the cell completely. By combining cross-linking and careful treatment of the bacterial cells with Triton X-100, we found that this protein is weakly bound to the cell surface, while the true transmembrane protein Mpn141 (adhesin P1) is firmly attached under the same experimental conditions. A transposon mutant in the mpn474 gene, which has no obvious phenotype, served as negative control for the immunodetection.
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Affiliation(s)
- Jan Hegermann
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Sven Halbedel
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Roger Dumke
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität, Medizinische Fakultät Carl Gustav Carus, Fetscherstr. 74, D-01307 Dresden, Germany
| | - Jörg Regula
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Razif R Gabdoulline
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany
| | - Frank Mayer
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Jörg Stülke
- Abteilung für Allgemeine Mikrobiologie, Institut für Mikrobiologie und Genetik, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Richard Herrmann
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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199
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Abstract
Structural maintenance of chromosomes (SMC) proteins form the cohesin and condensin complexes and play important roles in sister chromatid pairing, chromosome segregation, and transcriptional regulation. Two papers in Nature Genetics now show that SMC-like proteins also participate in epigenetic processes such as X inactivation in mammals and RNA-directed DNA methylation in plants.
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Affiliation(s)
- Edith Heard
- CNRS UMR 218, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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200
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Luo H, Li Y, Mu JJ, Zhang J, Tonaka T, Hamamori Y, Jung SY, Wang Y, Qin J. Regulation of intra-S phase checkpoint by ionizing radiation (IR)-dependent and IR-independent phosphorylation of SMC3. J Biol Chem 2008; 283:19176-83. [PMID: 18442975 DOI: 10.1074/jbc.m802299200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Structure maintenance of chromosome 1 (SMC1) is phosphorylated by ataxia telangiectasia-mutated (ATM) in response to ionizing radiation (IR) to activate intra-S phase checkpoint. A role of CK2 in DNA damage response has been implicated in many previous works, but the molecular mechanism for its activation is not clear. In the present work, we report that SMC3 is phosphorylated at Ser-1067 and Ser-1083 in vivo. Ser-1083 phosphorylation is IR-inducible, depends on ATM and Nijmegen breakage syndrome 1 (NBS1), and is required for intra-S phase checkpoint. Interestingly, Ser-1067 phosphorylation is constitutive and is not induced by IR but also affects intra-S phase checkpoint. Phosphorylation of Ser-1083 is weakened in cells expressing S1067A mutant, suggesting interplay between Ser-1067 and Ser-1083 phosphorylation in DNA damage response. Consistently, small interfering RNA knockdown of CK2 leads to attenuated phosphorylation of Ser-1067 as well as intra-S phase checkpoint defect. Our data provide evidence that phosphorylation of a core cohesin subunit SMC3 by ATM plays an important role in DNA damage response and suggest that a constitutive phosphorylation by CK2 may affect intra-S phase checkpoint by modulating SMC3 phosphorylation by ATM.
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Affiliation(s)
- Hao Luo
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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