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Funk HM, Brooks JH, Detmer AE, Creech NN, Guy MP. Identification of Amino Acids in Trm734 Required for 2'- O-Methylation of the tRNA Phe Wobble Residue. ACS OMEGA 2024; 9:25063-25072. [PMID: 38882062 PMCID: PMC11170731 DOI: 10.1021/acsomega.4c02313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024]
Abstract
All organisms methylate their nucleic acids, and this methylation is critical for proper gene expression at both the transcriptional and translational levels. For proper translation in eukaryotes, 2'-O-methylation of C32 (Cm32) and G34 (Gm34) in the anticodon loop of tRNAPhe is critical, with defects in these modifications associated with human disease. In yeast, Cm32 is formed by an enzyme that consists of the methyltransferase Trm7 in complex with the auxiliary protein Trm732, and Gm34 is formed by an enzyme that consists of Trm7 in complex with Trm734. The role of Trm732 and Trm734 in tRNA modification is not fully understood, although previous studies have suggested that Trm734 is important for tRNA binding. In this report, we generated Trm734 variants and tested their ability to work with Trm7 to modify tRNAPhe. Using this approach, we identified several regions of amino acids that are important for Trm734 activity and/or stability. Based on the previously determined Trm7-Trm734 crystal structure, these crucial amino acids are near the active site of Trm7 and are not directly involved in Trm7-Trm734 protein-protein interactions. Immunoprecipitation experiments with these Trm734 variants and Trm7 confirm that these residues are not involved in Trm7-Trm734 binding. Further experiments should help determine if these residues are important for tRNA binding or have another role in the modification of the tRNA. Furthermore, our discovery of a nonfunctional, stable Trm734 variant will be useful in determining if the reported roles of Trm734 in other biological processes such as retromer processing and resistance to Ty1 transposition are due to tRNA modification defects or to other bona fide cellular roles of Trm734.
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Affiliation(s)
- Holly M Funk
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Jennifer H Brooks
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Alisha E Detmer
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Natalie N Creech
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Michael P Guy
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
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2
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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3
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Beckwith SL, Nomberg EJ, Newman AC, Taylor JV, Guerrero RC, Garfinkel DJ. An interchangeable prion-like domain is required for Ty1 retrotransposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530227. [PMID: 36909481 PMCID: PMC10002725 DOI: 10.1101/2023.02.27.530227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Retrotransposons and retroviruses shape genome evolution and can negatively impact genome function. Saccharomyces cerevisiae and its close relatives harbor several families of LTR-retrotransposons, the most abundant being Ty1 in several laboratory strains. The cytosolic foci that nucleate Ty1 virus-like particle (VLP) assembly are not well-understood. These foci, termed retrosomes or T-bodies, contain Ty1 Gag and likely Gag-Pol and the Ty1 mRNA destined for reverse transcription. Here, we report a novel intrinsically disordered N-terminal pr ion-like d omain (PrLD) within Gag that is required for transposition. This domain contains amino-acid composition similar to known yeast prions and is sufficient to nucleate prionogenesis in an established cell-based prion reporter system. Deleting the Ty1 PrLD results in dramatic VLP assembly and retrotransposition defects but does not affect Gag protein level. Ty1 Gag chimeras in which the PrLD is replaced with other sequences, including yeast and mammalian prionogenic domains, display a range of retrotransposition phenotypes from wildtype to null. We examine these chimeras throughout the Ty1 replication cycle and find that some support retrosome formation, VLP assembly, and retrotransposition, including the yeast Sup35 prion and the mouse PrP prion. Our interchangeable Ty1 system provides a useful, genetically tractable in vivo platform for studying PrLDs, complete with a suite of robust and sensitive assays, and host modulators developed to study Ty1 retromobility. Our work invites study into the prevalence of PrLDs in additional mobile elements. Significance Retrovirus-like retrotransposons help shape the genome evolution of their hosts and replicate within cytoplasmic particles. How their building blocks associate and assemble within the cell is poorly understood. Here, we report a novel pr ion-like d omain (PrLD) in the budding yeast retrotransposon Ty1 Gag protein that builds virus-like particles. The PrLD has similar sequence properties to prions and disordered protein domains that can drive the formation of assemblies that range from liquid to solid. We demonstrate that the Ty1 PrLD can function as a prion and that certain prion sequences can replace the PrLD and support Ty1 transposition. This interchangeable system is an effective platform to study additional disordered sequences in living cells.
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Affiliation(s)
- Sean L. Beckwith
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Emily J. Nomberg
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Abigail C. Newman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jeannette V. Taylor
- Robert P. Apkarian Integrated Electron Microscopy Core at Emory University, Atlanta, GA, 30322, USA
| | - Ricardo C. Guerrero
- Robert P. Apkarian Integrated Electron Microscopy Core at Emory University, Atlanta, GA, 30322, USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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4
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Barkova A, Adhya I, Conesa C, Asif-Laidin A, Bonnet A, Rabut E, Chagneau C, Lesage P, Acker J. A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition. Mob DNA 2022; 13:26. [PMCID: PMC9673352 DOI: 10.1186/s13100-022-00284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few of them interact physically with Ty1 integrase (IN).
Results
Here, we perform a proteomic screen to establish Ty1 IN interactome. Among the 265 potential interacting partners, we focus our study on the conserved CK2 kinase. We confirm the interaction between IN and CK2, demonstrate that IN is a substrate of CK2 in vitro and identify the modified residues. We find that Ty1 IN is phosphorylated in vivo and that these modifications are dependent in part on CK2. No significant change in Ty1 retromobility could be observed when we introduce phospho-ablative mutations that prevent IN phosphorylation by CK2 in vitro. However, the absence of CK2 holoenzyme results in a strong stimulation of Ty1 retrotransposition, characterized by an increase in Ty1 mRNA and protein levels and a high accumulation of cDNA.
Conclusion
Our study shows that Ty1 IN is phosphorylated, as observed for retroviral INs and highlights an important role of CK2 in the regulation of Ty1 retrotransposition. In addition, the proteomic approach enabled the identification of many new Ty1 IN interacting partners, whose potential role in the control of Ty1 mobility will be interesting to study.
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5
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Salinero AC, Emerson S, Cormier TC, Yin J, Morse RH, Curcio MJ. Reliance of Host-Encoded Regulators of Retromobility on Ty1 Promoter Activity or Architecture. Front Mol Biosci 2022; 9:896215. [PMID: 35847981 PMCID: PMC9283973 DOI: 10.3389/fmolb.2022.896215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
The Ty1 retrotransposon family is maintained in a functional but dormant state by its host, Saccharomyces cerevisiae. Several hundred RHF and RTT genes encoding co-factors and restrictors of Ty1 retromobility, respectively, have been identified. Well-characterized examples include MED3 and MED15, encoding subunits of the Mediator transcriptional co-activator complex; control of retromobility by Med3 and Med15 requires the Ty1 promoter in the U3 region of the long terminal repeat. To characterize the U3-dependence of other Ty1 regulators, we screened a library of 188 known rhf and rtt mutants for altered retromobility of Ty1his3AI expressed from the strong, TATA-less TEF1 promoter or the weak, TATA-containing U3 promoter. Two classes of genes, each including both RHFs and RTTs, were identified. The first class comprising 82 genes that regulated Ty1his3AI retromobility independently of U3 is enriched for RHF genes that restrict the G1 phase of the cell cycle and those involved in transcriptional elongation and mRNA catabolism. The second class of 51 genes regulated retromobility of Ty1his3AI driven only from the U3 promoter. Nineteen U3-dependent regulators (U3DRs) also controlled retromobility of Ty1his3AI driven by the weak, TATA-less PSP2 promoter, suggesting reliance on the low activity of U3. Thirty-one U3DRs failed to modulate PPSP2-Ty1his3AI retromobility, suggesting dependence on the architecture of U3. To further investigate the U3-dependency of Ty1 regulators, we developed a novel fluorescence-based assay to monitor expression of p22-Gag, a restriction factor expressed from the internal Ty1i promoter. Many U3DRs had minimal effects on levels of Ty1 RNA, Ty1i RNA or p22-Gag. These findings uncover a role for the Ty1 promoter in integrating signals from diverse host factors to modulate Ty1 RNA biogenesis or fate.
