1
|
Strasser AS, Gonzalez-Reiche AS, Zhou X, Valdebenito-Maturana B, Ye X, Zhang B, Wu M, van Bakel H, Jabs EW. Limb reduction in an Esco2 cohesinopathy mouse model is mediated by p53-dependent apoptosis and vascular disruption. Nat Commun 2024; 15:7154. [PMID: 39168984 PMCID: PMC11339411 DOI: 10.1038/s41467-024-51328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
Roberts syndrome (RBS) is an autosomal recessive disorder with profound growth deficiency and limb reduction caused by ESCO2 loss-of-function variants. Here, we elucidate the pathogenesis of limb reduction in an Esco2fl/fl;Prrx1-CreTg/0 mouse model using bulk- and single-cell-RNA-seq and gene co-expression network analyses during embryogenesis. Our results reveal morphological and vascular defects culminating in hemorrhage of mutant limbs at E12.5. Underlying this abnormal developmental progression is a pre-apoptotic, mesenchymal cell population specific to mutant limb buds enriched for p53-related signaling beginning at E9.5. We then characterize these p53-related processes of cell cycle arrest, DNA damage, cell death, and the inflammatory leukotriene signaling pathway in vivo. In utero treatment with pifithrin-α, a p53 inhibitor, rescued the hemorrhage in mutant limbs. Lastly, significant enrichments were identified among genes associated with RBS, thalidomide embryopathy, and other genetic limb reduction disorders, suggesting a common vascular etiology among these conditions.
Collapse
Affiliation(s)
- Arielle S Strasser
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Braulio Valdebenito-Maturana
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Xiaoqian Ye
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Department of Clinical Genomics, Mayo Clinic, 200 First Street, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street, Rochester, MN, USA.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Department of Clinical Genomics, Mayo Clinic, 200 First Street, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street, Rochester, MN, USA.
- Department of Cell, Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA.
| |
Collapse
|
2
|
Attou A, Zülske T, Wedemann G. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions. Biophys J 2022; 121:4788-4799. [PMID: 36325618 PMCID: PMC9811664 DOI: 10.1016/j.bpj.2022.10.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.
Collapse
Affiliation(s)
- Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| |
Collapse
|
3
|
Koh YE, Choi EH, Kim JW, Kim KP. The Kleisin Subunits of Cohesin are Involved in the Fate Determination of Embryonic Stem Cells. Mol Cells 2022; 45:820-832. [PMID: 36172976 PMCID: PMC9676991 DOI: 10.14348/molcells.2022.2042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/20/2022] [Accepted: 07/24/2022] [Indexed: 11/27/2022] Open
Abstract
As a potential candidate to generate an everlasting cell source to treat various diseases, embryonic stem cells are regarded as a promising therapeutic tool in the regenerative medicine field. Cohesin, a multi-functional complex that controls various cellular activities, plays roles not only in organizing chromosome dynamics but also in controlling transcriptional activities related to self-renewal and differentiation of stem cells. Here, we report a novel role of the α-kleisin subunits of cohesin (RAD21 and REC8) in the maintenance of the balance between these two stem-cell processes. By knocking down REC8, RAD21, or the non-kleisin cohesin subunit SMC3 in mouse embryonic stem cells, we show that reduction in cohesin level impairs their self-renewal. Interestingly, the transcriptomic analysis revealed that knocking down each cohesin subunit enables the differentiation of embryonic stem cells into specific lineages. Specifically, embryonic stem cells in which cohesin subunit RAD21 were knocked down differentiated into cells expressing neural alongside germline lineage markers. Thus, we conclude that cohesin appears to control the fate determination of embryonic stem cells.
Collapse
Affiliation(s)
- Young Eun Koh
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
- Genexine Inc., Bio Innovation Park, Seoul 07789, Korea
| | - Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Jung-Woong Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Korea
| |
Collapse
|
4
|
Mehta G, Sanyal K, Abhishek S, Rajakumara E, Ghosh SK. Minichromosome maintenance proteins in eukaryotic chromosome segregation. Bioessays 2021; 44:e2100218. [PMID: 34841543 DOI: 10.1002/bies.202100218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023]
Abstract
Minichromosome maintenance (Mcm) proteins are well-known for their functions in DNA replication. However, their roles in chromosome segregation are yet to be reviewed in detail. Following the discovery in 1984, a group of Mcm proteins, known as the ARS-nonspecific group consisting of Mcm13, Mcm16-19, and Mcm21-22, were characterized as bonafide kinetochore proteins and were shown to play significant roles in the kinetochore assembly and high-fidelity chromosome segregation. This review focuses on the structure, function, and evolution of this group of Mcm proteins. Our in silico analysis of the physical interactors of these proteins reveals that they share non-overlapping functions despite being copurified in biochemically stable complexes. We have discussed the contrasting results reported in the literature and experimental strategies to address them. Taken together, this review focuses on the structure-function of the ARS-nonspecific Mcm proteins and their evolutionary flexibility to maintain genome stability in various organisms.
Collapse
Affiliation(s)
- Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | - Suman Abhishek
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| |
Collapse
|
5
|
Cao L, Wang S, Zhao L, Qin Y, Wang H, Cheng Y. The Inactivation of Arabidopsis UBC22 Results in Abnormal Chromosome Segregation in Female Meiosis, but Not in Male Meiosis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112418. [PMID: 34834780 PMCID: PMC8625819 DOI: 10.3390/plants10112418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/18/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Protein ubiquitination is important for the regulation of meiosis in eukaryotes, including plants. However, little is known about the involvement of E2 ubiquitin-conjugating enzymes in plant meiosis. Arabidopsis UBC22 is a unique E2 enzyme, able to catalyze the formation of ubiquitin dimers through lysine 11 (K11). Previous work has shown that ubc22 mutants are defective in megasporogenesis, with most ovules having no or abnormally functioning megaspores; furthermore, some mutant plants show distinct phenotypes in vegetative growth. In this study, we showed that chromosome segregation and callose deposition were abnormal in mutant female meiosis while male meiosis was not affected. The meiotic recombinase DMC1, required for homologous chromosome recombination, showed a dispersed distribution in mutant female meiocytes compared to the presence of strong foci in WT female meiocytes. Based on an analysis of F1 plants produced from crosses using a mutant as the female parent, about 24% of female mutant gametes had an abnormal content of DNA, resulting in frequent aneuploids among the mutant plants. These results show that UBC22 is critical for normal chromosome segregation in female meiosis but not for male meiosis, and they provide important leads for studying the role of UBC22 and K11-linked ubiquitination.
Collapse
Affiliation(s)
- Ling Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (L.Z.); (Y.Q.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Lihua Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (L.Z.); (Y.Q.)
