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Guo D, Xu W, Cui T, Rong Q, Wu Q. Protein-coding circular RNA enhances antiviral immunity via JAK/STAT pathway in Drosophila. mBio 2024:e0146924. [PMID: 39158293 DOI: 10.1128/mbio.01469-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/11/2024] [Indexed: 08/20/2024] Open
Abstract
RNA interference (RNAi) drives powerful antiviral immunity in plants and animals so that many viruses must express viral suppressor of RNAi (VSR) to establish virulent infection. However, little is known about the immune responses conferring resistance against viruses that have evolved the counter-defensive strategy to suppress antiviral RNAi. In this study, we discover that Drosophila cells infected with Drosophila C virus (DCV), a natural viral pathogen of Drosophila known to harbor a potent VSR, exhibit heightened expression of circular RNA circZfh1. circZfh1 confers virus resistance in the presence of viral suppression of antiviral RNAi. Furthermore, we validate that circZfh1 encodes a 274-amino acid protein, CRAV, essential for its antiviral activity. Notably, CRAV differs from its parental Zfh1 gene in a different reading frame, with the C-terminal 69 amino acids unique to CRAV. Our analysis also reveals the presence of CRAV in species within the melanogaster subgroup, with the C-terminal unique fragment undergoing accelerated evolution. Expression of CRAV upregulates the expression of the cytokine Upd3, which binds to its receptor, stimulating the JAK-STAT pathway and enhancing the immune response to DCV infection. Notably, CRISPR/Cas9 knockout of circZfh1 significantly enhances DCV replication in vitro and in vivo, with circZfh1-knockout adult flies displaying heightened disease susceptibility to DCV. In summary, our findings unveil a Drosophila protein-coding circular RNA that activates an innate immune signaling pathway crucial for virus resistance following the suppression of antiviral RNAi by viruses, thereby elucidating a novel counter-defensive strategy.IMPORTANCEEukaryotic hosts possess a complex, multilayered immune system that guards against pathogen invasion. In fruit flies, RNA interference (RNAi) drives robust antiviral immunity, prompting many viruses to express viral suppressors of RNAi (VSRs) to establish virulent infections. However, little is known about immune responses that confer resistance against viruses with potent VSRs. In this study, we discovered that Drosophila cells infected with Drosophila C virus (DCV), a natural viral pathogen possessing a potent VSR, upregulated the expression of circular RNA circZfh1. circZfh1 exhibits DCV-specific antiviral activity, encoding a 274-amino acid protein, CRAV, crucial for its antiviral effects. As a different reading frame from its parental Zfh1 gene, the C-terminal 69 amino acids are unique to CRAV, undergoing faster evolution. CRAV activates the JAK-STAT pathway, enhancing the immune response to DCV infection. Therefore, our work uncovers a new strategy for suppressing viral counter-defense through protein-coding circular RNA in fruit flies.
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Affiliation(s)
- Dongyang Guo
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Wen Xu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Ting Cui
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Qiqi Rong
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
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2
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Nikolenko JV, Georgieva SG, Kopytova DV. Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes. Mol Biol 2023. [DOI: 10.1134/s0026893323010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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3
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CMTr cap-adjacent 2'-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses. Nat Commun 2022; 13:1209. [PMID: 35260552 PMCID: PMC8904806 DOI: 10.1038/s41467-022-28549-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Cap-adjacent nucleotides of animal, protist and viral mRNAs can be O-methylated at the 2‘ position of the ribose (cOMe). The functions of cOMe in animals, however, remain largely unknown. Here we show that the two cap methyltransferases (CMTr1 and CMTr2) of Drosophila can methylate the ribose of the first nucleotide in mRNA. Double-mutant flies lack cOMe but are viable. Consistent with prominent neuronal expression, they have a reward learning defect that can be rescued by conditional expression in mushroom body neurons before training. Among CMTr targets are cell adhesion and signaling molecules. Many are relevant for learning, and are also targets of Fragile X Mental Retardation Protein (FMRP). Like FMRP, cOMe is required for localization of untranslated mRNAs to synapses and enhances binding of the cap binding complex in the nucleus. Hence, our study reveals a mechanism to co-transcriptionally prime mRNAs by cOMe for localized protein synthesis at synapses. The two cap methyltransferases (CMTrs) redundantly methylate riboses of first cap adjacent nucleotides in messenger RNAs in Drosophila. Here, CMTrs are required for reward learning and localization of untranslated messenger RNAs to synapses.
