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Zhao B, Hu L, Kaundal S, Neetu N, Lee CH, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Venkataram Prasad BV. Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories. Nat Commun 2024; 15:2460. [PMID: 38503747 PMCID: PMC10950856 DOI: 10.1038/s41467-024-46627-8] [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: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
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Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Soni Kaundal
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Neetu Neetu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher H Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Xayathed Somoulay
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Gwen M Taylor
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA.
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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2
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Zhao B, Hu L, Kuandal S, Neetu N, Lee C, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Prasad BVV. Structure of Orthoreovirus RNA Chaperone σNS, a Component of Viral Replication Factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551319. [PMID: 37577609 PMCID: PMC10418060 DOI: 10.1101/2023.07.31.551319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The reovirus σNS RNA-binding protein is required for formation of intracellular compartments during viral infection that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of an R6A mutant of σNS that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure of selenomethionine-substituted σNS-R6A reveals that the mutant protein forms a stable antiparallel dimer, with each subunit having a well-folded central core and a projecting N-terminal arm. The dimers interact with each other by inserting the N-terminal arms into a hydrophobic pocket of the neighboring dimers on either side to form a helical assembly that resembles filaments of WT σNS in complex with RNA observed using cryo-EM. The interior of the crystallographic helical assembly is positively charged and of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same hydrophobic pocket as the N-terminal arm, as demonstrated in the crystal structure of σNS-R6A in complex with bile acid, suggesting that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS. This idea is supported by the structure of σNS lacking the N-terminal arm. We discovered that σNS displays RNA helix destabilizing and annealing activities, likely essential for presenting mRNA to the viral RNA-dependent RNA polymerase for genome replication. The RNA chaperone activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
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3
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Kiliszek A, Rypniewski W, Błaszczyk L. Exploring structural determinants and the role of nucleolin in formation of the long-range interactions between untranslated regions of p53 mRNA. RNA (NEW YORK, N.Y.) 2023; 29:630-643. [PMID: 36653114 PMCID: PMC10158990 DOI: 10.1261/rna.079378.122] [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: 07/24/2022] [Accepted: 01/02/2023] [Indexed: 05/06/2023]
Abstract
p53 protein is a key regulator of cellular homeostasis by coordinating the framework of antiproliferative pathways as a response to various stress factors. Although the main mechanism of stress-dependent induction of p53 protein relies on post-translational modifications influencing its stability and activity, a growing amount of evidence suggests that complex regulation of p53 expression occurs also at the mRNA level. This study explores structural determinants of long-range RNA-RNA interactions in p53 mRNA, crucial for stress-dependent regulation of p53 protein translation. We demonstrate that the 8-nt bulge motif plays a key structural role in base-pairing of complementary sequences from the 5' and 3' untranslated regions of p53 mRNA. We also show that one of the p53 translation regulators, nucleolin, displays an RNA chaperone activity and facilitates the association of sequences involved in the formation of long-range interactions in p53 mRNA. Nucleolin promotes base-pairing of complementary sequences through the bulge motif, because mutations of this region reduce or inhibit pairing while compensatory mutations restore this interaction. Mutational analysis of nucleolin reveals that all four RNA recognition motifs are indispensable for optimal RNA chaperone activity of nucleolin. These observations help to decipher the unique mechanism of p53 protein translation regulation pointing to bulge motif and nucleolin as the critical factors during intramolecular RNA-RNA recognition in p53 mRNA.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
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4
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Macromolecular Structure Assembly as a Novel Antibiotic Target. Antibiotics (Basel) 2022; 11:antibiotics11070937. [PMID: 35884191 PMCID: PMC9311618 DOI: 10.3390/antibiotics11070937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022] Open
Abstract
This review discusses the inhibition of macromolecular structure formation as a novel and under-investigated drug target. The disruption of cell wall structures by penicillin-binding protein interactions is one potential target. Inhibition of DNA polymerase III assembly by novel drugs is a second target that should be investigated. RNA polymerase protein structural interactions are a third potential target. Finally, disruption of ribosomal subunit biogenesis represents a fourth important target that can be further investigated. Methods to examine these possibilities are discussed.
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5
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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6
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de Vries S, Benes V, Naarmann-de Vries IS, Rücklé C, Zarnack K, Marx G, Ostareck DH, Ostareck-Lederer A. P23 Acts as Functional RBP in the Macrophage Inflammation Response. Front Mol Biosci 2021; 8:625608. [PMID: 34179071 PMCID: PMC8226254 DOI: 10.3389/fmolb.2021.625608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Macrophages exert the primary cellular immune response. Pathogen components like bacterial lipopolysaccharides (LPS) stimulate macrophage migration, phagocytotic activity and cytokine expression. Previously, we identified the poly(A)+ RNA interactome of RAW 264.7 macrophages. Of the 402 RNA-binding proteins (RBPs), 32 were classified as unique in macrophages, including nineteen not reported to interact with nucleic acids before. Remarkably, P23 a HSP90 co-chaperone, also known as cytosolic prostaglandin E2 synthase (PTGES3), exhibited differential poly(A)+ RNA binding in untreated and LPS-induced macrophages. To identify mRNAs bound by P23 and to elucidate potential regulatory RBP functions in macrophages, we immunoprecipitated P23 from cytoplasmic extracts of cross-linked untreated and LPS-induced cells. RNAseq revealed that enrichment of 44 mRNAs was reduced in response to LPS. Kif15 mRNA, which encodes kinesin family member 15 (KIF15), a motor protein implicated in cytoskeletal reorganization and cell mobility was selected for further analysis. Noteworthy, phagocytic activity of LPS-induced macrophages was enhanced by P23 depletion. Specifically, in untreated RAW 264.7 macrophages, decreased P23 results in Kif15 mRNA destabilization, diminished KIF15 expression and accelerated macrophage migration. We show that the unexpected RBP function of P23 contributes to the regulation of macrophage phagocytotic activity and migration.
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Affiliation(s)
- Sebastian de Vries
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Cornelia Rücklé
- Buchmann Institute of Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany
| | - Katharina Zarnack
- Buchmann Institute of Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany
| | - Gernot Marx
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | - Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
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Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021; 27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
Abstract
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding of misfolded substrates into functional conformations. The best characterized tRNA chaperone is the La protein, which interacts with nascent RNA polymerase III transcripts to promote folding and offers protection from exonucleases. More recently, certain tRNA modification enzymes have also been demonstrated to possess tRNA folding activity distinct from their catalytic activity, suggesting that they may act as tRNA chaperones. In this review, we will discuss pioneering studies relating post-transcriptional modification to tRNA stability and decay pathways, present recent advances into the mechanism by which the RNA chaperone La assists pre-tRNA maturation, and summarize emerging research directions aimed at characterizing modification enzymes as tRNA chaperones. Together, these findings shed light on the importance of tRNA folding and how tRNA chaperones, in particular, increase the fraction of nascent pre-tRNAs that adopt a folded, functional conformation.
