DOCSLIB.ORG

(SMC) Proteins in Eukaryotes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(SMC) Proteins in Eukaryotes bioRxiv preprint doi: https://doi.org/10.1101/2021.05.15.444277; this version posted May 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Assessing the ubiquity and origins of 2 structural maintenance of 3 chromosomes (SMC) proteins in 4 eukaryotes 5 6 Mari Yoshinaga1 and Yuji Inagaki1,2. 7 8 1 Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 9 Ibaraki, Japan. 10 2 Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. 11 12 Corresponding author: Yuji Inagaki, [email protected] 13 14 15 Keywords: condensin, cohesin, chromosome assembly, chromosome segregation, DNA 16 repair, ATPase. 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.15.444277; this version posted May 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 18 ABSTRACT 19 Structural maintenance of chromosomes (SMC) protein complexes are common in 20 Bacteria, Archaea, and Eukaryota. SMC proteins, together with the proteins related to 21 SMC (SMC-related proteins), constitute a superfamily of ATPases. Bacteria/Archaea 22 and Eukaryotes are distinctive from one another in terms of the repertory of SMC 23 proteins. A single type of SMC protein is dimerized in the bacterial and archaeal 24 complexes, whereas eukaryotes possess six distinct SMC subfamilies (SMC1-6), 25 constituting three heterodimeric complexes, namely cohesin, condensin, and SMC5/6 26 complex. Thus, to bridge the homodimeric SMC complexes in Bacteria and Archaea to 27 the heterodimeric SMC complexes in Eukaryota, we need to invoke multiple 28 duplications of a SMC gene followed by functional divergence. However, to our 29 knowledge, the evolution of the SMC proteins in Eukaryota had not been examined for 30 more than a decade. In this study, we reexamined the ubiquity of SMC1-6 in 31 phylogenetically diverse eukaryotes that cover the major eukaryotic taxonomic groups 32 recognized to date (101 species in total) and provide two novel insights into the SMC 33 evolution in eukaryotes. First, multiple secondary losses of SMC5 and SMC6 occurred 34 in the eukaryotic evolution. Second, the SMC proteins constituting cohesin and 35 condensin (i.e., SMC1-4), and SMC5 and SMC6 were derived from closely related but 36 distinct ancestral proteins. Finally, we discuss how SMC1-4 were evolved from the 37 ancestral SMC protein(s) in the very early stage of eukaryotic evolution. 38 39 INTRODUCTION 40 Chromosomes comprise DNA molecules, which are the body of genetic information, 41 and a large number of proteins with diverse functions. In eukaryotes, cohesin and 42 condensin, together with many other proteins, maintain the integrity of chromosome 43 structure. Cohesin and condensin participate in protein complexes (Anderson et al. 44 2002) that bundle sister chromosomes together during mitosis (Christian H et al. 2008) 45 and meiosis (Ishiguro 2019), and aggregate chromosomes (Sutani and Yanagida 1997), 46 respectively. Cohesin is constituted by two Structural Maintenance of Chromosomes 47 (SMC) proteins (SMC1 and SMC3) (Losada et al. 1998) and accessory subunits 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.15.444277; this version posted May 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 48 Rad21/Scc1 and STAG1/Scc3 (Birkenbihl and Subramani 1995; Carramolino et al. 49 1997; Tóth et al. 1999). Condensin contains SMC2 and SMC4 (Hirano and Mitchison 50 1994), and a different set of accessory subunits CAP-D2, CAP-G, and CAP-H (Hirano et 51 al. 1997). There are two additional SMC proteins, SMC5 and SMC6 (Lehmann et al. 52 1995; Fousteri and Lehmann 2000), which comprise the “SMC5/6” complex together 53 with six accessory proteins (Nse1-6) (Andrews et al. 2005; Fujioka et al. 2002; Hu et al. 54 2005; Pebernard et al. 2004; Pebernard et al. 2006) and involve mainly in DNA repair 55 but also replication fork stability (Aragón 2018). 