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https://www.readbyqxmd.com/read/27924829/diverse-specificity-of-cellulosome-attachment-to-the-bacterial-cell-surface
#1
Joana L A Brás, Benedita A Pinheiro, Kate Cameron, Fiona Cuskin, Aldino Viegas, Shabir Najmudin, Pedro Bule, Virginia M R Pires, Maria João Romão, Edward A Bayer, Holly L Spencer, Steven Smith, Harry J Gilbert, Victor D Alves, Ana Luísa Carvalho, Carlos M G A Fontes
During the course of evolution, the cellulosome, one of Nature's most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924011/roles-for-aprin-pds5b-in-homologous-recombination-and-in-ovarian-cancer-prediction
#2
Anthony M Couturier, Hubert Fleury, Anne-Marie Patenaude, Victoria L Bentley, Amélie Rodrigue, Yan Coulombe, Joshi Niraj, Joris Pauty, Jason N Berman, Graham Dellaire, Javier M Di Noia, Anne-Marie Mes-Masson, Jean-Yves Masson
APRIN (PDS5 cohesin associated factor B) interacts with both the cohesin complex and the BRCA2 tumor suppressor. How APRIN influences cohesion and DNA repair processes is not well understood. Here, we show that APRIN is recruited to DNA damage sites. We find that APRIN interacts directly with RAD51, PALB2 and BRCA2. APRIN stimulates RAD51-mediated DNA strand invasion. APRIN also binds DNA with an affinity for D-loop structures and single-strand (ss) DNA. APRIN is a new homologous recombination (HR) mediator as it counteracts the RPA inhibitory effect on RAD51 loading to ssDNA...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27917322/bioinformatical-analysis-of-eukaryotic-shugoshins-reveals-meiosis-specific-features-of-vertebrate-shugoshins
#3
Tatiana M Grishaeva, Darya Kulichenko, Yuri F Bogdanov
BACKGROUND: Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms. METHODS: A bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed...
2016: PeerJ
https://www.readbyqxmd.com/read/27916662/acetylation-of-pcna-sliding-surface-by-eco1-promotes-genome-stability-through-homologous-recombination
#4
Pierre Billon, Jian Li, Jean-Philippe Lambert, Yizhang Chen, Véronique Tremblay, Joseph S Brunzelle, Anne-Claude Gingras, Alain Verreault, Tomohiko Sugiyama, Jean-Francois Couture, Jacques Côté
During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage...
November 16, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27916276/a-surveillance-mechanism-ensures-repair-of-dna-lesions-during-zygotic-reprogramming
#5
Sabrina Ladstätter, Kikuë Tachibana-Konwalski
Sexual reproduction culminates in a totipotent zygote with the potential to produce a whole organism. Sperm chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications generate a totipotent embryo. Active DNA demethylation of the paternal genome has been proposed to involve base excision and DNA repair-based mechanisms. The nature and consequence of DNA lesions generated during reprogramming are not known. Using mouse genetics and chemical biology, we discovered that Tet3-dependent zygotic reprogramming generates paternal DNA lesions that are monitored by a surveillance mechanism...
November 21, 2016: Cell
https://www.readbyqxmd.com/read/27906978/correction-of-rings-and-rods-regulating-cohesin-entrapment-of-dna-to-generate-intra-and-intermolecular-tethers
#6
Robert V Skibbens
[This corrects the article DOI: 10.1371/journal.pgen.1006337.].
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27906670/stag3-regulates-microtubule-stability-to-maintain-euploidy-during-mouse-oocyte-meiotic-maturation
#7
Mianqun Zhang, Xiaoxin Dai, Yalu Sun, Yajuan Lu, Changyin Zhou, Yilong Miao, Ying Wang, Bo Xiong
Stag3, a meiosis-specific subunit of cohesin complex, has been demonstrated to function in both male and female reproductive systems in mammals. However, its roles during oocyte meiotic maturation have not been fully defined. In the present study, we report that Stag3 uniquely accumulates on the spindle apparatus and colocalizes with microtubule fibers during mouse oocyte meiotic maturation. Depletion of Stag3 by gene-targeting morpholino disrupts normal spindle assembly and chromosome alignment in oocytes...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27889450/rpa-mediates-recruitment-of-mrx-to-forks-and-double-strand-breaks-to-hold-sister-chromatids-together
#8
Andrew Seeber, Anna Maria Hegnauer, Nicole Hustedt, Ishan Deshpande, Jérôme Poli, Jan Eglinger, Philippe Pasero, Heinz Gut, Miki Shinohara, Karl-Peter Hopfner, Kenji Shimada, Susan M Gasser
The Mre11-Rad50-Xrs2 (MRX) complex is related to SMC complexes that form rings capable of holding two distinct DNA strands together. MRX functions at stalled replication forks and double-strand breaks (DSBs). A mutation in the N-terminal OB fold of the 70 kDa subunit of yeast replication protein A, rfa1-t11, abrogates MRX recruitment to both types of DNA damage. The rfa1 mutation is functionally epistatic with loss of any of the MRX subunits for survival of replication fork stress or DSB recovery, although it does not compromise end-resection...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27880868/origin-and-evolution-of-the-metazoan-non-coding-regulatory-genome
#9
REVIEW
Federico Gaiti, Andrew D Calcino, Miloš Tanurdžić, Bernard M Degnan
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa...