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Affiliation(s)
- Alicia C. Salinero
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
| | - Simey Emerson
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Tayla C. Cormier
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - John Yin
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
| | - M. Joan Curcio
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
- *Correspondence: M. Joan Curcio,
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6
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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7
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Corda Y, Maestroni L, Luciano P, Najem MY, Géli V. Genome stability is guarded by yeast Rtt105 through multiple mechanisms. Genetics 2021; 217:6126811. [PMID: 33724421 DOI: 10.1093/genetics/iyaa035] [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: 06/11/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
Ty1 mobile DNA element is the most abundant and mutagenic retrotransposon present in the genome of the budding yeast Saccharomyces cerevisiae. Protein regulator of Ty1 transposition 105 (Rtt105) associates with large subunit of RPA and facilitates its loading onto a single-stranded DNA at replication forks. Here, we dissect the role of RTT105 in the maintenance of genome stability under normal conditions and upon various replication stresses through multiple genetic analyses. RTT105 is essential for viability in cells experiencing replication problems and in cells lacking functional S-phase checkpoints and DNA repair pathways involving homologous recombination. Our genetic analyses also indicate that RTT105 is crucial when cohesion is affected and is required for the establishment of normal heterochromatic structures. Moreover, RTT105 plays a role in telomere maintenance as its function is important for the telomere elongation phenotype resulting from the Est1 tethering to telomeres. Genetic analyses indicate that rtt105Δ affects the growth of several rfa1 mutants but does not aggravate their telomere length defects. Analysis of the phenotypes of rtt105Δ cells expressing NLS-Rfa1 fusion protein reveals that RTT105 safeguards genome stability through its role in RPA nuclear import but also by directly affecting RPA function in genome stability maintenance during replication.
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Affiliation(s)
- Yves Corda
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Pierre Luciano
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Maria Y Najem
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Géli
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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8
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Chromatin Structure and Drug Resistance in Candida spp. J Fungi (Basel) 2020; 6:jof6030121. [PMID: 32751495 PMCID: PMC7559719 DOI: 10.3390/jof6030121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/14/2022] Open
Abstract
Anti-microbial resistance (AMR) is currently one of the most serious threats to global human health and, appropriately, research to tackle AMR garnishes significant investment and extensive attention from the scientific community. However, most of this effort focuses on antibiotics, and research into anti-fungal resistance (AFR) is vastly under-represented in comparison. Given the growing number of vulnerable, immunocompromised individuals, as well as the positive impact global warming has on fungal growth, there is an immediate urgency to tackle fungal disease, and the disturbing rise in AFR. Chromatin structure and gene expression regulation play pivotal roles in the adaptation of fungal species to anti-fungal stress, suggesting a potential therapeutic avenue to tackle AFR. In this review we discuss both the genetic and epigenetic mechanisms by which chromatin structure can dictate AFR mechanisms and will present evidence of how pathogenic yeast, specifically from the Candida genus, modify chromatin structure to promote survival in the presence of anti-fungal drugs. We also discuss the mechanisms by which anti-chromatin therapy, specifically lysine deacetylase inhibitors, influence the acquisition and phenotypic expression of AFR in Candida spp. and their potential as effective adjuvants to mitigate against AFR.
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9
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Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res 2020; 47:10942-10955. [PMID: 31586407 PMCID: PMC6847430 DOI: 10.1093/nar/gkz856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/20/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022] Open
Abstract
The complex between Trm7 and Trm734 (Trm7–Trm734) from Saccharomyces cerevisiae catalyzes 2′-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7–Trm734 complex. Purified recombinant Trm7–Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7–Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7–Trm734. Small angle X-ray scattering reveals that Trm7–Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7–Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Keisuke Okada
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kazuaki Yoshii
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Shiraishi
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shinya Saijo
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
- To whom correspondence should be addressed. Tel: +81 89 927 8548; Fax: +81 89 927 9941;
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10
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Maxwell PH. Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. Mob DNA 2020; 11:16. [PMID: 32336995 PMCID: PMC7175516 DOI: 10.1186/s13100-020-00215-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogens Candida albicans and Cryptococcus neoformans, and the nonpathogenic species Saccharomyces cerevisiae and Schizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons from Saccharomyces cerevisiae and Tf1 and Tf2 retrotransposons from Schizosaccharomyces pombe to emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
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11
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Angelova MT, Dimitrova DG, Da Silva B, Marchand V, Jacquier C, Achour C, Brazane M, Goyenvalle C, Bourguignon-Igel V, Shehzada S, Khouider S, Lence T, Guerineau V, Roignant JY, Antoniewski C, Teysset L, Bregeon D, Motorin Y, Schaefer MR, Carré C. tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. Nucleic Acids Res 2020; 48:2050-2072. [PMID: 31943105 PMCID: PMC7038984 DOI: 10.1093/nar/gkaa002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022] Open
Abstract
2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.
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Affiliation(s)
- Margarita T Angelova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Caroline Jacquier
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Cyrinne Achour
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Mira Brazane
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Catherine Goyenvalle
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Valérie Bourguignon-Igel
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.,Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Salman Shehzada
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Souraya Khouider
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Tina Lence
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Guerineau
- Institut de Chimie de Substances Naturelles, Centre de Recherche de Gif CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Yves Roignant
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Damien Bregeon
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Yuri Motorin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Clément Carré
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
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12
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Barkova A, Asif-Laidin A, Lesage P. Genome-Wide Mapping of Yeast Retrotransposon Integration Target Sites. Methods Enzymol 2018; 612:197-223. [PMID: 30502942 DOI: 10.1016/bs.mie.2018.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are present in virtually all organisms. TE integration into genomes contributes to their structure and evolution, but can also be harmful in some cases. Deciphering where and how TE integration is targeted is fundamental to understand their intricate relationship with their host and explore the outcome of TE mobility on genome evolution and cell fitness. In general, TEs display integration site preference, which differs between elements. High-throughput mapping of de novo insertions by deep sequencing has recently allowed identifying genome-wide integration preferences of several TEs. These studies have provided invaluable clues to address the molecular determinants of integration site preference. Here, we provide a step-by-step methodology to generate massive de novo insertion events and prepare a library of genomic DNA for next-generation sequencing. We also describe a primary bioinformatic procedure to map these insertions in the genome. The whole procedure comes from our recent work on the integration of Ty1 in Saccharomyces cerevisiae, but could be easily adapted to the study of other TEs.
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Affiliation(s)
- Anastasia Barkova
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France
| | - Amna Asif-Laidin
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France.
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13
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Lin H, Cliften PF, Dutcher SK. MAPINS, a Highly Efficient Detection Method That Identifies Insertional Mutations and Complex DNA Rearrangements. PLANT PHYSIOLOGY 2018; 178:1436-1447. [PMID: 30206105 PMCID: PMC6288735 DOI: 10.1104/pp.18.00474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
Insertional mutagenesis, in which a piece of exogenous DNA is integrated randomly into the genomic DNA of the recipient cell, is a useful method to generate new mutants with phenotypes of interest. The unicellular green alga Chlamydomonas reinhardtii is an outstanding model for studying many biological processes. We developed a new computational algorithm, MAPINS (mapping insertions), to efficiently identify insertion sites created by the integration of an APHVIII (aminoglycoside 3'-phosphotransferase VIII) cassette that confers paromomycin resistance. Using whole-genome sequencing data, this method eliminates the need for genomic DNA manipulation and retains all the sequencing information provided by paired-end sequencing. We experimentally verified 38 insertion sites out of 41 sites (93%) identified by MAPINS from 20 paromomycin-resistant strains. Using meiotic analysis of 18 of these strains, we identified insertion sites that completely cosegregate with paromomycin resistance. In six of the seven strains with a mutant phenotype, we demonstrated complete cosegregation of the mutant phenotype and the verified insertion site. In addition, we provide direct evidence of complex rearrangements of genomic DNA in five strains, three of which involve the APHVIII insertion site. We suggest that strains obtained by insertional mutagenesis are more complicated than expected from previous analyses in Chlamydomonas To map the locations of some complex insertions, we designed 49 molecular markers based on differences identified via whole-genome sequencing between wild-type strains CC-124 and CC-125. Overall, MAPINS provides a low-cost, efficient method to characterize insertional mutants in Chlamydomonas.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Paul F Cliften
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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14
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Cheung S, Manhas S, Measday V. Retrotransposon targeting to RNA polymerase III-transcribed genes. Mob DNA 2018; 9:14. [PMID: 29713390 PMCID: PMC5911963 DOI: 10.1186/s13100-018-0119-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae (S. cerevisiae) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1-copia (Pseudoviridae) or Ty3-gypsy (Metaviridae) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes. This particular genomic locus provides a safe environment for Ty element insertion without disruption of the host genome and is a targeting strategy used by retrotransposons that insert into compact genomes of hosts such as S. cerevisiae and the social amoeba Dictyostelium. The mechanism by which Ty1 targeting is achieved has been recently solved due to the discovery of an interaction between Ty1 Integrase (IN) and RNA Pol III subunits. We describe the methods used to identify the Ty1-IN interaction with Pol III and the Ty1 targeting consequences if the interaction is perturbed. The details of Ty1 targeting are just beginning to emerge and many unexplored areas remain including consideration of the 3-dimensional shape of genome. We present a variety of other retrotransposon families that insert adjacent to Pol III-transcribed genes and the mechanism by which the host machinery has been hijacked to accomplish this targeting strategy. Finally, we discuss why retrotransposons selected Pol III-transcribed genes as a target during evolution and how retrotransposons have shaped genome architecture.