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (L.Z.); (Y.Q.)
| | - Hong Wang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.C.); (L.Z.); (Y.Q.)
| |
Collapse
|
6
|
Fauser J, Itzen A, Gulen B. Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology. Bioconjug Chem 2021; 32:879-890. [PMID: 33861574 DOI: 10.1021/acs.bioconjchem.1c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
Collapse
Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| |
Collapse
|
7
|
Yoshimura A, Sutani T, Shirahige K. Functional control of Eco1 through the MCM complex in sister chromatid cohesion. Gene 2021; 784:145584. [PMID: 33753149 DOI: 10.1016/j.gene.2021.145584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 10/21/2022]
Abstract
Sister chromatid cohesion (SCC) is essential for the maintenance of genome integrity. The establishment of SCC is coupled to DNA replication, and this is achieved in budding yeast Saccharomyces cerevisiae by a mechanism that is dependent on the interaction between Eco1 acetyltransferase and PCNA in the DNA replication complex. In vertebrates, the Eco1 homolog ESCO2 has been reported to interact with MCM complex in the DNA replication complex to establish DNA replication-dependent cohesion. Here we show that budding yeast Eco1 is also physically interacted with the MCM complex. We found that Eco1 was specifically bound to Mcm2 subunit in the MCM complex and they interacted via their N-terminal regions, using yeast two-hybrid system. The underlying mechanism of the interaction was different between yeast and vertebrates. Intensive molecular dissection of Eco1 identified residues important for interaction with Mcm2 and/or PCNA. Mutant forms of Eco1 (Eco1mWW and Eco1mGRK), where sets of the identified residues were substituted with alanine, resulted in impaired SCC, decreased level of acetylation of Smc3, and a reduction of Eco1 protein amount in yeast cells. We, hence, suggest that Eco1 is stabilized by its interactions with MCM complex and PCNA, which allows it to promote DNA replication-coupled SCC establishment.
Collapse
Affiliation(s)
- Atsunori Yoshimura
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Sutani
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
8
|
Yi F, Zhang Y, Wang Z, Wang Z, Li Z, Zhou T, Xu H, Liu J, Jiang B, Li X, Wang L, Bai N, Guo Q, Guan Y, Feng Y, Mao Z, Fan G, Zhang S, Wang C, Cao L, O'Rourke BP, Wang Y, Wu Y, Wu B, You S, Zhang N, Guan J, Song X, Sun Y, Wei S, Cao L. The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis. SCIENCE ADVANCES 2021; 7:7/9/eabe5518. [PMID: 33627431 PMCID: PMC7904255 DOI: 10.1126/sciadv.abe5518] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Improper distribution of chromosomes during mitosis can contribute to malignant transformation. Higher eukaryotes have evolved a mitotic catastrophe mechanism for eliminating mitosis-incompetent cells; however, the signaling cascade and its epigenetic regulation are poorly understood. Our analyses of human cancerous tissue revealed that the NAD-dependent deacetylase SIRT2 is up-regulated in early-stage carcinomas of various organs. Mass spectrometry analysis revealed that SIRT2 interacts with and deacetylates the structural maintenance of chromosomes protein 1 (SMC1A), which then promotes SMC1A phosphorylation to properly drive mitosis. We have further demonstrated that inhibition of SIRT2 activity or continuously increasing SMC1A-K579 acetylation causes abnormal chromosome segregation, which, in turn, induces mitotic catastrophe in cancer cells and enhances their vulnerability to chemotherapeutic agents. These findings suggest that regulation of the SIRT2-SMC1A axis through deacetylation-phosphorylation permits escape from mitotic catastrophe, thus allowing early precursor lesions to overcome oncogenic stress.
Collapse
Affiliation(s)
- Fei Yi
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Ying Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Zhijun Wang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Zhuo Wang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Ziwei Li
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Tingting Zhou
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Hongde Xu
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Jingwei Liu
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Bo Jiang
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Xiaoman Li
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Liang Wang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Ning Bai
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Qiqiang Guo
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Yi Guan
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Yanling Feng
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200082, China
| | - Guangjian Fan
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Shengping Zhang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Chuangui Wang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Longyue Cao
- Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Brian P O'Rourke
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yang Wang
- Panjin Liaohe Oilfield Gem Flower Hospital, Panjin, Liaoning Province 124010, China
| | - Yanmei Wu
- Panjin Liaohe Oilfield Gem Flower Hospital, Panjin, Liaoning Province 124010, China
| | - Boquan Wu
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Shilong You
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Junlin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaoyu Song
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China.
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
| | - Shi Wei
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249-7331, USA.
| | - Liu Cao
- Institute of Translational Medicine, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, , No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, China.
| |
Collapse
|
9
|
Ding N, Zhang X, Zhang XD, Jing J, Liu SS, Mu YP, Peng LL, Yan YJ, Xiao GM, Bi XY, Chen H, Li FH, Yao B, Zhao AZ. Impairment of spermatogenesis and sperm motility by the high-fat diet-induced dysbiosis of gut microbes. Gut 2020; 69:1608-1619. [PMID: 31900292 PMCID: PMC7456731 DOI: 10.1136/gutjnl-2019-319127] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE High-fat diet (HFD)-induced metabolic disorders can lead to impaired sperm production. We aim to investigate if HFD-induced gut microbiota dysbiosis can functionally influence spermatogenesis and sperm motility. DESIGN Faecal microbes derived from the HFD-fed or normal diet (ND)-fed male mice were transplanted to the mice maintained on ND. The gut microbes, sperm count and motility were analysed. Human faecal/semen/blood samples were collected to assess microbiota, sperm quality and endotoxin. RESULTS Transplantation of the HFD gut microbes into the ND-maintained (HFD-FMT) mice resulted in a significant decrease in spermatogenesis and sperm motility, whereas similar transplantation with the microbes from the ND-fed mice failed to do so. Analysis of the microbiota showed a profound increase in genus Bacteroides and Prevotella, both of which likely contributed to the metabolic endotoxaemia in the HFD-FMT mice. Interestingly, the gut microbes from clinical subjects revealed a strong negative correlation between the abundance of Bacteroides-Prevotella and sperm motility, and a positive correlation between blood endotoxin and Bacteroides abundance. Transplantation with HFD microbes also led to intestinal infiltration of T cells and macrophages as well as a significant increase of pro-inflammatory cytokines in the epididymis, suggesting that epididymal inflammation have likely contributed to the impairment of sperm motility. RNA-sequencing revealed significant reduction in the expression of those genes involved in gamete meiosis and testicular mitochondrial functions in the HFD-FMT mice. CONCLUSION We revealed an intimate linkage between HFD-induced microbiota dysbiosis and defect in spermatogenesis with elevated endotoxin, dysregulation of testicular gene expression and localised epididymal inflammation as the potential causes. TRIAL REGISTRATION NUMBER NCT03634644.
Collapse
Affiliation(s)
- Ning Ding
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | | | - Xue Di Zhang
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Jun Jing
- Jinling Hospital Department Reproductive Medical Center, Nanjing Medicine University, Nanjing, Jiangsu, China,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shan Shan Liu
- Department of Laboratory, Women and Children 's Hospital of Qingdao, Qingdao, Shandong, China
| | - Yun Ping Mu
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Li Li Peng
- The School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Yun Jing Yan
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Geng Miao Xiao
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Xin Yun Bi
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Hao Chen
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Fang Hong Li
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| | - Bing Yao
- Jinling Hospital Department Reproductive Medical Center, Nanjing Medicine University, Nanjing, Jiangsu, China .,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Allan Z Zhao
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China
| |
Collapse
|
10
|
Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
Collapse
Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| |
Collapse
|
11
|
Hsieh YYP, Makrantoni V, Robertson D, Marston AL, Murray AW. Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis. PLoS Biol 2020; 18:e3000635. [PMID: 32155147 PMCID: PMC7138332 DOI: 10.1371/journal.pbio.3000635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/07/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
The role of proteins often changes during evolution, but we do not know how cells adapt when a protein is asked to participate in a different biological function. We forced the budding yeast, Saccharomyces cerevisiae, to use the meiosis-specific kleisin, recombination 8 (Rec8), during the mitotic cell cycle, instead of its paralog, Scc1. This perturbation impairs sister chromosome linkage, advances the timing of genome replication, and reduces reproductive fitness by 45%. We evolved 15 parallel populations for 1,750 generations, substantially increasing their fitness, and analyzed the genotypes and phenotypes of the evolved cells. Only one population contained a mutation in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and delay genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow cells to use an existing protein to participate in new biological functions.