November 20, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27875311/single-binding-mode-integration-of-hemicellulose-degrading-enzymes-via-adaptor-scaffoldins-in-ruminococcus-flavefaciens-cellulosome
#10
Pedro Bule, Victor Diogo Alves, André Leitão, Luis M A Ferreira, Edward A Bayer, Steven P Smith, Harry J Gilbert, Shabir Najmudin, Carlos M G A Fontes
The assembly of one of Nature most elaborate multi-enzyme complexes, the cellulosome, results from the binding of enzyme-borne dockerins to reiterated cohesin domains located in a non-catalytic primary scaffoldin. Generally, dockerins present two similar cohesin binding interfaces that support a dual binding mode. The dynamic integration of enzymes in cellulosomes, afforded by the dual binding mode, is believed to incorporate additional flexibility in highly populated multi-enzyme complexes. Ruminococcus flavefaciens, the primary degrader of plant structural carbohydrates in the rumen of mammals, uses a portfolio of more than 220 different enzymes to assemble the most intricate cellulosome known to date...
November 14, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27872142/cohesin-acetylation-and-wapl-pds5-oppositely-regulate-translocation-of-cohesin-along-dna
#11
Mai Kanke, Eri Tahara, Pim J Huis In't Veld, Tomoko Nishiyama
Cohesin is a ring-shaped protein complex that plays a crucial role in sister chromatid cohesion and gene expression. The dynamic association of cohesin with chromatin is essential for these functions. However, the exact nature of cohesin dynamics, particularly cohesin translocation, remains unclear. We evaluated the dynamics of individual cohesin molecules on DNA and found that the cohesin core complex possesses an intrinsic ability to traverse DNA in an adenosine triphosphatase (ATPase)-dependent manner. Translocation ability is suppressed in the presence of Wapl-Pds5 and Sororin; this suppression is alleviated by the acetylation of cohesin and the action of mitotic kinases...
November 21, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27863240/insulated-neighborhoods-structural-and-functional-units-of-mammalian-gene-control
#12
REVIEW
Denes Hnisz, Daniel S Day, Richard A Young
Understanding how transcriptional enhancers control over 20,000 protein-coding genes to maintain cell-type-specific gene expression programs in all human cells is a fundamental challenge in regulatory biology. Recent studies suggest that gene regulatory elements and their target genes generally occur within insulated neighborhoods, which are chromosomal loop structures formed by the interaction of two DNA sites bound by the CTCF protein and occupied by the cohesin complex. Here, we review evidence that insulated neighborhoods provide for specific enhancer-gene interactions, are essential for both normal gene activation and repression, form a chromosome scaffold that is largely preserved throughout development, and are perturbed by genetic and epigenetic factors in disease...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27855157/a-helping-hand-rna-binding-proteins-guide-gene-binding-choices-by-cohesin-complexes
#13
Alyssa N Coyne, Daniela C Zarnescu
No abstract text is available yet for this article.
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27851967/a-compendium-of-chromatin-contact-maps-reveals-spatially-active-regions-in-the-human-genome
#14
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr, Bing Ren
The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27826041/smc1a-recruits-tumor-associated-fibroblasts-tafs-and-promotes-colorectal-cancer-metastasis
#15
Pengyang Zhou, Nan Xiao, Jian Wang, Zhanhuai Wang, Shuchun Zheng, Siyang Shan, Jianping Wang, Jinlin Du, Jianwei Wang
Tumor-associated-fibroblasts (TAFs) are the most important host cells in the stroma and take part in extracellular matrix construction and cancer colony development. During cancer colonization, seed cells from primary tumor can reconstruct the microenvironment by recruiting circulating cancer cells and TAFs to the metastasis site. Previous studies have established that SMC1A, a subunit of cohesin, is an important trigger signal for liver metastasis in colorectal cancer. We investigated the particular effects as well as the underlying mechanism of SMC1A on TAFs recruitment during liver metastasis of colorectal cancer...