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Affiliation(s)
- Stephanie Cheung
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Savrina Manhas
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Food Science, Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Room 325-2205 East Mall, Vancouver, British Columbia V6T 1Z4 Canada
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15
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Manhas S, Ma L, Measday V. The yeast Ty1 retrotransposon requires components of the nuclear pore complex for transcription and genomic integration. Nucleic Acids Res 2018; 46:3552-3578. [PMID: 29514267 PMCID: PMC5909446 DOI: 10.1093/nar/gky109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/01/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Nuclear pore complexes (NPCs) orchestrate cargo between the cytoplasm and nucleus and regulate chromatin organization. NPC proteins, or nucleoporins (Nups), are required for human immunodeficiency virus type 1 (HIV-1) gene expression and genomic integration of viral DNA. We utilize the Ty1 retrotransposon of Saccharomyces cerevisiae (S. cerevisiae) to study retroviral integration because retrotransposons are the progenitors of retroviruses and have conserved integrase (IN) enzymes. Ty1-IN targets Ty1 elements into the genome upstream of RNA polymerase (Pol) III transcribed genes such as transfer RNA (tRNA) genes. Evidence that S. cerevisiae tRNA genes are recruited to NPCs prompted our investigation of a functional role for the NPC in Ty1 targeting into the genome. We find that Ty1 mobility is reduced in multiple Nup mutants that cannot be accounted for by defects in Ty1 gene expression, cDNA production or Ty1-IN nuclear entry. Instead, we find that Ty1 insertion upstream of tRNA genes is impaired. We also identify Nup mutants with wild type Ty1 mobility but impaired Ty1 targeting. The NPC nuclear basket, which interacts with chromatin, is required for both Ty1 expression and nucleosome targeting. Deletion of components of the NPC nuclear basket causes mis-targeting of Ty1 elements to the ends of chromosomes.
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Affiliation(s)
- Savrina Manhas
- Department of Biochemistry and Molecular Biology, 2350 Health Sciences Mall, Life Sciences Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Lina Ma
- Wine Research Centre, 2205 East Mall, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, 2350 Health Sciences Mall, Life Sciences Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Wine Research Centre, 2205 East Mall, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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16
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Rowley PA, Patterson K, Sandmeyer SB, Sawyer SL. Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS Genet 2018; 14:e1007325. [PMID: 29694349 PMCID: PMC5918913 DOI: 10.1371/journal.pgen.1007325] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Yeasts serve as hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the mobility of Ty retrotransposons. Specifically, changing the genetic sequence of NUP84 or NUP82 to match that of other Saccharomyces species alters the mobility of S. cerevisiae Ty1 and Ty3. Importantly, all tested housekeeping functions of NUP84 and NUP82 remained equivalent across species. Signatures of natural selection, resulting in altered interactions with viruses and parasitic genetic elements, are common in host defense proteins. Yet, few instances have been documented in essential housekeeping proteins. The nuclear pore complex is the gatekeeper of the nucleus. This study shows how the evolution of this large, ubiquitous eukaryotic complex can alter the replication of a molecular parasite, but concurrently maintain essential host functionalities regarding nucleocytoplasmic trafficking.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Suzanne B. Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
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17
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Salinero AC, Knoll ER, Zhu ZI, Landsman D, Curcio MJ, Morse RH. The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters. PLoS Genet 2018; 14:e1007232. [PMID: 29462141 PMCID: PMC5834202 DOI: 10.1371/journal.pgen.1007232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/02/2018] [Accepted: 01/30/2018] [Indexed: 12/24/2022] Open
Abstract
The Ty1 retrotransposons present in the genome of Saccharomyces cerevisiae belong to the large class of mobile genetic elements that replicate via an RNA intermediary and constitute a significant portion of most eukaryotic genomes. The retromobility of Ty1 is regulated by numerous host factors, including several subunits of the Mediator transcriptional co-activator complex. In spite of its known function in the nucleus, previous studies have implicated Mediator in the regulation of post-translational steps in Ty1 retromobility. To resolve this paradox, we systematically examined the effects of deleting non-essential Mediator subunits on the frequency of Ty1 retromobility and levels of retromobility intermediates. Our findings reveal that loss of distinct Mediator subunits alters Ty1 retromobility positively or negatively over a >10,000-fold range by regulating the ratio of an internal transcript, Ty1i, to the genomic Ty1 transcript. Ty1i RNA encodes a dominant negative inhibitor of Ty1 retromobility that blocks virus-like particle maturation and cDNA synthesis. These results resolve the conundrum of Mediator exerting sweeping control of Ty1 retromobility with only minor effects on the levels of Ty1 genomic RNA and the capsid protein, Gag. Since the majority of characterized intrinsic and extrinsic regulators of Ty1 retromobility do not appear to effect genomic Ty1 RNA levels, Mediator could play a central role in integrating signals that influence Ty1i expression to modulate retromobility. Retrotransposons are mobile genetic elements that copy their RNA genomes into DNA and insert the DNA copies into the host genome. These elements contribute to genome instability, control of host gene expression and adaptation to changing environments. Retrotransposons depend on numerous host factors for their own propagation and control. The retrovirus-like retrotransposon, Ty1, in the yeast Saccharomyces cerevisiae has been an invaluable model for retrotransposon research, and hundreds of host factors that regulate Ty1 retrotransposition have been identified. Non-essential subunits of the Mediator transcriptional co-activator complex have been identified as one set of host factors implicated in Ty1 regulation. Here, we report a systematic investigation of the effects of loss of these non-essential subunits of Mediator on Ty1 retrotransposition. Our findings reveal a heretofore unknown mechanism by which Mediator influences the balance between transcription from two promoters in Ty1 to modulate expression of an autoinhibitory transcript known as Ty1i RNA. Our results provide new insights into host control of retrotransposon activity via promoter choice and elucidate a novel mechanism by which the Mediator co-activator governs this choice.
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Affiliation(s)
- Alicia C. Salinero
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
| | - Elisabeth R. Knoll
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
| | - Z. Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States of America
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, United States of America
| | - M. Joan Curcio
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail: (MJC); (RHM)
| | - Randall H. Morse
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail: (MJC); (RHM)
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18
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Rai SK, Sangesland M, Lee M, Esnault C, Cui Y, Chatterjee AG, Levin HL. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes. PLoS Genet 2017; 13:e1006775. [PMID: 29232693 PMCID: PMC5741268 DOI: 10.1371/journal.pgen.1006775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/22/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. Retroviruses and retrotransposons are genetic elements that propagate by integrating into chromosomes of eukaryotic cells. Genetic disorders are being treated with retrovirus-based vectors that integrate corrective genes into the chromosomes of patients. Unfortunately, the vectors can alter expression of adjacent genes and depending on the position of integration, cancer genes can be induced. It is therefore essential that we understand how integration sites are selected. Interestingly, different retroviruses and retrotransposons have different profiles of integration sites. While specific proteins have been identified that select target sites, it’s not known what other cellular factors promote integration. In this paper, we report a comprehensive screen of host factors that promote LTR-retrotransposon integration in the widely-studied yeast, Schizosaccharomyces pombe. Unexpectedly, we found a wide range of pathways and host factors participate in integration. And importantly, we found the cellular processes that promote integration relative to recombination in S. pombe are the same that drive integration of LTR-retrotransposons in the distantly related yeast Saccharomyces cerevisiae. This suggests a specific set of cellular pathways are responsible for integration in a wide range of eukaryotic hosts.
