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Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency. PLoS Genet 2022; 18:e1010267. [PMID: 35714159 PMCID: PMC9246224 DOI: 10.1371/journal.pgen.1010267] [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: 01/25/2022] [Revised: 06/30/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated in a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target. Human genetic diseases, including cancers, are frequently driven by substantial changes to chromosomes, including translocations, where one arm of a chromosome is exchanged for another. The human nucleic acid binding protein Translin was first identified by its ability to bind to the chromosomal sites at which some of these translocations occur. This resulted in Translin being implicated in the mechanism that generated the translocation and thus the associated disease state. However, since its discovery there has been little evidence to directly indicate Translin does contribute to this process. It is, however, known to contribute to a number of biological functions including, amongst others, neurological regulation, sleep control, vascular stiffening, cancer immunomodulation and it has been recently identified as a potential therapeutic target in some cancers. Here we demonstrate that Translin has conserved function in genome stability maintenance when other primary pathways are defective, a function independent of a key binding partner protein, Trax. Specifically, we demonstrate that Translin contributes to minimizing the deleterious genome destabilizing effects of retaining gene expression machineries on chromosomes. This offers the first evidence for how Translin might contribute to genetic disease-causing chromosomal changes and offers insight to inform therapeutic design.
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2
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Gupta A, Pillai VS, Chittela RK. Translin: A multifunctional protein involved in nucleic acid metabolism. J Biosci 2019; 44:139. [PMID: 31894120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Translin, a highly conserved, DNA/RNA binding protein, is abundantly expressed in brain, testis and in certain malignancies. It was discovered initially in the quest to find proteins that bind to alternating polypurines-polypyrimidines repeats. It has been implicated to have a role in RNA metabolism (tRNA processing, RNAi, RNA transport, etc.), transcription, DNA damage response, etc. Studies from human, mice, drosophila and yeast have revealed that it forms an octameric ring, which is important for its function. Translin is a cytoplasmic protein, but under genotoxic stress, it migrates into the nucleus, binds to the break point hot spots and therefore, thought to be involved in chromosomal translocation events as well as DNA damage related response. Its structure is known and DNA binding regions, GTP binding region and regions responsible for homotypic and heterotypic interaction are known. It forms a ball like structure with open central channel for accommodating the substrate nucleic acids. Besides this, translin protein binds to 3' and 5' UTR of certain mRNAs and probably regulates their availability for translation. It is also involved in mRNA transport and cell cycle progression. It forms a heteromeric complex with translin associated factor-X (TRAX) to form C3PO complex which is involved in RNA silencing process. Recently, it has been shown that translin is upregulated under starvation conditions in Drosophila and is involved in the integration of sleep and metabolic rate of the flies. Earlier studies classified translin as a DNA repair protein; however subsequent studies showed that it is a multifunctional protein. With this background, in this review we have summarized the translin biochemical activities, cellular function as well as structural properties of this important protein.
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Affiliation(s)
- Alka Gupta
- Molecular Damage and Repair Section, Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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3
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Gupta A, Pillai VS, Chittela RK. Translin: A multifunctional protein involved in nucleic acid metabolism. J Biosci 2019. [DOI: 10.1007/s12038-019-9947-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Mo X, Yang X, Yuan YA. Structural insights into Drosophila-C3PO complex assembly and 'Dynamic Side Port' model in substrate entry and release. Nucleic Acids Res 2019; 46:8590-8604. [PMID: 29860349 PMCID: PMC6144819 DOI: 10.1093/nar/gky465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/17/2018] [Indexed: 01/22/2023] Open
Abstract
In Drosophila and human, component 3 promoter of RISC (C3PO), a heteromeric complex, enhances RISC assembly and promotes RISC activity. Here, we report crystal structure of full-length Drosophila C3PO (E126Q), an inactive C3PO mutant displaying much weaker RNA binding ability, at 2.1 Å resolution. In addition, we also report the cryo-EM structures of full-length Drosophila C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT, sumo-TRAX + Translin) particles trapped at different conformations at 12, 19.7 and 12.8 Å resolutions, respectively. Crystal structure of C3PO (E126Q) displays a half-barrel architecture consisting of two Trax/Translin heterodimers, whereas cryo-EM structures of C3PO (E126Q), C3PO (WT) and SUMO-C3PO (WT) adopt a closed football-like shape with a hollow interior cavity. Remarkably, both cryo-EM structures of Drosophila C3PO (E126Q) and Drosophila SUMO-C3PO (WT) particles contain a wide side port (∼25 Å × ∼30 Å versus ∼15 Å × ∼20 Å) for RNA substrate entry and release, formed by a pair of anti-parallel packed long α1 helices of TRAX subunits. Notably, cryo-EM structure of SUMO-C3PO showed that four copies of extra densities belonging to N-terminal SUMO tag are located at the outside shell of SUMO-C3PO particle, which demonstrated that the stoichiometry of TRAX/Translin for the in vitro expressed and assembled full-length Drosophila-SUMO–C3PO particle is 4:4, suggesting Drosophila C3PO is composed by TRAX/translin at a ratio of 4:4. Remarkably, the comparison of the cryo-EM structures suggests that the C3PO side ports regulated by α1 helices of TRAX molecules are highly dynamic. Hence, we propose that C3PO particles could adopt a ‘Dynamic Side Port’ model to capture/digest nucleic acid duplex substrate and release the digested fragments through the dynamic side ports.
