1
|
Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. The DNA polymerases of Drosophila melanogaster. Fly (Austin) 2020; 14:49-61. [PMID: 31933406 PMCID: PMC7714529 DOI: 10.1080/19336934.2019.1710076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.
Collapse
Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Elena Speretta
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Kate Warner
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Michele Magrane
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro" , Bari, Italy
| | - Sue Cotterill
- Department Basic Medical Sciences, St Georges University London , London, UK
| | - Mitch McVey
- Department of Biology, Tufts University , Medford, MA, USA
| | - Yikang Rong
- School of Life Sciences, Sun Yat-sen University , Guangzhou, China
| | - Masamitsu Yamaguchi
- Department of Applied Biology and Advanced Insect Research Promotion Center, Kyoto Institute of Technology , Kyoto, Japan
| |
Collapse
|
2
|
Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
Collapse
Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
| | | |
Collapse
|
3
|
Namekawa S, Hamada F, Sawado T, Ishii S, Nara T, Ishizaki T, Ohuchi T, Arai T, Sakaguchi K. Dissociation of DNA polymerase alpha-primase complex during meiosis in Coprinus cinereus. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2137-46. [PMID: 12752433 DOI: 10.1046/j.1432-1033.2003.03565.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Previously, the activity of DNA polymerase alpha was found in the meiotic prophase I including non-S phase stages, in the basidiomycetes, Coprinus cinereus. To study DNA polymerase alpha during meiosis, we cloned cDNAs for the C. cinereus DNA polymerase alpha catalytic subunit (p140) and C. cinereus primase small subunit (p48). Northern analysis indicated that both p140 and p48 are expressed not only at S phase but also during the leptotene/zygotene stages of meiotic prophase I. In situ immuno-staining of cells at meiotic prophase I revealed a sub population of p48 that does not colocalize with p140 in nuclei. We also purified the pol alpha-primase complex from meiotic cells by column chromatography and characterized its biochemical properties. We found a subpopulation of primase that was separated from the pol alpha-primase complex by phosphocellulose column chromatography. Glycerol gradient density sedimentation results indicated that the amount of intact pol alpha-primase complex in crude extract is reduced, and that a smaller complex appears upon meiotic development. These results suggest that the form of the DNA polymerase alpha-primase complex is altered during meiotic development.
Collapse
Affiliation(s)
- Satoshi Namekawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Kuroda K, Ueda R. Phosphorylation and dephosphorylation of the B subunit of DNA polymerase alpha-primase complex in the early embryogenesis of Drosophila. Biochem Biophys Res Commun 1999; 254:372-7. [PMID: 9918845 DOI: 10.1006/bbrc.1998.9944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the early embryos of Drosophila, the B subunit of the DNA polymerase alpha-primase complex was found to migrate more slowly during the first 13 mitotic cycles than that from cycle 14 using SDS-polyacrylamide gel electrophoresis. Lambda phosphatase treatment showed that the reduced migration was caused by phosphorylation of the B subunit. Detailed analysis using the partially purified B subunit indicated that most of the B subunit until cycle 13 was a phosphorylated form while the B subunit of cycle 14 was a dephosphorylated form.
Collapse
Affiliation(s)
- K Kuroda
- Mitsubishi Kasei Institute of Life Sciences, Tokyo, Machida, 194-8511, Japan.