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Affiliation(s)
- Sudhir Kumar Rai
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Maya Sangesland
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michael Lee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Caroline Esnault
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Yujin Cui
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Atreyi Ghatak Chatterjee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Henry L. Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
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19
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Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae. Genetics 2017; 207:1441-1456. [PMID: 29046400 PMCID: PMC5714458 DOI: 10.1534/genetics.117.300388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/12/2017] [Indexed: 11/26/2022] Open
Abstract
Transposons can impact the host genome by altering gene expression and participating in chromosome rearrangements. Therefore, organisms evolved different ways to minimize the level of transposition. In Saccharomyces cerevisiae and its close relative S. paradoxus, Ty1 copy number control (CNC) is mediated by the self-encoded restriction factor p22, which is derived from the GAG capsid gene and inhibits virus-like particle (VLP) assembly and function. Based on secondary screens of Ty1 cofactors, we identified LOC1, a RNA localization/ribosome biogenesis gene that affects Ty1 mobility predominantly in strains harboring Ty1 elements. Ribosomal protein mutants rps0bΔ and rpl7aΔ displayed similar CNC-specific phenotypes as loc1Δ, suggesting that ribosome biogenesis is critical for CNC. The level of Ty1 mRNA and Ty1 internal (Ty1i) transcripts encoding p22 was altered in these mutants, and displayed a trend where the level of Ty1i RNA increased relative to full-length Ty1 mRNA. The level of p22 increased in these mutants, and the half-life of p22 also increased in a loc1Δ mutant. Transcriptomic analyses revealed small changes in the level of Ty1 transcripts or efficiency of translation initiation in a loc1Δ mutant. Importantly, a loc1Δ mutant had defects in assembly of Gag complexes and packaging Ty1 RNA. Our results indicate that defective ribosome biogenesis enhances CNC by increasing the level of p22, and raise the possibility for versatile links between VLP assembly, its cytoplasmic environment, and a novel stress response.
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20
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Jezek M, Gast A, Choi G, Kulkarni R, Quijote J, Graham-Yooll A, Park D, Green EM. The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance. Epigenetics 2016; 12:93-104. [PMID: 27911222 DOI: 10.1080/15592294.2016.1265712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of Saccharomyces cerevisiae have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
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Affiliation(s)
- Meagan Jezek
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Alison Gast
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Grace Choi
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Rushmie Kulkarni
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Jeremiah Quijote
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Andrew Graham-Yooll
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - DoHwan Park
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Erin M Green
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
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21
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Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK. URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells. J Biol Chem 2016; 291:25516-25528. [PMID: 27780869 PMCID: PMC5207251 DOI: 10.1074/jbc.m116.741660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells.
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Affiliation(s)
- Paolo Mita
- From the Institute of Systems Genetics and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jeffrey N Savas
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Erica M Briggs
- the Departments of Biochemistry and Molecular Pharmacology
| | - Susan Ha
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Veena Gnanakkan
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - John R Yates
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Diane M Robins
- the Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Gregory David
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jef D Boeke
- From the Institute of Systems Genetics and
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Michael J Garabedian
- Urology, and
- Microbiology at New York University School of Medicine, New York, New York 10016
| | - Susan K Logan
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
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22
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Affiliation(s)
- John Novembre
- Department of Human Genetics and Department of Ecology and Evolutionary Biology, University of Chicago, Illinois 60637
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23
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Abstract
Long terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element of Saccharomyces cerevisiae is one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3-Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3-Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3-Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.
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24
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Tucker JM, Garfinkel DJ. Ty1 escapes restriction by the self-encoded factor p22 through mutations in capsid. Mob Genet Elements 2016; 6:e1154639. [PMID: 27141327 DOI: 10.1080/2159256x.2016.1154639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/04/2016] [Accepted: 02/11/2016] [Indexed: 12/26/2022] Open
Abstract
Ty1 is a long terminal repeat (LTR) retrotransposon belonging to the Ty1/copia family and is present in up to 32 full-length copies in Saccharomyces. Like retroviruses, Ty1 contains GAG and POL genes, LTRs, and replicates via an RNA intermediate within a virus-like particle (VLP). Although Ty1 retrotransposition is not infectious, uncontrolled replication can lead to detrimental effects on the host genome, including insertional mutagenesis and chromosomal rearrangements. Ty1 copy number control (CNC) limits replication and is mediated through a self-encoded protein called p22. p22 is translated from a subgenomic Ty1 RNA and encodes an amino-truncated version of the Gag protein. We highlight a recent study identifying Ty1 Gag, which comprises the VLP capsid and provides nucleic acid chaperone functions, as a direct target of p22-mediated inhibition. CNC-resistant (CNCR) mutations map within predicted helical domains of Gag, including those in the Ty1/copia pfam domain Retrotran_gag_2 (formerly UBN2) and a central region we refer to as the CNCR domain. CNCR Gag forms VLPs that exclude p22, thus restoring Ty1 replication. We discuss possible mechanisms for p22 inclusion in Ty1 VLPs and compare Ty1 CNC with retroviral restriction factors targeting capsid (CA).
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Affiliation(s)
- Jessica M Tucker
- Department of Biochemistry & Molecular Biology, University of Georgia , Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry & Molecular Biology, University of Georgia , Athens, GA, USA
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25
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Cheung S, Ma L, Chan PHW, Hu HL, Mayor T, Chen HT, Measday V. Ty1 Integrase Interacts with RNA Polymerase III-specific Subcomplexes to Promote Insertion of Ty1 Elements Upstream of Polymerase (Pol) III-transcribed Genes. J Biol Chem 2016; 291:6396-411. [PMID: 26797132 DOI: 10.1074/jbc.m115.686840] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 01/01/2023] Open
Abstract
Retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate and are derived from retroviruses. The Ty1 retrotransposon of Saccharomyces cerevisiae belongs to the Ty1/Copia superfamily, which is present in every eukaryotic genome. Insertion of Ty1 elements into the S. cerevisiae genome, which occurs upstream of genes transcribed by RNA Pol III, requires the Ty1 element-encoded integrase (IN) protein. Here, we report that Ty1-IN interacts in vivo and in vitro with RNA Pol III-specific subunits to mediate insertion of Ty1 elements upstream of Pol III-transcribed genes. Purification of Ty1-IN from yeast cells followed by mass spectrometry (MS) analysis identified an enrichment of peptides corresponding to the Rpc82/34/31 and Rpc53/37 Pol III-specific subcomplexes. GFP-Trap purification of multiple GFP-tagged RNA Pol III subunits from yeast extracts revealed that the majority of Pol III subunits co-purify with Ty1-IN but not two other complexes required for Pol III transcription, transcription initiation factors (TF) IIIB and IIIC. In vitro binding studies with bacterially purified RNA Pol III proteins demonstrate that Rpc31, Rpc34, and Rpc53 interact directly with Ty1-IN. Deletion of the N-terminal 280 amino acids of Rpc53 abrogates insertion of Ty1 elements upstream of the hot spot SUF16 tRNA locus and abolishes the interaction of Ty1-IN with Rpc37. The Rpc53/37 complex therefore has an important role in targeting Ty1-IN to insert Ty1 elements upstream of Pol III-transcribed genes.
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Affiliation(s)
- Stephanie Cheung
- From the Department of Biochemistry and Molecular Biology, Wine Research Centre, and
| | | | - Patrick H W Chan
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Hui-Lan Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115
| | - Thibault Mayor
- From the Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada and
| | - Hung-Ta Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115
| | - Vivien Measday
- From the Department of Biochemistry and Molecular Biology, Wine Research Centre, and
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26
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Suresh S, Ahn HW, Joshi K, Dakshinamurthy A, Kananganat A, Garfinkel DJ, Farabaugh PJ. Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon. Mob DNA 2015; 6:22. [PMID: 26664557 PMCID: PMC4673737 DOI: 10.1186/s13100-015-0053-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/30/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A large number of Saccharomyces cerevisiae cellular factors modulate the movement of the retrovirus-like transposon Ty1. Surprisingly, a significant number of chromosomal genes required for Ty1 transposition encode components of the translational machinery, including ribosomal proteins, ribosomal biogenesis factors, protein trafficking proteins and protein or RNA modification enzymes. RESULTS To assess the mechanistic connection between Ty1 mobility and the translation machinery, we have determined the effect of these mutations on ribosome biogenesis and Ty1 transcriptional and post-transcriptional regulation. Lack of genes encoding ribosomal proteins or ribosome assembly factors causes reduced accumulation of the ribosomal subunit with which they are associated. In addition, these mutations cause decreased Ty1 + 1 programmed translational frameshifting, and reduced Gag protein accumulation despite at least normal levels of Ty1 mRNA. Several ribosome subunit mutations increase the level of both an internally initiated Ty1 transcript and its encoded truncated Gag-p22 protein, which inhibits transposition. CONCLUSIONS Together, our results suggest that this large class of cellular genes modulate Ty1 transposition through multiple pathways. The effects are largely post-transcriptional acting at a variety of levels that may include translation initiation, protein stability and subcellular protein localization.