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Nikolenko JV, Vdovina YA, Fefelova EI, Glukhova AA, Nabirochkina EN, Kopytova DV. The SAGA Deubiquitinilation (DUB) Module Participates in Pol III-Dependent Transcription. Mol Biol 2021. [DOI: 10.1134/s0026893321020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Mazina MY, Vorobyeva NE. Chromatin Modifiers in Transcriptional Regulation: New Findings and Prospects. Acta Naturae 2021; 13:16-30. [PMID: 33959384 PMCID: PMC8084290 DOI: 10.32607/actanaturae.11101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/17/2020] [Indexed: 02/04/2023] Open
Abstract
Histone-modifying and remodeling complexes are considered the main coregulators that affect transcription by changing the chromatin structure. Coordinated action by these complexes is essential for the transcriptional activation of any eukaryotic gene. In this review, we discuss current trends in the study of histone modifiers and chromatin remodelers, including the functional impact of transcriptional proteins/ complexes i.e., "pioneers"; remodeling and modification of non-histone proteins by transcriptional complexes; the supplementary functions of the non-catalytic subunits of remodelers, and the participation of histone modifiers in the "pause" of RNA polymerase II. The review also includes a scheme illustrating the mechanisms of recruitment of the main classes of remodelers and chromatin modifiers to various sites in the genome and their functional activities.
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Affiliation(s)
- M. Yu. Mazina
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
| | - N. E. Vorobyeva
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
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6
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Fursova NA, Mazina MY, Nikolenko JV, Vorobyova NE, Krasnov AN. Drosophila Zinc Finger Protein CG9890 Is Colocalized with Chromatin Modifying and Remodeling Complexes on Gene Promoters and Involved in Transcription Regulation. Acta Naturae 2020; 12:114-119. [PMID: 33456983 PMCID: PMC7800599 DOI: 10.32607/actanaturae.11056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we conducted a genome-wide study of the zinc finger protein
CG9890 and showed that it is localized mostly on the promoters of active genes.
The CG9890 binding sites are low-nucleosome-density regions and are colocalized
with the chromatin modifying and remodeling complexes SAGA and dSWI/SNF, as
well as with the ORC replication complex. The CG9890 protein was shown to be
involved in the regulation of the expression of some genes on the promoters of
which it is located, with the ecdysone cascade genes accounting for a
significant percentage of these genes. Thus, the CG9890 protein is a new member
of the transcriptional network which is localized on active promoters,
interacts with the main transcription and replication complexes, and is
involved in the regulation of both basal and inducible transcription.
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Affiliation(s)
- N. A. Fursova
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. Y. Mazina
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - J. V. Nikolenko
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - N. E. Vorobyova
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - A. N. Krasnov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
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Cornelio-Parra DV, Goswami R, Costanzo K, Morales-Sosa P, Mohan RD. Function and regulation of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) deubiquitinase module. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194630. [PMID: 32911111 DOI: 10.1016/j.bbagrm.2020.194630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/27/2022]
Abstract
The Spt-Ada-Gcn5 Acetyltransferase (SAGA) chromatin modifying complex is a critical regulator of gene expression and is highly conserved across species. Subunits of SAGA arrange into discrete modules with lysine aceyltransferase and deubiquitinase activities housed separately. Mutation of the SAGA deubiquitinase module can lead to substantial biological misfunction and diseases such as cancer, neurodegeneration, and blindness. Here, we review the structure and functions of the SAGA deubiquitinase module and regulatory mechanisms acting to control these.
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Nuño-Cabanes C, Rodríguez-Navarro S. The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194607. [PMID: 32712338 DOI: 10.1016/j.bbagrm.2020.194607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Gene expression, the decoding of DNA information into accessible instructions for protein synthesis, is a complex process in which multiple steps, including transcription, mRNA processing and mRNA export, are regulated by different factors. One of the first steps in this process involves chemical and structural changes in chromatin to allow transcription. For such changes to occur, histone tail and DNA epigenetic modifications foster the binding of transcription factors to promoter regions. The SAGA coactivator complex plays a crucial role in this process by mediating histone acetylation through Gcn5, and histone deubiquitination through Ubp8 enzymes. However, most SAGA subunits interact physically with other proteins beyond the SAGA complex. These interactions could represent SAGA-independent functions or a mechanism to widen SAGA multifunctionality. Among the different mechanisms to perform more than one function, protein moonlighting defines unrelated molecular activities for the same polypeptide sequence. Unlike pleiotropy, where a single gene can affect different phenotypes, moonlighting necessarily involves separate functions of a protein at the molecular level. In this review we describe in detail some of the alternative physical interactions of several SAGA subunits. In some cases, the alternative role constitutes a clear moonlighting function, whereas in most of them the lack of molecular evidence means that we can only define these interactions as promiscuous that require further work to verify if these are moonlighting functions.