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Pokornowska M, Milewski MC, Ciechanowska K, Szczepańska A, Wojnicka M, Radogostowicz Z, Figlerowicz M, Kurzynska-Kokorniak A. The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Cell Mol Life Sci 2020; 77:3231-3244. [PMID: 31655860 PMCID: PMC7391396 DOI: 10.1007/s00018-019-03344-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/24/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.
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Affiliation(s)
- Maria Pokornowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Kinga Ciechanowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Agnieszka Szczepańska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marta Wojnicka
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ziemowit Radogostowicz
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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9
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Lee K, Park SJ, Colas des Francs-Small C, Whitby M, Small I, Kang H. The coordinated action of PPR4 and EMB2654 on each intron half mediates trans-splicing of rps12 transcripts in plant chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1193-1207. [PMID: 31442349 DOI: 10.1111/tpj.14509] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/24/2019] [Accepted: 08/12/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat proteins PPR4 and EMB2654 have been shown to be required for the trans-splicing of plastid rps12 transcripts in Zea mays (maize) and Arabidopsis, respectively, but their roles in this process are not well understood. We investigated the functions of the Arabidopsis and Oryza sativa (rice) orthologs of PPR4, designated AtPPR4 (At5g04810) and OsPPR4 (Os4g58780). Arabidopsis atppr4 and rice osppr4 mutants are embryo-lethal and seedling-lethal 3 weeks after germination, respectively, showing that PPR4 is essential in the development of both dicot and monocot plants. Artificial microRNA-mediated mutants of AtPPR4 displayed a specific defect in rps12 trans-splicing, with pale-green, yellowish or albino phenotypes, according to the degree of knock-down of AtPPR4 expression. Comparison of RNA footprints in atppr4 and emb2654 mutants showed a similar concordant loss of extensive footprints at the 3' end of intron 1a and at the 5' end of intron 1b in both cases. EMB2654 is known to bind within the footprint region in intron 1a and we show that AtPPR4 binds to the footprint region in intron 1b, via its PPR motifs. Binding of both PPR4 and EMB2654 is essential to juxtapose the two intron halves and to maintain the RNAs in a splicing-competent structure for the efficient trans-splicing of rps12 intron 1, which is crucial for chloroplast biogenesis and plant development. The similarity of EMB2654 and PPR4 orthologs and their respective binding sites across land plant phylogeny indicates that their coordinate function in rps12 trans-splicing has probably been conserved for 500 million years.
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Affiliation(s)
- Kwanuk Lee
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Catherine Colas des Francs-Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael Whitby
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61186, Korea
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10
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Li J, Zhang B, Zhou L, Qi L, Yue L, Zhang W, Cheng H, Whitman WB, Dong X. The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis. PLoS Genet 2019; 15:e1008328. [PMID: 31404065 PMCID: PMC6705878 DOI: 10.1371/journal.pgen.1008328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/22/2019] [Accepted: 07/22/2019] [Indexed: 11/27/2022] Open
Abstract
TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Bo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Liguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Huicai Cheng
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang, China
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
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11
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Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU. The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity. Nucleic Acids Res 2019; 46:10353-10367. [PMID: 30060205 PMCID: PMC6212840 DOI: 10.1093/nar/gky668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 02/01/2023] Open
Abstract
Sequence-deficient mitochondrial pre-mRNAs in African trypanosomes are substrates of a U-nucleotide-specific RNA editing reaction to generate translation-competent mRNAs. The reaction is catalyzed by a macromolecular protein complex termed the editosome. Editosomes execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis for this activity is unknown. Here we test five of the OB-fold proteins of the Trypanosoma brucei editosome as candidates. We demonstrate that all proteins execute RNA-chaperone activity albeit to different degrees. We further show that the activities correlate to the surface areas of the proteins and we map the protein-induced RNA-structure changes using SHAPE-chemical probing. To provide a structural context for our findings we calculate a coarse-grained model of the editosome. The model has a shell-like structure: Structurally well-defined protein domains are separated from an outer shell of intrinsically disordered protein domains, which suggests a surface-driven mechanism for the chaperone activity.
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Affiliation(s)
- Christin Voigt
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Mateusz Dobrychlop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Elisabeth Kruse
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna M Kasprzak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Cristian Del Campo
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - W-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Janusz M Bujnicki
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.,Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - H Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
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12
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Falk J, Bronstein L, Hanst M, Drossel B, Koeppl H. Context in synthetic biology: Memory effects of environments with mono-molecular reactions. J Chem Phys 2019; 150:024106. [DOI: 10.1063/1.5053816] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Johannes Falk
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Leo Bronstein
- Bioinspired Communication Systems, Technische Universität Darmstadt, Rundeturmstr. 12, 64283 Darmstadt, Germany
- Institute of Biostatistics and Clinical Research, University of Münster, Schmeddingstr. 56, 48149 Münster, Germany
| | - Maleen Hanst
- Bioinspired Communication Systems, Technische Universität Darmstadt, Rundeturmstr. 12, 64283 Darmstadt, Germany
| | - Barbara Drossel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Heinz Koeppl
- Bioinspired Communication Systems, Technische Universität Darmstadt, Rundeturmstr. 12, 64283 Darmstadt, Germany
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13
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Nawaz G, Kang H. Rice OsRH58, a chloroplast DEAD-box RNA helicase, improves salt or drought stress tolerance in Arabidopsis by affecting chloroplast translation. BMC PLANT BIOLOGY 2019; 19:17. [PMID: 30626336 PMCID: PMC6327599 DOI: 10.1186/s12870-018-1623-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/28/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Despite increasing characterization of DEAD-box RNA helicases (RHs) in chloroplast gene expression regulation at posttranscriptional levels in plants, their functional roles in growth responses of crops, including rice (Oryza sativa), to abiotic stresses are yet to be characterized. In this study, rice OsRH58 (LOC_Os01g73900), a chloroplast-localized DEAD-box RH, was characterized for its expression patterns upon stress treatment and its functional roles using transgenic Arabidopsis plants under normal and abiotic stress conditions. RESULTS Chloroplast localization of OsRH58 was confirmed by analyzing the expression of OsRH58-GFP fusion proteins in tobacco leaves. Expression of OsRH58 in rice was up-regulated by salt, drought, or heat stress, whereas its expression was decreased by cold, UV, or ABA treatment. The OsRH58-expressing Arabidopsis plants were taller and had more seeds than the wild type under favorable conditions. The transgenic plants displayed faster seed germination, better seedling growth, and a higher survival rate than the wild type under high salt or drought stress. Importantly, levels of several chloroplast proteins were increased in the transgenic plants under salt or dehydration stress. Notably, OsRH58 harbored RNA chaperone activity. CONCLUSIONS These findings suggest that the chloroplast-transported OsRH58 possessing RNA chaperone activity confers stress tolerance by increasing translation of chloroplast mRNAs.