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Affiliation(s)
- Susmitha Suresh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Hyo Won Ahn
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Kartikeya Joshi
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - Arun Dakshinamurthy
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
- />Present address: Department of Nanosciences and Technology, Karunya University, Karunya Nagar, Coimbatore, 641 114 Tamil Nadu India
| | - Arun Kananganat
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
| | - David J. Garfinkel
- />Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Philip J. Farabaugh
- />Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, MD 21250 USA
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27
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Maxwell PH. What might retrotransposons teach us about aging? Curr Genet 2015; 62:277-82. [PMID: 26581630 DOI: 10.1007/s00294-015-0538-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 01/17/2023]
Abstract
Retrotransposons are activated as organisms age, based on work from several model systems. Since these mobile DNA elements can promote genome instability, this has raised the possibility that they can contribute to loss of cellular function with age. Many questions remain to be addressed about the relationship between retrotransposons and aging, so it is unclear if changes in their activity will be found to contribute to aging or to be a consequence of aging. A few broad perspectives are presented regarding how continued work on these elements could provide important insights into the aging process, regardless of whether their mobility is ultimately found to significantly contribute to reduced lifespan and healthspan.
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Affiliation(s)
- Patrick H Maxwell
- Department of Biological Sciences, Rensselaer Polytechnic Institute, CBIS Room 2123, 110 8th Street, Troy, NY, 12180, USA.
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28
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Abstract
tRNA modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. There are 7 cytoplasmic tRNA modifications in the yeast Saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. These enzymes include the deaminase Tad2-Tad3, and the methyltransferases Trm6-Trm61, Trm8-Trm82, Trm7-Trm732, and Trm7-Trm734, Trm9-Trm112, and Trm11-Trm112. We describe the occurrence and biological role of each modification, evidence for a required partner protein in S. cerevisiae and other eukaryotes, evidence for a single subunit in bacteria, and evidence for the role of the non-catalytic binding partner. Although it is unclear why these eukaryotic enzymes require partner proteins, studies of some 2-subunit modification enzymes suggest that the partner proteins help expand substrate range or allow integration of cellular activities.
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Affiliation(s)
- Michael P Guy
- a Department of Biochemistry and Biophysics; Center for RNA Biology ; University of Rochester School of Medicine ; Rochester , NY USA
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29
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Abstract
Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer.
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30
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Nishida Y, Pachulska-Wieczorek K, Błaszczyk L, Saha A, Gumna J, Garfinkel DJ, Purzycka KJ. Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions. Nucleic Acids Res 2015; 43:7414-31. [PMID: 26160887 PMCID: PMC4551931 DOI: 10.1093/nar/gkv695] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/26/2015] [Indexed: 12/13/2022] Open
Abstract
Ty1 Gag comprises the capsid of virus-like particles and provides nucleic acid chaperone (NAC) functions during retrotransposition in budding yeast. A subgenomic Ty1 mRNA encodes a truncated Gag protein (p22) that is cleaved by Ty1 protease to form p18. p22/p18 strongly inhibits transposition and can be considered an element-encoded restriction factor. Here, we show that only p22 and its short derivatives restrict Ty1 mobility whereas other regions of GAG inhibit mobility weakly if at all. Mutational analyses suggest that p22/p18 is synthesized from either of two closely spaced AUG codons. Interestingly, AUG1p18 and AUG2p18 proteins display different properties, even though both contain a region crucial for RNA binding and NAC activity. AUG1p18 shows highly reduced NAC activity but specific binding to Ty1 RNA, whereas AUG2p18 shows the converse behavior. p22/p18 affects RNA encapsidation and a mutant derivative defective for RNA binding inhibits the RNA chaperone activity of the C-terminal region (CTR) of Gag-p45. Moreover, affinity pulldowns show that p18 and the CTR interact. These results support the idea that one aspect of Ty1 restriction involves inhibition of Gag-p45 NAC functions by p22/p18-Gag interactions.
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Affiliation(s)
- Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Leszek Błaszczyk
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julita Gumna
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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31
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Abstract
Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
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32
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Saha A, Mitchell JA, Nishida Y, Hildreth JE, Ariberre JA, Gilbert WV, Garfinkel DJ. A trans-dominant form of Gag restricts Ty1 retrotransposition and mediates copy number control. J Virol 2015; 89:3922-38. [PMID: 25609815 PMCID: PMC4403431 DOI: 10.1128/jvi.03060-14] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/15/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Saccharomyces cerevisiae and Saccharomyces paradoxus lack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. Glutathione S-transferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation. IMPORTANCE Retrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both "host and parasite." To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication.
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Affiliation(s)
- Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Jessica A Mitchell
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Jonathan E Hildreth
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Joshua A Ariberre
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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33
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Ho KL, Ma L, Cheung S, Manhas S, Fang N, Wang K, Young B, Loewen C, Mayor T, Measday V. A role for the budding yeast separase, Esp1, in Ty1 element retrotransposition. PLoS Genet 2015; 11:e1005109. [PMID: 25822502 PMCID: PMC4378997 DOI: 10.1371/journal.pgen.1005109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/27/2015] [Indexed: 12/18/2022] Open
Abstract
Separase/Esp1 is a protease required at the onset of anaphase to cleave cohesin and thereby enable sister chromatid separation. Esp1 also promotes release of the Cdc14 phosphatase from the nucleolus to enable mitotic exit. To uncover other potential roles for separase, we performed two complementary genome-wide genetic interaction screens with a strain carrying the budding yeast esp1-1 separase mutation. We identified 161 genes that when mutated aggravate esp1-1 growth and 44 genes that upon increased dosage are detrimental to esp1-1 viability. In addition to the expected cell cycle and sister chromatid segregation genes that were identified, 24% of the genes identified in the esp1-1 genetic screens have a role in Ty1 element retrotransposition. Retrotransposons, like retroviruses, replicate through reverse transcription of an mRNA intermediate and the resultant cDNA product is integrated into the genome by a conserved transposon or retrovirus encoded integrase protein. We purified Esp1 from yeast and identified an interaction between Esp1 and Ty1 integrase using mass spectrometry that was subsequently confirmed by co-immunoprecipitation analysis. Ty1 transposon mobility and insertion upstream of the SUF16 tRNA gene are both reduced in an esp1-1 strain but increased in cohesin mutant strains. Securin/Pds1, which is required for efficient localization of Esp1 to the nucleus, is also required for efficient Ty1 transposition. We propose that Esp1 serves two roles to mediate Ty1 transposition - one to remove cohesin and the second to target Ty1-IN to chromatin.
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Affiliation(s)
- Krystina L. Ho
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lina Ma
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Cheung
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Savrina Manhas
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Fang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaiqian Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barry Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vivien Measday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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34
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Guy MP, Phizicky EM. Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (NEW YORK, N.Y.) 2015; 21:61-74. [PMID: 25404562 PMCID: PMC4274638 DOI: 10.1261/rna.047639.114] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Post-transcriptional tRNA modifications are critical for efficient and accurate translation, and have multiple different roles. Lack of modifications often leads to different biological consequences in different organisms, and in humans is frequently associated with neurological disorders. We investigate here the conservation of a unique circuitry for anticodon loop modification required for healthy growth in the yeast Saccharomyces cerevisiae. S. cerevisiae Trm7 interacts separately with Trm732 and Trm734 to 2'-O-methylate three substrate tRNAs at anticodon loop residues C₃₂ and N₃₄, and these modifications are required for efficient wybutosine formation at m(1)G₃₇ of tRNA(Phe). Moreover, trm7Δ and trm732Δ trm734Δ mutants grow poorly due to lack of functional tRNA(Phe). It is unknown if this circuitry is conserved and important for tRNA(Phe) modification in other eukaryotes, but a likely human TRM7 ortholog is implicated in nonsyndromic X-linked intellectual disability. We find that the distantly related yeast Schizosaccharomyces pombe has retained this circuitry for anticodon loop modification, that S. pombe trm7Δ and trm734Δ mutants have more severe phenotypes than the S. cerevisiae mutants, and that tRNA(Phe) is the major biological target. Furthermore, we provide evidence that Trm7 and Trm732 function is widely conserved throughout eukaryotes, since human FTSJ1 and THADA, respectively, complement growth defects of S. cerevisiae trm7Δ and trm732Δ trm734Δ mutants by modifying C₃₂ of tRNA(Phe), each working with the corresponding S. cerevisiae partner protein. These results suggest widespread importance of 2'-O-methylation of the tRNA anticodon loop, implicate tRNA(Phe) as the crucial substrate, and suggest that this modification circuitry is important for human neuronal development.
