The Mitotic Exit Network Integrates Temporal and Spatial Signals By
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice
Loyola University Chicago Loyola eCommons Biology: Faculty Publications and Other Works Faculty Publications 2013 Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice Mihaela Palicev Gunter P. Wagner James P. Noonan Benedikt Hallgrimsson James M. Cheverud Loyola University Chicago, [email protected] Follow this and additional works at: https://ecommons.luc.edu/biology_facpubs Part of the Biology Commons Recommended Citation Palicev, M, GP Wagner, JP Noonan, B Hallgrimsson, and JM Cheverud. "Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice." Genome Biology and Evolution 5(10), 2013. This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Biology: Faculty Publications and Other Works by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. © Palicev et al., 2013. GBE Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice Mihaela Pavlicev1,2,*, Gu¨ nter P. Wagner3, James P. Noonan4, Benedikt Hallgrı´msson5,and James M. Cheverud6 1Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria 2Department of Pediatrics, Cincinnati Children‘s Hospital Medical Center, Cincinnati, Ohio 3Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University 4Department of Genetics, Yale University School of Medicine 5Department of Cell Biology and Anatomy, The McCaig Institute for Bone and Joint Health and the Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada 6Department of Anatomy and Neurobiology, Washington University *Corresponding author: E-mail: [email protected]. -
Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases. -
Supplementary Information Integrative Analyses of Splicing in the Aging Brain: Role in Susceptibility to Alzheimer’S Disease
Supplementary Information Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease Contents 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project 1.2. Mount Sinai Brain Bank Alzheimer’s Disease 1.3. CommonMind Consortium 1.4. Data Availability 2. Supplementary Tables 3. Supplementary Figures Note: Supplementary Tables are provided as separate Excel files. 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project Gene expression data1. Gene expression data were generated using RNA- sequencing from Dorsolateral Prefrontal Cortex (DLPFC) of 540 individuals, at an average sequence depth of 90M reads. Detailed description of data generation and processing was previously described2 (Mostafavi, Gaiteri et al., under review). Samples were submitted to the Broad Institute’s Genomics Platform for transcriptome analysis following the dUTP protocol with Poly(A) selection developed by Levin and colleagues3. All samples were chosen to pass two initial quality filters: RNA integrity (RIN) score >5 and quantity threshold of 5 ug (and were selected from a larger set of 724 samples). Sequencing was performed on the Illumina HiSeq with 101bp paired-end reads and achieved coverage of 150M reads of the first 12 samples. These 12 samples will serve as a deep coverage reference and included 2 males and 2 females of nonimpaired, mild cognitive impaired, and Alzheimer's cases. The remaining samples were sequenced with target coverage of 50M reads; the mean coverage for the samples passing QC is 95 million reads (median 90 million reads). The libraries were constructed and pooled according to the RIN scores such that similar RIN scores would be pooled together. -
Tunable Ultrasensitivity: Functional Decoupling and Biological Insights Guanyu Wang & Mengshi Zhang
www.nature.com/scientificreports OPEN Tunable ultrasensitivity: functional decoupling and biological insights Guanyu Wang & Mengshi Zhang Sensitivity has become a basic concept in biology, but much less is known about its tuning, probably Received: 21 October 2015 because allosteric cooperativity, the best known mechanism of sensitivity, is determined by rigid Accepted: 30 December 2015 conformations of interacting molecules and is thus difficult to tune. Reversible covalent modification Published: 05 February 2016 (RCM), owing to its systems-level ingenuity, can generate concentration based, tunable sensitivity. Using a mathematical model of regulated RCM, we find sensitivity tuning can be decomposed into two orthogonal modes, which provide great insights into vital biological processes such as tissue development and cell cycle progression. We find that decoupling of the two modes of sensitivity tuning is critical to fidelity of cell fate decision; the decoupling is thus important in development. The decomposition also allows us to solve the ‘wasteful degradation conundrum’ in budding yeast cell cycle checkpoint, which further leads to discovery of a subtle but essential difference between positive feedback and double negative feedback. The latter guarantees revocability of stress-induced cell cycle arrest; while the former does not. By studying concentration conditions in the system, we extend applicability of ultrasensitivity and explain the ubiquity of reversible covalent modification. Sensitivity is important in biology—a cell often needs to make clear-cut decisions such as whether to commit apoptosis or which cell type to become. The best known mechanism of sensitivity is cooperative binding of substrate with enzyme that has more than one binding site. -