Collapse
Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Vasso Makrantoni
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Robertson
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adèle L. Marston
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew W. Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| |
Collapse
|
12
|
A 'parameiosis' drives depolyploidization and homologous recombination in Candida albicans. Nat Commun 2019; 10:4388. [PMID: 31558727 PMCID: PMC6763455 DOI: 10.1038/s41467-019-12376-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/28/2019] [Indexed: 12/14/2022] Open
Abstract
Meiosis is a conserved tenet of sexual reproduction in eukaryotes, yet this program is seemingly absent from many extant species. In the human fungal pathogen Candida albicans, mating of diploid cells generates tetraploid products that return to the diploid state via a non-meiotic process of depolyploidization known as concerted chromosome loss (CCL). Here, we report that recombination rates are more than three orders of magnitude higher during CCL than during normal mitotic growth. Furthermore, two conserved ‘meiosis-specific’ factors play central roles in CCL as SPO11 mediates DNA double-strand break formation while both SPO11 and REC8 regulate chromosome stability and promote inter-homolog recombination. Unexpectedly, SPO11 also promotes DNA repair and recombination during normal mitotic divisions. These results indicate that C. albicans CCL represents a ‘parameiosis’ that blurs the conventional boundaries between mitosis and meiosis. They also reveal parallels with depolyploidization in mammalian cells and provide potential insights into the evolution of meiosis. Mating of Candida albicans produces tetraploid products that return to the diploid state via a non-meiotic process known as concerted chromosome loss (CCL). Here, Anderson et al. show high recombination rates during CCL and identify factors that are essential for chromosome stability and recombination during CCL.
Collapse
|
13
|
Zhu Z, Wang X. Roles of cohesin in chromosome architecture and gene expression. Semin Cell Dev Biol 2019; 90:187-193. [PMID: 30096363 DOI: 10.1016/j.semcdb.2018.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 12/18/2022]
Abstract
Cohesin-mediated chromatin organization plays an important role in formation and stabilization of chromosome architecture and gene regulation. Mechanisms by which cohesin shapes chromosome and regulates gene expression remain unclear. The present article overviews biological characters and functions of cohesin and core subunits and explores roles of regulatory factors (e.g. Pds5, Wapl, and Eco1) in dynamic behaviors of cohesin. Cohesin interacts with CCCTC binding factor (CTCF) and other factors to maintain and stabilize multi-dimensional organizations of topological loops and distances between sites during cell segmentation. We also describe functional roles of cohesin in cell cycle by entrapping sister chromatids to form embrace and handcuff models, loading onto chromatin, establishing cohesion function, and regulating removal of cohesin and associated factors from the chromosome arm through prophase pathway or at onset of anaphase. It is questioned whether those factors associated with cohesin-regulated processes can be identified as biology- or disease-specific biomarkers and druggable targets to dynamically monitor changes during phasing, staging, progressing, and responding of diseases. It is also expected to explore heterogenetic roles of cohesin between single cells and regulatory roles of cohesin in trans-omic profiles and functions. Further understanding of cohesin functions will be beneficial to improve diagnosis and treatment of cohesinopathies.
Collapse
Affiliation(s)
- Zhenhua Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
| |
Collapse
|
14
|
Perez S, Gevor M, Davidovich A, Kaspi A, Yamin K, Domovich T, Meirson T, Matityahu A, Brody Y, Stemmer SM, El-Osta A, Haviv I, Onn I, Gal-Tanamy M. Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions. Nucleic Acids Res 2019; 47:2455-2471. [PMID: 30698808 PMCID: PMC6412124 DOI: 10.1093/nar/gkz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/30/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis, which often results in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). HCV possesses an RNA genome and its replication is confined to the cytoplasm. Yet, infection with HCV leads to global changes in gene expression, and chromosomal instability (CIN) in the host cell. The mechanisms by which the cytoplasmic virus affects these nuclear processes are elusive. Here, we show that HCV modulates the function of the Structural Maintenance of Chromosome (SMC) protein complex, cohesin, which tethers remote regions of chromatin. We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. These changes regulate the expression of genes associated with virus-induced pathways. Furthermore, siRNA downregulation of viral-induced RAD21 reduces HCV infection. During mitosis, HCV infection induces hypercondensation of chromosomes and the appearance of multi-centrosomes. We provide evidence that the underlying mechanism involves the viral NS3/4 protease and the cohesin regulator, WAPL. Altogether, our results provide the first evidence that HCV induces changes in gene expression and chromosome structure of infected cells by modulating cohesin.
Collapse
Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Gevor
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Katreena Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tom Domovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tomer Meirson
- Cell Migration and Invasion Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yehuda Brody
- The Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| |
Collapse
|
15
|
Carvajal-Maldonado D, Byrum AK, Jackson J, Wessel S, Lemaçon D, Guitton-Sert L, Quinet A, Tirman S, Graziano S, Masson JY, Cortez D, Gonzalo S, Mosammaparast N, Vindigni A. Perturbing cohesin dynamics drives MRE11 nuclease-dependent replication fork slowing. Nucleic Acids Res 2019; 47:1294-1310. [PMID: 29917110 PMCID: PMC6379725 DOI: 10.1093/nar/gky519] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
Pds5 is required for sister chromatid cohesion, and somewhat paradoxically, to remove cohesin from chromosomes. We found that Pds5 plays a critical role during DNA replication that is distinct from its previously known functions. Loss of Pds5 hinders replication fork progression in unperturbed human and mouse cells. Inhibition of MRE11 nuclease activity restores fork progression, suggesting that Pds5 protects forks from MRE11-activity. Loss of Pds5 also leads to double-strand breaks, which are again reduced by MRE11 inhibition. The replication function of Pds5 is independent of its previously reported interaction with BRCA2. Unlike Pds5, BRCA2 protects forks from nucleolytic degradation only in the presence of genotoxic stress. Moreover, our iPOND analysis shows that the loading of Pds5 and other cohesion factors on replication forks is not affected by the BRCA2 status. Pds5 role in DNA replication is shared by the other cohesin-removal factor Wapl, but not by the cohesin complex component Rad21. Interestingly, depletion of Rad21 in a Pds5-deficient background rescues the phenotype observed upon Pds5 depletion alone. These findings support a model where loss of either component of the cohesin releasin complex perturbs cohesin dynamics on replication forks, hindering fork progression and promoting MRE11-dependent fork slowing.