56 SMC proteins, together with MukB, Rad50, and RecN, belong to a large ATPase 57 superfamily with unique structural characteristics (Niki et al. 1991; Funayama et al. 58 1999; Löwe et al. 2001). SMC proteins comprise “head” that hydrolyzes ATP, “hinge” 59 that facilitates the dimerization of two SMC proteins (SMC1 and SMC3 in cohesin, 60 SMC2 and SMC4 in condensin, and SMC5 and SMC6 in the SMC5/6 complex), and 61 antiparallel coiled coils connecting the head and hinge (Melby et al. 1998). As ATPases, 62 SMC proteins bear seven motifs such as Walker A (P-loop), Walker B, ABC signature 63 motif (C-loop), A-loop, D-loop, H-loop (switch motif), R-loop, and Q-loop, all of which are 64 required ATP binding and hydrolysis. In the ATPases belonging to the SMC superfamily, 65 the Walker A motif, A-loop, R-loop, and Q-loop are located at the N-terminus of the 66 molecule, being remote from the rest of the motifs at the C-terminus (Palou et al. 2018). 67 Thus, SMC proteins most likely form hairpin-like structures to make all of the sequence 68 motifs for ATP binding in close proximity in the tertiary structures (Melby et al. 1998). 69 The vast majority of the members of Bacteria and Archaea possess a single SMC 70 protein for DNA strand aggregation. In contrast to the eukaryotic SMC complexes 71 containing heterodimeric SMC proteins, the SMC complexes in Bacteria and Archaea 72 comprise two identical SMC proteins (i.e., homodimeric), together with accessory 73 subunits (Britton et al. 1998; Soppa 2001). It is noteworthy that the SMC protein is not 74 conserved strictly in Bacteria or Archaea (Soppa 2001). For instance, the absence of 75 the conventional SMC protein in the Crenarchaeota genus Sulfolobus was 76 experimentally shown to be complemented by the proteins that are distantly related to 77 the authentic SMC, namely coalescin (Takemata et al. 2019). 3 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.15.444277; this version posted May 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 78 To our knowledge, no study on the diversity and evolution of SMC proteins 79 sampled from phylogenetically diverse eukaryotes has been done since Cobbe and 80 Heck (2004). Their phylogenetic analyses recovered individual clades of SMC1-6, and 81 further united (i) SMC1 and SMC4 clades, (ii) SMC2 and SMC3 clades, and (iii) SMC5 82 and SMC6 clades together. Henceforth here in this work, we designated the three 83 unions as “SMC1+4 clan,” “SMC2+3 clan,” and “SMC5+6 clan,” respectively. Based on 84 the phylogenies inferred from the SMC proteins in the three domains of Life, the authors 85 proposed that SMC1-6 were yielded through gene duplication events that occurred in 86 the early eukaryotic evolution. 87 The pioneering work by Cobbe and Heck (2004) was a significant first step to 88 decipher the origin and evolution of SMC proteins in eukaryotes, albeit they provided no 89 clear scenario explaining how a primordial SMC protein diversified into SMC1-6 prior to 90 the divergence of the extant eukaryotes. Thus, we reassessed the ubiquity of SMC1-6 91 in eukaryotes and the phylogenetic relationship among the six eukaryotic SMC 92 subfamilies in this study. Fortunately, recent advances in sequencing technology allow 93 us to search for SMC proteins in the transcriptome and/or genome data of 94 phylogenetically much broader eukaryotic lineages than those sampled from metazoans, 95 fungi (including a microsporidian), land plants, and trypanosomatids analyzed in Cobbe 96 and Heck (2004). Furthermore, computer programs for the maximum-likelihood (ML) 97 phylogenetic methods, as well as hardwares, have been improved significantly since 98 2004. Thus, hundreds of SMC proteins from diverse eukaryotes can be subjected to the 99 ML analyses now, in contrast to Cobbe and Heck (2004) wherein only a distance tree 100 was inferred from the alignment of 148 SMC sequences. 101 Our survey of SMC1-6 in 101 eukaryotes confirmed the early divergence of the 102 six SMC subfamilies in eukaryotes, albeit the secondary loss of SMC5 and SMC6 most 103 likely has occurred in separate branches of the tree of eukaryotes. Moreover, the 104 phylogenetic analysis of SMC1-6, bacterial and archaeal SMC, and Rad50/SbcC (304 105 sequences in total) disfavored the single origin of the six SMC subfamilies in eukaryotes 106 and instead suggested that the ancestral molecule of SMC5 and SMC6 is distinct from 107 that of SMC1-4. We finally explored multiple scenarios to explain how the repertory of 108 the SMC subfamilies was shaped in the very early evolution of eukaryotes. 4 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.15.444277; this version posted May 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license.