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Affiliation(s)
- Xiaobing Mo
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Xia Yang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Yuren Adam Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.,Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Jiangsu 215123, China
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5
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Gomez-Escobar N, Almobadel N, Alzahrani O, Feichtinger J, Planells-Palop V, Alshehri Z, Thallinger GG, Wakeman JA, McFarlane RJ. Translin and Trax differentially regulate telomere-associated transcript homeostasis. Oncotarget 2017; 7:33809-20. [PMID: 27183912 PMCID: PMC5085120 DOI: 10.18632/oncotarget.9278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
Translin and Trax proteins are highly conserved nucleic acid binding proteins that have been implicated in RNA regulation in a range of biological processes including tRNA processing, RNA interference, microRNA degradation during oncogenesis, spermatogenesis and neuronal regulation. Here, we explore the function of this paralogue pair of proteins in the fission yeast. Using transcript analysis we demonstrate a reciprocal mechanism for control of telomere-associated transcripts. Mutation of tfx1+ (Trax) elevates transcript levels from silenced sub-telomeric regions of the genome, but not other silenced regions, such as the peri-centromeric heterochromatin. In the case of some sub-telomeric transcripts, but not all, this elevation is dependent on the Trax paralogue, Tsn1 (Translin). In a reciprocal fashion, Tsn1 (Translin) serves to repress levels of transcripts (TERRAs) from the telomeric repeats, whereas Tfx1 serves to maintain these elevated levels. This reveals a novel mechanism for the regulation of telomeric transcripts. We extend this to demonstrate that human Translin and Trax also control telomere-associated transcript levels in human cells in a telomere-specific fashion.
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Affiliation(s)
- Natalia Gomez-Escobar
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Nasser Almobadel
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Othman Alzahrani
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Julia Feichtinger
- Computational Biotechnology and Bioinformatics Group, Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria.,Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Vicente Planells-Palop
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Zafer Alshehri
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Gerhard G Thallinger
- Computational Biotechnology and Bioinformatics Group, Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria.,Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Jane A Wakeman
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Ramsay J McFarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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6
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Sahu S, Williams L, Perez A, Philip F, Caso G, Zurawsky W, Scarlata S. Regulation of the activity of the promoter of RNA-induced silencing, C3PO. Protein Sci 2017; 26:1807-1818. [PMID: 28714243 DOI: 10.1002/pro.3219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 12/29/2022]
Abstract
RNA-induced silencing is a process which allows cells to regulate the synthesis of specific proteins. RNA silencing is promoted by the protein C3PO (component 3 of RISC). We have previously found that phospholipase Cβ, which increases intracellular calcium levels in response to specific G protein signals, inhibits C3PO activity towards certain genes. Understanding the parameters that control C3PO activity and which genes are impacted by G protein activation would help predict which genes are more vulnerable to downregulation. Here, using a library of 1018 oligonucleotides, we show that C3PO binds oligonucleotides with structural specificity but little sequence specificity. Alternately, C3PO hydrolyzes oligonucleotides with a rate that is sensitive to substrate stability. Importantly, we find that oligonucleotides with higher Tm values are inhibited by bound PLCβ. This finding is supported by microarray analysis in cells over-expressing PLCβ1. Taken together, this study allows predictions of the genes whose post-transcriptional regulation is responsive to the G protein/phospholipase Cβ/calcium signaling pathway.