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Affiliation(s)
- Michael P Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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35
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El Hage A, Webb S, Kerr A, Tollervey D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet 2014; 10:e1004716. [PMID: 25357144 PMCID: PMC4214602 DOI: 10.1371/journal.pgen.1004716] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023] Open
Abstract
During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5′-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes. R-loops (RNA-DNA hybrids) are potentially deleterious for gene expression and genome stability, but can be beneficial, for example, during immunoglobulin gene class-switch recombination. Here we made use of antibody S9.6, with specificity for RNA-DNA duplexes independently of their sequence. The genome-wide distribution of R-loops in wild-type yeast showed association with the highly transcribed ribosomal DNA, and protein-coding genes, particularly the second exon of spliced genes. On RNA polymerase III loci such as the highly transcribed transfer RNA genes (tRNAs), R-loop accumulation was strongly detected in the absence of both ribonucleases H1 and H2 (RNase H1 and H2), indicating that R-loops are inherently formed but rapidly cleared by RNase H. Importantly, stable R-loops lead to reduced synthesis of tRNA precursors in mutants lacking RNase H and DNA topoisomerase activities. RNA-DNA hybrids associated with TY1 cDNA retrotransposition intermediates were elevated in the absence of RNase H, and this was accompanied by increased retrotransposition, in particular to 5′-flanking regions of tRNAs. Our findings show that RNase H participates in silencing of TY1 life cycle. Surprisingly, R-loops associated with mitochondrial transcription units were suppressed specifically by RNase H1. These findings have potentially important implications for understanding human diseases caused by mutations in RNase H.
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Affiliation(s)
- Aziz El Hage
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
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Stoycheva T. Methylmethane Sulfonate Increases the Level of Superoxide Anions in Yeast Cells. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ. Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. Epigenetics 2014; 9:513-22. [PMID: 24442241 DOI: 10.4161/epi.27645] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A complex interplay between multiple chromatin modifiers is critical for cells to regulate chromatin structure and accessibility during essential DNA-templated processes such as transcription. However, the coordinated activities of these chromatin modifiers in the regulation of gene expression are not fully understood. We previously determined that the budding yeast histone H4 methyltransferase Set5 functions together with Set1, the H3K4 methyltransferase, in specific cellular contexts. Here, we sought to understand the relationship between these evolutionarily conserved enzymes in the regulation of gene expression. We generated a comprehensive genetic interaction map of the functionally uncharacterized Set5 methyltransferase and expanded the existing genetic interactome of the global chromatin modifier Set1, revealing functional overlap of the two enzymes in chromatin-related networks, such as transcription. Furthermore, gene expression profiling via RNA-Seq revealed an unexpected synergistic role of Set1 and Set5 in repressing transcription of Ty transposable elements and genes located in subtelomeric regions. This study uncovers novel pathways in which the methyltransferase Set5 participates and, more importantly, reveals a partnership between Set1 and Set5 in transcriptional repression near repetitive DNA elements in budding yeast. Together, our results define a new functional relationship between histone H3 and H4 methyltransferases, whose combined activity may be implicated in preserving genomic integrity.
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Affiliation(s)
| | - Devin A King
- Department of Biology; Stanford University; Stanford, CA USA
| | - Erin M Green
- Department of Biology; Stanford University; Stanford, CA USA
| | | | - Richard Alexander
- Department of Cellular and Molecular Pharmacology; University of California San Francisco; San Francisco, CA USA
| | - Sean R Collins
- Department of Chemical and Systems Biology; Stanford University; Stanford, CA USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology; University of California San Francisco; San Francisco, CA USA
| | - Or P Gozani
- Department of Biology; Stanford University; Stanford, CA USA
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38
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mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases. Proc Natl Acad Sci U S A 2013; 110:E1641-50. [PMID: 23572591 DOI: 10.1073/pnas.1218515110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent global proteomic and genomic studies have determined that lysine acetylation is a highly abundant posttranslational modification. The next challenge is connecting lysine acetyltransferases (KATs) to their cellular targets. We hypothesize that proteins that physically interact with KATs may not only predict the cellular function of the KATs but may be acetylation targets. We have developed a mass spectrometry-based method that generates a KAT protein interaction network from which we simultaneously identify both in vivo acetylation sites and in vitro acetylation sites. This modified chromatin-immunopurification coupled to an in vitro KAT assay with mass spectrometry (mChIP-KAT-MS) was applied to the Saccharomyces cerevisiae KAT nucleosome acetyltransferase of histone H4 (NuA4). Using mChIP-KAT-MS, we define the NuA4 interactome and in vitro-enriched acetylome, identifying over 70 previously undescribed physical interaction partners for the complex and over 150 acetyl lysine residues, of which 108 are NuA4-specific in vitro sites. Through this method we determine NuA4 acetylation of its own subunit Epl1 is a means of self-regulation and identify a unique link between NuA4 and the spindle pole body. Our work demonstrates that this methodology may serve as a valuable tool in connecting KATs with their cellular targets.
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Checkley MA, Mitchell JA, Eizenstat LD, Lockett SJ, Garfinkel DJ. Ty1 gag enhances the stability and nuclear export of Ty1 mRNA. Traffic 2013; 14:57-69. [PMID: 22998189 PMCID: PMC3548082 DOI: 10.1111/tra.12013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 11/28/2022]
Abstract
Retrotransposon and retroviral RNA delivery to particle assembly sites is essential for their replication. mRNA and Gag from the Ty1 retrotransposon colocalize in cytoplasmic foci, which are required for transposition and may be the sites for virus-like particle (VLP) assembly. To determine which Ty1 components are required to form mRNA/Gag foci, localization studies were performed in a Ty1-less strain expressing galactose-inducible Ty1 plasmids (pGTy1) containing mutations in GAG or POL. Ty1 mRNA/Gag foci remained unaltered in mutants defective in Ty1 protease (PR) or deleted for POL. However, Ty1 mRNA containing a frameshift mutation (Ty1fs) that prevents the synthesis of all proteins accumulated in the nucleus. Ty1fs RNA showed a decrease in stability that was mediated by the cytoplasmic exosome, nonsense-mediated decay (NMD) and the processing body. Localization of Ty1fs RNA remained unchanged in an nmd2Δ mutant. When Gag and Ty1fs mRNA were expressed independently, Gag provided in trans increased Ty1fs RNA level and restored localization of Ty1fs RNA in cytoplasmic foci. Endogenously expressed Gag also localized to the nuclear periphery independent of RNA export. These results suggest that Gag is required for Ty1 mRNA stability, efficient nuclear export and localization into cytoplasmic foci.
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Affiliation(s)
- Mary Ann Checkley
- Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jessica A. Mitchell
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Linda D. Eizenstat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | | | - David J. Garfinkel
- Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
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Zhou ZX, Zhang MJ, Peng X, Takayama Y, Xu XY, Huang LZ, Du LL. Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method. Genome Res 2012; 23:705-15. [PMID: 23249883 PMCID: PMC3613587 DOI: 10.1101/gr.146357.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Spontaneous DNA damage may occur nonrandomly in the genome, especially when genome maintenance mechanisms are undermined. We developed single-strand DNA (ssDNA)–associated protein immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double-strand breaks (DSBs) as well as endogenously programmed DSBs for mating-type switching. Applying Rad52 SPI-seq to fission yeast mutants defective in DNA helicase Pfh1 or histone H3K56 deacetylase Hst4, led to global views of DNA lesion hotspots emerging in these mutants. We also found serendipitously that histone dosage aberration can activate retrotransposon Tf2 and cause the accumulation of a Tf2 cDNA species bound by Rad52. SPI-seq should be widely applicable for mapping sites of DNA damage and uncovering the causes of genome instability.
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Affiliation(s)
- Zhi-Xiong Zhou
- Graduate Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Clemens K, Bilanchone V, Beliakova-Bethell N, Larsen LSZ, Nguyen K, Sandmeyer S. Sequence requirements for localization and packaging of Ty3 retroelement RNA. Virus Res 2012; 171:319-31. [PMID: 23073180 DOI: 10.1016/j.virusres.2012.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 10/06/2012] [Accepted: 10/08/2012] [Indexed: 12/22/2022]
Abstract
Retroviruses and retrotransposons package genomic RNA into virus-like particles (VLPs) in a poorly understood process. Expression of the budding yeast retrotransposon Ty3 results in the formation of cytoplasmic Ty3 VLP assembly foci comprised of Ty3 RNA and proteins, and cellular factors associated with RNA processing body (PB) components, which modulate translation and effect nonsense-mediated decay (NMD). A series of Ty3 RNA variants were tested to understand the effects of read-through translation via programmed frameshifting on RNA localization and packaging into VLPs, and to identify the roles of coding and non-coding sequences in those processes. These experiments showed that a low level of read-through translation of the downstream open reading frame (as opposed to no translation or translation without frameshifting) is important for localization of full-length Ty3 RNA to foci. Ty3 RNA variants associated with PB components via independent determinants in the native Ty3 untranslated regions (UTRs) and in GAG3-POL3 sequences flanked by UTRs adapted from non-Ty3 transcripts. However, despite localization, RNAs containing GAG3-POL3 but lacking Ty3 UTRs were not packaged efficiently. Surprisingly, sequences within Ty3 UTRs, which bind the initiator tRNA(Met) proposed to provide the dimerization interface, were not required for packaging of full-length Ty3 RNA into VLPs. In summary, our results demonstrate that Gag3 is sufficient and required for localization and packaging of RNAs containing Ty3 UTRs and support a role for POL3 sequences, translation of which is attenuated by programmed frameshifting, in both localization and packaging of the Ty3 full-length gRNA.