Load more

Recommended publications
  • Expanding the Chlamydiae Tree
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions.
    [Show full text]
  • Dynamic Molecular Linkers of the Genome: the First Decade of SMC Proteins
    Downloaded from genesdev.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Dynamic molecular linkers of the genome: the first decade of SMC proteins Ana Losada1 and Tatsuya Hirano2,3 1Spanish National Cancer Center (CNIO), Madrid E-28029, Spain; 2Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA Structural maintenance of chromosomes (SMC) proteins in eukaryotes. The proposed actions of cohesin and con- are chromosomal ATPases, highly conserved from bac- densins offer a plausible, if not complete, explanation for teria to humans, that play fundamental roles in many the sudden appearance of thread-like “substances” (the aspects of higher-order chromosome organization and chromosomes) and their longitudinal splitting during dynamics. In eukaryotes, SMC1 and SMC3 act as the mitosis, first described by Walther Flemming (1882). core of the cohesin complexes that mediate sister chro- Remarkably, SMC proteins are conserved among the matid cohesion, whereas SMC2 and SMC4 function as three phyla of life, indicating that the basic strategy of the core of the condensin complexes that are essential chromosome organization may be evolutionarily con- for chromosome assembly and segregation. Another served from bacteria to humans. An emerging theme is complex containing SMC5 and SMC6 is implicated in that SMC proteins are dynamic molecular linkers of the DNA repair and checkpoint responses. The SMC com- genome that actively fold, tether, and manipulate DNA plexes form unique ring- or V-shaped structures with strands. Their diverse functions range far beyond chro- long coiled-coil arms, and function as ATP-modulated, mosome segregation, and involve nearly all aspects of dynamic molecular linkers of the genome.
    [Show full text]
  • Localization of Condensin Subunit XCAP-E in Interphase Nucleus, Nucleoid and Nuclear
    1 Localization of condensin subunit XCAP-E in interphase nucleus, nucleoid and nuclear matrix of XL2 cells. Elmira Timirbulatova, Igor Kireev, Vladimir Ju. Polyakov, and Rustem Uzbekov* Division of Electron Microscopy, A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia. *Author for correspondence: telephone. 007-095-939-55-28; FAX 007-095-939-31-81 e-mail: [email protected] Key words: XCAP-E; nucleolus; condensin; nuclear matrix; Xenopus. Abbreviations: DAPI , 4’, 6 diamidino-2-phenylindole; DNP, deoxyribonucleoprotein; DRB, 5,6-dichloro-1b-d-ribofuranosylbenzimidazole; SMC, structural maintenance of chromosomes; XCAP-E, Xenopus chromosome associated protein E. 2 Abstract The Xenopus XCAP-E protein is a component of condensin complex In the present work we investigate its localization in interphase XL2 cells and nucleoids. We shown, that XCAP-E is localizes in granular and in dense fibrillar component of nucleolus and also in small karyoplasmic structures (termed “SMC bodies”). Extraction by 2M NaCl does not influence XCAP-E distribution in nucleolus and “SMC bodies”. DNAse I treatment of interphase cells permeabilized by Triton X-100 or nucleoids resulted in partial decrease of labeling intensity in the nucleus, whereas RNAse A treatment resulted in practically complete loss of labeling of nucleolus and “SMC bodies” labeling. In mitotic cells, however, 2M NaCl extraction results in an intense staining of the chromosome region although the labeling was visible along the whole length of sister chromatids, with a stronger staining in centromore region. The data are discussed in view of a hypothesis about participation of XCAP-E in processing of ribosomal RNA.