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Affiliation(s)
- Shriya Sahu
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York
| | - Leo Williams
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York
| | - Alberto Perez
- Laufer Center for Computational Biology, Stony Brook University, Stony Brook, New York
| | - Finly Philip
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York
| | - Giuseppe Caso
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York
| | - Walter Zurawsky
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, 01609
| | - Suzanne Scarlata
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York.,Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, 01609
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7
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Zhang J, Liu H, Yao Q, Yu X, Chen Y, Cui R, Wu B, Zheng L, Zuo J, Huang Z, Ma J, Gan J. Structural basis for single-stranded RNA recognition and cleavage by C3PO. Nucleic Acids Res 2016; 44:9494-9504. [PMID: 27596600 PMCID: PMC5100593 DOI: 10.1093/nar/gkw776] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/23/2016] [Indexed: 12/12/2022] Open
Abstract
Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced silencing complex, the effector complex of RNA interference (RNAi). Here, we report three crystal structures of Nanoarchaeum equitans (Ne) C3PO. The apo-NeC3PO structure adopts an open form and unravels a potential substrates entryway for the first time. The NeC3PO:ssRNA and NeC3PO:ssDNA complexes fold like closed football with the substrates captured at the inner cavities. The NeC3PO:ssRNA structure represents the only catalytic form C3PO complex available to date; with mutagenesis and in vitro cleavage assays, the structure provides critical insights into the substrate binding and the two-cation-assisted catalytic mechanisms that are shared by eukaryotic C3POs. The work presented here further advances our understanding on the RNAi pathway.
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Affiliation(s)
- Jing Zhang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hehua Liu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiang Yu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiqing Chen
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Junjun Zuo
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA .,College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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8
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Phospholipase Cβ connects G protein signaling with RNA interference. Adv Biol Regul 2015; 61:51-7. [PMID: 26746047 DOI: 10.1016/j.jbior.2015.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 11/24/2022]
Abstract
Phosphoinositide-specific-phospholipase Cβ (PLCβ) is the main effector of Gαq stimulation which is coupled to receptors that bind acetylcholine, bradykinin, dopamine, angiotensin II as well as other hormones and neurotransmitters. Using a yeast two-hybrid and other approaches, we have recently found that the same region of PLCβ that binds Gαq also interacts with Component 3 Promoter of RNA induced silencing complex (C3PO), which is required for efficient activity of the RNA-induced silencing complex. In purified form, C3PO competes with Gαq for PLCβ binding and at high concentrations can quench PLCβ activation. Additionally, we have found that the binding of PLCβ to C3PO inhibits its nuclease activity leading to reversal of RNA-induced silencing of specific genes. In cells, we found that PLCβ distributes between the plasma membrane where it localizes with Gαq, and in the cytosol where it localizes with C3PO. When cells are actively processing small interfering RNAs the interaction between PLCβ and C3PO gets stronger and leads to changes in the cellular distribution of PLCβ. The magnitude of attenuation is specific for different silencing RNAs. Our studies imply a direct link between calcium responses mediated through Gαq and post-transcriptional gene regulation through PLCβ.
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9
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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10
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Eliahoo E, Marx A, Manor H, Alian A. A novel open-barrel structure of octameric translin reveals a potential RNA entryway. J Mol Biol 2014; 427:756-762. [PMID: 25433126 DOI: 10.1016/j.jmb.2014.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
Abstract
The single-stranded DNA (ssDNA)/RNA binding protein translin was suggested to be involved in chromosomal translocations, telomere metabolism, and mRNA transport and translation. Oligonucleotide binding surfaces map within a closed cavity of translin octameric barrels, raising the question as to how DNA/RNA gain access to this inner cavity, particularly given that, to date, none of the barrel structures reported hint to an entryway. Here, we argue against a mechanism by which translin octamers may "dissociate and reassemble" upon RNA binding and report a novel "open"-barrel structure of human translin revealing a feasible DNA/RNA entryway into the cavity. Additionally, we report that translin not only is confined to binding of ssDNA oligonucleotides, or single-stranded extensions of double-stranded DNA (dsDNA), but also can bind single-stranded sequences internally embedded in dsDNA molecules.
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Affiliation(s)
- Elad Eliahoo
- Department of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel
| | - Ailie Marx
- Department of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel
| | - Haim Manor
- Department of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel
| | - Akram Alian
- Department of Biology, Technion-Israel Institute of Technology, Haifa 320003, Israel.