Collapse
Affiliation(s)
- Denisse Carvajal-Maldonado
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Andrea K Byrum
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sarah Wessel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Delphine Lemaçon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Stephanie Tirman
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Simona Graziano
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Susana Gonzalo
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| |
Collapse
|
16
|
Villa-Hernández S, Bermejo R. Cohesin dynamic association to chromatin and interfacing with replication forks in genome integrity maintenance. Curr Genet 2018; 64:1005-1013. [PMID: 29549581 DOI: 10.1007/s00294-018-0824-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 01/09/2023]
Abstract
Proliferating cells need to accurately duplicate and pass their genetic material on to daughter cells. Problems during replication and partition challenge the structural and numerical integrity of chromosomes. Diverse mechanisms, as the DNA replication checkpoint, survey the correct progression of replication and couple it with other cell cycle events to preserve genome integrity. The structural maintenance of chromosomes (SMC) cohesin complex primarily contributes to chromosome duplication by mediating the tethering of newly replicated sister chromatids, thus assisting their equal segregation in mitosis. In addition, cohesin exerts important functions in genome organization, gene expression and DNA repair. These are determined by cohesin's ability to bring together different DNA segments and, hence, by the fashion and dynamics of its interaction with chromatin. It recently emerged that cohesin contributes to the protection of stalled replication forks through a mechanism requiring its timely mobilization from unreplicated DNA and relocation to nascent strands. This mechanism relies on DNA replication checkpoint-dependent cohesin ubiquitylation and promotes nascent sister chromatid entrapment, likely contributing to preserve stalled replisome-fork architectural integrity. Here we review how cohesin dynamic association to chromatin is controlled through post-translational modifications to dictate its functions during chromosome duplication. We also discuss recent insights on the mechanism that mediates interfacing of replisome components with chromatin-bound cohesin and its contribution to the establishment of sister chromatid cohesion and the protection of stalled replication forks.
Collapse
Affiliation(s)
- Sara Villa-Hernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040, Madrid, Spain
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040, Madrid, Spain.
| |
Collapse
|
17
|
Mehta G, Anbalagan GK, Bharati AP, Gadre P, Ghosh SK. An interplay between Shugoshin and Spo13 for centromeric cohesin protection and sister kinetochore mono-orientation during meiosis I in Saccharomyces cerevisiae. Curr Genet 2018; 64:1141-1152. [PMID: 29644457 DOI: 10.1007/s00294-018-0832-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Meiosis is a specialized cell division process by which haploid gametes are produced from a diploid mother cell. Reductional chromosome segregation during meiosis I (MI) is achieved by two unique and conserved events: centromeric cohesin protection (CCP) and sister kinetochore mono-orientation (SKM). In Saccharomyces cerevisiae, a meiosis-specific protein Spo13 plays a role in both these centromere-specific events. Despite genome-wide association of Spo13, we failed to detect its function in global processes such as cohesin loading, cohesion establishment and homologs pairing. While Shugoshin (Sgo1) and protein phosphatase 2A (PP2ARts1) play a central role in CCP, it is not fully understood whether Spo13 functions in the process through a Sgo1- PP2ARts1-dependent or -independent mechanism. To delineate this and to find the relative contribution of each of these proteins in CCP and SKM, we meticulously observed the sister chromatid segregation pattern in the wild type, sgo1Δ, rts1Δ and spo13Δ single mutants and in their respective double mutants. We found that Spo13 protects centromeric cohesin through a Sgo1- PP2ARts1-independent mechanism. To our surprise, we observed a hitherto unknown role of Sgo1 in SKM. Further investigation revealed that Sgo1-mediated recruitment of aurora kinase Ipl1 to the centromere facilitates monopolin loading at the kinetochore during MI. Hence, this study uncovers the role of Sgo1 in SKM and demonstartes how the regulators (Sgo1, PP2ARts1, Spo13) work in a coordinated manner to achieve faithful chromosome segregation during meiosis, the failure of which leads to aneuploidy and birth defects.
Collapse
Affiliation(s)
- Gunjan Mehta
- National Cancer Institute, National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | | | - Akhilendra Pratap Bharati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Purna Gadre
- B231, Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India.
| |
Collapse
|
18
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 PMCID: PMC5699866 DOI: 10.7554/elife.28231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 12/12/2022] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1’s function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment. Most of the DNA in a cell is stored in structures called chromosomes. During every cell cycle, each cell needs to replicate its chromosomes, hold the two chromosome copies (also known as “sister chromatids”) together before cell division, and distribute them equally to the two new cells. Each step must be executed accurately otherwise the new cells will have extra or missing chromosomes – a condition that is seen in many cancer cells and that can cause embryos to die. Since these processes are so essential to life, they are highly similar in a range of species, from single-celled organisms such as yeast to multicellular organisms like humans. However, it was not clear when and how sister chromatids first join together, or how this process is linked to DNA replication. The DNA in the sister chromatids is wrapped around proteins called histones to form a structure known as chromatin. An enzyme called Bre1 plays roles in gene transcription and DNA replication and repair by adding ubiquitin molecules to a histone called H2B. Now, by using genetic, molecular and cell biological approaches to study baker and brewer yeast cells, Zhang et al. show that the activity of Bre1 helps to hold sister chromatids together. Specifically, Bre1 recruits proteins to the chromatin before and during DNA replication, which help to initiate replication and to establish cohesion between the sister chromatids. The ubiquitin molecule attached to H2B by Bre1 is also essential for establishing cohesion, acting as a mark that helps to link the two processes. In the future it will be worthwhile to investigate whether genetic mutations that prevent sister chromatids adhering to each other is a major cause of the chromosome abnormalities seen in cancer cells. This knowledge may be useful for diagnosing cancers. Drugs that prevent the activity of Bre1 and other proteins involved in holding together sister chromatids could also be developed as potential cancer treatments that kill cancer cells by causing instability in their number of chromosomes.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
19
|
Zhang W, Yeung CHL, Wu L, Yuen KWY. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae. eLife 2017; 6:28231. [PMID: 29058668 DOI: 10.7554/elife.28231.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/22/2017] [Indexed: 05/25/2023] Open
Abstract
Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae, together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. Deletion of BRE1 or LGE1 also results in whole chromosome instability. We discovered a novel role for Bre1, Lge1 and H2Bub1 in chromosome segregation and sister chromatid cohesion. Bre1's function in G1 and S phases contributes to cohesion establishment, but it is not required for cohesion maintenance in G2 phase. Bre1 is dispensable for the loading of cohesin complex to chromatin in G1, but regulates the localization of replication factor Mcm10 and cohesion establishment factors Ctf4, Ctf18 and Eco1 to early replication origins in G1 and S phases, and promotes cohesin subunit Smc3 acetylation for cohesion stabilization. H2Bub1 epigenetically marks the origins, potentially signaling the coupling of DNA replication and cohesion establishment.
Collapse
Affiliation(s)
- Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | | | - Liwen Wu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
20
|
Rizvi SMA, Prajapati HK, Ghosh SK. The 2 micron plasmid: a selfish genetic element with an optimized survival strategy within Saccharomyces cerevisiae. Curr Genet 2017; 64:25-42. [PMID: 28597305 DOI: 10.1007/s00294-017-0719-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 11/27/2022]
Abstract
Since its discovery in the early 70s, the 2 micron plasmid of Saccharomyces cerevisiae continues to intrigue researchers with its high protein-coding capacity and a selfish nature yet high stability, earning it the title of a 'miniaturized selfish genetic element'. It codes for four proteins (Rep1, Rep2, Raf1, and Flp) vital for its own survival and recruits several host factors (RSC2, Cohesin, Cse4, Kip1, Bik1, Bim1, and microtubules) for its faithful segregation during cell division. The plasmid maintains a high-copy number with the help of Flp-mediated recombination. The plasmids organize in the form of clusters that hitch-hike the host chromosomes presumably with the help of the plasmid-encoded Rep proteins and host factors such as microtubules, Kip1 motor, and microtubule-associated proteins Bik1 and Bim1. Although there is no known yeast cell phenotype associated with the 2 micron plasmid, excessive copies of the plasmid are lethal for the cells, warranting a tight control over the plasmid copy number. This control is achieved through a combination of feedback loops involving the 2 micron encoded proteins. Thus, faithful segregation and a concomitant tightly controlled plasmid copy number ensure an optimized benign parasitism of the 2 micron plasmid within budding yeast.