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Affiliation(s)
- Ghazala Nawaz
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186 South Korea
- Department of Botany, Kohat University of Science and Technology, Indus Highway Kohat, Kohat, Khyber Pakhtunkhwa 26000 Pakistan
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186 South Korea
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14
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Melencion SMB, Chi YH, Pham TT, Paeng SK, Wi SD, Lee C, Ryu SW, Koo SS, Lee SY. RNA Chaperone Function of a Universal Stress Protein in Arabidopsis Confers Enhanced Cold Stress Tolerance in Plants. Int J Mol Sci 2017; 18:ijms18122546. [PMID: 29186920 PMCID: PMC5751149 DOI: 10.3390/ijms18122546] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 02/07/2023] Open
Abstract
The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA. Therefore, we investigated the relationship of AtUSP with RNA metabolism. We found that AtUSP can bind nucleic acids, including single- and double-stranded DNA and luciferase mRNA. AtUSP also displayed strong nucleic acid-melting activity. We expressed AtUSP in RL211 Escherichia coli, which contains a hairpin-loop RNA structure upstream of chloramphenicol acetyltransferase (CAT), and observed that AtUSP exhibited anti-termination activity that enabled CAT gene expression. AtUSP expression in the cold-sensitive Escherichia coli (E. coli) mutant BX04 complemented the cold sensitivity of the mutant cells. As these properties are typical characteristics of RNA chaperones, we conclude that AtUSP functions as a RNA chaperone under cold-shock conditions. Thus, the enhanced tolerance of AtUSP OE lines to cold stress is mediated by the RNA chaperone function of AtUSP.
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Affiliation(s)
- Sarah Mae Boyles Melencion
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Yong Hun Chi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Thuy Thi Pham
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Changyu Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seoung Woo Ryu
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sung Sun Koo
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
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15
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Diab A, Foca A, Zoulim F, Durantel D, Andrisani O. The diverse functions of the hepatitis B core/capsid protein (HBc) in the viral life cycle: Implications for the development of HBc-targeting antivirals. Antiviral Res 2017; 149:211-220. [PMID: 29183719 DOI: 10.1016/j.antiviral.2017.11.015] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/08/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022]
Abstract
Virally encoded proteins have evolved to perform multiple functions, and the core protein (HBc) of the hepatitis B virus (HBV) is a perfect example. While HBc is the structural component of the viral nucleocapsid, additional novel functions for the nucleus-localized HBc have recently been described. These results extend for HBc, beyond its structural role, a regulatory function in the viral life cycle and potentially a role in pathogenesis. In this article, we review the diverse roles of HBc in HBV replication and pathogenesis, emphasizing how the unique structure of this protein is key to its various functions. We focus in particular on recent advances in understanding the significance of HBc phosphorylations, its interaction with host proteins and the role of HBc in regulating the transcription of host genes. We also briefly allude to the emerging niche for new direct-acting antivirals targeting HBc, known as Core (protein) Allosteric Modulators (CAMs).
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Affiliation(s)
- Ahmed Diab
- Department of Basic Medical Sciences and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA; INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France; University of Lyon, Université Claude-Bernard (UCBL), UMR_S1052, UCBL, 69008, Lyon, France
| | - Adrien Foca
- INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France; University of Lyon, Université Claude-Bernard (UCBL), UMR_S1052, UCBL, 69008, Lyon, France
| | - Fabien Zoulim
- INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France; University of Lyon, Université Claude-Bernard (UCBL), UMR_S1052, UCBL, 69008, Lyon, France; Hepato-Gastroenterology Unit, Croix-Rousse Hospital, Hospices Civils de Lyon (HCL), 69002, Lyon, France; Labex DEVweCAN, 69008, Lyon, France
| | - David Durantel
- INSERM U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France; University of Lyon, Université Claude-Bernard (UCBL), UMR_S1052, UCBL, 69008, Lyon, France; Hepato-Gastroenterology Unit, Croix-Rousse Hospital, Hospices Civils de Lyon (HCL), 69002, Lyon, France.
| | - Ourania Andrisani
- Department of Basic Medical Sciences and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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16
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Reuter M, Krüger DH. The nucleocapsid protein of hantaviruses: much more than a genome-wrapping protein. Virus Genes 2017; 54:5-16. [PMID: 29159494 DOI: 10.1007/s11262-017-1522-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/11/2017] [Indexed: 12/11/2022]
Abstract
The nucleocapsid (N) protein of hantaviruses represents an impressive example of a viral multifunctional protein. It encompasses properties as diverse as genome packaging, RNA chaperoning, intracellular protein transport, DNA degradation, intervention in host translation, and restricting host immune responses. These functions all rely on the capability of N to interact with RNA and other viral and cellular proteins. We have compiled data on the N protein of different hantavirus species together with information of the recently published three-dimensional structural data of the protein. The array of diverse functional activities accommodated in the hantaviral N protein goes far beyond to be a static structural protein and makes it an interesting target in the development of antiviral therapeutics.
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Affiliation(s)
- Monika Reuter
- Institute of Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Detlev H Krüger
- Institute of Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
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17
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Analysis of the Roles of the Arabidopsis nMAT2 and PMH2 Proteins Provided with New Insights into the Regulation of Group II Intron Splicing in Land-Plant Mitochondria. Int J Mol Sci 2017; 18:ijms18112428. [PMID: 29149092 PMCID: PMC5713396 DOI: 10.3390/ijms18112428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
Plant mitochondria are remarkable with respect to the presence of numerous group II introns which reside in many essential genes. The removal of the organellar introns from the coding genes they interrupt is essential for respiratory functions, and is facilitated by different enzymes that belong to a diverse set of protein families. These include maturases and RNA helicases related proteins that function in group II intron splicing in different organisms. Previous studies indicate a role for the nMAT2 maturase and the RNA helicase PMH2 in the maturation of different pre-RNAs in Arabidopsis mitochondria. However, the specific roles of these proteins in the splicing activity still need to be resolved. Using transcriptome analyses of Arabidopsis mitochondria, we show that nMAT2 and PMH2 function in the splicing of similar subsets of group II introns. Fractionation of native organellar extracts and pulldown experiments indicate that nMAT2 and PMH2 are associated together with their intron-RNA targets in large ribonucleoprotein particle in vivo. Moreover, the splicing efficiencies of the joint intron targets of nMAT2 and PMH2 are more strongly affected in a double nmat2/pmh2 mutant-line. These results are significant as they may imply that these proteins serve as components of a proto-spliceosomal complex in plant mitochondria.
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18
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Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. RNA binding and chaperone activity of the E. coli cold-shock protein CspA. Nucleic Acids Res 2017; 45:4255-4268. [PMID: 28126922 PMCID: PMC5397153 DOI: 10.1093/nar/gkx044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/17/2017] [Indexed: 11/14/2022] Open
Abstract
Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.