    [Show full text]
  • NCAPD3 Antibody (C-Term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP16786B
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 NCAPD3 Antibody (C-term) Affinity Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP16786B Specification NCAPD3 Antibody (C-term) - Product Information Application WB,E Primary Accession P42695 Other Accession NP_056076.1 Reactivity Human Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Calculated MW 168891 Antigen Region 1050-1078 NCAPD3 Antibody (C-term) - Additional Information NCAPD3 Antibody (C-term) (Cat. Gene ID 23310 #AP16786b) western blot analysis in K562 cell line lysates (35ug/lane).This Other Names Condensin-2 complex subunit D3, Non-SMC demonstrates the NCAPD3 antibody detected condensin II complex subunit D3, hCAP-D3, the NCAPD3 protein (arrow). NCAPD3, CAPD3, KIAA0056 Target/Specificity NCAPD3 Antibody (C-term) - Background This NCAPD3 antibody is generated from rabbits immunized with a KLH conjugated Condensin complexes I and II play essential synthetic peptide between 1050-1078 roles in amino acids from the C-terminal region of mitotic chromosome assembly and human NCAPD3. segregation. Both condensins contain 2 invariant structural maintenance of Dilution chromosome (SMC) WB~~1:1000 subunits, SMC2 (MIM 605576) and SMC4 (MIM 605575), but they contain Format different sets of non-SMC subunits. NCAPD3 is Purified polyclonal antibody supplied in PBS 1 of 3 non-SMC with 0.09% (W/V) sodium azide. This subunits that define condensin II (Ono et al., antibody is purified through a protein A 2003 [PubMed column, followed by peptide affinity 14532007]). purification. NCAPD3 Antibody (C-term) - References Storage Maintain refrigerated at 2-8°C for up to 2 Rose, J.E., et al.
    [Show full text]
  • Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
    Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae
    [Show full text]
  • A Commercial Antibody to the Human Condensin II Subunit NCAPH2 Cross-Reacts with a SWI/SNF Complex Component
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.07.372599; this version posted November 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. A commercial antibody to the human condensin II subunit NCAPH2 cross-reacts with a SWI/SNF complex component Erin E. Cutts1*, Gillian C Taylor2*, Mercedes Pardo1, Lu Yu1, Jimi C Wills3, Jyoti S. Choudhary1, Alessandro Vannini1#, Andrew J Wood2# 1 Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, United Kingdom 2 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK. 3 Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. * Equal contribution # correspondence to: [email protected], [email protected]. Summary Condensin complexes compact and disentangle chromosomes in preparation for cell division. Commercially available antibodies raised against condensin subunits have been widely used to characterise their cellular interactome. Here we have assessed the specificity of a polyclonal antibody (Bethyl A302- 276A) that is commonly used as a probe for NCAPH2, the kleisin subunit of condensin II, in mammalian cells. We find that, in addition to its intended target, this antibody cross-reacts with one or more components of the SWI/SNF family of chromatin remodelling complexes in an NCAPH2- independent manner. This cross-reactivity with an abundant chromatin- associated factor is likely to affect the interpretation of protein and chromatin immunoprecipitation experiments that make use of this antibody probe.