Collapse
Affiliation(s)
- Syed Meraj Azhar Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Hemant Kumar Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India.
| |
Collapse
|
21
|
Montaño-Gutierrez LF, Ohta S, Kustatscher G, Earnshaw WC, Rappsilber J. Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data. Mol Biol Cell 2017; 28:673-680. [PMID: 28057767 PMCID: PMC5328625 DOI: 10.1091/mbc.e16-06-0370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 11/30/2022] Open
Abstract
Nano Random Forests is a machine learning-based approach to extract valuable information about multiprotein complexes in collections of proteomics experiments. In mitotic chromosome data, it retrieves known relationships among kinetochore substructures and provides highly specific predictions about uncharacterized protein function. Ever-increasing numbers of quantitative proteomics data sets constitute an underexploited resource for investigating protein function. Multiprotein complexes often follow consistent trends in these experiments, which could provide insights about their biology. Yet, as more experiments are considered, a complex’s signature may become conditional and less identifiable. Previously we successfully distinguished the general proteomic signature of genuine chromosomal proteins from hitchhikers using the Random Forests (RF) machine learning algorithm. Here we test whether small protein complexes can define distinguishable signatures of their own, despite the assumption that machine learning needs large training sets. We show, with simulated and real proteomics data, that RF can detect small protein complexes and relationships between them. We identify several complexes in quantitative proteomics results of wild-type and knockout mitotic chromosomes. Other proteins covary strongly with these complexes, suggesting novel functional links for later study. Integrating the RF analysis for several complexes reveals known interdependences among kinetochore subunits and a novel dependence between the inner kinetochore and condensin. Ribosomal proteins, although identified, remained independent of kinetochore subcomplexes. Together these results show that this complex-oriented RF (NanoRF) approach can integrate proteomics data to uncover subtle protein relationships. Our NanoRF pipeline is available online.
Collapse
Affiliation(s)
- Luis F Montaño-Gutierrez
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Shinya Ohta
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.,Center for Innovative and Translational Medicine, Medical School, Kochi University, Kochi 783-8505, Japan
| | - Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom .,Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| |
Collapse
|
22
|
Kumar R. Separase: Function Beyond Cohesion Cleavage and an Emerging Oncogene. J Cell Biochem 2017; 118:1283-1299. [PMID: 27966791 DOI: 10.1002/jcb.25835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
Proper and timely segregation of genetic endowment is necessary for survival and perpetuation of every species. Mis-segregation of chromosomes and resulting aneuploidy leads to genetic instability, which can jeopardize the survival of an individual or population as a whole. Abnormality with segregation of genetic contents has been associated with several medical consequences including cancer, sterility, mental retardation, spontaneous abortion, miscarriages, and other birth related defects. Separase, by irreversible cleavage of cohesin complex subunit, paves the way for metaphase/anaphase transition during the cell cycle. Both over or reduced expression and altered level of separase have been associated with several medical consequences including cancer, as a result separase now emerges as an important oncogene and potential molecular target for medical intervenes. Recently, separase is also found to be essential in separation and duplication of centrioles. Here, I review the role of separase in mitosis, meiosis, non-canonical roles of separase, separase regulation, as a regulator of centriole disengagement, nonproteolytic roles, diverse substrates, structural insights, and association of separase with cancer. At the ends, I proposed a model which showed that separase is active throughout the cell cycle and there is a mere increase in separase activity during metaphase contrary to the common believes that separase is inactive throughout cell cycle except for metaphase. J. Cell. Biochem. 118: 1283-1299, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, Maharashtra, India
| |
Collapse
|
23
|
Agostinho A, Höög C. REC8 density along chromosomes prevents illegitimate synapsis. Cell Cycle 2016; 15:2543-2544. [PMID: 27359070 DOI: 10.1080/15384101.2016.1204853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Ana Agostinho
- a Department of Cell and Molecular Biology , Karolinska Institutet , Stockholm , Sweden
| | - Christer Höög
- a Department of Cell and Molecular Biology , Karolinska Institutet , Stockholm , Sweden
| |
Collapse
|
24
|
Kim HS, Fernandes G, Lee CW. Protein Phosphatases Involved in Regulating Mitosis: Facts and Hypotheses. Mol Cells 2016; 39:654-62. [PMID: 27669825 PMCID: PMC5050529 DOI: 10.14348/molcells.2016.0214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 12/19/2022] Open
Abstract
Almost all eukaryotic proteins are subject to post-translational modifications during mitosis and cell cycle, and in particular, reversible phosphorylation being a key event. The recent use of high-throughput experimental analyses has revealed that more than 70% of all eukaryotic proteins are regulated by phosphorylation; however, the mechanism of dephosphorylation, counteracting phosphorylation, is relatively unknown. Recent discoveries have shown that many of the protein phosphatases are involved in the temporal and spatial control of mitotic events, such as mitotic entry, mitotic spindle assembly, chromosome architecture changes and cohesion, and mitotic exit. This implies that certain phosphatases are tightly regulated for timely dephosphorylation of key mitotic phosphoproteins and are essential for control of various mitotic processes. This review describes the physiological and pathological roles of mitotic phosphatases, as well as the versatile role of various protein phosphatases in several mitotic events.
Collapse
Affiliation(s)
- Hyun-Soo Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419,
Korea
| | - Gary Fernandes
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419,
Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419,
Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351,
Korea
| |
Collapse
|
25
|
Abstract
Heterochromatin is the transcriptionally repressed portion of eukaryotic chromatin that maintains a condensed appearance throughout the cell cycle. At sites of ribosomal DNA (rDNA) heterochromatin, epigenetic states contribute to gene silencing and genome stability, which are required for proper chromosome segregation and a normal life span. Here, we focus on recent advances in the epigenetic regulation of rDNA silencing in Saccharomyces cerevisiae and in mammals, including regulation by several histone modifications and several protein components associated with the inner nuclear membrane within the nucleolus. Finally, we discuss the perturbations of rDNA epigenetic pathways in regulating cellular aging and in causing various types of diseases.
Collapse
|
26
|
The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells. Microbiol Spectr 2016; 2. [PMID: 25541598 DOI: 10.1128/microbiolspec.plas-0003-2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.
Collapse
|
27
|
Turner RL, Groitl P, Dobner T, Ornelles DA. Adenovirus replaces mitotic checkpoint controls. J Virol 2015; 89:5083-96. [PMID: 25694601 PMCID: PMC4403466 DOI: 10.1128/jvi.00213-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/17/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Infection with adenovirus triggers the cellular DNA damage response, elements of which include cell death and cell cycle arrest. Early adenoviral proteins, including the E1B-55K and E4orf3 proteins, inhibit signaling in response to DNA damage. A fraction of cells infected with an adenovirus mutant unable to express the E1B-55K and E4orf3 genes appeared to arrest in a mitotic-like state. Cells infected early in G1 of the cell cycle were predisposed to arrest in this state at late times of infection. This arrested state, which displays hallmarks of mitotic catastrophe, was prevented by expression of either the E1B-55K or the E4orf3 genes. However, E1B-55K mutant virus-infected cells became trapped in a mitotic-like state in the presence of the microtubule poison colcemid, suggesting that the two viral proteins restrict entry into mitosis or facilitate exit from mitosis in order to prevent infected cells from arresting in mitosis. The E1B-55K protein appeared to prevent inappropriate entry into mitosis through its interaction with the cellular tumor suppressor protein p53. The E4orf3 protein facilitated exit from mitosis by possibly mislocalizing and functionally inactivating cyclin B1. When expressed in noninfected cells, E4orf3 overcame the mitotic arrest caused by the degradation-resistant R42A cyclin B1 variant. IMPORTANCE Cells that are infected with adenovirus type 5 early in G1 of the cell cycle are predisposed to arrest in a mitotic-like state in a p53-dependent manner. The adenoviral E1B-55K protein prevents entry into mitosis. This newly described activity for the E1B-55K protein appears to depend on the interaction between the E1B-55K protein and the tumor suppressor p53. The adenoviral E4orf3 protein facilitates exit from mitosis, possibly by altering the intracellular distribution of cyclin B1. By preventing entry into mitosis and by promoting exit from mitosis, these adenoviral proteins act to prevent the infected cell from arresting in a mitotic-like state.