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Affiliation(s)
- Enrico Rennella
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Tomáš Sára
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Michael Juen
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Wunderlich
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Lionel Imbert
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Zsofia Solyom
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Katharina Weinhäupl
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Robert Konrat
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
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19
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Zhang B, Yue L, Zhou L, Qi L, Li J, Dong X. Conserved TRAM Domain Functions as an Archaeal Cold Shock Protein via RNA Chaperone Activity. Front Microbiol 2017; 8:1597. [PMID: 28878753 PMCID: PMC5572242 DOI: 10.3389/fmicb.2017.01597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Cold shock proteins (Csps) enable organisms to acclimate to and survive in cold environments and the bacterial CspA family exerts the cold protection via its RNA chaperone activity. However, most Archaea do not contain orthologs to the bacterial csp. TRAM, a conserved domain among RNA modification proteins ubiquitously distributed in organisms, occurs as an individual protein in most archaeal phyla and has a structural similarity to Csp proteins, yet its biological functions remain unknown. Through physiological and biochemical studies on four TRAM proteins from a cold adaptive archaeon Methanolobus psychrophilus R15, this work demonstrated that TRAM is an archaeal Csp and exhibits RNA chaperone activity. Three TRAM encoding genes (Mpsy_0643, Mpsy_3043, and Mpsy_3066) exhibited remarkable cold-shock induced transcription and were preferentially translated at lower temperature (18°C), while the fourth (Mpsy_2002) was constitutively expressed. They were all able to complement the cspABGE mutant of Escherichia coli BX04 that does not grow in cold temperatures and showed transcriptional antitermination. TRAM3066 (gene product of Mpsy_3066) and TRAM2002 (gene product of Mpsy_2002) displayed sequence-non-specific RNA but not DNA binding activity, and TRAM3066 assisted RNases in degradation of structured RNA, thus validating the RNA chaperone activity of TRAMs. Given the chaperone activity, TRAM is predicted to function beyond a Csp.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Liguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,School of Life Sciences, University of Chinese Academy of SciencesBeijing, China
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20
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Attaiech L, Glover JNM, Charpentier X. RNA Chaperones Step Out of Hfq's Shadow. Trends Microbiol 2017; 25:247-249. [PMID: 28189381 DOI: 10.1016/j.tim.2017.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
The stability and function of regulatory small RNAs (sRNAs) often require a specialized RNA-binding protein called an RNA chaperone. Recent findings show that proteins containing a ProQ/FinO domain constitute a new class of RNA chaperones that could play key roles in post-transcriptional gene regulation throughout bacterial species.
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Affiliation(s)
- Laetitia Attaiech
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, 69100, Villeurbanne, France.
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, 69100, Villeurbanne, France
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21
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Friedrich S, Schmidt T, Schierhorn A, Lilie H, Szczepankiewicz G, Bergs S, Liebert UG, Golbik RP, Behrens SE. Arginine methylation enhances the RNA chaperone activity of the West Nile virus host factor AUF1 p45. RNA (NEW YORK, N.Y.) 2016; 22:1574-1591. [PMID: 27520967 PMCID: PMC5029455 DOI: 10.1261/rna.055269.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
A prerequisite for the intracellular replication process of the Flavivirus West Nile virus (WNV) is the cyclization of the viral RNA genome, which enables the viral replicase to initiate RNA synthesis. Our earlier studies indicated that the p45 isoform of the cellular AU-rich element binding protein 1 (AUF1) has an RNA chaperone activity, which supports RNA cyclization and viral RNA synthesis by destabilizing a stem structure at the WNV RNA's 3'-end. Here we show that in mammalian cells, AUF1 p45 is consistently modified by arginine methylation of its C terminus. By a combination of different experimental approaches, we can demonstrate that the methyltransferase PRMT1 is necessary and sufficient for AUF1 p45 methylation and that PRMT1 is required for efficient WNV replication. Interestingly, in comparison to the nonmethylated AUF1 p45, the methylated AUF1 p45(aDMA) exhibits a significantly increased affinity to the WNV RNA termini. Further data also revealed that the RNA chaperone activity of AUF1 p45(aDMA) is improved and the methylated protein stimulates viral RNA synthesis considerably more efficiently than the nonmethylated AUF1 p45. In addition to its destabilizing RNA chaperone activity, we identified an RNA annealing activity of AUF1 p45, which is not affected by methylation. Arginine methylation of AUF1 p45 thus represents a specific determinant of its RNA chaperone activity while functioning as a WNV host factor. Our data suggest that the methylation modifies the conformation of AUF1 p45 and in this way affects its RNA binding and restructuring activities.
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Affiliation(s)
- Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | | | - Sandra Bergs
- Institute of Virology, Leipzig University, 04130 Leipzig, Germany
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04130 Leipzig, Germany
| | - Ralph P Golbik
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
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22
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Modulation of the cytoplasmic functions of mammalian post-transcriptional regulatory proteins by methylation and acetylation: a key layer of regulation waiting to be uncovered? Biochem Soc Trans 2016; 43:1285-95. [PMID: 26614674 DOI: 10.1042/bst20150172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-transcriptional control of gene expression is critical for normal cellular function and viability and many of the proteins that mediate post-transcriptional control are themselves subject to regulation by post-translational modification (PTM), e.g. phosphorylation. However, proteome-wide studies are revealing new complexities in the PTM status of mammalian proteins, in particular large numbers of novel methylated and acetylated residues are being identified. Here we review studied examples of methylation/acetylation-dependent regulation of post-transcriptional regulatory protein (PTRP) function and present collated PTM data that points to the huge potential for regulation of mRNA fate by these PTMs.
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23
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Rakesh R, Joseph AP, Bhaskara RM, Srinivasan N. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. RNA Biol 2016; 13:1025-1040. [PMID: 27618338 DOI: 10.1080/15476286.2016.1218590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a "fuzzy complex" with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5' end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity.