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain.
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9
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Zhang L, Xu W, Gao X, Li W, Qi S, Guo D, Ajayi OE, Ding SW, Wu Q. lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila. Cell Host Microbe 2020; 27:115-128.e8. [PMID: 31917956 DOI: 10.1016/j.chom.2019.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/10/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
Antiviral immunity in insects is mediated by the RNA interference (RNAi) pathway. Viruses evade antiviral RNAi by expressing virulence factors known as viral suppressors of RNAi (VSR). Here, we report the identification of VINR, a Drosophila VSR-interacting long non-coding (lnc) RNA that activates non-canonical innate immune signaling upon detection of the dsRNA-binding VSR of Drosophila C virus (DCV). VINR is required for the induction of antimicrobial peptide (AMP) genes but dispensable for antiviral RNAi. VINR functions by preventing the ubiquitin proteasome-dependent degradation of Cactin, a coiled-coil and arginine-serine-rich domain-containing protein that regulates a non-cannonical antimicrobial pathway for AMP induction. CRISPR-Cas9 knockout of VINR in Drosophila cells enhances DCV replication independently of antiviral RNAi, and VINR-knockout adult flies exhibit enhanced disease susceptibility to DCV and bacteria. Our findings reveal a counter counter-defense strategy activated by a lncRNA in response to the viral suppression of the primary antiviral RNAi immunity.
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Affiliation(s)
- Liqin Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wen Xu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinlei Gao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenjie Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shuishui Qi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dongyang Guo
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Olugbenga Emmanuel Ajayi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside CA, USA
| | - Qingfa Wu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
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10
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Nikolenko JV, Kurshakova MM, Krasnov AN. Multifunctional ENY2 Protein Interacts with RNA Helicase MLE. DOKL BIOCHEM BIOPHYS 2020; 489:407-410. [DOI: 10.1134/s1607672919060140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Indexed: 11/23/2022]
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11
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Nabirochkina EN, Kurshakova MM, Georgieva SG, Kopytova DV. The role of SAGA in the transcription and export of mRNA. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
SAGA/TFTC, which is a histone acetyltransferase complex, plays an important role in the regulation of transcription. We have identified that the metazoan TFTC/STAGA complexes had histone H2A and H2B deubiquitinase activity that is carried out by a DUBm (deubiquitination module). We studied the DUBm of SAGA in Drosophila melanogaster and identified Drosophila homologs of yeast DUBm components. Two subunits of DUBm (Sus1/ENY2 and Sgf11) were shown to have functions separate from DUBm function. Thus, Sus1/ENY2 was shown to be present in several different complexes. Sgf11 was found to be associated with the cap-binding complex (CBC) and recruited onto growing messenger ribonucleic acid (mRNA). Also, we have shown that Sgf11 interacted with the TREX-2/AMEX mRNA export complex and was essential for mRNA export from the nucleus. Immunostaining of the polytene chromosomes of Drosophila larvae revealed that Sgf11 is present at the sites of localization of snRNA genes. It was also found in immunostaining experiments that dPbp45, the subunit of the PBP complex, the key player in the snRNA transcription process, is associated not only with the snRNA gene localization sites, but with other sites of active transcription by PolII. We also revealed that Sgf11 was present at many active transcription sites in interbands and puffs on polytene chromosomes, Sgf11 was localized at all Brf1 (the component of the RNA polymerase III basal transcription complex) sites. We concluded that SAGA coactivated transcription of both the PolII and PolIII-dependent snRNA genes.
