1
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Kurshakova MM, Yakusheva YA, Georgieva SG. TREX-2-ORC Complex of D. melanogaster Participates in Nuclear Export of Histone mRNA. DOKL BIOCHEM BIOPHYS 2024; 514:11-15. [PMID: 38189888 PMCID: PMC11021305 DOI: 10.1134/s160767292370059x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 01/09/2024]
Abstract
The TREX-2-ORC protein complex of D. melanogaster is necessary for the export of the bulk of synthesized poly(A)-containing mRNA molecules from the nucleus to the cytoplasm through the nuclear pores. However, the role of this complex in the export of other types of RNA remains unknown. We have shown that TREX-2-ORC participates in the nuclear export of histone mRNAs: it associates with histone mRNPs, binds to histone H3 mRNA at the 3'-terminal part of the coding region, and participates in the export of histone mRNAs from the nucleus to the cytoplasm.
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Affiliation(s)
- M M Kurshakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Y A Yakusheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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2
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Vdovina YA, Georgieva SG, Kopytova DV. Interaction of mRNA with the C-Terminal Domain of PCID2, a Subunit of the TREX-2 Complex, Is Required for Its Export from the Nucleus to the Cytoplasm in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2023; 513:328-331. [PMID: 38066318 PMCID: PMC10810031 DOI: 10.1134/s1607672923700527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 01/26/2024]
Abstract
Following the transcription step, the newly synthesized mRNA is exported from the nucleus to the cytoplasm and further to the translation site. The TREX-2 complex is involved in the step of mRNA export from the nucleus to the cytoplasm. This complex in Drosophila melanogaster consists of four proteins: Xmas-2, PCID2, ENY2, and Sem1p. In our work, we have shown that deletion of the C-terminal sequence of PCID2 leads to a decrease in the interaction of the protein with RNA and to impaired mRNA export from the nucleus to the cytoplasm in D. melanogaster.
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Affiliation(s)
- Yu A Vdovina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - S G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Kopytova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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3
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Kurshakova MM, Georgieva SG, Kopytova DV. The Human TREX-2 Complex Interacts with Subunits of the ORC Complex. DOKL BIOCHEM BIOPHYS 2023; 513:346-349. [PMID: 38066323 PMCID: PMC10810029 DOI: 10.1134/s1607672923700552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 01/26/2024]
Abstract
The TREX-2 protein complex is the key complex involved in the export of mRNA from the nucleus to the cytoplasm through the nuclear pores. Previously, a joint protein complex of TREX-2 with ORC was isolated in D. melanogaster. It was shown that the interaction of TREX-2 with ORC is necessary for efficient mRNA export from the nucleus to the cytoplasm. In this work, we showed that the TREX-2-ORC joint complex is also formed in human cells.
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Affiliation(s)
- M M Kurshakova
- Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - S G Georgieva
- Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Kopytova
- Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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4
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Lee H, Kim S, Lee D. The versatility of the proteasome in gene expression and silencing: Unraveling proteolytic and non-proteolytic functions. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194978. [PMID: 37633648 DOI: 10.1016/j.bbagrm.2023.194978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The 26S proteasome consists of a 20S core particle and a 19S regulatory particle and critically regulates gene expression and silencing through both proteolytic and non-proteolytic functions. The 20S core particle mediates proteolysis, while the 19S regulatory particle performs non-proteolytic functions. The proteasome plays a role in regulating gene expression in euchromatin by modifying histones, activating transcription, initiating and terminating transcription, mRNA export, and maintaining transcriptome integrity. In gene silencing, the proteasome modulates the heterochromatin formation, spreading, and subtelomere silencing by degrading specific proteins and interacting with anti-silencing factors such as Epe1, Mst2, and Leo1. This review discusses the proteolytic and non-proteolytic functions of the proteasome in regulating gene expression and gene silencing-related heterochromatin formation. This article is part of a special issue on the regulation of gene expression and genome integrity by the ubiquitin-proteasome system.
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Affiliation(s)
- Hyesu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sungwook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
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5
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Pan H, Qin Y, Zhu J, Wang W, Liu Z, Huang X, Lam SM, Shui G, Wang Y, Jiang Y, Huang X. Centrins control chicken cone cell lipid droplet dynamics through lipid-droplet-localized SPDL1. Dev Cell 2023; 58:2528-2544.e8. [PMID: 37699389 DOI: 10.1016/j.devcel.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023]
Abstract
As evolutionarily conserved organelles, lipid droplets (LDs) carry out numerous functions and have various subcellular localizations in different cell types and species. In avian cone cells, there is a single apically localized LD. We demonstrated that CIDEA (cell death inducing DFFA like effector a) and microtubules promote the formation of the single LD in chicken cone cells. Centrins, which are well-known centriole proteins, target to the cone cell LD via their C-terminal calcium-binding domains. Centrins localize on cone cell LDs with the help of SPDL1-L (spindle apparatus coiled-coil protein 1-L), a previously uncharacterized isoform of the kinetochore-associated dynein adaptor SPDL1. The loss of CETN3 or overexpression of a truncated CETN1 abrogates the apical localization of the cone cell LD. Simulation analysis showed that multiple LDs or a single mispositioned LD reduces the light sensitivity. Collectively, our findings identify a role of centrins in the regulation of cone cell LD localization, which is important for the light sensitivity of cone cells.
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Affiliation(s)
- Huimin Pan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqiang Qin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinglin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhonghua Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou 450001, China.
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6
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Joshua IM, Lin M, Mardjuki A, Mazzola A, Höfken T. A Protein-Protein Interaction Analysis Suggests a Wide Range of New Functions for the p21-Activated Kinase (PAK) Ste20. Int J Mol Sci 2023; 24:15916. [PMID: 37958899 PMCID: PMC10647699 DOI: 10.3390/ijms242115916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The p21-activated kinases (PAKs) are important signaling proteins. They contribute to a surprisingly wide range of cellular processes and play critical roles in a number of human diseases including cancer, neurological disorders and cardiac diseases. To get a better understanding of PAK functions, mechanisms and integration of various cellular activities, we screened for proteins that bind to the budding yeast PAK Ste20 as an example, using the split-ubiquitin technique. We identified 56 proteins, most of them not described previously as Ste20 interactors. The proteins fall into a small number of functional categories such as vesicle transport and translation. We analyzed the roles of Ste20 in glucose metabolism and gene expression further. Ste20 has a well-established role in the adaptation to changing environmental conditions through the stimulation of mitogen-activated protein kinase (MAPK) pathways which eventually leads to transcription factor activation. This includes filamentous growth, an adaptation to nutrient depletion. Here we show that Ste20 also induces filamentous growth through interaction with nuclear proteins such as Sac3, Ctk1 and Hmt1, key regulators of gene expression. Combining our observations and the data published by others, we suggest that Ste20 has several new and unexpected functions.
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Affiliation(s)
| | - Meng Lin
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
| | - Ariestia Mardjuki
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
| | - Alessandra Mazzola
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Department of Biopathology and Medical and Forensic Biotechnologies, University of Palermo, 90133 Palermo, Italy
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, Uxbridge UB8 3PH, UK; (I.M.J.)