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Affiliation(s)
- Kristina Clemens
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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Guy MP, Podyma BM, Preston MA, Shaheen HH, Krivos KL, Limbach PA, Hopper AK, Phizicky EM. Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA (NEW YORK, N.Y.) 2012; 18:1921-33. [PMID: 22912484 PMCID: PMC3446714 DOI: 10.1261/rna.035287.112] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/19/2012] [Indexed: 05/17/2023]
Abstract
Post-transcriptional modification of the tRNA anticodon loop is critical for translation. Yeast Trm7 is required for 2'-O-methylation of C(32) and N(34) of tRNA(Phe), tRNA(Trp), and tRNA(Leu(UAA)) to form Cm(32) and Nm(34), and trm7-Δ mutants have severe growth and translation defects, but the reasons for these defects are not known. We show here that overproduction of tRNA(Phe) suppresses the growth defect of trm7-Δ mutants, suggesting that the crucial biological role of Trm7 is the modification of tRNA(Phe). We also provide in vivo and in vitro evidence that Trm7 interacts with ORF YMR259c (now named Trm732) for 2'-O-methylation of C(32), and with Rtt10 (named Trm734) for 2'-O-methylation of N(34) of substrate tRNAs and provide evidence for a complex circuitry of anticodon loop modification of tRNA(Phe), in which formation of Cm(32) and Gm(34) drives modification of m(1)G(37) (1-methylguanosine) to yW (wyebutosine). Further genetic analysis shows that the slow growth of trm7-Δ mutants is due to the lack of both Cm(32) and Nm(34), and the accompanying loss of yW, because trm732-Δ trm734-Δ mutants phenocopy trm7-Δ mutants, whereas each single mutant is healthy; nonetheless, TRM732 and TRM734 each have distinct roles, since mutations in these genes have different genetic interactions with trm1-Δ mutants, which lack m(2,2)G(26) in their tRNAs. We speculate that 2'-O-methylation of the anticodon loop may be important throughout eukaryotes because of the widespread conservation of Trm7, Trm732, and Trm734 proteins, and the corresponding modifications, and because the putative human TRM7 ortholog FTSJ1 is implicated in nonsyndromic X-linked mental retardation.
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Affiliation(s)
- Michael P. Guy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Brandon M. Podyma
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Melanie A. Preston
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Hussam H. Shaheen
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kady L. Krivos
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Anita K. Hopper
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
- Corresponding authorE-mail
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Risler JK, Kenny AE, Palumbo RJ, Gamache ER, Curcio MJ. Host co-factors of the retrovirus-like transposon Ty1. Mob DNA 2012; 3:12. [PMID: 22856544 PMCID: PMC3522557 DOI: 10.1186/1759-8753-3-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/18/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Long-terminal repeat (LTR) retrotransposons have complex modes of mobility involving reverse transcription of their RNA genomes in cytoplasmic virus-like particles (VLPs) and integration of the cDNA copies into the host genome. The limited coding capacity of retrotransposons necessitates an extensive reliance on host co-factors; however, it has been challenging to identify co-factors that are required for endogenous retrotransposon mobility because retrotransposition is such a rare event. RESULTS To circumvent the low frequency of Ty1 LTR-retrotransposon mobility in Saccharomyces cerevisiae, we used iterative synthetic genetic array (SGA) analysis to isolate host mutations that reduce retrotransposition. Query strains that harbor a chromosomal Ty1his3AI reporter element and either the rtt101Δ or med1Δ mutation, both of which confer a hypertransposition phenotype, were mated to 4,847 haploid ORF deletion strains. Retrotransposition was measured in the double mutant progeny, and a set of 275 ORF deletions that suppress the hypertransposition phenotypes of both rtt101Δ and med1Δ were identified. The corresponding set of 275 retrotransposition host factors (RHFs) includes 45 previously identified Ty1 or Ty3 co-factors. More than half of the RHF genes have statistically robust human homologs (E < 1 x 10-10). The level of unintegrated Ty1 cDNA in 181 rhfΔ single mutants was altered <2-fold, suggesting that the corresponding co-factors stimulate retrotransposition at a step after cDNA synthesis. However, deletion of 43 RHF genes, including specific ribosomal protein and ribosome biogenesis genes and RNA degradation, modification and transport genes resulted in low Ty1 cDNA levels. The level of Ty1 Gag but not RNA was reduced in ribosome biogenesis mutants bud21Δ, hcr1Δ, loc1Δ, and puf6Δ. CONCLUSION Ty1 retrotransposition is dependent on multiple co-factors acting at different steps in the replication cycle. Human orthologs of these RHFs are potential, or in a few cases, presumptive HIV-1 co-factors in human cells. RHF genes whose absence results in decreased Ty1 cDNA include characterized RNA metabolism and modification genes, consistent with their having roles in early steps in retrotransposition such as expression, nuclear export, translation, localization, or packaging of Ty1 RNA. Our results suggest that Bud21, Hcr1, Loc1, and Puf6 promote efficient synthesis or stability of Ty1 Gag.
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Affiliation(s)
- Jenni K Risler
- Laboratory of Molecular Genetics, Wadsworth Center, Albany, NY, 12201, USA.
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44
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Baller JA, Gao J, Stamenova R, Curcio MJ, Voytas DF. A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. Genome Res 2012; 22:704-13. [PMID: 22219511 DOI: 10.1101/gr.129585.111] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ty1, the most abundant retrotransposon in Saccharomyces cerevisiae, integrates preferentially upstream of genes transcribed by RNA polymerase III (Pol III). Targeting is likely due to interactions between the Ty1 integration complex and a feature of chromatin characteristic of sites of Pol III transcription. To better understand Ty1 targeting determinants, >150,000 Ty1 insertions were mapped onto the S. cerevisiae genome sequence. Logistic regression was used to assess relationships between patterns of Ty1 integration and various genomic features, including genome-wide data sets of histone modifications and transcription-factor binding sites. Nucleosomes were positively associated with Ty1 insertions, and fine-scale mapping of insertions upstream of genes transcribed by Pol III indicated that Ty1 preferentially integrates into nucleosome-bound DNA near the H2A/H2B interface. Outside of genes transcribed by Pol III, Ty1 avoids coding sequences, a pattern that is not due to selection, but rather reflects a preference for nucleosome-rich sites flanking genes. Ty1 insertion sites were also mapped in four mutant lines that affect Ty1 transposition frequency or integration specificity (rrm3Δ, hos2Δ, rtt109Δ, and rad6Δ). Patterns of integration were largely preserved in the mutants, although significantly more insertions into coding sequences were observed in the rad6Δ strain, suggesting a loosening of target specificity in this mutant that lacks an enzyme involved in ubiquitinating H2A. Overall, our data suggest that nucleosomes are necessary for Ty1 integration, and that a secondary factor, likely a histone modification or nucleosome-bound factor enriched at sites of Pol III transcription, determines preferred target sites.