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Affiliation(s)
- Ramachandran Rakesh
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India
| | - Agnel Praveen Joseph
- b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
| | - Ramachandra M Bhaskara
- a Molecular Biophysics Unit, Indian Institute of Science , Bangalore , India.,b National Center for Biological Sciences, TIFR, GKVK Campus , Bangalore , India
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24
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Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Föhr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A. Identification of RNA-binding Proteins in Macrophages by Interactome Capture. Mol Cell Proteomics 2016; 15:2699-714. [PMID: 27281784 DOI: 10.1074/mcp.m115.056564] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
Pathogen components, such as lipopolysaccharides of Gram-negative bacteria that activate Toll-like receptor 4, induce mitogen activated protein kinases and NFκB through different downstream pathways to stimulate pro- and anti-inflammatory cytokine expression. Importantly, post-transcriptional control of the expression of Toll-like receptor 4 downstream signaling molecules contributes to the tight regulation of inflammatory cytokine synthesis in macrophages. Emerging evidence highlights the role of RNA-binding proteins (RBPs) in the post-transcriptional control of the innate immune response. To systematically identify macrophage RBPs and their response to LPS stimulation, we employed RNA interactome capture in LPS-induced and untreated murine RAW 264.7 macrophages. This combines RBP-crosslinking to RNA, cell lysis, oligo(dT) capture of polyadenylated RNAs and mass spectrometry analysis of associated proteins. Our data revealed 402 proteins of the macrophage RNA interactome including 91 previously not annotated as RBPs. A comparison with published RNA interactomes classified 32 RBPs uniquely identified in RAW 264.7 macrophages. Of these, 19 proteins are linked to biochemical activities not directly related to RNA. From this group, we validated the HSP90 cochaperone P23 that was demonstrated to exhibit cytosolic prostaglandin E2 synthase 3 (PTGES3) activity, and the hematopoietic cell-specific LYN substrate 1 (HCLS1 or HS1), a hematopoietic cell-specific adapter molecule, as novel macrophage RBPs. Our study expands the mammalian RBP repertoire, and identifies macrophage RBPs that respond to LPS. These RBPs are prime candidates for the post-transcriptional regulation and execution of LPS-induced signaling pathways and the innate immune response. Macrophage RBP data have been deposited to ProteomeXchange with identifier PXD002890.
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Affiliation(s)
- Anke Liepelt
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Isabel S Naarmann-de Vries
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Nadine Simons
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Katrin Eichelbaum
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Sophia Föhr
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Stuart K Archer
- ¶EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Garran Rd, Acton (Canberra) ACT 2601, Australia
| | - Alfredo Castello
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Björn Usadel
- ‖Institute of Biology I, RWTH Aachen, Worringer Weg 2, 52074 Aachen, Germany
| | - Jeroen Krijgsveld
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Thomas Preiss
- ¶EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Garran Rd, Acton (Canberra) ACT 2601, Australia; **Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Gernot Marx
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Matthias W Hentze
- §European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Dirk H Ostareck
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany;
| | - Antje Ostareck-Lederer
- From the ‡Department of Intensive Care and Intermediate Care, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany;
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Gu L, Jung HJ, Kim BM, Xu T, Lee K, Kim YO, Kang H. A chloroplast-localized S1 domain-containing protein SRRP1 plays a role in Arabidopsis seedling growth in the presence of ABA. JOURNAL OF PLANT PHYSIOLOGY 2015; 189:34-41. [PMID: 26513458 DOI: 10.1016/j.jplph.2015.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 05/07/2023]
Abstract
Although the roles of S1 domain-containing proteins have been characterized in diverse cellular processes in the cytoplasm, the functional roles of a majority of S1 domain-containing proteins targeted to the chloroplast are largely unknown. Here, we characterized the function of a nuclear-encoded chloroplast-targeted protein harboring two S1 domains, designated SRRP1 (for S1 RNA-binding ribosomal protein 1), in Arabidopsis thaliana. Subcellular localization analysis of SRRP1-GFP fusion proteins revealed that SRRP1 is localized to the chloroplast. The T-DNA tagged loss-of-function srrp1 mutants displayed poorer seedling growth and less cotyledon greening than the wild-type plants on MS medium supplemented with abscisic acid (ABA), suggesting that SRRP1 plays a role in seedling growth in the presence of ABA. Splicing of the trnL intron and processing of 5S rRNA in chloroplasts were altered in the mutant plants. Importantly, SRRP1 complemented the growth-defective phenotypes of an RNA chaperone-deficient Escherichia coli mutant at low temperatures and had nucleic acid-melting ability, indicating that SRRP1 possesses RNA chaperone activity. Taken together, these results suggest that SRRP1, the chloroplast-localized S1 domain-containing protein, harboring RNA chaperone activity affects the splicing and processing of chloroplast transcripts and plays a role in Arabidopsis seedling growth in the presence of ABA.
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Affiliation(s)
- Lili Gu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Bo Mi Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Tao Xu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea; College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, PR China
| | - Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Yeon-Ok Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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Han JH, Lee K, Lee KH, Jung S, Jeon Y, Pai HS, Kang H. A nuclear-encoded chloroplast-targeted S1 RNA-binding domain protein affects chloroplast rRNA processing and is crucial for the normal growth of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:277-89. [PMID: 26031782 DOI: 10.1111/tpj.12889] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/05/2015] [Accepted: 05/13/2015] [Indexed: 05/22/2023]
Abstract
Despite the fact that a variety of nuclear-encoded RNA-binding proteins (RBPs) are targeted to the chloroplast and play essential roles during post-transcriptional RNA metabolism in the chloroplast, the physiological roles of the majority of chloroplast-targeted RBPs remain elusive. Here, we investigated the functional role of a nuclear-encoded S1 domain-containing RBP, designated SDP, in the growth and development of Arabidopsis thaliana. Confocal analysis of the SDP-green fluorescent protein revealed that SDP was localized to the chloroplast. The loss-of-function sdp mutant displayed retarded seed germination and pale-green phenotypes, and grew smaller than the wild-type plants. Chlorophyll a content and photosynthetic activity of the sdp mutant were much lower than those of wild-type plants, and the structures of the chloroplast and the prolamellar body were abnormal in the sdp mutant. The processing of rRNAs in the chloroplast was defective in the sdp mutant, and SDP was able to bind chloroplast 23S, 16S, 5S and 4.5S rRNAs. Notably, SDP possesses RNA chaperone activity. Transcript levels of the nuclear genes involved in chlorophyll biosynthesis were altered in the sdp mutant. Collectively, these results suggest that chloroplast-targeted SDP harboring RNA chaperone activity affects rRNA processing, chloroplast biogenesis and photosynthetic activity, which is crucial for normal growth of Arabidopsis.
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Affiliation(s)
- Ji Hoon Han
- Department of Plant Biotechnology, Chonnam National University, Gwangju, 500-757, Korea
| | - Kwanuk Lee
- Department of Plant Biotechnology, Chonnam National University, Gwangju, 500-757, Korea
| | - Kwang Ho Lee
- Department of Wood Science and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Korea
| | - Sunyo Jung
- School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, 702-701, Korea
| | - Young Jeon
- Department of Systems Biology, Yonsei University, Seoul, 120-749, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 120-749, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, Chonnam National University, Gwangju, 500-757, Korea
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A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Nature 2014; 515:591-5. [PMID: 25209668 DOI: 10.1038/nature13709] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
To prime reverse transcription, retroviruses require annealing of a transfer RNA molecule to the U5 primer binding site (U5-PBS) region of the viral genome. The residues essential for primer annealing are initially locked in intramolecular interactions; hence, annealing requires the chaperone activity of the retroviral nucleocapsid (NC) protein to facilitate structural rearrangements. Here we show that, unlike classical chaperones, the Moloney murine leukaemia virus NC uses a unique mechanism for remodelling: it specifically targets multiple structured regions in both the U5-PBS and tRNA(Pro) primer that otherwise sequester residues necessary for annealing. This high-specificity and high-affinity binding by NC consequently liberates these sequestered residues--which are exactly complementary--for intermolecular interactions. Furthermore, NC utilizes a step-wise, entropy-driven mechanism to trigger both residue-specific destabilization and residue-specific release. Our structures of NC bound to U5-PBS and tRNA(Pro) reveal the structure-based mechanism for retroviral primer annealing and provide insights as to how ATP-independent chaperones can target specific RNAs amidst the cellular milieu of non-target RNAs.