- Institute of Biochemistry, Kiel University, 24118 Kiel, Germany
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7
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Vdovina YA, Kurshakova MM, Georgieva SG, Kopytova DV. PCID2 Subunit of the Drosophila TREX-2 Complex Has Two RNA-Binding Regions. Curr Issues Mol Biol 2023; 45:5662-5676. [PMID: 37504273 PMCID: PMC10378293 DOI: 10.3390/cimb45070357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
Drosophila PCID2 is a subunit of the TREX-2 mRNA nuclear export complex. Although the complex has long been studied in eukaryotes, it is still unclear how TREX-2 interacts with mRNA in multicellular organisms. Here, the interaction between Drosophila PCID2 and the ras2 RNA was studied by EMSA. We show that the C-terminal region of the WH domain of PCID2 specifically binds the 3'-noncoding region of the ras2 RNA. While the same region of PCID2 interacts with the Xmas-2 subunit of the TREX-2 complex, PCID2 interacts with RNA independently of Xmas-2. An additional RNA-binding region (M region) was identified in the N-terminal part of the PCI domain and found to bind RNA nonspecifically. Point mutations of evolutionarily conserved amino acid residues in this region completely abolish the PCID2-RNA interaction, while a deletion of the C-terminal domain only partly decreases it. Thus, the specific interaction of PCID2 with RNA requires nonspecific PCID2-RNA binding.
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Affiliation(s)
- Yulia A Vdovina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria M Kurshakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sofia G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Daria V Kopytova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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8
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Kurshakova MM, Georgieva SG, Kopytova DV. The Xmas-2 Protein of Drosophila melanogaster Undergoes Cleavage into Two Fragments. DOKL BIOCHEM BIOPHYS 2023; 509:37-40. [PMID: 37340289 DOI: 10.1134/s1607672923700163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/22/2023]
Abstract
The TREX-2 complex integrates several stages of gene expression, such as transcriptional activation and mRNA export. In D. melanogaster, TREX-2 consists of four major proteins: Xmas-2, ENY2, PCID2, and Sem1p. The Xmas-2 protein is the core subunit of the complex, with which other TREX-2 subunits interact. Xmas-2 homologues were found in all higher eukaryotes. Previously, it was shown that the human Xmas-2 homologue, GANP protein, can undergo cleavage into two parts, probably during apoptosis. We showed that the Xmas-2 protein of D. melanogaster can also split into two fragments. The resulting fragments of the protein correspond to the two large Xmas-2 domains. Protein splitting is observed both in vivo and in vitro. However, Xmas-2 cleavage in D. melanogaster is observed under normal conditions and is probably a part of the mechanism of transcription and mRNA export regulation in D. melanogaster.
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Affiliation(s)
- M M Kurshakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Kopytova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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9
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Rodríguez-Banqueri A, Moliner-Culubret M, Mendes SR, Guevara T, Eckhard U, Gomis-Rüth FX. Structural insights into latency of the metallopeptidase ulilysin (lysargiNase) and its unexpected inhibition by a sulfonyl-fluoride inhibitor of serine peptidases. Dalton Trans 2023; 52:3610-3622. [PMID: 36857690 DOI: 10.1039/d3dt00458a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Peptidases are regulated by latency and inhibitors, as well as compatibilization and cofactors. Ulilysin from Methanosarcina acetivorans, also called lysargiNase, is an archaeal metallopeptidase (MP) that is biosynthesized as a zymogen with a 60-residue N-terminal prosegment (PS). In the presence of calcium, it self-activates to yield the mature enzyme, which specifically cleaves before basic residues and thus complements trypsin in proteomics workflows. Here, we obtained a low-resolution crystal structure of proulilysin, in which 28 protomers arranged as 14 dimers form a continuous double helix of 544 Å pitch that parallels cell axis b of the crystal. The PS includes two α-helices and obstructs the active-site cleft of the catalytic domain (CD) by traversing it in the opposite orientation of a substrate, and a cysteine blocks the catalytic zinc according to a "cysteine-switch mechanism". Moreover, the PS interacts through its first helix with an "S-loop" of the CD, which acts as an "activation segment" that lacks one of two essential calcium cations. Upon PS removal during maturation, the S-loop adopts its competent conformation and binds the second calcium ion. Next, we found that in addition to general MP inhibitors, ulilysin was competitively and reversibly inhibited by 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF; Ki = 4 μM). This is a compound that normally forms an irreversible covalent complex with serine peptidases but does not inhibit MPs. A high-resolution crystal structure of the complex revealed that the inhibitor penetrates the specificity pocket of ulilysin. A primary amine of the inhibitor salt-bridges an aspartate at the pocket bottom, thus mimicking the basic side chain of substrates. In contrast, the sulfonyl fluoride warhead is not involved and the catalytic zinc ion is freely accessible. Thus, the usage of inhibitor cocktails of peptidases, which typically contain AEBSF at ∼25-fold higher concentrations than the determined Ki, should be avoided when working with ulilysin. Finally, the structure of the complex, which occurred as a crystallographic dimer recurring in previous mature ulilysin structures, unveiled an N-terminal product fragment that delineated the non-primed side of the cleft. These results complement prior structures of ulilysin with primed-side product fragments and inhibitors.
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Affiliation(s)
- Arturo Rodríguez-Banqueri
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Marina Moliner-Culubret
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Soraia R Mendes
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Tibisay Guevara
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - Ulrich Eckhard
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory; Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC); Barcelona Science Park; c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain.
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10
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Moretti E, Noto D, Corsaro R, Collodel G. Focus on centrin in normal and altered human spermatozoa. Syst Biol Reprod Med 2023; 69:175-187. [PMID: 36892570 DOI: 10.1080/19396368.2023.2181115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
This review provides details on the role of centrin in human spermatozoa and in various forms of male infertility. Centrin is a calcium (Ca2+)-binding phosphoprotein that is located in the centrioles - which are typical structures of the sperm connecting piece and play a key role in centrosome dynamics during sperm morphogenesis - as well as in zygotes and early embryos during spindle assembly. In humans, three different centrin genes encoding three isoforms have been discovered. Centrin 1, the only one expressed in spermatozoa, seems to be lost inside the oocyte after fertilization. The sperm connecting piece is characterized by the presence of numerous proteins including centrin, that deserves particular attention because, in humans, it is enriched during maturation of the centrioles. In normal sperm, centrin 1 is visible as two distinct spots in the head-tail junction; however, in some defective spermatozoa, centrin 1 distribution is altered. Centrin has been studied in humans and animal models. Its mutations may lead to several structural alterations, such as serious defects in the connective piece and, subsequently, fertilization failure or incomplete embryonic development. However, the effects of these abnormalities on male fertility have not been fully studied. Because the presence and the function of centrin in the sperm connecting piece appears important for reproductive success, additional studies are needed to bring medical benefits in resolving some cases of idiopathic infertility.