Non-Essential Sites Improve Phosphorylation Switch
Non-Essential Sites Improve Phosphorylation Switch Liming Wang, Qing Nie, and German Enciso* Department of Mathematics Center for Mathematical and Complex Biological Systems Center for Complex Biological Systems University of California Irvine, CA 92697 *Corresponding author: [email protected] Running title: non-essential sites improve switch Keywords: multi-site phosphorylation, ultrasensitivity, Hill coefficient, Sic1 Subject of Categories: Signal Transduction Total character count: ~ 22,600 Abstract Multisite phosphorylation is a common form of post-translational protein regulation which has been used to increase the switch-like behavior of the protein response to increasing kinase concentrations. In this paper, we show that phosphorylation sites that are not necessary for protein activation can strongly enhance the switch-like response. In the case of unordered phosphorylation, this holds when a sufficient amount of sites are phosphorylated regardless of their exact position, as occurs in bulk electrostatic activation. We obtained analytic estimates for the Hill coefficient of the switch-like response, and we observed that a trade-off exists between the switch and the kinase threshold for activation. This finding suggests a possible evolutionary mechanism for the relatively large numbers of phosphorylation sites found in various proteins. Introduction Protein phosphorylation is a ubiquitous form of post-translational modification. Since covalently bound phosphate groups are strongly hydrophilic and negatively charged, they can activate or inhibit a protein by changing its conformation or the way it interacts with other proteins. This is a key element of countless molecular systems including many forms of signal transduction, the regulation of the cell cycle and protein degradation. Multiple phosphorylations are often observed on the same protein; for instance, the epidermal growth factor receptor (EGFR) protein becomes activated when it is phosphorylated at multiple tyrosine residues by another EGFR (Alberts, 2002). -
Mitosis Vs. Meiosis
Mitosis vs. Meiosis In order for organisms to continue growing and/or replace cells that are dead or beyond repair, cells must replicate, or make identical copies of themselves. In order to do this and maintain the proper number of chromosomes, the cells of eukaryotes must undergo mitosis to divide up their DNA. The dividing of the DNA ensures that both the “old” cell (parent cell) and the “new” cells (daughter cells) have the same genetic makeup and both will be diploid, or containing the same number of chromosomes as the parent cell. For reproduction of an organism to occur, the original parent cell will undergo Meiosis to create 4 new daughter cells with a slightly different genetic makeup in order to ensure genetic diversity when fertilization occurs. The four daughter cells will be haploid, or containing half the number of chromosomes as the parent cell. The difference between the two processes is that mitosis occurs in non-reproductive cells, or somatic cells, and meiosis occurs in the cells that participate in sexual reproduction, or germ cells. The Somatic Cell Cycle (Mitosis) The somatic cell cycle consists of 3 phases: interphase, m phase, and cytokinesis. 1. Interphase: Interphase is considered the non-dividing phase of the cell cycle. It is not a part of the actual process of mitosis, but it readies the cell for mitosis. It is made up of 3 sub-phases: • G1 Phase: In G1, the cell is growing. In most organisms, the majority of the cell’s life span is spent in G1. • S Phase: In each human somatic cell, there are 23 pairs of chromosomes; one chromosome comes from the mother and one comes from the father. -
The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression
International Journal of Molecular Sciences Review The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression Tingting Zou and Zhenghong Lin * School of Life Sciences, Chongqing University, Chongqing 401331, China; [email protected] * Correspondence: [email protected] Abstract: The cell cycle is a collection of events by which cellular components such as genetic materials and cytoplasmic components are accurately divided into two daughter cells. The cell cycle transition is primarily driven by the activation of cyclin-dependent kinases (CDKs), which activities are regulated by the ubiquitin-mediated proteolysis of key regulators such as cyclins, CDK inhibitors (CKIs), other kinases and phosphatases. Thus, the ubiquitin-proteasome system (UPS) plays a pivotal role in the regulation of the cell cycle progression via recognition, interaction, and ubiquitination or deubiquitination of key proteins. The illegitimate degradation of tumor suppressor or abnormally high accumulation of oncoproteins often results in deregulation of cell proliferation, genomic instability, and cancer occurrence. In this review, we demonstrate the diversity and complexity of the regulation of UPS machinery of the cell cycle. A profound understanding of the ubiquitination machinery will provide new insights into the regulation of the cell cycle transition, cancer treatment, and the development of anti-cancer drugs. Keywords: cell cycle regulation; CDKs; cyclins; CKIs; UPS; E3 ubiquitin ligases; Deubiquitinases (DUBs) Citation: Zou, T.; Lin, Z. The Involvement of Ubiquitination Machinery in Cell Cycle Regulation and Cancer Progression. 