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28
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Gu L, Xu T, Lee K, Lee KH, Kang H. A chloroplast-localized DEAD-box RNA helicaseAtRH3 is essential for intron splicing and plays an important role in the growth and stress response in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:309-18. [PMID: 25043599 DOI: 10.1016/j.plaphy.2014.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/03/2014] [Indexed: 05/06/2023]
Abstract
Although many DEAD-box RNA helicases (RHs) are targeted to chloroplasts, the functional roles of the majority of RHs are still unknown. Recently, the chloroplast-localized Arabidopsis thaliana AtRH3 has been demonstrated to play important roles in intron splicing, ribosome biogenesis, and seedling growth. To further understand the functional role of AtRH3 in intron splicing and growth and the stress response in Arabidopsis, the newly-generated artificial microRNA-mediated knockdown plants as well as the previously characterized T-DNA tagged rh3-4 mutant were analyzed under normal and stress conditions. The rh3 mutants displayed retarded growth and pale-green phenotypes, and the growth of mutant plants was inhibited severely under salt or cold stress but marginally under dehydration stress conditions. Splicing of several intron-containing chloroplast genes was defective in the mutant plants. Importantly, splicing of ndhA and ndhB genes was severely inhibited in the mutant plants compared with the wild-type plants under salt or cold stress but not under dehydration stress conditions. Moreover, AtRH3 complemented the growth-defect phenotype of the RNA chaperone-deficient Escherichia coli mutant and had the ability to disrupt RNA and DNA base pairs, indicating that AtRH3 possesses RNA chaperone activity. Taken together, these results demonstrate that AtRH3 plays a prominent role in the growth and stress response of Arabidopsis, and suggest that proper splicing of introns governed by RNA chaperone activity of AtRH3 is crucial for chloroplast function and the growth and stress response of plants.
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Affiliation(s)
- Lili Gu
- Department of Plant Biotechnology and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Tao Xu
- Department of Plant Biotechnology and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kwanuk Lee
- Department of Plant Biotechnology and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kwang Ho Lee
- Department of Wood Science and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology and Landscape Architecture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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Plasmodium knowlesi thioredoxin peroxidase 1 binds to nucleic acids and has RNA chaperone activity. Parasitol Res 2014; 113:3957-62. [DOI: 10.1007/s00436-014-4060-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/23/2014] [Indexed: 10/24/2022]
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30
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Xu T, Gu L, Choi MJ, Kim RJ, Suh MC, Kang H. Comparative functional analysis of wheat (Triticum aestivum) zinc finger-containing glycine-rich RNA-binding proteins in response to abiotic stresses. PLoS One 2014; 9:e96877. [PMID: 24800811 PMCID: PMC4011930 DOI: 10.1371/journal.pone.0096877] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/13/2014] [Indexed: 11/19/2022] Open
Abstract
Although the functional roles of zinc finger-containing glycine-rich RNA-binding proteins (RZs) have been characterized in several plant species, including Arabidopsis thaliana and rice (Oryza sativa), the physiological functions of RZs in wheat (Triticum aestivum) remain largely unknown. Here, the functional roles of the three wheat RZ family members, named TaRZ1, TaRZ2, and TaRZ3, were investigated using transgenic Arabidopsis plants under various abiotic stress conditions. Expression of TaRZs was markedly regulated by salt, dehydration, or cold stress. The TaRZ1 and TaRZ3 proteins were localized to the nucleus, whereas the TaRZ2 protein was localized to the nucleus, endoplasmic reticulum, and cytoplasm. Germination of all three TaRZ-expressing transgenic Arabidopsis seeds was retarded compared with that of wild-type seeds under salt stress conditions, whereas germination of TaRZ2- or TaRZ3-expressing transgenic Arabidopsis seeds was retarded under dehydration stress conditions. Seedling growth of TaRZ1-expressing transgenic plants was severely inhibited under cold or salt stress conditions, and seedling growth of TaRZ2-expressing plants was inhibited under salt stress conditions. By contrast, expression of TaRZ3 did not affect seedling growth of transgenic plants under any of the stress conditions. In addition, expression of TaRZ2 conferred freeze tolerance in Arabidopsis. Taken together, these results suggest that different TaRZ family members play various roles in seed germination, seedling growth, and freeze tolerance in plants under abiotic stress.
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Affiliation(s)
- Tao Xu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Lili Gu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Min Ji Choi
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Ryeo Jin Kim
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
- * E-mail:
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Mohamadkhani A. Long Noncoding RNAs in Interaction With RNA Binding Proteins in Hepatocellular Carcinoma. HEPATITIS MONTHLY 2014; 14:e18794. [PMID: 24910706 PMCID: PMC4030262 DOI: 10.5812/hepatmon.18794] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Gene expression microarrays' analyses provide a description of long noncoding RNAs (lncRNAs) with lack of coding protein function that is often important in human cancer. OBJECTIVES A number of lncRNAs that have been well characterized in hepatocellular carcinoma (HCC) have been scheduled in this study to discuss for protein-lncRNA interaction. MATERIALS AND METHODS The identified lncRNAs were analyzed by bioinformatics tools, starBase and lncRNA db, to anticipate the RNA-binding proteins (RBPs) that tend to interact to HCC-related lncRNAs. The most important predicted RBPs in interaction with well-known lncRNAs in HCC were briefly discussed. RESULTS The lncRNAs HOTTIP, H19, HOTAIR, MALAT1, antisense Igf2r (AIR), HOXA13, GTL2 (also called MEG3) and uc002mb have been reported in association with HCC. Besides, this study predicted that eIF4AIII, PTB and FUS were the most involved RBPs in interaction with HCC-related lncRNAs. CONCLUSIONS This information provides an explanation for the previously valuable literature on the functions of lncRNAs and suggest for the novel therapeutic targeting.