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Affiliation(s)
- Elena Moretti
- Department Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Daria Noto
- Department Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Roberta Corsaro
- Department Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Giulia Collodel
- Department Molecular and Developmental Medicine, University of Siena, Siena, Italy
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11
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Bensidoun P, Reiter T, Montpetit B, Zenklusen D, Oeffinger M. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell 2022; 82:3856-3871.e6. [PMID: 36220102 PMCID: PMC10300651 DOI: 10.1016/j.molcel.2022.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
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Affiliation(s)
- Pierre Bensidoun
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Taylor Reiter
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Daniel Zenklusen
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada.
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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12
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Conformational Plasticity of Centrin 1 from Toxoplasma gondii in Binding to the Centrosomal Protein SFI1. Biomolecules 2022; 12:biom12081115. [PMID: 36009009 PMCID: PMC9406199 DOI: 10.3390/biom12081115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/01/2022] Open
Abstract
Centrins are calcium (Ca2+)-binding proteins that are involved in many cellular functions including centrosome regulation. A known cellular target of centrins is SFI1, a large centrosomal protein containing multiple repeats that represent centrin-binding motifs. Recently, a protein homologous to yeast and mammalian SFI1, denominated TgSFI1, which shares SFI1-repeat organization, was shown to colocalize at centrosomes with centrin 1 from Toxoplasma gondii (TgCEN1). However, the molecular details of the interaction between TgCEN1 and TgSFI1 remain largely unknown. Herein, combining different biophysical methods, including isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, we determined the binding properties of TgCEN1 and its individual N- and C-terminal domains to synthetic peptides derived from distinct repeats of TgSFI1. Overall, our data indicate that the repeats in TgSFI1 constitute binding sites for TgCEN1, but the binding modes of TgCEN1 to the repeats differ appreciably in terms of binding affinity, Ca2+ sensitivity, and lobe-specific interaction. These results suggest that TgCEN1 displays remarkable conformational plasticity, allowing for the distinct repeats in TgSFI1 to possess precise modes of TgCEN1 binding and regulation during Ca2+ sensing, which appears to be crucial for the dynamic association of TgCEN1 with TgSFI1 in the centrosome architecture.
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13
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Lim S, Liu Y, Rhie BH, Kim C, Ryu HY, Ahn SH. Sus1 maintains a normal lifespan through regulation of TREX-2 complex-mediated mRNA export. Aging (Albany NY) 2022; 14:4990-5012. [PMID: 35771153 PMCID: PMC9271307 DOI: 10.18632/aging.204146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Eukaryotic gene expression requires multiple cellular events, including transcription and RNA processing and transport. Sus1, a common subunit in both the Spt-Ada-Gcn5 acetyltransferase (SAGA) and transcription and export complex-2 (TREX-2) complexes, is a key factor in coupling transcription activation to mRNA nuclear export. Here, we report that the SAGA DUB module and TREX-2 distinctly regulate yeast replicative lifespan in a Sir2-dependent and -independent manner, respectively. The growth and lifespan impaired by SUS1 loss depend on TREX-2 but not on the SAGA DUB module. Notably, an increased dose of the mRNA export factors Mex67 and Dbp5 rescues the growth defect, shortened lifespan, and nuclear accumulation of poly(A)+ RNA in sus1Δ cells, suggesting that boosting the mRNA export process restores the mRNA transport defect and the growth and lifespan damage in sus1Δ cells. Moreover, Sus1 is required for the proper association of Mex67 and Dbp5 with the nuclear rim. Together, these data indicate that Sus1 links transcription and mRNA nuclear export to the lifespan control pathway, suggesting that prevention of an abnormal accumulation of nuclear RNA is necessary for maintenance of a normal lifespan.
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Affiliation(s)
- Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Byung-Ho Rhie
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Chun Kim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, Gyeonggi-do 15588, Republic of Korea
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14
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Nuclear mRNA Export and Aging. Int J Mol Sci 2022; 23:ijms23105451. [PMID: 35628261 PMCID: PMC9142925 DOI: 10.3390/ijms23105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
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15
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Troilo F, Pedretti M, Travaglini-Allocatelli C, Astegno A, Di Matteo A. Rapid kinetics of calcium dissociation from plant calmodulin and calmodulin-like proteins and effect of target peptides. Biochem Biophys Res Commun 2022; 590:103-108. [PMID: 34974297 DOI: 10.1016/j.bbrc.2021.12.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/02/2022]
Abstract
Calcium (Ca2+) signaling represents a universal information code in plants, playing crucial roles spanning developmental processes to stress responses. Ca2+ signals are decoded into defined plant adaptive responses by different Ca2+ sensing proteins, including calmodulin (CaM) and calmodulin-like (CML) proteins. Although major advances have been achieved in describing how these Ca2+ decoding proteins interact and regulate downstream target effectors, the molecular details of these processes remain largely unknown. Herein, the kinetics of Ca2+ dissociation from a conserved CaM and two CML isoforms from A. thaliana has been studied by fluorescence stopped-flow spectroscopy. Kinetic data were obtained for the isolated Ca2+-bound proteins as well as for the proteins complexed with different target peptides. Moreover, the lobe specific interactions between the Ca2+ sensing proteins and their targets were characterized by using a panel of protein mutants deficient in Ca2+ binding at the N-lobe or C-lobe. Results were analyzed and discussed in the context of the Ca2+-decoding and Ca2+-controlled target binding mechanisms in plants.
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Affiliation(s)
- Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
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16
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Structural Basis for the Functional Diversity of Centrins: A Focus on Calcium Sensing Properties and Target Recognition. Int J Mol Sci 2021; 22:ijms222212173. [PMID: 34830049 PMCID: PMC8622359 DOI: 10.3390/ijms222212173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 11/23/2022] Open
Abstract
Centrins are a family of small, EF hand-containing proteins that are found in all eukaryotes and are often complexed with centrosome-related structures. Since their discovery, centrins have attracted increasing interest due to their multiple, diverse cellular functions. Centrins are similar to calmodulin (CaM) in size, structure and domain organization, although in contrast to CaM, the majority of centrins possess at least one calcium (Ca2+) binding site that is non-functional, thus displaying large variance in Ca2+ sensing abilities that could support their functional versatility. In this review, we summarize current knowledge on centrins from both biophysical and structural perspectives with an emphasis on centrin-target interactions. In-depth analysis of the Ca2+ sensing properties of centrins and structures of centrins complexed with target proteins can provide useful insight into the mechanisms of the different functions of centrins and how these proteins contribute to the complexity of the Ca2+ signaling cascade. Moreover, it can help to better understand the functional redundancy of centrin isoforms and centrin-binding proteins.