Collapse
Affiliation(s)
- Roberta L Turner
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Peter Groitl
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Thomas Dobner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - David A Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| |
Collapse
|
28
|
Sun L, Hartson SD, Matts RL. Identification of proteins associated with Aha1 in HeLa cells by quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:365-80. [PMID: 25614414 DOI: 10.1016/j.bbapap.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/20/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023]
Abstract
The identification of the activator of heat shock protein 90 (Hsp90) ATPase's (Aha1) protein-protein interaction (PPI) network will provide critical insights into the relationship of Aha1 with multi-molecular complexes and shed light onto Aha1's interconnections with Hsp90-regulated biological functions. Flag-tagged Aha1 was over-expressed in HeLa cells and isolated by anti-Flag affinity pull downs, followed by trypsin digestion and identification co-adsorbing proteins by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). A probability-based identification of Aha1 PPIs was generated from the LC-MS/MS analysis by using a relative quantification strategy, spectral counting (SC). By comparing the SC-based protein levels between Aha1 pull-down samples and negative controls, 164 Aha1-interacting proteins were identified that were quantitatively enriched in the pull-down samples over the controls. The identified Aha1-interacting proteins are involved in a wide number of intracellular bioprocesses, including DNA maintenance, chromatin structure, RNA processing, translation, nucleocytoplasmic and vesicle transport, among others. The interactions of 33 of the identified proteins with Aha1 were further confirmed by Western blotting, demonstrating the reliability of our affinity-purification-coupled quantitative SC-MS strategy. Our proteomic data suggests that Aha1 may participate in diverse biological pathways to facilitate Hsp90 chaperone functions in response to stress.
Collapse
Affiliation(s)
- Liang Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| |
Collapse
|
29
|
Agarwal M, Mehta G, Ghosh SK. Role of Ctf3 and COMA subcomplexes in meiosis: Implication in maintaining Cse4 at the centromere and numeric spindle poles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:671-84. [PMID: 25562757 DOI: 10.1016/j.bbamcr.2014.12.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/24/2014] [Accepted: 12/29/2014] [Indexed: 12/16/2022]
Abstract
During mitosis and meiosis, kinetochore, a conserved multi-protein complex, connects microtubule with the centromere and promotes segregation of the chromosomes. In budding yeast, central kinetochore complex named Ctf19 has been implicated in various functions and is believed to be made up of three biochemically distinct subcomplexes: COMA, Ctf3 and Iml3-Chl4. In this study, we aimed to identify whether Ctf3 and COMA subcomplexes have any unshared function at the kinetochore. Our data suggests that both these subcomplexes may work as a single functional unit without any unique functions, which we tested. Analysis of severity of the defects in the mutants suggests that COMA is epistatic to Ctf3 subcomplex. Interestingly, we noticed that these subcomplexes affect the organization of mitotic and meiotic kinetochores with subtle differences and they promote maintenance of Cse4 at the centromeres specifically during meiosis which is similar to the role of Mis6 (Ctf3 homolog) in fission yeast during mitosis. Interestingly, analysis of ctf3Δ and ctf19Δ mutants revealed a novel role of Ctf19 complex in regulation of SPB cohesion and duplication in meiosis.
Collapse
Affiliation(s)
- Meenakshi Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India
| | - Gunjan Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India.
| |
Collapse
|
30
|
de Mendonca POR, Costa IC, Lotfi CFP. The involvement of Nek2 and Notch in the proliferation of rat adrenal cortex triggered by POMC-derived peptides. PLoS One 2014; 9:e108657. [PMID: 25279464 PMCID: PMC4184836 DOI: 10.1371/journal.pone.0108657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
The adrenal gland is a dynamic organ that undergoes constant cell turnover. This allows for rapid organ remodeling in response to the physiological demands of the HPA axis, which is controlled by proopiomelanocortin (POMC)-derived peptides, such as adrenocorticotropic hormone (ACTH) and N-Terminal peptides (N-POMC). In the rat adrenal cortex, POMC-derived peptides trigger a mitogenic effect, and this process increases cyclins D and E, while inhibiting p27Kip1. The goal of the present study was to further explore the mitogenic effect of ACTH and synthetic N-POMC1–28 peptides by investigating the differences in the expression of key genes involved in the cell cycle of the rat adrenal cortex, following inhibition of the HPA axis. Moreover, we evaluated the differences between the inner and outer fractions of the adrenal cortex (ZF-fraction and ZG-fraction) in terms of their response patterns to different stimuli. In the current study, the inhibition of the HPA axis repressed the expression of Ccnb2, Camk2a, and Nek2 genes throughout the adrenal cortex, while treatments with POMC-derived peptides stimulated Nek2, gene and protein expression, and Notch2 gene expression. Furthermore, Notch1 protein expression was restricted to the subcapsular region of the cortex, an area of the adrenal cortex that is well-known for proliferation. We also showed that different regions of the adrenal cortex respond to HPA-axis inhibition and to induction with POMC-derived peptides at different times. These results suggest that cells in the ZG and ZF fractions could be at different phases of the cell cycle. Our results contribute to the understanding of the mechanisms involved in cell cycle regulation in adrenocortical cells triggered by N-POMC peptides and ACTH, and highlight the involvement of genes such as Nek2 and Notch.
Collapse
Affiliation(s)
| | - Ismael Cabral Costa
- Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | |
Collapse
|
31
|
The origins and processing of ultra fine anaphase DNA bridges. Curr Opin Genet Dev 2014; 26:1-5. [PMID: 24795279 DOI: 10.1016/j.gde.2014.03.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/13/2014] [Accepted: 03/12/2014] [Indexed: 01/26/2023]
Abstract
Ultra-fine DNA bridges (UFBs) are a recently identified class of mitotic DNA structures that cannot be visualized using conventional DNA staining methods (e.g. using DAPI). Their existence can currently only be revealed by immuno-fluorescent staining for proteins that bind to them, including PICH and BLM. UFBs become visible in the anaphase of mitosis, and can persist into telophase in rare cases. There are at least three different types of UFBs that can be distinguished according to the chromosomal loci from which they originate. However, it remains largely unknown how these UFBs are generated or resolved in the cell. In this article, we will review our current understanding of different types of UFBs and the potential functional role of the proteins that have been shown to be associated with them.