November 4, 2016: Cancer Letters
https://www.readbyqxmd.com/read/27803161/molecular-basis-for-cohesin-acetylation-by-establishment-of-sister-chromatid-cohesion-n-acetyltransferase-esco1
#16
Yadilette Rivera-Colón, Andrew Maguire, Glen P Liszczak, Adam S Olia, Ronen Marmorstein
Protein acetylation is a prevalent posttranslational modification that is regulated by diverse acetyltransferase enzymes. While histone acetyltransferases (HATs) have been well characterized both structurally and mechanistically, far less is known about non-histone acetyltransferase enzymes. The human ESCO1 and ESCO2 paralogs acetylate the cohesin complex subunit SMC3 to regulate the separation of sister chromatids during mitosis and meiosis. Missense mutations within the acetyltransferase domain of these proteins correlate with diseases, including endometrial cancers and Roberts Syndrome...
November 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27799150/rapid-movement-and-transcriptional-re-localization-of-human-cohesin-on-dna
#17
Iain F Davidson, Daniela Goetz, Maciej P Zaczek, Maxim I Molodtsov, Pim J Huis In 't Veld, Florian Weissmann, Gabriele Litos, David A Cisneros, Maria Ocampo-Hafalla, Rene Ladurner, Frank Uhlmann, Alipasha Vaziri, Jan-Michael Peters
The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown...
October 31, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27798625/the-genomic-landscape-of-core-binding-factor-acute-myeloid-leukemias
#18
Zachary J Faber, Xiang Chen, Amanda Larson Gedman, Kristy Boggs, Jinjun Cheng, Jing Ma, Ina Radtke, Jyh-Rong Chao, Michael P Walsh, Guangchun Song, Anna K Andersson, Jinjun Dang, Li Dong, Yu Liu, Robert Huether, Zhongling Cai, Heather Mulder, Gang Wu, Michael Edmonson, Michael Rusch, Chunxu Qu, Yongjin Li, Bhavin Vadodaria, Jianmin Wang, Erin Hedlund, Xueyuan Cao, Donald Yergeau, Joy Nakitandwe, Stanley B Pounds, Sheila Shurtleff, Robert S Fulton, Lucinda L Fulton, John Easton, Evan Parganas, Ching-Hon Pui, Jeffrey E Rubnitz, Li Ding, Elaine R Mardis, Richard K Wilson, Tanja A Gruber, Charles G Mullighan, Richard F Schlenk, Peter Paschka, Konstanze Döhner, Hartmut Döhner, Lars Bullinger, Jinghui Zhang, Jeffery M Klco, James R Downing
Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML...
October 31, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27798241/an-acetyltransferase-independent-function-of-eso1-regulates-centromere-cohesion
#19
Su-Jiun Lin, Claudia Tapia-Alveal, Omar J Jabado, Doris Germain, Matthew J O'Connell
Eukaryotes contain three essential Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin and Smc5/6. Cohesin forms a ring-shaped structure that embraces sister chromatids to promote their cohesion. The cohesiveness of cohesin is promoted by acetylation of N-terminal lysines of the Smc3 subunit by the acetyltransferases Eco1 in Saccharomyces cerevisiae, and by the homolog Eso1 in Schizosaccharomyces pombe In both yeasts, these acetyltransferases are essential for cell viability. However, while non-acetylatable Smc3 mutants are lethal in S...
October 19, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27797083/the-use-of-laser-microirradiation-to-investigate-the-roles-of-cohesins-in-dna-repair
#20
Xiangduo Kong, Alexander R Ball, Kyoko Yokomori
In addition to their mitotic and transcriptional functions, cohesin plays critical roles in DNA damage response (DDR) and repair. Specifically, cohesin promotes homologous recombination (HR) repair of DNA double-strand breaks (DSBs), which is conserved from yeast to humans, and is a critical effector of ATM/ATR DDR kinase-mediated checkpoint control in mammalian cells. Optical laser microirradiation has been instrumental in revealing the damage site-specific functions of cohesin and, more recently, uncovering the unique role of cohesin-SA2, one of the two cohesin complexes uniquely present in higher eukaryotes, in DNA repair in human cells...
2017: Methods in Molecular Biology
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