| | | |
Collapse
|
5
|
Sawado T, Sakaguchi K. A DNA polymerase alpha catalytic subunit is purified independently from the tissues at meiotic prometaphase I of a basidiomycete, Coprinus cinereus. Biochem Biophys Res Commun 1997; 232:454-60. [PMID: 9125200 DOI: 10.1006/bbrc.1997.6306] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A 135kDa DNA polymerase alpha lacking primase activity has been purified to near homogeneity from Coprinus meiotic tissues. The activity of the DNA polymerase was sensitive to aphidicolin and N-ethylmaleimide, but was insensitive to dideoxythymidine triphosphate. DNA synthesis was proceeded with a low processivity. Neither activity nor processivity were affected by PCNA in the presence or absence of KCI. Monovalent cation inhibited its activity. These biochemical properties are almost identical to those of Coprinus DNA polymerase alpha -primase complex. However, the 135kDa DNA polymerase did not use activated DNA as a template-primer, inconsistent with Coprinus DNA polymerase alpha-primase complex. The 135kDa DNA polymerase was purified from the tissues at meiotic pro-metaphase I, suggesting that the alpha- DNA polymerase-primase complex dissociates as the meiotic cell cycle progresses and only the catalytic subunit remains at this stage.
Collapse
Affiliation(s)
- T Sawado
- Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Chiba-ken, Japan
| | | |
Collapse
|
6
|
Aoyagi N, Oshige M, Hirose F, Kuroda K, Matsukage A, Sakaguchi K. DNA polymerase epsilon from Drosophila melanogaster. Biochem Biophys Res Commun 1997; 230:297-301. [PMID: 9016770 DOI: 10.1006/bbrc.1996.5945] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We identified a DNA polymerase species in Drosophila melanogaster embryos, and purified it. This polymerase shared some common properties with DNA polymerase epsilon from mammals and yeast as follows; it has a preference for poly(dA)/oligo(dT) as a template/primer, it is highly processive in DNA synthesis, it co-fractionates with 3'-5' exonuclease activity, it is sensitive to aphidicolin and is resistance to ddTTP. The polymerase activity was inhibited in the immuno-precipitation assay with anti-pol-epsilon antibodies, which were produced against a polypeptide coded on the cDNA of a putative Drosophila pol-epsilon we isolated previously. Using these antibodies, Western blot analysis revealed that this polymerase is a 250kDa polypeptide, which is the same size as observed in mammals and yeast. These results indicate that Drosophila produces the epsilon-class of DNA polymerase, and like mammals or yeast, possesses the 5 typical classes of DNA polymerases (alpha to epsilon) in its embryos.
Collapse
Affiliation(s)
- N Aoyagi
- Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda-shi, Japan
| | | | | | | | | | | |
Collapse
|
7
|
Yamaguchi M, Hirose F, Nishimoto Y, Naruge T, Ikeda M, Hachiya T, Tamai K, Kuroda K, Matsukage A. Expression patterns of DNA replication enzymes and the regulatory factor DREF during Drosophila development analyzed with specific antibodies. Biol Cell 1995; 85:147-55. [PMID: 8785516 DOI: 10.1016/0248-4900(96)85275-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Specific antibodies were prepared against Drosophila DNA polymerase epsilon and DREF, a regulatory factor for DNA replication-related genes. Using these antibodies together with those for DNA polymerase alpha and proliferating cell nuclear antigen (PCNA), we examined expression patterns and sub-cellular distributions of these proteins during Drosophila development. DNA polymerase alpha, epsilon and PCNA proteins were maternally stored in unfertilized eggs and maintained at high levels during embryogenesis. With distinct nuclear localization, proteins were observed in embryos at interphase stages throughout the 13 nuclear division cycles, suggesting that they all participate in rapid nuclear DNA replication during these cycles. In contrast, maternal storage of a DREF protein was relatively low and its level increased throughout embryogenesis. Strong nuclear staining with the anti-DREF antibody was not observed until the nuclear division cycle 8. Immunostaining of various larval tissues from transgenic flies carrying the PCNA gene promoter-lacZ fusion gene revealed co-expression of DREF, PCNA and lacZ, suggesting that DREF regulates the expression of PCNA gene in these tissues. In addition, we detected a relatively high level of DREF in adult males as well as females. Since DNA polymerase alpha, epsilon and PCNA are hardly detectable in adult males, DREF very likely regulates genes other than those closely linked to DNA replication in adult males.
Collapse
Affiliation(s)
- M Yamaguchi
- Laboratory of Cell Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|