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12
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Popova VV, Orlova AV, Kurshakova MM, Nikolenko JV, Nabirochkina EN, Georgieva SG, Kopytova DV. The role of SAGA coactivator complex in snRNA transcription. Cell Cycle 2018; 17:1859-1870. [PMID: 29995556 DOI: 10.1080/15384101.2018.1489175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The general snRNA gene transcription apparatus has been extensively studied. However, the role of coactivators in this process is far from being clearly understood. Here, we have demonstrated that the Drosophila SAGA complex interacts with the PBP complex, the key component of the snRNA gene transcription apparatus, and is present at the promoter regions of the snRNA genes transcribed by both the RNA polymerase II and RNA polymerase III (U6 snRNA). We show that SAGA interacts with the Brf1 transcription factor, which is a part of the RNA polymerase III transcription apparatus and is present at promoters of a number of Pol III-transcribed genes. Mutations inactivating several SAGA subunit genes resulted in reduced snRNA levels in adult flies, indicating that SAGA is indeed the transcriptional coactivator for the snRNA genes. The transcription of the Pol II and Pol III-transcribed U genes was reduced by mutations in all tested SAGA complex subunits. Therefore, the transcription of the Pol II and Pol III-transcribed U genes was reduced by the mutations in the deubiquitinase module, as well as in the acetyltransferase module of the SAGA, indicating that the whole complex is essential for their transcription. Therefore, the SAGA complex activates snRNA genes suggesting its wide involvement in the regulation of gene transcription, and consequently, in the maintenance of cellular homeostasis.
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Affiliation(s)
- V V Popova
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - A V Orlova
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - M M Kurshakova
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - J V Nikolenko
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - E N Nabirochkina
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - S G Georgieva
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - D V Kopytova
- a Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
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13
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Mazina MY, Kovalenko EV, Derevyanko PK, Nikolenko JV, Krasnov AN, Vorobyeva NE. One signal stimulates different transcriptional activation mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:178-189. [PMID: 29410380 DOI: 10.1016/j.bbagrm.2018.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/10/2017] [Accepted: 01/15/2018] [Indexed: 12/30/2022]
Abstract
Transcriptional activation is often represented as a "one-step process" that involves the simultaneous recruitment of co-activator proteins, leading to a change in gene status. Using Drosophila developmental ecdysone-dependent genes as a model, we demonstrated that activation of transcription is instead a continuous process that consists of a number of steps at which different phases of transcription (initiation or elongation) are stimulated. Thorough evaluation of the behaviour of multiple transcriptional complexes during the early activation process has shown that the pathways by which activation proceeds for different genes may vary considerably, even in response to the same induction signal. RNA polymerase II recruitment is an important step that is involved in one of the pathways. RNA polymerase II recruitment is accompanied by the recruitment of a significant number of transcriptional coactivators as well as slight changes in the chromatin structure. The second pathway involves the stimulation of transcriptional elongation as its key step. The level of coactivator binding to the promoter shows almost no increase, whereas chromatin modification levels change significantly.
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Affiliation(s)
- Marina Yu Mazina
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Elena V Kovalenko
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Polina K Derevyanko
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Julia V Nikolenko
- Group of Studying an Association of Transcription and mRNA Transport, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Aleksey N Krasnov
- Group of Studying an Association of Transcription and mRNA Transport, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Nadezhda E Vorobyeva
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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14
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Melo-Cardenas J, Zhang Y, Zhang DD, Fang D. Ubiquitin-specific peptidase 22 functions and its involvement in disease. Oncotarget 2018; 7:44848-44856. [PMID: 27057639 PMCID: PMC5190139 DOI: 10.18632/oncotarget.8602] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 03/10/2016] [Indexed: 12/24/2022] Open
Abstract
Deubiquitylases remove ubiquitin moieties from different substrates to regulate protein activity and cell homeostasis. Since this posttranslational modification plays a role in several different cellular functions, its deregulation has been associated with different pathologies. Aberrant expression of the Ubiquitin-Specific Peptidase 22 (USP22) has been associated with poor cancer prognosis and neurological disorders. However, little is known about USP22 role in these pathologies or in normal physiology. This review summarizes the current knowledge about USP22 function from yeast to human and provides an overview of the possible mechanisms by which USP22 is emerging as a potential oncogene.