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17
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De Magistris P. The Great Escape: mRNA Export through the Nuclear Pore Complex. Int J Mol Sci 2021; 22:ijms222111767. [PMID: 34769195 PMCID: PMC8583845 DOI: 10.3390/ijms222111767] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins that are crucial for its metabolism, some of which; like Mex67/MTR2-NXF1/NXT1; are key players for its translocation to the cytoplasm. In this review, I will summarize our current body of knowledge on the basic characteristics of mRNA export through the NPC. To be granted passage, the mRNP cargo needs to bind transport receptors, which facilitate the nuclear export. During NPC transport, mRNPs undergo compositional and conformational changes. The interactions between mRNP and the central channel of NPC are described; together with the multiple quality control steps that mRNPs undergo at the different rings of the NPC to ensure only proper export of mature transcripts to the cytoplasm. I conclude by mentioning new opportunities that arise from bottom up approaches for a mechanistic understanding of nuclear export.
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18
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Evolution and diversification of the nuclear pore complex. Biochem Soc Trans 2021; 49:1601-1619. [PMID: 34282823 PMCID: PMC8421043 DOI: 10.1042/bst20200570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022]
Abstract
The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.
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19
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The interplay of self-assembly and target binding in centrin 1 from Toxoplasma gondii. Biochem J 2021; 478:2571-2587. [PMID: 34114596 PMCID: PMC8286830 DOI: 10.1042/bcj20210295] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/17/2022]
Abstract
Centrins are conserved calcium (Ca2+)-binding proteins typically associated with centrosomes that have been implicated in several biological processes. In Toxoplasma gondii, a parasite that causes toxoplasmosis, three centrin isoforms have been recognized. We have recently characterized the metal binding and structural features of isoform 1 (TgCEN1), demonstrating that it possesses properties consistent with a role as a Ca2+ sensor and displays a Ca2+-dependent tendency to self-assemble. Herein, we expanded our studies, focusing on the self-association and target binding properties of TgCEN1 by combining biophysical techniques including dynamic light scattering, isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy. We found that the self-assembly process of TgCEN1 depends on different physicochemical factors, including Ca2+ concentration, temperature, and protein concentration, and is mediated by both electrostatic and hydrophobic interactions. The process is completely abolished upon removal of the first 21-residues of the protein and is significantly reduced in the presence of a binding target peptide derived from the human XPC protein (P17-XPC). Titration of P17-XPC to the intact protein and isolated domains showed that TgCEN1 possesses two binding sites with distinct affinities and Ca2+ sensitivity; a high-affinity site in the C-lobe which may be constitutively bound to the peptide and a low-affinity site in the N-lobe which is active only upon Ca2+ stimulus. Overall, our results suggest a specific mechanism of TgCEN1 for Ca2+-modulated target binding and support a N-to-C self-assembly mode, in which the first 21-residues of one molecule likely interact with the C-lobe of the other.
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20
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Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
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21
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Kurshakova MM, Kopytova DV, Georgieva SG. Study of the Interaction between Xmas-2, the Main Protein of TREX-2 mRNA Export Complex, and the Orc3 Protein, a Subunit of ORC Complex of D. melanogaster. DOKL BIOCHEM BIOPHYS 2021; 496:18-21. [PMID: 33689068 DOI: 10.1134/s1607672921010063] [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: 09/23/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/23/2022]
Abstract
The TREX-2 protein complex is the key participant in the export of mRNA from the nucleus to the cytoplasm through the nuclear pores. Previously, a protein complex of D. melanogaster consisting of TREX-2 and ORC complexes was purified. It was shown that, in the TREX-2-ORC complex, the Xmas-2 protein, which is the platform for TREX-2 assembly, interacts with the Orc3 protein. The aim of this work was to investigate what regions of the Xmas-2 amino acid sequence are involved in the interaction with Orc3. It was shown that the interaction of Xmas-2 with Orc3 requires a C-terminal region of Xmas-2 located downstream of the CID domain.
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Affiliation(s)
- M M Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - D V Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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22
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D'Andréa ÉD, Retel JS, Diehl A, Schmieder P, Oschkinat H, Pires JR. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. J Struct Biol 2021; 213:107715. [PMID: 33705979 DOI: 10.1016/j.jsb.2021.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The 106-residue protein Q4DY78 (UniProt accession number) from Trypanosoma cruzi is highly conserved in the related kinetoplastid pathogens Trypanosoma brucei and Leishmania major. Given the essentiality of its orthologue in T. brucei, the high sequence conservation with other trypanosomatid proteins, and the low sequence similarity with mammalian proteins, Q4DY78 is an attractive protein for structural characterization. Here, we solved the structure of Q4DY78 by solution NMR and evaluated its backbone dynamics. Q4DY78 is composed of five α -helices and a small, two-stranded antiparallel β-sheet. The backbone RMSD is 0.22 ± 0.05 Å for the representative ensemble of the 20 lowest-energy structures. Q4DY78 is overall rigid, except for N-terminal residues (V8 to I10), residues at loop 4 (K57 to G65) and residues at the C-terminus (F89 to F112). Q4DY78 has a short motif FPCAP that could potentially mediate interactions with the host cytoskeleton via interaction with EVH1 (Drosophila Enabled (Ena)/Vasodilator-stimulated phosphoprotein (VASP) homology 1) domains. Albeit Q4DY78 lacks calcium-binding motifs, its fold resembles that of eukaryotic calcium-binding proteins such as calcitracin, calmodulin, and polcacin Bet V4. We characterized this novel protein with a calcium binding fold without the capacity to bind calcium.
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Affiliation(s)
- Éverton Dias D'Andréa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil
| | - Joren Sebastian Retel
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Anne Diehl
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany; Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, Berlin 14195, Germany
| | - José Ricardo Pires
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil.
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23
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Glukhova AA, Kurshakova MM, Nabirochkina EN, Georgieva SG, Kopytova DV. PCID2, a subunit of the Drosophila TREX-2 nuclear export complex, is essential for both mRNA nuclear export and its subsequent cytoplasmic trafficking. RNA Biol 2021; 18:1969-1980. [PMID: 33602059 DOI: 10.1080/15476286.2021.1885198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The TREX-2 complex is essential for the general nuclear mRNA export in eukaryotes. TREX-2 interacts with the nuclear pore and transcriptional apparatus and links transcription to the mRNA export. However, it remains poorly understood how the TREX-2-dependent nuclear export is connected to the subsequent stages of mRNA trafficking. Here, we show that the PCID2 subunit of Drosophila TREX-2 is present in the cytoplasm of the cell. The cytoplasmic PCID2 directly interacts with the NudC protein and this interaction maintains its stability in the cytoplasm. Moreover, PCID2 is associated with the cytoplasmic mRNA and microtubules. The PCID2 knockdown blocks nuclear export of mRNA and also affects the general mRNA transport into the cytoplasm. These data suggest that PCID2 could be the link between the nuclear TREX-2-dependent export and the subsequent cytoplasmic trafficking of mRNA.
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Affiliation(s)
- A A Glukhova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - M M Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - E N Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - S G Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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24
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Lee ES, Wolf EJ, Ihn SSJ, Smith HW, Emili A, Palazzo AF. TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes. Nucleic Acids Res 2021; 48:11645-11663. [PMID: 33091126 PMCID: PMC7672458 DOI: 10.1093/nar/gkaa919] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] Open
Abstract
While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.