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11
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Cheng JY, Wang SH, Lin J, Tsai YC, Yu J, Wu JC, Hung JT, Lin JJ, Wu YY, Yeh KT, Yu AL. Globo-H Ceramide Shed from Cancer Cells Triggers Translin-Associated Factor X-Dependent Angiogenesis. Cancer Res 2014; 74:6856-66. [DOI: 10.1158/0008-5472.can-14-1651] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Identification of proteins that form specific complexes with the highly conserved protein Translin in Schizosaccharomyces pombe. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:767-77. [DOI: 10.1016/j.bbapap.2013.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/18/2013] [Accepted: 12/22/2013] [Indexed: 11/23/2022]
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13
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Llaguno MC, Xu H, Shi L, Huang N, Zhang H, Liu Q, Jiang QX. Chemically functionalized carbon films for single molecule imaging. J Struct Biol 2014; 185:405-17. [PMID: 24457027 DOI: 10.1016/j.jsb.2014.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 01/08/2014] [Accepted: 01/11/2014] [Indexed: 11/25/2022]
Abstract
Many biological complexes are naturally low in abundance and pose a significant challenge to their structural and functional studies. Here we describe a new method that utilizes strong oxidation and chemical linkage to introduce a high density of bioactive ligands onto nanometer-thick carbon films and enable selective enrichment of individual macromolecular complexes at subnanogram levels. The introduced ligands are physically separated. Ni-NTA, Protein G and DNA/RNA oligonucleotides were covalently linked to the carbon surface. They embody negligible mass and their stability makes the functionalized films able to survive long-term storage and tolerate variations in pH, temperature, salts, detergents, and solvents. We demonstrated the application of the new method to the electron microscopic imaging of the substrate-bound C3PO, an RNA-processing enzyme important for the RNA interference pathway. On the ssRNA-linked carbon surface, the formation of C3PO oligomers at subnanomolar concentrations likely mimics their assembly onto ssRNA substrates presented by their native partners. Interestingly, the 3D reconstructions by negative stain EM reveal a side port in the C3PO/ssRNA complex, and the 15Å cryoEM map showed extra density right above the side port, which probably represents the ssRNA. These results suggest a new way for ssRNAs to interact with the active sites of the complex. Together our data demonstrate that the surface-engineered carbon films are suitable for selectively enriching low-abundance biological complexes at nanomolar level and for developing novel applications on a large number of surface-presented molecules.
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Affiliation(s)
- Marc C Llaguno
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Hui Xu
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Liang Shi
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Nian Huang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Biophysics, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Hong Zhang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Biophysics, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Qinghua Liu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Qiu-Xing Jiang
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA.
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14
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Sahu S, Philip F, Scarlata S. Hydrolysis rates of different small interfering RNAs (siRNAs) by the RNA silencing promoter complex, C3PO, determines their regulation by phospholipase Cβ. J Biol Chem 2013; 289:5134-44. [PMID: 24338081 DOI: 10.1074/jbc.m113.531467] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C3PO plays a key role in promoting RNA-induced gene silencing. C3PO consists of two subunits of the endonuclease translin-associated factor X (TRAX) and six subunits of the nucleotide-binding protein translin. We have found that TRAX binds strongly to phospholipase Cβ (PLCβ), which transmits G protein signals from many hormones and sensory inputs. The association between PLCβ and TRAX is thought to underlie the ability of PLCβ to reverse gene silencing by small interfering RNAs. However, this reversal only occurs for some genes (e.g. GAPDH and LDH) but not others (e.g. Hsp90 and cyclophilin A). To understand this specificity, we carried out studies using fluorescence-based methods. In cells, we find that PLCβ, TRAX, and their complexes are identically distributed through the cytosol suggesting that selectivity is not due to large scale sequestration of either the free or complexed proteins. Using purified proteins, we find that PLCβ binds ∼5-fold more weakly to translin than to TRAX but ∼2-fold more strongly to C3PO. PLCβ does not alter TRAX-translin assembly to C3PO, and brightness studies suggest one PLCβ binds to one C3PO octamer without a change in the number of TRAX/translin molecules suggesting that PLCβ binds to an external site. Functionally, we find that C3PO hydrolyzes siRNA(GAPDH) at a faster rate than siRNA(Hsp90). However, when PLCβ is bound to C3PO, the hydrolysis rate of siRNA(GAPDH) becomes comparable with siRNA(Hsp90). Our results show that the selectivity of PLCβ toward certain genes lies in the rate at which the RNA is hydrolyzed by C3PO.
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Affiliation(s)
- Shriya Sahu
- From the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
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15
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Philip F, Sahu S, Caso G, Scarlata S. Role of phospholipase C-β in RNA interference. Adv Biol Regul 2013; 53:319-330. [PMID: 23916604 PMCID: PMC3805765 DOI: 10.1016/j.jbior.2013.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 06/02/2023]
Abstract
Phospholipase C-β (PLCβ) enzymes are activated by G proteins in response to agents such as hormones and neurotransmitters, and have been implicated in leukemias and neurological disorders. PLCβ activity causes an increase in intracellular calcium which ultimately leads to profound changes in the cell. PLCβ localizes to three cellular compartments: the plasma membrane, the cytosol and the nucleus. Under most cell conditions, the majority of PLCβ localizes to the plasma membrane where it interacts with G proteins. In trying to determine the factors that localize PLCβ to the cytosol and nucleus, we have recently identified the binding partner, TRAX. TRAX is a nuclease and part of the machinery involved in RNA interference. This review discusses the interaction between PLCβ and TRAX, and its repercussions in G protein signaling and RNA silencing.
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Affiliation(s)
- Finly Philip
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
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