1. Introduction Int. J. Mol. Sci. 2021, 22, 5754. https://doi.org/10.3390/ijms22115754 The cell cycle is a ubiquitous, complex, and highly regulated process that is involved in the sequential events during which a cell duplicates its genetic materials, grows, and di- Academic Editors: Kwang-Hyun Bae vides into two daughter cells. -
Polo-Like Kinase 1: Target and Regulator of Anaphase-Promoting Complex/Cyclosome–Dependent Proteolysis Frank Eckerdt1 and Klaus Strebhardt2
Review Polo-Like Kinase 1: Target and Regulator of Anaphase-Promoting Complex/Cyclosome–Dependent Proteolysis Frank Eckerdt1 and Klaus Strebhardt2 1Department of Pharmacology, University of Colorado School of Medicine, Denver, Colorado and 2Department of Gynecology and Obstetrics, Medical School, J.W. Goethe-University, Frankfurt, Germany Abstract to the regulation of the APC/C, an E3 ubiquitin ligase that is Polo-like kinase 1 (Plk1) is a key regulator of progression responsible for the timely destruction of various mitotic proteins, through mitosis. Although Plk1 seems to be dispensable for thereby regulating chromosome segregation, exit from mitosis, entry into mitosis, its role in spindle formation and exit from and a stable subsequent G1 phase (3).The APC/C is first activated by the ancillary protein Cdc20, targeting proteins containing a mitosis is crucial. Recent evidence suggests that a major role Cdc20 of Plk1 in exit from mitosis is the regulation of inhibitors of destruction box (D box), like securin.Once APC/C has the anaphase-promoting complex/cyclosome (APC/C), such as initiated mitotic exit, Cdc20 itself is degraded and is replaced by Cdh1, allowing the degradation of a wider spectrum of substrates. the early mitotic inhibitor 1 (Emi1) and spindle checkpoint Cdh1 proteins. Thus, Plk1 and the APC/C control mitotic regulators The APC/C complex targets not only D box–containing proteins but also proteins exhibiting a KEN box and/or an A box by both phosphorylation and targeted ubiquitylation to Cdh1 ensure the fidelity of chromosome separation at the meta- (e.g., cyclin B1 and Aurora A). Plk1 itself is an APC/C target. -
Multisite Protein Phosphorylation Makes a Good Threshold but Can Be a Poor Switch
Multisite protein phosphorylation makes a good threshold but can be a poor switch Jeremy Gunawardena* Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115 Communicated by Marc W. Kirschner, Harvard Medical School, Boston, MA, August 23, 2005 (received for review March 7, 2005) Phosphorylation and dephosphorylation play a fundamental role an additional mechanism for creating ultrasensitivity. Catalytic in eukaryotic signaling. Some 30% of proteins are phosphorylated activity is distributive if at most one modification (phosphory- at any time, many on multiple sites, raising the question of how the lation or dephosphorylation) takes place before enzyme and cellular phosphorylation state is regulated. Previous work for one substrate molecules part company. It is processive if two or more and two phosphorylation sites has revealed mechanisms, such as modifications take place during a single encounter. For n ϭ 2, distributive phosphorylation, for switch-like regulation of maxi- Huang and Ferrell (5) showed that distributive P&D causes the mally phosphorylated phosphoforms. These insights have led to steady state proportion of doubly phosphorylated substrate to the influential view that more phosphorylation sites leads to depend ultrasensitively on kinase concentration. In vitro exper- steeper switching, as proposed for substrates like cyclin E and the iments showed that Mek phosphorylation of Erk2 was distrib- cyclin-dependent kinase inhibitor Sic1. An analytical study of the utive (6, 7), and later work found the same for the mitogen- ordered distributive case reveals a more complex story. Multisite activated protein kinase phosphatase MKP3 (8). Ultrasensitivity phosphorylation creates an efficient threshold: The proportion of in the mitogen-activated protein kinase cascade is thought to maximally phosphorylated substrate is maintained close to 0 when underlie the all-or-none maturation of Xenopus oocytes (9). -
The APC/C in Female Mammalian Meiosis I