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Affiliation(s)
- Eliza S Lee
- University of Toronto, Department of Biochemistry, Canada
| | - Eric J Wolf
- University of Toronto, Department of Molecular Genetics, Canada
| | - Sean S J Ihn
- University of Toronto, Department of Biochemistry, Canada
| | | | - Andrew Emili
- University of Toronto, Department of Molecular Genetics, Canada.,Boston University School of Medicine, Department of Biochemistry, Boston, MA, USA
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25
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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26
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Nabirochkina EN, Kopytova DV. The Xmas-2 Homologues, the Main Component of the TREX-2 mRNA Export Complex. DOKL BIOCHEM BIOPHYS 2020; 495:325-328. [PMID: 33368044 DOI: 10.1134/s1607672920060101] [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: 07/17/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 11/23/2022]
Abstract
TREX-2 complex is responsible for general mRNA export from nucleus to cytoplasm in eukaryote. The main protein of TREX-2 complex of D. melanogaster is protein Xmas-2. Its homologues in yeast and humans are Sac3 and GANP proteins, respectively. All three proteins contain the highly conserved domain Sac3-GANP, which is essential for interaction of TREX-2 complex with mRNA and another protein of the complex, PCID2. We identified two Xmas-2 homologues in D. melanogaster using the Sac3-GANP family domain sequence. These proteins have a common domain responsible for interaction with the PCID2 protein and RNA and are present in other eukaryotes. The function of these proteins is unknown. However, on the basis of their structural organization, we can assume that they interact with nucleic acids.
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Affiliation(s)
- E N Nabirochkina
- Institute of Gene Biology, Russian Academy of Science, Moscow, Russia
| | - D V Kopytova
- Institute of Gene Biology, Russian Academy of Science, Moscow, Russia.
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27
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Eyboulet F, Jeronimo C, Côté J, Robert F. The deubiquitylase Ubp15 couples transcription to mRNA export. eLife 2020; 9:e61264. [PMID: 33226341 PMCID: PMC7682988 DOI: 10.7554/elife.61264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
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Affiliation(s)
- Fanny Eyboulet
- Institut de recherches cliniques de MontréalMontréalCanada
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - Célia Jeronimo
- Institut de recherches cliniques de MontréalMontréalCanada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du CHU de Québec-Université LavalQuébec CityCanada
| | - François Robert
- Institut de recherches cliniques de MontréalMontréalCanada
- Département de Médecine, Faculté de Médecine, Université de MontréalMontréalCanada
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28
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Mahesh G, Rivas GBS, Caster C, Ost EB, Amunugama R, Jones R, Allen DL, Hardin PE. Proteomic analysis of Drosophila CLOCK complexes identifies rhythmic interactions with SAGA and Tip60 complex component NIPPED-A. Sci Rep 2020; 10:17951. [PMID: 33087840 PMCID: PMC7578830 DOI: 10.1038/s41598-020-75009-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks keep time via ~ 24 h transcriptional feedback loops. In Drosophila, CLOCK-CYCLE (CLK-CYC) activators and PERIOD-TIMELESS (PER-TIM) repressors are feedback loop components whose transcriptional status varies over a circadian cycle. Although changes in the state of activators and repressors has been characterized, how their status is translated to transcriptional activity is not understood. We used mass spectrometry to identify proteins that interact with GFP-tagged CLK (GFP-CLK) in fly heads at different times of day. Many expected and novel interacting proteins were detected, of which several interacted rhythmically and were potential regulators of protein levels, activity or transcriptional output. Genes encoding these proteins were tested to determine if they altered circadian behavior via RNAi knockdown in clock cells. The NIPPED-A protein, a scaffold for the SAGA and Tip60 histone modifying complexes, interacts with GFP-CLK as transcription is activated, and reducing Nipped-A expression lengthens circadian period. RNAi analysis of other SAGA complex components shows that the SAGA histone deubiquitination (DUB) module lengthened period similarly to Nipped-A RNAi knockdown and weakened rhythmicity, whereas reducing Tip60 HAT expression drastically weakened rhythmicity. These results suggest that CLK-CYC binds NIPPED-A early in the day to promote transcription through SAGA DUB and Tip60 HAT activity.
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Affiliation(s)
- Guruswamy Mahesh
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Gustavo B S Rivas
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Courtney Caster
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Evan B Ost
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | | | | | | | - Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA.
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Gales JP, Kubina J, Geldreich A, Dimitrova M. Strength in Diversity: Nuclear Export of Viral RNAs. Viruses 2020; 12:E1014. [PMID: 32932882 PMCID: PMC7551171 DOI: 10.3390/v12091014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
The nuclear export of cellular mRNAs is a complex process that requires the orchestrated participation of many proteins that are recruited during the early steps of mRNA synthesis and processing. This strategy allows the cell to guarantee the conformity of the messengers accessing the cytoplasm and the translation machinery. Most transcripts are exported by the exportin dimer Nuclear RNA export factor 1 (NXF1)-NTF2-related export protein 1 (NXT1) and the transcription-export complex 1 (TREX1). Some mRNAs that do not possess all the common messenger characteristics use either variants of the NXF1-NXT1 pathway or CRM1, a different exportin. Viruses whose mRNAs are synthesized in the nucleus (retroviruses, the vast majority of DNA viruses, and influenza viruses) exploit both these cellular export pathways. Viral mRNAs hijack the cellular export machinery via complex secondary structures recognized by cellular export factors and/or viral adapter proteins. This way, the viral transcripts succeed in escaping the host surveillance system and are efficiently exported for translation, allowing the infectious cycle to proceed. This review gives an overview of the cellular mRNA nuclear export mechanisms and presents detailed insights into the most important strategies that viruses use to export the different forms of their RNAs from the nucleus to the cytoplasm.
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Affiliation(s)
- Jón Pol Gales
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
| | - Julie Kubina
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
- SVQV UMR-A 1131, INRAE, Université de Strasbourg, F-68000 Colmar, France
| | - Angèle Geldreich
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
| | - Maria Dimitrova
- Institut de Biologie Moléculaire des Plantes, The French National Center for Scientific Research (CNRS) UPR2357, Université de Strasbourg, F-67084 Strasbourg, France; (J.P.G.); (J.K.); (A.G.)