Collapse
|
32
|
Caburet S, Arboleda VA, Llano E, Overbeek PA, Barbero JL, Oka K, Harrison W, Vaiman D, Ben-Neriah Z, García-Tuñón I, Fellous M, Pendás AM, Veitia RA, Vilain E. Mutant cohesin in premature ovarian failure. N Engl J Med 2014; 370:943-949. [PMID: 24597867 PMCID: PMC4068824 DOI: 10.1056/nejmoa1309635] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Premature ovarian failure is a major cause of female infertility. The genetic causes of this disorder remain unknown in most patients. Using whole-exome sequence analysis of a large consanguineous family with inherited premature ovarian failure, we identified a homozygous 1-bp deletion inducing a frameshift mutation in STAG3 on chromosome 7. STAG3 encodes a meiosis-specific subunit of the cohesin ring, which ensures correct sister chromatid cohesion. Female mice devoid of Stag3 are sterile, and their fetal oocytes are arrested at early prophase I, leading to oocyte depletion at 1 week of age.
Collapse
Affiliation(s)
- Sandrine Caburet
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Valerie A Arboleda
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Elena Llano
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Paul A Overbeek
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Jose Luis Barbero
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Kazuhiro Oka
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Wilbur Harrison
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Daniel Vaiman
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Ziva Ben-Neriah
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Ignacio García-Tuñón
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Marc Fellous
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Alberto M Pendás
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Reiner A Veitia
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| | - Eric Vilain
- Institut Jacques Monod, Université Paris Diderot (S.C., M.F., R.A.V.), and Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, INSERM (D.V., M.F.) - both in Paris; the Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles (V.A.A., E.V.); Departamento de Fisiología y Farmacología, Universidad de Salamanca (E.L.), and Instituto de Biología Molecular y Celular del Cáncer (E.L., I.G.-T., A.M.P.) - both in Salaman ca, Spain; the Department of Molecular Cellular Biology, Baylor College of Medicine, Houston (P.A.O., K.O., W.H.); Centro de In vestigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid (J.L.B.); and the Department of Genetics, Hadassah University Hospital, Jerusalem (Z.B.-N.)
| |
Collapse
|
33
|
Wood AM, Garza-Gongora AG, Kosak ST. A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:178-90. [PMID: 24412853 PMCID: PMC3954575 DOI: 10.1016/j.bbagrm.2014.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 01/14/2023]
Abstract
The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
Collapse
Affiliation(s)
- Ashley M Wood
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arturo G Garza-Gongora
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
34
|
Mehta GD, Agarwal M, Ghosh SK. Functional characterization of kinetochore protein, Ctf19 in meiosis I: an implication of differential impact of Ctf19 on the assembly of mitotic and meiotic kinetochores in Saccharomyces cerevisiae. Mol Microbiol 2014; 91:1179-99. [PMID: 24446862 DOI: 10.1111/mmi.12527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 11/29/2022]
Abstract
Meiosis is a specialized cell division process through which chromosome numbers are reduced by half for the generation of gametes. Kinetochore, a multiprotein complex that connects centromeres to microtubules, plays essential role in chromosome segregation. Ctf19 is the key central kinetochore protein that recruits all the other non-essential proteins of the Ctf19 complex in budding yeast. Earlier studies have shown the role of Ctf19 complex in enrichment of cohesin around the centromeres both during mitosis and meiosis, leading to sister chromatid cohesion and meiosis II disjunction. Here we show that Ctf19 is also essential for the proper execution of the meiosis I specific unique events, such as non-homologous centromere coupling, homologue pairing, chiasmata resolution and proper orientation of homologues and sister chromatids with respect to the spindle poles. Additionally, this investigation reveals that proper kinetochore function is required for faithful chromosome condensation in meiosis. Finally, this study suggests that absence of Ctf19 affects the integrity of meiotic kinetochore differently than that of the mitotic kinetochore. Consequently, absence of Ctf19 leads to gross chromosome missegregation during meiosis as compared with mitosis. Hence, this study reports for the first time the differential impact of a non-essential kinetochore protein on the mitotic and meiotic kinetochore ensembles and hence chromosome segregation.
Collapse
Affiliation(s)
- Gunjan D Mehta
- Department of Biosciences and Bioengineering, Wadhawani Research Centre of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 40076, India
| | | | | |
Collapse
|
35
|
Jiang R, Gao ZL, Sun M, Zhang XY, Wang JC, Wu H. Zinc finger X-chromosomal protein promotes growth and tumorigenesis in human osteosarcoma cells. Pak J Med Sci 2013; 29:997-1002. [PMID: 24353675 PMCID: PMC3817752 DOI: 10.12669/pjms.294.3498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/19/2013] [Accepted: 06/13/2013] [Indexed: 11/22/2022] Open
Abstract
Objective: To investigate the role of Zinc finger X-chromosomal protein (ZFX) in oncogenesis of Osteosarcoma tumor. Methods: Here, we first conducted an expression analysis of ZFX in Osteosarcoma cell lines. Then, we constructed ZFX-specific small interfering RNA (siRNA)-lentiviral vector that is capable of effectively inhibiting the expression of ZFX gene in human Osteosarcoma Saos-2 cells, and investigated systemically the impacts of ZFX silence on the growth and invasive ability of the cancer cells in vitro. Furthermore, we determined the effects of ZFX knockdown on the cell cycle distribution and apoptosis of Saos-2 cells. Results: We found that ZFX inhibition resulted in significantly impaired proliferation and colony formation as well as mitigated invasiveness of Saos-2 cells. Importantly, si-ZFX infected cells exhibited a greater portion of cells at G1 phase, but a minor portion of S and G2/M phase cells. Moreover, a greater portion of sub-G1 apoptotic cells was observed in si-ZFX infected cells. Conclusions: These results strongly suggest that ZFX is a novel proliferation regulator that promotes growth of Osteosarcoma cells, and downregulation of ZFX expression induces growth suppression of Saos-2 cells via arrested G0/G1 phase cell cycle and apoptosis pathways, thereby indicating that ZFX may serve as a new molecular target for Osteosarcoma tumor therapy.
Collapse
Affiliation(s)
- Rui Jiang
- Rui Jiang, Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, PR China
| | - Zhong-Li Gao
- Zhong-li Gao, Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, PR China
| | - Mei Sun
- Mei Sun, Department of Pathology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun 130041, PR China
| | - Xing-Yi Zhang
- Xing-yi Zhang, Department of Thoracic Surgery, Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, PR China
| | - Jin-Cheng Wang
- Jin-chengWang, Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, PR China
| | - Han Wu
- Han Wu Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun 130033, PR China
| |
Collapse
|
36
|
Miles S, Li L, Davison J, Breeden LL. Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet 2013; 9:e1003854. [PMID: 24204289 PMCID: PMC3814307 DOI: 10.1371/journal.pgen.1003854] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/19/2013] [Indexed: 01/03/2023] Open
Abstract
Pure populations of quiescent yeast can be obtained from stationary phase cultures that have ceased proliferation after exhausting glucose and other carbon sources from their environment. They are uniformly arrested in the G1 phase of the cell cycle, and display very high thermo-tolerance and longevity. We find that G1 arrest is initiated before all the glucose has been scavenged from the media. Maintaining G1 arrest requires transcriptional repression of the G1 cyclin, CLN3, by Xbp1. Xbp1 is induced as glucose is depleted and it is among the most abundant transcripts in quiescent cells. Xbp1 binds and represses CLN3 transcription and in the absence of Xbp1, or with extra copies of CLN3, cells undergo ectopic divisions and produce very small cells. The Rad53-mediated replication stress checkpoint reinforces the arrest and becomes essential when Cln3 is overproduced. The XBP1 transcript also undergoes metabolic oscillations under glucose limitation and we identified many additional transcripts that oscillate out of phase with XBP1 and have Xbp1 binding sites in their promoters. Further global analysis revealed that Xbp1 represses 15% of all yeast genes as they enter the quiescent state and over 500 of these transcripts contain Xbp1 binding sites in their promoters. Xbp1-repressed transcripts are highly enriched for genes involved in the regulation of cell growth, cell division and metabolism. Failure to repress some or all of these targets leads xbp1 cells to enter a permanent arrest or senescence with a shortened lifespan. Complex organisms depend on populations of non-dividing quiescent cells for their controlled growth, development and tissue renewal. These quiescent cells are maintained in a resting state, and divide only when stimulated to do so. Unscheduled exit or failure to enter this quiescent state results in uncontrolled proliferation and cancer. Yeast cells also enter a stable, protected and reversible quiescent state. As with higher cells, they exit the cell cycle from G1, reduce growth, conserve and recycle cellular contents. These similarities, and the fact that the mechanisms that start and stop the cell cycle are fundamentally conserved lead us to think that understanding how yeast enter, maintain and reverse quiescence could give important leads into the same processes in complex organisms. We show that yeast cells maintain G1 arrest by expressing a transcription factor that represses conserved activators (cyclins) and hundreds of other genes that are important for cell division and cell growth. Failure to repress some or all of these targets leads to extra cell divisions, prevents reversible arrest and shortens life span. Many Xbp1 targets are conserved cell cycle regulators and may also be actively repressed in the quiescent cells of more complex organisms.