    [Show full text]
  • Whole-Proteome Tree of Life Suggests a Deep Burst of Organism Diversity
    Whole-proteome tree of life suggests a deep burst of organism diversity JaeJin Choia,b,c and Sung-Hou Kima,b,c,1 aDepartment of Chemistry, University of California, Berkeley, CA 94720; bCenter for Computational Biology, University of California, Berkeley, CA 94720; and cMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Contributed by Sung-Hou Kim, December 11, 2019 (sent for review September 12, 2019; reviewed by Se-Ran Jun and Charles G. Kurland) An organism tree of life (organism ToL) is a conceptual and addition, an important issue of rooting gene ToLs has not been well metaphorical tree to capture a simplified narrative of the evolution- resolved and still is being debated (ref. 13 and references within). ary course and kinship among the extant organisms. Such a tree These and other issues of gene ToLs highlight the need for cannot be experimentally validated but may be reconstructed based alternative surrogates for the organism ToL built based on as on characteristics associated with the organisms. Since the whole- completely different assumptions as possible from those of gene genome sequence of an organism is, at present, the most compre- ToLs. A “genome ToL” (see below) constructed based on in- hensive descriptor of the organism, a whole-genome sequence-based formation theory (14) may provide an independent and alter- ToL can be an empirically derivable surrogate for the organism ToL. native view of the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. Genome ToL We have constructed three types of ToLs for diversely sampled Following the commonly used definition of gene ToL (see organisms using the sequences of whole genome, of whole tran- above), the term genome ToL is used in this study for the ToLs scriptome, and of whole proteome.
    [Show full text]
  • Building the Interphase Nucleus: a Study on the Kinetics of 3D Chromosome Formation, Temporal Relation to Active Transcription, and the Role of Nuclear Rnas
    University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2020-07-28 Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs Kristin N. Abramo University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Bioinformatics Commons, Cell Biology Commons, Computational Biology Commons, Genomics Commons, Laboratory and Basic Science Research Commons, Molecular Biology Commons, Molecular Genetics Commons, and the Systems Biology Commons Repository Citation Abramo KN. (2020). Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs. GSBS Dissertations and Theses. https://doi.org/10.13028/a9gd-gw44. Retrieved from https://escholarship.umassmed.edu/ gsbs_diss/1099 Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. ABRAMO Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPOPHY July 28, 2020 Program in Systems Biology, Interdisciplinary Graduate Program BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N.
    [Show full text]
  • Understanding Molecular Functions of the SMC5/6 Complex
    G C A T T A C G G C A T genes Review Scaffolding for Repair: Understanding Molecular Functions of the SMC5/6 Complex Mariana Diaz 1,2 and Ales Pecinka 1,* ID 1 Institute of Experimental Botany of the Czech Academy of Sciences (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelu˚ 31, 77900 Olomouc-Holice, Czech Republic 2 Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829 Cologne, Germany; [email protected] * Correspondence: [email protected]; Tel.: +420-585-238-709 Received: 15 November 2017; Accepted: 4 January 2018; Published: 12 January 2018 Abstract: Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex. SMC5/6 complex was originally identified based on the sensitivity of its mutants to genotoxic stress but there is increasing number of studies demonstrating its roles in the control of DNA replication, sister chromatid resolution and genomic location-dependent promotion or suppression of homologous recombination. Some of these functions appear to be due to a very dynamic interaction with cohesin or other repair complexes. Studies in Arabidopsis indicate that, besides its canonical function in repair of damaged DNA, the SMC5/6 complex plays important roles in regulating plant development, abiotic stress responses, suppression of autoimmune responses and sexual reproduction.
    [Show full text]
  • Condensation of Prometaphase Chromo-Somes
    Condensation of Prometaphase Chromo- somes D'Eustachio, P., Matthews, L., Orlic-Milacic, M. European Bioinformatics Institute, New York University Langone Medical Center, Ontario Institute for Cancer Research, Oregon Health and Science University. The contents of this document may be freely copied and distributed in any media, provided the authors, plus the institutions, are credited, as stated under the terms of Creative Commons Attribution 4.0 Inter- national (CC BY 4.0) License. For more information see our license. 09/03/2019 Introduction Reactome is open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross- referenced to many bioinformatics databases. A system of evidence tracking ensures that all assertions are backed up by the primary literature. Reactome is used by clinicians, geneticists, genomics research- ers, and molecular biologists to interpret the results of high-throughput experimental studies, by bioin- formaticians seeking to develop novel algorithms for mining knowledge from genomic studies, and by systems biologists building predictive models of normal and disease variant pathways. The development of Reactome is supported by grants from the US National Institutes of Health (P41 HG003751), University of Toronto (CFREF Medicine by Design), European Union (EU STRP, EMI-CD), and the European Molecular Biology Laboratory (EBI Industry program). Literature references Fabregat, A., Sidiropoulos, K., Viteri, G., Forner, O., Marin-Garcia, P., Arnau, V. et al. (2017). Reactome pathway ana- lysis: a high-performance in-memory approach. BMC bioinformatics, 18, 142. ↗ Sidiropoulos, K., Viteri, G., Sevilla, C., Jupe, S., Webber, M., Orlic-Milacic, M.