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Affiliation(s)
- Joshua A Baller
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
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45
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Kottom TJ, Limper AH. Substrate analysis of the Pneumocystis carinii protein kinases PcCbk1 and PcSte20 using yeast proteome microarrays provides a novel method for Pneumocystis signalling biology. Yeast 2011; 28:707-19. [PMID: 21905091 DOI: 10.1002/yea.1900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 07/14/2011] [Accepted: 08/04/2011] [Indexed: 11/08/2022] Open
Abstract
Pneumocystis carinii (Pc) undergoes morphological transitions between cysts and trophic forms. We have previously described two Pc serine/threonine kinases, termed PcCbk1 and PcSte20, with PcSte20 belonging to a family of kinases involved in yeast mating, while PcCbk1 is a member of a group of protein kinases involved in regulation of cell cycle, shape, and proliferation. As Pc remains genetically intractable, knowledge on specific substrates phosphorylated by these kinases remains limited. Utilizing the phylogenetic relatedness of Pc to Saccharomyces cerevisiae, we interrogated a yeast proteome microarray containing >4000 purified protein based peptides, leading to the identification of 18 potential PcCbk1 and 15 PcSte20 substrates (Z-score > 3.0). A number of these potential protein substrates are involved in bud site selection, polarized growth, and response to mating α factor and pseudohyphal and invasive growth. Full-length open reading frames suggested by the PcCbk1 and PcSte20 protoarrays were amplified and expressed. These five proteins were used as substrates for PcCbk1 or PcSte20, with each being highly phosphorylated by the respective kinase. Finally, to demonstrate the utility of this method to identify novel PcCbk1 and PcSte20 substrates, we analysed DNA sequence data from the partially complete Pc genome database and detected partial sequence information of potential PcCbk1 kinase substrates PcPxl1 and PcInt1. We additionally identified the potential PcSte20 kinase substrate PcBdf2. Full-length Pc substrates were cloned and expressed in yeast, and shown to be phosphorylated by the respective Pc kinases. In conclusion, the yeast protein microarray represents a novel crossover technique for identifying unique potential Pc kinase substrates.
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Affiliation(s)
- Theodore J Kottom
- Thoracic Diseases Research Unit, Department of Medicine and Biochemistry, 8-24 Stabile, Mayo Clinic, Rochester, MN 55905, USA
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46
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Shi Y, Stefan CJ, Rue SM, Teis D, Emr SD. Two novel WD40 domain-containing proteins, Ere1 and Ere2, function in the retromer-mediated endosomal recycling pathway. Mol Biol Cell 2011; 22:4093-107. [PMID: 21880895 PMCID: PMC3204071 DOI: 10.1091/mbc.e11-05-0440] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Regulated responses to extracellular signals depend on cell-surface proteins that are internalized and recycled back to the plasma membrane. Two novel WD40 domain proteins, Ere1 and Ere2 (endosomal recycling proteins), are found to mediate cargo-specific recognition by the retromer pathway. Regulated secretion, nutrient uptake, and responses to extracellular signals depend on cell-surface proteins that are internalized and recycled back to the plasma membrane. However, the underlying mechanisms that govern membrane protein recycling to the cell surface are not fully known. Using a chemical-genetic screen in yeast, we show that the arginine transporter Can1 is recycled back to the cell surface via two independent pathways mediated by the sorting nexins Snx4/41/42 and the retromer complex, respectively. In addition, we identify two novel WD40-domain endosomal recycling proteins, Ere1 and Ere2, that function in the retromer pathway. Ere1 is required for Can1 recycling via the retromer-mediated pathway, but it is not required for the transport of other retromer cargoes, such as Vps10 and Ftr1. Biochemical studies reveal that Ere1 physically interacts with internalized Can1. Ere2 is present in a complex containing Ere1 on endosomes and functions as a regulator of Ere1. Taken together, our results suggest that Snx4/41/42 and the retromer comprise two independent pathways for the recycling of internalized cell-surface proteins. Moreover, a complex containing the two novel proteins Ere1 and Ere2 mediates cargo-specific recognition by the retromer pathway.
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Affiliation(s)
- Yufeng Shi
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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47
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Bleykasten-Grosshans C, Neuvéglise C. Transposable elements in yeasts. C R Biol 2011; 334:679-86. [PMID: 21819950 DOI: 10.1016/j.crvi.2011.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/31/2011] [Indexed: 11/19/2022]
Abstract
With the development of new sequencing technologies in the past decade, yeast genomes have been extensively sequenced and their structures investigated. Transposable elements (TEs) are ubiquitous in eukaryotes and constitute a limited part of yeast genomes. However, due to their ability to move in genomes and generate dispersed repeated sequences, they contribute to modeling yeast genomes and thereby induce plasticity. This review assesses the TE contents of yeast genomes investigated so far. Their diversity and abundance at the inter- and intraspecific levels are presented, and their effects on gene expression and genome stability is considered. Recent results concerning TE-host interactions are also analyzed.
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Affiliation(s)
- Claudine Bleykasten-Grosshans
- CNRS UMR 7156, Laboratoire Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, 28 rue Goethe, 67083 Strasbourg cedex, France.
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Demogines A, East AM, Lee JH, Grossman SR, Sabeti PC, Paull TT, Sawyer SL. Ancient and recent adaptive evolution of primate non-homologous end joining genes. PLoS Genet 2010; 6:e1001169. [PMID: 20975951 PMCID: PMC2958818 DOI: 10.1371/journal.pgen.1001169] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 09/21/2010] [Indexed: 02/07/2023] Open
Abstract
In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to characterize the molecular evolution of the human NHEJ pathway, we generated large simian primate sequence datasets for NHEJ genes. Codon-based models of gene evolution yielded statistical support for the recurrent positive selection of five NHEJ genes during primate evolution: XRCC4, NBS1, Artemis, POLλ, and CtIP. Analysis of human polymorphism data using the composite of multiple signals (CMS) test revealed that XRCC4 has also been subjected to positive selection in modern humans. Crystal structures are available for XRCC4, Nbs1, and Polλ; and residues under positive selection fall exclusively on the surfaces of these proteins. Despite the positive selection of such residues, biochemical experiments with variants of one positively selected site in Nbs1 confirm that functions necessary for DNA repair and checkpoint signaling have been conserved. However, many viruses interact with the proteins of the NHEJ pathway as part of their infectious lifecycle. We propose that an ongoing evolutionary arms race between viruses and NHEJ genes may be driving the surprisingly rapid evolution of these critical genes. Because all cells experience DNA damage, they must also have mechanisms for repairing DNA. When the proteins that repair DNA malfunction, mutation and disease often result. Based on their fundamental importance, DNA repair proteins would be expected to be well preserved over evolutionary time in order to ensure optimal DNA repair function. However, a previous genome-wide study of molecular evolution in Saccharomyces yeast identified the non-homologous end joining (NHEJ) DNA repair pathway as one of the two most rapidly evolving pathways in the yeast genome. In order to analyze the evolution of this pathway in humans, we have generated large evolutionary sequence sets of NHEJ genes from our primate relatives. Similar to the scenario in yeast, several genes in this pathway are evolving rapidly in primate genomes and in modern human populations. Thus, complex and seemingly opposite selective forces are shaping the evolution of these important DNA repair genes. The finding that NHEJ genes are rapidly evolving in species groups as diverse as yeasts and primates indicates a systematic perturbation of the NHEJ pathway, one that is potentially important to human health.
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Affiliation(s)
- Ann Demogines
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alysia M. East
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ji-Hoon Lee
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- The Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Sharon R. Grossman
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Pardis C. Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tanya T. Paull
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- The Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Sara L. Sawyer
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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49
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BUD22 affects Ty1 retrotransposition and ribosome biogenesis in Saccharomyces cerevisiae. Genetics 2010; 185:1193-205. [PMID: 20498295 DOI: 10.1534/genetics.110.119115] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A variety of cellular factors affect the movement of the retrovirus-like transposon Ty1. To identify genes involved in Ty1 virus-like particle (VLP) function, the level of the major capsid protein (Gag-p45) and its proteolytic precursor (Gag-p49p) was monitored in a subset of Ty1 cofactor mutants. Twenty-nine of 87 mutants contained alterations in the level of Gag; however, only bud22Delta showed a striking defect in Gag processing. BUD22 affected the +1 translational frameshifting event required to express the Pol proteins protease, integrase, and reverse transcriptase. Therefore, it is possible that the bud22Delta mutant may not produce enough functional Ty1 protease to completely process Gag-p49 to p45. Furthermore, BUD22 is required for 18S rRNA processing and 40S subunit biogenesis and influences polysome density. Together our results suggest that BUD22 is involved in a step in ribosome biogenesis that not only affects general translation, but also may alter the frameshifting efficiency of ribosomes, an event central to Ty1 retrotransposition.
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Han JS. Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions. Mob DNA 2010; 1:15. [PMID: 20462415 PMCID: PMC2881922 DOI: 10.1186/1759-8753-1-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 05/12/2010] [Indexed: 12/22/2022] Open
Abstract
Non-long terminal repeat (non-LTR) retrotransposons are present in most eukaryotic genomes. In some species, such as humans, these elements are the most abundant genome sequence and continue to replicate to this day, creating a source of endogenous mutations and potential genotoxic stress. This review will provide a general outline of the replicative cycle of non-LTR retrotransposons. Recent findings regarding the host regulation of non-LTR retrotransposons will be summarized. Finally, future directions of interest will be discussed.
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Affiliation(s)
- Jeffrey S Han
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD, USA.
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