Collapse
Affiliation(s)
- Shawna Miles
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lihong Li
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jerry Davison
- Computational Biology, Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda L. Breeden
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
37
|
Mehta GD, Kumar R, Srivastava S, Ghosh SK. Cohesin: functions beyond sister chromatid cohesion. FEBS Lett 2013; 587:2299-312. [PMID: 23831059 DOI: 10.1016/j.febslet.2013.06.035] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/24/2013] [Indexed: 11/22/2022]
Abstract
Faithful segregation of chromosomes during mitosis and meiosis is the cornerstone process of life. Cohesin, a multi-protein complex conserved from yeast to human, plays a crucial role in this process by keeping the sister chromatids together from S-phase to anaphase onset during mitosis and meiosis. Technological advancements have discovered myriad functions of cohesin beyond its role in sister chromatid cohesion (SCC), such as transcription regulation, DNA repair, chromosome condensation, homolog pairing, monoorientation of sister kinetochore, etc. Here, we have focused on such functions of cohesin that are either independent of or dependent on its canonical role of sister chromatid cohesion. At the end, human diseases associated with malfunctioning of cohesin, albeit with mostly unperturbed sister chromatid cohesion, have been discussed.
Collapse
Affiliation(s)
- Gunjan D Mehta
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai 400076, India
| | | | | | | |
Collapse
|
38
|
Sousounis K, Looso M, Maki N, Ivester CJ, Braun T, Tsonis PA. Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns. PLoS One 2013; 8:e61445. [PMID: 23613853 PMCID: PMC3628982 DOI: 10.1371/journal.pone.0061445] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/09/2013] [Indexed: 12/11/2022] Open
Abstract
Regeneration of the lens in newts is quite a unique process. The lens is removed in its entirety and regeneration ensues from the pigment epithelial cells of the dorsal iris via transdifferentiation. The same type of cells from the ventral iris are not capable of regenerating a lens. It is, thus, expected that differences between dorsal and ventral iris during the process of regeneration might provide important clues pertaining to the mechanism of regeneration. In this paper, we employed next generation RNA-seq to determine gene expression patterns during lens regeneration in Notophthalmus viridescens. The expression of more than 38,000 transcripts was compared between dorsal and ventral iris. Although very few genes were found to be dorsal- or ventral-specific, certain groups of genes were up-regulated specifically in the dorsal iris. These genes are involved in cell cycle, gene regulation, cytoskeleton and immune response. In addition, the expression of six highly regulated genes, TBX5, FGF10, UNC5B, VAX2, NR2F5, and NTN1, was verified using qRT-PCR. These graded gene expression patterns provide insight into the mechanism of lens regeneration, the markers that are specific to dorsal or ventral iris, and layout a map for future studies in the field.
Collapse
Affiliation(s)
- Konstantinos Sousounis
- Department of Biology and Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, Ohio, United States of America
| | - Mario Looso
- Department of Bioinformatics, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Nobuyasu Maki
- Department of Biology and Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, Ohio, United States of America
| | - Clifford J. Ivester
- Department of Biology and Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, Ohio, United States of America
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail: (TB); (PAT)
| | - Panagiotis A. Tsonis
- Department of Biology and Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, Ohio, United States of America
- * E-mail: (TB); (PAT)
| |
Collapse
|
39
|
Wassmann K. Sister chromatid segregation in meiosis II: deprotection through phosphorylation. Cell Cycle 2013; 12:1352-9. [PMID: 23574717 DOI: 10.4161/cc.24600] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Meiotic divisions (meiosis I and II) are specialized cell divisions to generate haploid gametes. The first meiotic division with the separation of chromosomes is named reductional division. The second division, which takes place immediately after meiosis I without intervening S-phase, is equational, with the separation of sister chromatids, similar to mitosis. This meiotic segregation pattern requires the two-step removal of the cohesin complex holding sister chromatids together: cohesin is removed from chromosome arms that have been subjected to homologous recombination in meiosis I and from the centromere region in meiosis II. Cohesin in the centromere region is protected from removal in meiosis I, but this protection has to be removed--deprotected--for sister chromatid segregation in meiosis II. Whereas the mechanisms of cohesin protection are quite well understood, the mechanisms of deprotection have been largely unknown until recently. In this review I summarize our current knowledge on cohesin deprotection.
Collapse
|
40
|
Horsfield JA, Print CG, Mönnich M. Diverse developmental disorders from the one ring: distinct molecular pathways underlie the cohesinopathies. Front Genet 2012; 3:171. [PMID: 22988450 PMCID: PMC3439829 DOI: 10.3389/fgene.2012.00171] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/17/2012] [Indexed: 11/13/2022] Open
Abstract
The multi-subunit protein complex, cohesin, is responsible for sister chromatid cohesion during cell division. The interaction of cohesin with DNA is controlled by a number of additional regulatory proteins. Mutations in cohesin, or its regulators, cause a spectrum of human developmental syndromes known as the “cohesinopathies.” Cohesinopathy disorders include Cornelia de Lange Syndrome and Roberts Syndrome. The discovery of novel roles for chromatid cohesion proteins in regulating gene expression led to the idea that cohesinopathies are caused by dysregulation of multiple genes downstream of mutations in cohesion proteins. Consistent with this idea, Drosophila, mouse, and zebrafish cohesinopathy models all show altered expression of developmental genes. However, there appears to be incomplete overlap among dysregulated genes downstream of mutations in different components of the cohesion apparatus. This is surprising because mutations in all cohesion proteins would be predicted to affect cohesin’s roles in cell division and gene expression in similar ways. Here we review the differences and similarities between genetic pathways downstream of components of the cohesion apparatus, and discuss how such differences might arise, and contribute to the spectrum of cohesinopathy disorders. We propose that mutations in different elements of the cohesion apparatus have distinct developmental outcomes that can be explained by sometimes subtly different molecular effects.
Collapse
Affiliation(s)
- Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago Dunedin, New Zealand
| | | | | |
Collapse
|