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Bombardi L, Pedretti M, Conter C, Dominici P, Astegno A. Distinct Calcium Binding and Structural Properties of Two Centrin Isoforms from Toxoplasma gondii. Biomolecules 2020; 10:E1142. [PMID: 32759683 PMCID: PMC7465447 DOI: 10.3390/biom10081142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 11/16/2022] Open
Abstract
Centrins are calcium (Ca2+)-binding proteins that have been implicated in several regulatory functions. In the protozoan parasite Toxoplasma gondii, the causative agent of toxoplasmosis, three isoforms of centrin have been identified. While increasing information is now available that links the function of centrins with defined parasite biological processes, knowledge is still limited on the metal-binding and structural properties of these proteins. Herein, using biophysical and structural approaches, we explored the Ca2+ binding abilities and the subsequent effects of Ca2+ on the structure of a conserved (TgCEN1) and a more divergent (TgCEN2) centrin isoform from T. gondii. Our data showed that TgCEN1 and TgCEN2 possess diverse molecular features, suggesting that they play nonredundant roles in parasite physiology. TgCEN1 binds two Ca2+ ions with high/medium affinity, while TgCEN2 binds one Ca2+ with low affinity. TgCEN1 undergoes significant Ca2+-dependent conformational changes that expose hydrophobic patches, supporting a role as a Ca2+ sensor in toxoplasma. In contrast, Ca2+ binding has a subtle influence on conformational features of TgCEN2 without resulting in hydrophobic exposure, suggesting a different Ca2+ relay mode for this isoform. Furthermore, TgCEN1 displays a Ca2+-dependent ability to self-assemble, while TgCEN2 did not. We discuss our findings in the context of Ca2+ signaling in toxoplasma.
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Affiliation(s)
| | | | | | | | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.B.); (M.P.); (C.C.); (P.D.)
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SAC3B is a target of CML19, the centrin 2 of Arabidopsis thaliana. Biochem J 2020; 477:173-189. [PMID: 31860002 DOI: 10.1042/bcj20190674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Arabidopsis centrin 2, also known as calmodulin-like protein 19 (CML19), is a member of the EF-hand superfamily of calcium (Ca2+)-binding proteins. In addition to the notion that CML19 interacts with the nucleotide excision repair protein RAD4, CML19 was suggested to be a component of the transcription export complex 2 (TREX-2) by interacting with SAC3B. However, the molecular determinants of this interaction have remained largely unknown. Herein, we identified a CML19-binding site within the C-terminus of SAC3B and characterized the binding properties of the corresponding 26-residue peptide (SAC3Bp), which exhibits the hydrophobic triad centrin-binding motif in a reversed orientation (I8W4W1). Using a combination of spectroscopic and calorimetric experiments, we shed light on the SAC3Bp-CML19 complex structure in solution. We demonstrated that the peptide interacts not only with Ca2+-saturated CML19, but also with apo-CML19 to form a protein-peptide complex with a 1 : 1 stoichiometry. Both interactions involve hydrophobic and electrostatic contributions and include the burial of Trp residues of SAC3Bp. However, the peptide likely assumes different conformations upon binding to apo-CML19 or Ca2+-CML19. Importantly, the peptide dramatically increases the affinity for Ca2+ of CML19, especially of the C-lobe, suggesting that in vivo the protein would be Ca2+-saturated and bound to SAC3B even at resting Ca2+-levels. Our results, providing direct evidence that Arabidopsis SAC3B is a CML19 target and proposing that CML19 can bind to SAC3B through its C-lobe independent of a Ca2+ stimulus, support a functional role for these proteins in TREX-2 complex and mRNA export.
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Woldegebriel R, Kvist J, Andersson N, Õunap K, Reinson K, Wojcik MH, Bijlsma EK, Hoffer MJV, Ryan MM, Stark Z, Walsh M, Cuppen I, van den Boogaard MJH, Bharucha-Goebel D, Donkervoort S, Winchester S, Zori R, Bönnemann CG, Maroofian R, O’Connor E, Houlden H, Zhao F, Carpén O, White M, Sreedharan J, Stewart M, Ylikallio E, Tyynismaa H. Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content. Hum Mol Genet 2020; 29:1426-1439. [PMID: 32202298 PMCID: PMC7297229 DOI: 10.1093/hmg/ddaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/15/2022] Open
Abstract
Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
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Affiliation(s)
- Rosa Woldegebriel
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
| | - Noora Andersson
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Genomics and Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique M Ryan
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Royal Children’s Hospital, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Zornitza Stark
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Maie Walsh
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
| | - Inge Cuppen
- Department of Pediatric Neurology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sara Winchester
- Child Neurology Center of Northwest Florida, Pensacola, FL, USA
| | - Roberto Zori
- Division of Genetics and Metabolism, University of Florida, Gainesville, FL, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Emer O’Connor
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Fang Zhao
- Department of Pathology and Genetics, HUSLAB Laboratories, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matthew White
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jemeen Sreedharan
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
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Xie Y, Ren Y. Mechanisms of nuclear mRNA export: A structural perspective. Traffic 2019; 20:829-840. [PMID: 31513326 DOI: 10.1111/tra.12691] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Export of mRNA from the nucleus to the cytoplasm is a critical process for all eukaryotic gene expression. As mRNA is synthesized, it is packaged with a myriad of RNA-binding proteins to form ribonucleoprotein particles (mRNPs). For each step in the processes of maturation and export, mRNPs must have the correct complement of proteins. Much of the mRNA export pathway revolves around the heterodimeric export receptor yeast Mex67•Mtr2/human NXF1•NXT1, which is recruited to signal the completion of nuclear mRNP assembly, mediates mRNP targeting/translocation through the nuclear pore complex (NPC), and is displaced at the cytoplasmic side of the NPC to release the mRNP into the cytoplasm. Directionality of the transport is governed by at least two DEAD-box ATPases, yeast Sub2/human UAP56 in the nucleus and yeast Dbp5/human DDX19 at the cytoplasmic side of the NPC, which respectively mediate the association and dissociation of Mex67•Mtr2/NXF1•NXT1 onto the mRNP. Here we review recent progress from structural studies of key constituents in different steps of nuclear mRNA export. These findings have laid the foundation for further studies to obtain a comprehensive mechanistic view of the mRNA export pathway.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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Abstract
The Three prime repair exonuclease 2 (TREX-2) complex functions as a platform to which many of the components of the nuclear mRNA processing machinery bind, facilitating integration of this phase of the gene expression pathway, as well as mediating the re-positioning of highly regulated actively transcribing genes (such as GAL1) to nuclear pores (NPCs) to accelerate their activation. In Saccharomyces cerevisiae the TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and two Sus1 chains are bound. A combination of X-ray crystallography and electron microscopy studies have established the structure of two major regions of this complex: the M-region that functions to bind nucleic acids and the CID region that functions to link the complex to nuclear pores. These structures have facilitated the engineering of mutants that have been used to define the contributions made by the TREX-2 complex to locating high-expressed genes to nuclear pores and the contributions made to mRNA nuclear export.