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Affiliation(s)
- Ashraf Mohamadkhani
- Liver and Pancreatobiliary Disease Research Center, Digestive Disease Research institute, Shartati Hospital, Tehran University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Ashraf Mohamadkhani, Liver and Pancreatobiliary Disease Research Center, Digestive Disease Research institute, Shartati Hospital, Tehran University of Medical Sciences, North Kargar Ave. Tehran, IR Iran. Tel: +98-2182415227, Fax: +98-2182415400, E-mail:
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32
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Dolan GF, Müller UF. Trans-splicing with the group I intron ribozyme from Azoarcus. RNA (NEW YORK, N.Y.) 2014; 20:202-213. [PMID: 24344321 PMCID: PMC3895272 DOI: 10.1261/rna.041012.113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/02/2013] [Indexed: 06/02/2023]
Abstract
Group I introns are ribozymes (catalytic RNAs) that excise themselves from RNA primary transcripts by catalyzing two successive transesterification reactions. These cis-splicing ribozymes can be converted into trans-splicing ribozymes, which can modify the sequence of a separate substrate RNA, both in vitro and in vivo. Previous work on trans-splicing ribozymes has mostly focused on the 16S rRNA group I intron ribozyme from Tetrahymena thermophila. Here, we test the trans-splicing potential of the tRNA(Ile) group I intron ribozyme from the bacterium Azoarcus. This ribozyme is only half the size of the Tetrahymena ribozyme and folds faster into its active conformation in vitro. Our results showed that in vitro, the Azoarcus and Tetrahymena ribozymes favored the same set of splice sites on a substrate RNA. Both ribozymes showed the same trans-splicing efficiency when containing their individually optimized 5' terminus. In contrast to the previously optimized 5'-terminal design of the Tetrahymena ribozyme, the Azoarcus ribozyme was most efficient with a trans-splicing design that resembled the secondary structure context of the natural cis-splicing Azoarcus ribozyme, which includes base-pairing between the substrate 5' portion and the ribozyme 3' exon. These results suggested preferred trans-splicing interactions for the Azoarcus ribozyme under near-physiological in vitro conditions. Despite the high activity in vitro, however, the splicing efficiency of the Azoarcus ribozyme in Escherichia coli cells was significantly below that of the Tetrahymena ribozyme.
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MESH Headings
- Azoarcus/enzymology
- Azoarcus/genetics
- Base Sequence
- Chloramphenicol O-Acetyltransferase/genetics
- Escherichia coli
- Inverted Repeat Sequences
- Molecular Sequence Data
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Substrate Specificity
- Tetrahymena thermophila/enzymology
- Trans-Splicing
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Nucleic acid chaperone activity associated with the arginine-rich domain of human hepatitis B virus core protein. J Virol 2013; 88:2530-43. [PMID: 24352445 DOI: 10.1128/jvi.03235-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Hepatitis B virus (HBV) DNA replication occurs within the HBV icosahedral core particles. HBV core protein (HBc) contains an arginine-rich domain (ARD) at its carboxyl terminus. This ARD domain of HBc 149-183 is known to be important for viral replication but not known to have a structure. Recently, nucleocapsid proteins of several viruses have been shown to contain nucleic acid chaperone activity, which can facilitate structural rearrangement of viral genome. Major features of nucleic acid chaperones include highly basic amino acid residues and flexible protein structure. To test the nucleic acid chaperone hypothesis for HBc ARD, we first used the disassembled full-length HBc from Escherichia coli to analyze the nucleic acid annealing and strand displacement activities. To exclude the potential contamination of chaperones from E. coli, we designed synthetic HBc ARD peptides with different lengths and serine phosphorylations. We demonstrated that HBc ARD peptide can behave like a bona fide nucleic acid chaperone and that the chaperone activity depends on basic residues of the ARD domain. The loss of chaperone activity by arginine-to-alanine substitutions in the ARD can be rescued by restoring basic residues in the ARD. Furthermore, the chaperone activity is subject to regulation by phosphorylation and dephosphorylation at the HBc ARD. Interestingly, the HBc ARD can enhance in vitro cleavage activity of RNA substrate by a hammerhead ribozyme. We discuss here the potential significance of the HBc ARD chaperone activity in the context of viral DNA replication, in particular, at the steps of primer translocations and circularization of linear replicative intermediates. IMPORTANCE Hepatitis B virus is a major human pathogen. At present, no effective treatment can completely eradicate the virus from patients with chronic hepatitis B. We report here a novel chaperone activity associated with the viral core protein. Our discovery could lead to a new drug design for more effective treatment against hepatitis B virus in the future.
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Xu T, Lee K, Gu L, Kim JI, Kang H. Functional characterization of a plastid-specific ribosomal protein PSRP2 in Arabidopsis thaliana under abiotic stress conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 73:405-411. [PMID: 24220572 DOI: 10.1016/j.plaphy.2013.10.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/22/2013] [Indexed: 06/02/2023]
Abstract
Plastids possess a small set of proteins unique to plastid ribosome, named plastid-specific ribosomal proteins (PSRPs). Among the six PSRPs found in Arabidopsis thaliana, PSRP2 is unique in that it harbors two RNA-recognition motifs found in diverse RNA-binding proteins. A recent report demonstrated that PSRP2 is not essential for ribosome function and plant growth under standard greenhouse conditions. Here, we investigated the functional role of PSRP2 during Arabidopsis seed germination and seedling growth under different light environments and various stress conditions, including high salinity, dehydration, and low temperature. The transgenic Arabidopsis plants overexpressing PSRP2 showed delayed germination compared with that of the wild-type plants under salt, dehydration, or low temperature stress conditions. The T-DNA insertion psrp2 mutant displayed better seedling growth but PSRP2-overexpressing transgenic plants showed poorer seedling growth than that of the wild-type plants under salt stress conditions. No noticeable differences in seedling growth were observed between the genotypes when grown under different light environments including dark, red, far-red, and blue light. Interestingly, the PSRP2 protein possessed RNA chaperone activity. Taken together, these results suggest that PSRP2 harboring RNA chaperone activity plays a role as a negative regulator in seed germination under all three abiotic stress conditions tested and in seedling growth of Arabidopsis under salt stress but not under cold or dehydration stress conditions.
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Affiliation(s)
- Tao Xu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Republic of Korea
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Xu T, Han JH, Kang H. Structural features important for the RNA chaperone activity of zinc finger-containing glycine-rich RNA-binding proteins from wheat (Triticum avestivum) and rice (Oryza sativa). PHYTOCHEMISTRY 2013; 94:28-35. [PMID: 23787154 DOI: 10.1016/j.phytochem.2013.05.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/13/2013] [Accepted: 05/29/2013] [Indexed: 06/02/2023]
Abstract
Despite the increase in understanding of RNA chaperone activity of zinc finger-containing glycine-rich RNA-binding proteins (RZs) during the cold adaptation process, the structural features relevant to the RNA chaperone activity of RZs still largely remain to be established. To investigate the structural determinants important for the RNA chaperone activity of RZs, domain-swapping and deletion analyses was carried out to assess the contribution of the N-terminal zinc finger RNA-recognition motif (RRM) domain and the C-terminal glycine-rich region of wheat (Triticum avestivum) and rice (Oryza sativa) RZs to RNA chaperone activity. Although the amino acid sequence similarity among wheat TaRZ2, wheat TaRZ3, and rice OsRZ1 was high, only TaRZ2 had RNA chaperone activity as evidenced by complementation ability in cold-sensitive Escherichia coli mutant cell under cold stress and in vivo and in vitro nucleic acid-melting activity. Domain-swapping and deletion analysis demonstrated that the overall folding of RZs governed by the N-terminal RRM domain and the C-terminal glycine-rich region, as well as the size of the disordered C-terminal glycine-rich region, are crucial for the RNA chaperone activity of RZs. Collectively, these results indicate that a specific modular arrangement of RRM domain and the disordered C-terminal region determines the RNA chaperone activity of RZs in cells.