    [Show full text]
  • Metagenomic Characterization of Unicellular Eukaryotes in the Urban Thessaloniki Bay
    Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay George Tsipas SCHOOL OF ECONOMICS, BUSINESS ADMINISTRATION & LEGAL STUDIES A thesis submitted for the degree of Master of Science (MSc) in Bioeconomy Law, Regulation and Management May, 2019 Thessaloniki – Greece George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ Student Name: George Tsipas SID: 268186037282 Supervisor: Prof. Dr. Savvas Genitsaris I hereby declare that the work submitted is mine and that where I have made use of another’s work, I have attributed the source(s) according to the Regulations set in the Student’s Handbook. May, 2019 Thessaloniki - Greece Page 2 of 63 George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ 1. Abstract The present research investigates through metagenomics sequencing the unicellular protistan communities in Thermaikos Gulf. This research analyzes the diversity, composition and abundance in this marine environment. Water samples were collected monthly from April 2017 to February 2018 in the port of Thessaloniki (Harbor site, 40o 37’ 55 N, 22o 56’ 09 E). The extraction of DNA was completed as well as the sequencing was performed, before the downstream read processing and the taxonomic classification that was assigned using PR2 database. A total of 1248 Operational Taxonomic Units (OTUs) were detected but only 700 unicellular eukaryotes were analyzed, excluding unclassified OTUs, Metazoa and Streptophyta. In this research-based study the most abundant and diverse taxonomic groups were Dinoflagellata and Protalveolata. Specifically, the most abundant groups of all samples are Dinoflagellata with 190 OTUs (27.70%), Protalveolata with 139 OTUs (20.26%) Ochrophyta with 73 OTUs (10.64%), Cercozoa with 67 OTUs (9.77%) and Ciliophora with 64 OTUs (9.33%).
    [Show full text]
  • Predatory Flagellates – the New Recently Discovered Deep Branches of the Eukaryotic Tree and Their Evolutionary and Ecological Significance
    Protistology 14 (1), 15–22 (2020) Protistology Predatory flagellates – the new recently discovered deep branches of the eukaryotic tree and their evolutionary and ecological significance Denis V. Tikhonenkov Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia | Submitted March 20, 2020 | Accepted April 6, 2020 | Summary Predatory protists are poorly studied, although they are often representing important deep-branching evolutionary lineages and new eukaryotic supergroups. This short review/opinion paper is inspired by the recent discoveries of various predatory flagellates, which form sister groups of the giant eukaryotic clusters on phylogenetic trees, and illustrate an ancestral state of one or another supergroup of eukaryotes. Here we discuss their evolutionary and ecological relevance and show that the study of such protists may be essential in addressing previously puzzling evolutionary problems, such as the origin of multicellular animals, the plastid spread trajectory, origins of photosynthesis and parasitism, evolution of mitochondrial genomes. Key words: evolution of eukaryotes, heterotrophic flagellates, mitochondrial genome, origin of animals, photosynthesis, predatory protists, tree of life Predatory flagellates and diversity of eu- of the hidden diversity of protists (Moon-van der karyotes Staay et al., 2000; López-García et al., 2001; Edg- comb et al., 2002; Massana et al., 2004; Richards The well-studied multicellular animals, plants and Bass, 2005; Tarbe et al., 2011; de Vargas et al., and fungi immediately come to mind when we hear 2015). In particular, several prevailing and very abun- the term “eukaryotes”. However, these groups of dant ribogroups such as MALV, MAST, MAOP, organisms represent a minority in the real diversity MAFO (marine alveolates, stramenopiles, opistho- of evolutionary lineages of eukaryotes.
    [Show full text]