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Affiliation(s)
- Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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Chen L, Bian S, Li H, Madura K. A role for Saccharomyces cerevisiae Centrin (Cdc31) in mitochondrial function and biogenesis. Mol Microbiol 2018; 110:831-846. [PMID: 30251372 DOI: 10.1111/mmi.14128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/24/2018] [Accepted: 09/09/2018] [Indexed: 11/28/2022]
Abstract
Centrins belong to a family of proteins containing calcium-binding EF-hand motifs that perform well-established roles in centrosome and spindle pole body (SPB) duplication. Yeast encodes a single Centrin protein (Cdc31) that binds components in the SPB. However, further studies revealed a role for Centrins in mRNA export, and interactions with contractile filaments and photoreceptors. In addition, human Centrin-2 can bind the DNA-lesion recognition factor XPC, and improve the efficiency of nucleotide excision repair. Similarly, we reported that yeast Cdc31 binds Rad4, a functional counterpart of the XPC DNA repair protein. We also found that Cdc31 is involved in the ubiquitin/proteasome system, and mutations interfere with intracellular protein turnover. In this report, we describe new findings that indicate a role for Cdc31 in the energy metabolism pathway. Cdc31 and cdc31 mutant proteins showed distinct interactions with proteins in energy metabolism, and mutants showed sensitivity to oxidative stress and poor growth on non-fermentable carbon. Significant alteration in mitochondrial morphology was also detected. Although it is unclear how Cdc31 contributes to so many unrelated mechanisms, we propose that by controlling SPB duplication Centrin proteins might link the cellular responses to DNA damage, oxidative load and proteotoxic stresses to growth control.
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Affiliation(s)
- Li Chen
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, 683 Hoes Lane, SPH-383, Piscataway, NJ, 08854, USA
| | - Shengjie Bian
- Center for Advanced Proteomics Research, New Jersey Medical School, Rutgers University, 185 S. Orange Ave., Newark, NJ, 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, New Jersey Medical School, Rutgers University, 185 S. Orange Ave., Newark, NJ, 07103, USA
| | - Kiran Madura
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, 683 Hoes Lane, SPH-383, Piscataway, NJ, 08854, USA
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AbuQattam A, Serrano-Quílez J, Rodríguez-Navarro S, Gallego J. An exon three-way junction structure modulates splicing and degradation of the SUS1 yeast pre-mRNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:673-686. [PMID: 29966763 DOI: 10.1016/j.bbagrm.2018.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 06/04/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022]
Abstract
The SUS1 gene of Saccharomyces cerevisiae is unusual as it contains two introns and undergoes alternative splicing, retaining one or both introns depending on growth conditions. The exon located between the two introns can be skipped during splicing and has been detected in circular form. This exon (E2) has also been found to influence the splicing of the flanking introns, an unusual situation in budding yeast where splicing mainly relies on intron recognition. Using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), NMR spectroscopy, gel electrophoresis and UV thermal denaturation experiments combined with computational predictions, we show that E2 of SUS1 comprises a conserved double-helical stem topped by a three-way junction. One of the hairpins emerging from the junction exhibited significant thermal stability and was capped by a purine-rich loop structurally related to the substrate loop of the VS ribozyme. Cellular assays revealed that three mutants containing altered E2 structures had impaired SUS1 expression, and that a compensatory mutation restoring the conserved stem recovered expression to wild-type levels. Semi-quantitative RT-PCR measurements paralleled these results, and revealed that mutations in E2 altered splicing and transcript degradation processes. Thus, exon structure plays an important role in SUS1 RNA metabolism.
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Affiliation(s)
- Ali AbuQattam
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain; Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, C/ E. Primo Yúfera 3, 46012 Valencia, Spain
| | - Joan Serrano-Quílez
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/ Jaime Roig 11, 46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, C/ E. Primo Yúfera 3, 46012 Valencia, Spain; Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/ Jaime Roig 11, 46010 Valencia, Spain.
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
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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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Pfab A, Bruckmann A, Nazet J, Merkl R, Grasser KD. The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex. J Mol Biol 2018; 430:1479-1494. [PMID: 29588169 DOI: 10.1016/j.jmb.2018.03.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 12/26/2022]
Abstract
The conserved nuclear protein ENY2 (Sus1 in yeast) is involved in coupling transcription and mRNA export in yeast and metazoa, as it is a component both of the transcriptional co-activator complex SAGA and of the mRNA export complex TREX-2. Arabidopsis thaliana ENY2 is widely expressed in the plant and it localizes to the nucleoplasm, but unlike its yeast/metazoan orthologs, it is not enriched in the nuclear envelope. Affinity purification of ENY2 in combination with mass spectrometry revealed that it co-purified with SAGA components, but not with the nuclear pore-associated TREX-2. In addition, further targeted proteomics analyses by reciprocal tagging established the composition of the Arabidopsis SAGA complex consisting of the four modules HATm, SPTm, TAFm and DUBm, and that several SAGA subunits occur in alternative variants. While the HATm, SPTm and TAFm robustly co-purified with each other, the deubiquitination module (DUBm) appears to associate with the other SAGA modules more weakly/dynamically. Consistent with a homology model of the Arabidopsis DUBm, the SGF11 protein interacts directly with ENY2 and UBP22. Plants depleted in the DUBm components, SGF11 or ENY2, are phenotypically only mildly affected, but they contain increased levels of ubiquitinated histone H2B, indicating that the SAGA-DUBm has histone deubiquitination activity in plants. In addition to transcription-related proteins (i.e., transcript elongation factors, Mediator), many splicing factors were found to associate with SAGA, linking the SAGA complex and ongoing transcription with mRNA processing.
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Affiliation(s)
- Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Julian Nazet
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Rainer Merkl
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
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Xiao C, Yu Q, Zhang B, Li J, Zhang D, Li M. The mRNA export factor Sac3 maintains nuclear homeostasis and regulates cytoskeleton organization in Candida albicans. Future Microbiol 2018; 13:283-296. [PMID: 29436239 DOI: 10.2217/fmb-2017-0191] [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: 11/21/2022] Open
Abstract
AIM In eukaryotes, the nuclear export of mRNAs is essential for gene expression and regulations of numerous cellular processes. This study aimed to identify the mRNA export factor Sac3 in Candida albicans. MATERIALS & METHODS A sac3Δ/Δ mutant was obtained using PCR-mediated homologous recombination. RESULTS Disruption of SAC3 caused abnormal accumulation of mRNA in the nuclei. Further investigations revealed that sac3Δ/Δ mutant exhibited a severely growth defect, which was related to abnormal aggregation of microtubules. Moreover, loss of Sac3 caused a defect in hyphal polarized growth, which was associated with depolarization of actin cytoskeleton. In addition, the virulence of sac3Δ/Δ mutant was seriously attenuated. CONCLUSION Our findings provide new insights into the mRNA export factor Sac3 in C. albicans.
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Affiliation(s)
- Chenpeng Xiao
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Jianrong Li
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Dan Zhang
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
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42
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Xiao C, Yu Q, Zhang B, Li J, Zhang D, Li M. Role of the mRNA export factor Sus1 in oxidative stress tolerance in Candida albicans. Biochem Biophys Res Commun 2018; 496:253-259. [DOI: 10.1016/j.bbrc.2018.01.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/06/2018] [Indexed: 10/18/2022]
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43
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Ávila AR, Cabezas-Cruz A, Gissot M. mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway. Parasit Vectors 2018; 11:62. [PMID: 29370868 PMCID: PMC5785795 DOI: 10.1186/s13071-018-2648-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/15/2018] [Indexed: 01/08/2023] Open
Abstract
Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.