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Affiliation(s)
- Johanna Melo-Cardenas
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yusi Zhang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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15
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Rashpa R, Vazquez-Pianzola P, Colombo M, Hernandez G, Beuchle D, Berger F, Peischl S, Bruggmann R, Suter B. Cbp80 is needed for the expression of piRNA components and piRNAs. PLoS One 2017; 12:e0181743. [PMID: 28746365 PMCID: PMC5528831 DOI: 10.1371/journal.pone.0181743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 07/06/2017] [Indexed: 11/19/2022] Open
Abstract
Cap binding protein 80 (Cbp80) is the larger subunit of the nuclear cap-binding complex (nCBC), which is known to play important roles in nuclear mRNA processing, export, stability and quality control events. Reducing Cbp80 mRNA levels in the female germline revealed that Cbp80 is also involved in defending the germline against transposable elements. Combining such knockdown experiments with large scale sequencing of small RNAs further showed that Cbp80 is involved in the initial biogenesis of piRNAs as well as in the secondary biogenesis pathway, the ping-pong amplification cycle. We further found that Cbp80 knockdown not only led to the upregulation of transposons, but also to delocalization of Piwi, Aub and Ago3, key factors in the piRNA biosynthesis pathway. Furthermore, compared to controls, levels of Piwi and Aub were also reduced upon knock down of Cbp80. On the other hand, with the same treatment we could not detect significant changes in levels or subcellular distribution (nuage localization) of piRNA precursor transcripts. This shows that Cbp80 plays an important role in the production and localization of the protein components of the piRNA pathway and it seems to be less important for the production and export of the piRNA precursor transcripts.
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Affiliation(s)
- Ravish Rashpa
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | - Martino Colombo
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Greco Hernandez
- Division of Basic Research, National Institute of Cancer, Tlalpan, Mexico
| | - Dirk Beuchle
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Fabienne Berger
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Beat Suter
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail: (PV-P); (BS)
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16
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Shaposhnikov AV, Lebedeva LA, Chernioglo ES, Kachaev ZM, Abdrakhmanov A, Shidlovskii YV. Preparation and analysis of nuclear protein extract from Drosophila melanogaster embryos for studying transcription factors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162016060108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Popova VV, Glukhova AA, Georgieva SG, Kopytova DV. Interactions of the TREX-2 complex with mRNP particle of β-tubulin 56D gene. Mol Biol 2016. [DOI: 10.1134/s0026893316060157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Kopytova D, Popova V, Kurshakova M, Shidlovskii Y, Nabirochkina E, Brechalov A, Georgiev G, Georgieva S. ORC interacts with THSC/TREX-2 and its subunits promote Nxf1 association with mRNP and mRNA export in Drosophila. Nucleic Acids Res 2016; 44:4920-33. [PMID: 27016737 PMCID: PMC4889942 DOI: 10.1093/nar/gkw192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/11/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates the pre-replication complex assembly. In the literature, there are several reports of interaction of ORC with different RNAs. Here, we demonstrate for the first time a direct interaction of ORC with the THSC/TREX-2 mRNA nuclear export complex. The THSC/TREX-2 was purified from the Drosophila embryonic extract and found to bind with a fraction of the ORC. This interaction occurred via several subunits and was essential for Drosophila viability. Also, ORC was associated with mRNP, which was facilitated by TREX-2. ORC subunits interacted with the Nxf1 receptor mediating the bulk mRNA export. The knockdown of Orc5 led to a drop in the Nxf1 association with mRNP, while Orc3 knockdown increased the level of mRNP-bound Nxf1. The knockdown of Orc5, Orc3 and several other ORC subunits led to an accumulation of mRNA in the nucleus, suggesting that ORC participates in the regulation of the mRNP export.
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Affiliation(s)
- Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Yulii Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Elena Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Brechalov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Georgii Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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Krasnov AN, Mazina MY, Nikolenko JV, Vorobyeva NE. On the way of revealing coactivator complexes cross-talk during transcriptional activation. Cell Biosci 2016; 6:15. [PMID: 26913181 PMCID: PMC4765067 DOI: 10.1186/s13578-016-0081-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/09/2016] [Indexed: 08/07/2023] Open
Abstract
Transcriptional activation is a complex, multistage process implemented by hundreds of proteins. Many transcriptional proteins are organized into coactivator complexes, which participate in transcription regulation at numerous genes and are a driver of this process. The molecular action mechanisms of coactivator complexes remain largely understudied. Relevant publications usually deal with the involvement of these complexes in the entire process of transcription, and only a few studies are aimed to elucidate their functions at its particular stages. This review summarizes available information on the participation of key coactivator complexes in transcriptional activation. The timing of coactivator complex binding/removal has been used for restructuring previously described information about the transcriptional process. Several major stages of transcriptional activation have been distinguished based on the presence of covalent histone modifications and general transcriptional factors, and the recruitment and/or removal phases have been determined for each coactivator included in analysis. Recruitment of Mediator, SWItch/Sucrose Non-Fermentable and NUcleosome Remodeling Factor complexes during transcription activation has been investigated thoroughly; CHD and INOsitol auxotrophy 80 families are less well studied. In most cases, the molecular mechanisms responsible for the removal of certain coactivator complexes after the termination of their functions at the promoters are still not understood. On the basis of the summarized information, we propose a scheme that illustrates the involvement of coactivator complexes in different stages of the transcription activation process. This scheme may help to gain a deeper insight into the molecular mechanism of functioning of coactivator complexes, find novel participants of the process, and reveal novel structural or functional connections between different coactivators.