REPRODUCTIONREVIEW The APC/C in female mammalian meiosis I Hayden Homer1,2 1Mammalian Oocyte and Embryo Research Laboratory, Cell and Developmental Biology, UCL, London WC1E 6BT, UK and 2Reproductive Medicine Unit, Institute for Women’s Health, UCLH Elizabeth Garrett Anderson Wing, London NW1 2BU, UK Correspondence should be addressed to H Homer; Email: [email protected] Abstract The anaphase-promoting complex or cyclosome (APC/C) orchestrates a meticulously controlled sequence of proteolytic events critical for proper cell cycle progression, the details of which have been most extensively elucidated during mitosis. It has become apparent, however, that the APC/C, particularly when acting in concert with its Cdh1 co-activator (APC/CCdh1), executes a staggeringly diverse repertoire of functions that extend its remit well outside the bounds of mitosis. Findings over the past decade have not only earmarked mammalian oocyte maturation as one such case in point but have also begun to reveal a complex pattern of APC/C regulation that underpins many of the oocyte’s unique developmental attributes. This review will encompass the latest findings pertinent to the APC/C, especially APC/CCdh1, in mammalian oocytes and how its activity and substrates shape the stop–start tempo of female mammalian first meiotic division and the challenging requirement for assembling spindles in the absence of centrosomes. Reproduction (2013) 146 R61–R71 Introduction associated somatic follicular compartment at the time of ovulation. Significantly, although primordial germ cells Meiosis is the unique cell division that halves the in the ovary commit to meiosis during fetal life, it is chromosome compliment by coupling two successive not until postnatal adulthood that mature oocytes (or nuclear divisions with a single round of DNA replication. -
1 Spindle Assembly Checkpoint Is Sufficient for Complete Cdc20
Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control Bashar Ibrahim Bio System Analysis Group, Friedrich-Schiller-University Jena, and Jena Centre for Bioinformatics (JCB), 07743 Jena, Germany Email: [email protected] Abstract The spindle checkpoint assembly (SAC) ensures genome fidelity by temporarily delaying anaphase onset, until all chromosomes are properly attached to the mitotic spindle. The SAC delays mitotic progression by preventing activation of the ubiquitin ligase anaphase-promoting complex (APC/C) or cyclosome; whose activation by Cdc20 is required for sister-chromatid separation marking the transition into anaphase. The mitotic checkpoint complex (MCC), which contains Cdc20 as a subunit, binds stably to the APC/C. Compelling evidence by Izawa and Pines (Nature 2014; 10.1038/nature13911) indicates that the MCC can inhibit a second Cdc20 that has already bound and activated the APC/C. Whether or not MCC per se is sufficient to fully sequester Cdc20 and inhibit APC/C remains unclear. Here, a dynamic model for SAC regulation in which the MCC binds a second Cdc20 was constructed. This model is compared to the MCC, and the MCC-and-BubR1 (dual inhibition of APC) core model variants and subsequently validated with experimental data from the literature. By using ordinary nonlinear differential equations and spatial simulations, it is shown that the SAC works sufficiently to fully sequester Cdc20 and completely inhibit APC/C activity. This study highlights the principle that a systems biology approach is vital for molecular biology and could also be used for creating hypotheses to design future experiments. Keywords: Mathematical biology, Spindle assembly checkpoint; anaphase promoting complex, MCC, Cdc20, systems biology 1 Introduction Faithful DNA segregation, prior to cell division at mitosis, is vital for maintaining genomic integrity. -
Bub1 Positions Mad1 Close to KNL1 MELT Repeats to Promote Checkpoint Signalling
ARTICLE Received 14 Dec 2016 | Accepted 3 May 2017 | Published 12 June 2017 DOI: 10.1038/ncomms15822 OPEN Bub1 positions Mad1 close to KNL1 MELT repeats to promote checkpoint signalling Gang Zhang1, Thomas Kruse1, Blanca Lo´pez-Me´ndez1, Kathrine Beck Sylvestersen1, Dimitriya H. Garvanska1, Simone Schopper1, Michael Lund Nielsen1 & Jakob Nilsson1 Proper segregation of chromosomes depends on a functional spindle assembly checkpoint (SAC) and requires kinetochore localization of the Bub1 and Mad1/Mad2 checkpoint proteins. Several aspects of Mad1/Mad2 kinetochore recruitment in human cells are unclear and in particular the underlying direct interactions. Here we show that conserved domain 1 (CD1) in human Bub1 binds directly to Mad1 and a phosphorylation site exists in CD1 that stimulates Mad1 binding and SAC signalling. Importantly, fusion of minimal kinetochore-targeting Bub1 fragments to Mad1 bypasses the need for CD1, revealing that the main function of Bub1 is to position Mad1 close to KNL1 MELTrepeats. Furthermore, we identify residues in Mad1 that are critical for Mad1 functionality, but not Bub1 binding, arguing for a direct role of Mad1 in the checkpoint. This work dissects functionally relevant molecular interactions required for spindle assembly checkpoint signalling at kinetochores in human cells. 1 The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark. Correspondence and requests for materials should be addressed to G.Z.