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Affiliation(s)
- Tao Xu
- Department of Plant Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
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Abstract
The historical origins and current interpretation of the molecular chaperone concept are presented, with the emphasis on the distinction between folding chaperones and assembly chaperones. Definitions of some basic terms in this field are offered and misconceptions pointed out. Two examples of assembly chaperone are discussed in more detail: the role of numerous histone chaperones in fundamental nuclear processes and the co-operation of assembly chaperones with folding chaperones in the production of the world's most important enzyme.
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Affiliation(s)
- R John Ellis
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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Hafner M, Max KEA, Bandaru P, Morozov P, Gerstberger S, Brown M, Molina H, Tuschl T. Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. RNA (NEW YORK, N.Y.) 2013; 19:613-26. [PMID: 23481595 PMCID: PMC3677277 DOI: 10.1261/rna.036491.112] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Human LIN28A and LIN28B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ∼3000 mRNAs at ∼9500 sites located in the 3' UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.
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Affiliation(s)
- Markus Hafner
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
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Diverse functional manifestations of intrinsic structural disorder in molecular chaperones. Biochem Soc Trans 2013; 40:963-8. [PMID: 22988848 DOI: 10.1042/bst20120108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
IDPs (intrinsically disordered proteins) represent a unique class of proteins which show diverse molecular mechanisms in key biological functions. The aim of the present mini-review is to summarize IDP chaperones that have increasingly been studied in the last few years, by focusing on the role of intrinsic disorder in their molecular mechanism. Disordered regions in both globular and disordered chaperones are often involved directly in chaperone action, either by modulating activity or through direct involvement in substrate identification and binding. They might also be responsible for the subcellular localization of the protein. In outlining the state of the art, we survey known IDP chaperones discussing the following points: (i) globular chaperones that have an experimentally proven functional disordered region(s), (ii) chaperones that are completely disordered along their entire length, and (iii) the possible mechanisms of action of disordered chaperones. Through all of these details, we chart out how far the field has progressed, only to emphasize the long road ahead before the chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.
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Kang H, Park SJ, Kwak KJ. Plant RNA chaperones in stress response. TRENDS IN PLANT SCIENCE 2013; 18:100-6. [PMID: 22947615 DOI: 10.1016/j.tplants.2012.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/02/2012] [Accepted: 08/13/2012] [Indexed: 05/18/2023]
Abstract
Post-transcriptional regulation of RNA metabolism is a key regulatory process in diverse cellular processes, including the stress response of plants, during which a variety of RNA-binding proteins (RBPs) function as central regulators in cells. RNA chaperones are RBPs found in all living organisms and function by providing assistance to the correct folding of RNA molecules during RNA metabolism. Although our understanding of the role of RNA chaperones in plants is far less advanced than in bacteria, viruses, and animals, recent progress in functional characterization and determination of RNA chaperone activity of several RBPs has shed new light on the emerging roles of RNA chaperones during the stress response of plants.
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Affiliation(s)
- Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Korea.
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Batisse J, Guerrero S, Bernacchi S, Sleiman D, Gabus C, Darlix JL, Marquet R, Tisné C, Paillart JC. The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication. Virus Res 2012; 169:361-76. [PMID: 22728817 DOI: 10.1016/j.virusres.2012.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/04/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022]
Abstract
The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented.
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Affiliation(s)
- Julien Batisse
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
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41
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Fu Y, Ramisetty SR, Hussain N, Baranger AM. MBNL1-RNA recognition: contributions of MBNL1 sequence and RNA conformation. Chembiochem 2012; 13:112-9. [PMID: 22106026 PMCID: PMC3890438 DOI: 10.1002/cbic.201100487] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Indexed: 12/14/2022]
Abstract
Muscleblind-like proteins (MBNL) are RNA-binding proteins that bind to the poly(CUG) and poly(CCUG) sequences that are the causative agents of myotonic dystrophy. It has been suggested that as a result of binding to the repeating RNA sequences, MBNL1 is abnormally expressed and translocated, which leads to many of the misregulated events in myotonic dystrophy. In this work, steady-state fluorescence quenching experiments suggest that MBNL1 alters the structure of helical RNA targets upon binding, which may explain the selectivity of MBNL1 for less structured RNA sites. The removal of one pair of zinc fingers greatly impairs the binding affinity of MBNL1, which indicates that the two pairs of zinc fingers might possibly interact with RNA targets cooperatively. Alanine scanning mutagenesis results suggest that the binding energy may be distributed across the protein. Overall, the results presented here suggest that small molecules that stabilize the helical structure of poly(CUG) and poly(CCUG) RNAs will inhibit the formation of complexes with MBNL1.
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Affiliation(s)
| | | | | | - Anne M. Baranger
- Department of Chemistry, University of Illinois, 600 South Mathews Ave. Urbana, IL 61801, Fax:(217) 244-8024
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Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV. Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol Evol 2011; 3:1390-404. [PMID: 22071789 PMCID: PMC3242500 DOI: 10.1093/gbe/evr116] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian genomes contain numerous genes for long noncoding RNAs (lncRNAs). The functions of the lncRNAs remain largely unknown but their evolution appears to be constrained by purifying selection, albeit relatively weakly. To gain insights into the mode of evolution and the functional range of the lncRNA, they can be compared with much better characterized protein-coding genes. The evolutionary rate of the protein-coding genes shows a universal negative correlation with expression: highly expressed genes are on average more conserved during evolution than the genes with lower expression levels. This correlation was conceptualized in the misfolding-driven protein evolution hypothesis according to which misfolding is the principal cost incurred by protein expression. We sought to determine whether long intergenic ncRNAs (lincRNAs) follow the same evolutionary trend and indeed detected a moderate but statistically significant negative correlation between the evolutionary rate and expression level of human and mouse lincRNA genes. The magnitude of the correlation for the lincRNAs is similar to that for equal-sized sets of protein-coding genes with similar levels of sequence conservation. Additionally, the expression level of the lincRNAs is significantly and positively correlated with the predicted extent of lincRNA molecule folding (base-pairing), however, the contributions of evolutionary rates and folding to the expression level are independent. Thus, the anticorrelation between evolutionary rate and expression level appears to be a general feature of gene evolution that might be caused by similar deleterious effects of protein and RNA misfolding and/or other factors, for example, the number of interacting partners of the gene product.
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Affiliation(s)
- David Managadze
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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