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Affiliation(s)
- Andréa Rodrigues Ávila
- Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR, 81350-010, Brazil. .,UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.
| | - Alexjandro Cabezas-Cruz
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.,Institute of Parasitology, Biology Center, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mathieu Gissot
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
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44
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Shi E, Zhang W, Zhao Y, Yang B. Modulation of XPC peptide on binding Tb 3+ to Euplotes octocarinatus centrin. Metallomics 2017; 9:1796-1808. [PMID: 29114686 DOI: 10.1039/c7mt00263g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Centrins are Ca2+-binding proteins found throughout eukaryotic organisms. Xeroderma pigmentosum group C protein (XPC), a dominant component of the nuclear excision repair (NER) pathway, is a critical target protein of centrins. A 22-residue peptide (K842-R863) from XPC was used to investigate the effect of metal ions (Ca2+ and Tb3+) on the peptide binding of Euplotes octocarinatus centrin (EoCen) by isothermal titration calorimetry (ITC) and fluorescence spectroscopy. ITC and tryptophan spectrofluorimetric titrations revealed that metal ions (Ca2+ and Tb3+) could enhance the affinity between EoCen and the XPC peptide, and the enhanced effects were closely related to the ion potential of metal ions. Since the ion potential of Tb3+ (e/r = 0.0325) is larger than that of Ca2+ (e/r = 0.0202), the conformational change in the protein induced by Tb3+ is larger than that induced by Ca2+, and the enhanced affinity of Tb3+ is stronger than that of Ca2+. This interaction was driven by enthalpy in the presence of EDTA and enthalpy and entropy in the presence of Ca2+ or Tb3+. Similar to that observed in the presence of EDTA, the N-terminal domain did not participate in the interaction with the XPC peptide even in the presence of metal ions. Resonance light scattering (RLS) and the band shift in native polyacrylamide gel electrophoresis (PAGE) suggested that peptide binding resulted in the dissociation of EoCen aggregates and complex formation via the monomer-peptide form. Tb3+-Sensitized emission suggested that peptide binding in turn also had an impact on the Tb3+ binding of the protein: the C-terminal domain was slightly strengthened and the N-terminal domain was weakened about 225 fold. RLS and native PAGE indicated that the self-assembly induced by Tb3+ binding to the N-terminal domain of EoCen was inhibited in the presence of the XPC peptide. This study elucidates the molecular mechanism of EoCen function in the cellular context.
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Affiliation(s)
- Enxian Shi
- Institute of Molecular Science, Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry, Shanxi University, Taiyuan 030006, P. R. China. and Department of Pharmacy, Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Wenlong Zhang
- Institute of Molecular Science, Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry, Shanxi University, Taiyuan 030006, P. R. China.
| | - Yaqin Zhao
- Institute of Molecular Science, Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry, Shanxi University, Taiyuan 030006, P. R. China.
| | - Binsheng Yang
- Institute of Molecular Science, Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry, Shanxi University, Taiyuan 030006, P. R. China.
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45
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Helmlinger D, Tora L. Sharing the SAGA. Trends Biochem Sci 2017; 42:850-861. [PMID: 28964624 PMCID: PMC5660625 DOI: 10.1016/j.tibs.2017.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components. This observation appears remarkably prevalent for chromatin-modifying and remodeling complexes. Here, we use the modular organization of the evolutionary conserved Spt-Ada-Gcn5 acetyltransferase (SAGA) complex as a paradigm to illustrate how co-activators share and combine a relatively limited set of functional tools.
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Affiliation(s)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
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46
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Gordon JMB, Aibara S, Stewart M. Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex. Nucleic Acids Res 2017; 45:5577-5585. [PMID: 28334829 PMCID: PMC5435946 DOI: 10.1093/nar/gkx158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/01/2017] [Indexed: 01/29/2023] Open
Abstract
Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805. Although the M-region of Sac3 was originally thought to encompass residues ∼250-550, we report here the 2.3Å resolution crystal structure of a complex containing Sac3 residues 60–550 that indicates that the TPR-like repeats of the M-region extend to residue 137 and that residues 90–125 form a novel loop that links Sac3 to Thp1. These new structural elements are important for growth and mRNA export in vivo. Although deleting Sac3 residues 1–90 produced a wild-type phenotype, deletion of the loop as well generated growth defects at 37°C, whereas the deletion of residues 1–250 impaired mRNA export and also generated longer lag times when glucose or raffinose was replaced by galactose as the carbon source.
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Affiliation(s)
- James M B Gordon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Shintaro Aibara
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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Abstract
Pre-mRNA processing protein 40 (Prp40) is a nuclear protein that has a role in pre-mRNA splicing. Prp40 possesses two leucine-rich nuclear export signals, but little is known about the function of Prp40 in the export process. Another protein that has a role in protein export is centrin, a member of the EF-hand superfamily of Ca2+-binding proteins. Prp40 was found to be a centrin target by yeast-two-hybrid screening using both Homo sapiens centrin 2 (Hscen2) and Chlamydomonas reinhardtii centrin (Crcen). We identified a centrin-binding site within H. sapiens Prp40 homolog A (HsPrp40A), which contains a hydrophobic triad W1L4L8 that is known to be important in the interaction with centrin. This centrin-binding site is highly conserved within the first nuclear export signal consensus sequence identified in Saccharomyces cerevisiae Prp40. Here, we examine the interaction of HsPrp40A peptide (HsPrp40Ap) with both Hscen2 and Crcen by isothermal titration calorimetry. We employed the thermodynamic parameterization to estimate the polar and apolar surface area of the interface. In addition, we have defined the molecular mechanism of thermally induced unfolding and dissociation of the Crcen-HsPrp40Ap complex using two-dimensional infrared correlation spectroscopy. These complementary techniques showed for the first time, to our knowledge, that HsPrp40Ap interacts with centrin in vitro, supporting a coupled functional role for these proteins in pre-mRNA splicing.
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48
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Shi E, Zhang W, Zhao Y, Yang B. Binding of Euplotes octocarinatus centrin to peptide from xeroderma pigmentosum group C protein (XPC). RSC Adv 2017. [DOI: 10.1039/c7ra03079g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Trp is buried in the hydrophobic cavity, the peptide folds into an α-helix, and the interaction is enthalpically driven from ITC.
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Affiliation(s)
- Enxian Shi
- Institute of Molecular Science
- Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry
- Shanxi University
- Taiyuan 030006
- PR China
| | - Wenlong Zhang
- Institute of Molecular Science
- Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry
- Shanxi University
- Taiyuan 030006
- PR China
| | - Yaqin Zhao
- Institute of Molecular Science
- Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry
- Shanxi University
- Taiyuan 030006
- PR China
| | - Binsheng Yang
- Institute of Molecular Science
- Key Laboratory of Chemical Biology of Molecular Engineering of Education Ministry
- Shanxi University
- Taiyuan 030006
- PR China
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49
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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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50
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Kurshakova MM, Georgieva SG, Kopytova DV. Protein complexes coordinating mRNA export from the nucleus into the cytoplasm. Mol Biol 2016. [DOI: 10.1134/s0026893316050095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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