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Affiliation(s)
- Aleksey N Krasnov
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Marina Yu Mazina
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Julia V Nikolenko
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Nadezhda E Vorobyeva
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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21
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Brechalov AV, Georgieva SG, Soshnikova NV. Mammalian cells contain two functionally distinct PBAF complexes incorporating different isoforms of PHF10 signature subunit. Cell Cycle 2014; 13:1970-9. [PMID: 24763304 PMCID: PMC4111760 DOI: 10.4161/cc.28922] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The PBAF subtype of the mammalian chromatin remodeling SWI/SNF complex has wide and diverse functions in transcription regulation and development, being both transcription activator and repressor. However, a mechanism accounting for such functional diversity remains unclear. Human PHF10/BAF45a subunit of the PBAF complex plays an important role in brain development but has not been studied sufficiently. We have shown that the PHF10 gene encodes 2 types of evolutionarily conserved, ubiquitously expressed isoforms that are incorporated into the PBAF complex in a mutually exclusive manner. One isoform contains C-terminal tandem PHD fingers, which in the other isoform are replaced by the consensus sequence for phosphorylation-dependent SUMO 1 conjugation (PDSM). PBAF complexes containing different PHF10 isoforms can bind to the promoters of the same genes but produce different effects on the recruitment of Pol II to the promoter and on the level of gene transcription. In addition, it is only the PBAF with PHD-containing isoform that activates proliferation. Our study demonstrates the existence of functionally different PBAF complexes in mammalian cell. It also provides an insight into the molecular structure and role of human PHF10/BAF45a and characterizes it as an essential PBAF subunit.
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Affiliation(s)
- Alexander V Brechalov
- Department of Eukaryote Transcription Factors; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Transcription Factors; Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
| | - Sofia G Georgieva
- Department of Eukaryote Transcription Factors; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Transcription Factors; Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
| | - Nataliya V Soshnikova
- Department of Eukaryote Transcription Factors; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
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22
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Gurskiy DY, Kopytova DV, Georgieva SG, Nabirochkina EN. SAGA complex: Role in viability and development. Mol Biol 2013. [DOI: 10.1134/s0026893313060071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gurskiy DY, Nabirochkina EN, Kopytova DV. Role of multifunctional coactivator complex SAGA in regulation of eukaryotic gene expression. Mol Biol 2013. [DOI: 10.1134/s002689331306006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vorobyeva NE, Mazina MU, Golovnin AK, Kopytova DV, Gurskiy DY, Nabirochkina EN, Georgieva SG, Georgiev PG, Krasnov AN. Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome. Nucleic Acids Res 2013; 41:5717-30. [PMID: 23609538 PMCID: PMC3675495 DOI: 10.1093/nar/gkt297] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite increasing data on the properties of replication origins, molecular mechanisms underlying origin recognition complex (ORC) positioning in the genome are still poorly understood. The Su(Hw) protein accounts for the activity of best-studied Drosophila insulators. Here, we show that Su(Hw) recruits the histone acetyltransferase complex SAGA and chromatin remodeler Brahma to Su(Hw)-dependent insulators, which gives rise to regions with low nucleosome density and creates conditions for ORC binding. Depletion in Su(Hw) leads to a dramatic drop in the levels of SAGA, Brahma and ORC subunits and a significant increase in nucleosome density on Su(Hw)-dependent insulators, whereas artificial Su(Hw) recruitment itself is sufficient for subsequent SAGA, Brahma and ORC binding. In contrast to the majority of replication origins that associate with promoters of active genes, Su(Hw)-binding sites constitute a small proportion (6%) of ORC-binding sites that are localized preferentially in transcriptionally inactive chromatin regions termed BLACK and BLUE chromatin. We suggest that the key determinants of ORC positioning in the genome are DNA-binding proteins that constitute different DNA regulatory elements, including insulators, promoters and enhancers. Su(Hw) is the first example of such a protein.
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Affiliation(s)
- Nadezhda E Vorobyeva
- Department of Transcriptional Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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