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Pillai V, Gupta A, Rao A, Chittela RK. Biochemical characterization of clinically relevant mutations of human Translin. Mol Cell Biochem 2022; 478:821-834. [PMID: 36098897 DOI: 10.1007/s11010-022-04556-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022]
Abstract
DNA damage in all living cells is repaired with very high efficiency and nucleic acid binding proteins play crucial roles in repair associated processes. Translin is one such evolutionarily conserved nucleic acid interacting protein speculated to be a part of the DNA repair protein network. It is also involved in activation of RNA-induced silencing complex (RISC) along with Translin-associated factor X (TRAX) as the C3PO (component 3 promoter of RISC) complex. In the present work, we characterized ten clinically relevant variants of the human Translin protein using bioinformatic, biochemical, and biophysical tools. Bioinformatic studies using DynaMut revealed 9 out of the 10 selected mutations the Translin protein. Further analysis revealed that some mutations lead to changes in interactions with neighbouring residues in the protein structure. Using site directed mutagenesis, the point substitution variants were generated, corresponding proteins were overexpressed and purified using Ni-NTA affinity chromatography. Purified proteins form octamers similar to wild type (WT) Translin, as observed using native polyacrylamide gel electrophoresis (PAGE), gel filtration, and dynamic light-scattering (DLS) analysis. These octamers are functional and bind to single-stranded DNA (ssDNA) as well as single-stranded RNA (ssRNA) substrates. The mutant Translin proteins interact with wild type TRAX and form corresponding C3PO complexes. The C3PO complexes formed by all Translin variants with TRAX are functional in-vitro and show endoribonuclease activity. However, significant differences were observed in the extent of RNase activity in vitro. In conclusion, the clinically relevant mutations in Translin protein analysed by us exert their effect by modulating the RNase activity of the protein without altering its DNA-dependant function.
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Affiliation(s)
- Vinayaki Pillai
- Applied Genomics Section, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400 094, India
| | - Alka Gupta
- Applied Genomics Section, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Avssn Rao
- Applied Genomics Section, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India. .,Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400 094, India.
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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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Gupta A, Pillai VS, Chittela RK. Role of amino acid residues important for nucleic acid binding in human Translin. Int J Biochem Cell Biol 2019; 115:105593. [PMID: 31442605 DOI: 10.1016/j.biocel.2019.105593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/25/2019] [Accepted: 08/19/2019] [Indexed: 11/15/2022]
Abstract
Translin is a multifunctional DNA/RNA binding protein involved in DNA repair and RNA metabolism. It has two basic regions and involvement of some residues in these regions in nucleic acid binding is established experimentally. Here we report the functional role of four residues of basic region II, Y85, R86, H88, R92 and one residue of C terminal region, K193 in nucleic acid binding using substitution mutant variants. CD analysis of the mutant proteins showed that secondary structure was maintained in all the mutant proteins in comparison to wild type protein. Octameric state was maintained in all the mutants of basic region as evidenced by TEM, DLS, native PAGE and gel filtration analyses. However, K193G mutation completely abolished the octameric state of Translin protein and consequently its ability to bind ssDNA/ssRNA. The mutants of the basic region II exhibited a differential effect on nucleic acid binding, with R86A and R92G as most deleterious. Interestingly, H88A mutant showed higher nucleic acid binding affinity in comparison to the wild type Translin. An in silico analysis of the mutant variant sequences predicted all the mutations to be destabilizing, causing increase in flexibility and also leading to disruption of local interactions. The differential effect of mutations on DNA/RNA binding where octameric state is maintained could be attributed to these predicted disturbances.
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Affiliation(s)
- Alka Gupta
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Vinayaki S Pillai
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400 094, India
| | - Rajani Kant Chittela
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400 094, India.
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Gupta A, Nair A, Ballal A, Chittela RK. C-terminal residues of rice translin are essential for octamer formation and nucleic acid binding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:600-608. [PMID: 28797959 DOI: 10.1016/j.plaphy.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/25/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Translin is a DNA/RNA binding protein involved in DNA repair and RNA metabolism. Previously, we had shown that rice translin (221 amino acids) exhibits biochemical activities similar to that of the human translin protein. Here we report the role of the C-terminal random coil in rice translin function by analyzing truncation (after 215th residue, Tra - 215) and substitution mutant proteins (Ser216Ala, Lys217Ala, Gln218Ala, Glu219Ala). Circular Dichroism (CD) analysis of Tra-215 showed deviations in comparison to Tra-WT. Truncation abolished the DNA binding activity and octamer formation as evidenced by the absence of ring like structures from TEM analysis. CD analysis of the substitution mutant proteins showed that the secondary structure was maintained in all the mutant proteins in comparison to wild type protein. Native PAGE and TEM analysis of the substitution mutants showed that Lys217Ala mutation completely abolished the octamer formation as rings and nucleic acid binding. Glu219Ala mutation also affected oligomerization but exhibited marginal RNA binding at higher protein concentrations and interestingly, failed to bind to DNA. However, Ser216Ala and Gln218Ala substitutions did not affect above mentioned activities of translin. Our results indicate that the C-terminal residues are one of the determinants of octamer formation in rice translin, with lysine at 217th position being the most important. Therefore, in conclusion, although the C-terminal residues do not form any defined secondary structure in the translin monomer, they are definitely involved in octamer formation and hence important for its molecular function. We have attempted to find the critical residues in translin function, which will advance our understanding of translin in DNA repair process in general and of rice translin in particular.
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Affiliation(s)
- Alka Gupta
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Mumbai, 400 094, India
| | - Anuradha Nair
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Mumbai, 400 094, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Mumbai, 400 094, India
| | - Rajani Kant Chittela
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; Homi Bhabha National Institute, Mumbai, 400 094, India.
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Rao VG, Sarafdar RB, Chowdhury TS, Sivadas P, Yang P, Dongre PM, D'Souza JS. Myc-binding protein orthologue interacts with AKAP240 in the central pair apparatus of the Chlamydomonas flagella. BMC Cell Biol 2016; 17:24. [PMID: 27287193 PMCID: PMC4901443 DOI: 10.1186/s12860-016-0103-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/02/2016] [Indexed: 12/20/2022] Open
Abstract
Background Flagella and cilia are fine thread-like organelles protruding from cells that harbour them. The typical ‘9 + 2’ cilia confer motility on these cells. Although the mechanistic details of motility remain elusive, the dynein-driven motility is regulated by various kinases and phosphatases. A-kinase anchoring proteins (AKAPs) are scaffolds that bind to a variety of such proteins. Usually, they are known to possess a dedicated domain that in vitro interacts with the regulatory subunits (RI and RII) present in the cAMP-dependent protein kinase (PKA) holoenzyme. These subunits conventionally harbour contiguous stretches of a.a. residues that reveal the presence of the Dimerization Docking (D/D) domain, Catalytic interface domain and cAMP-Binding domain. The Chlamydomonas reinhardtii flagella harbour two AKAPs; viz., the radial spoke AKAP97 or RSP3 and the central pair AKAP240. Both these were identified on the basis of their RII-binding property. Interestingly, AKAP97 binds in vivo to two RII-like proteins (RSP7 and RSP11) that contain only the D/D domain. Results We found a Chlamydomonas Flagellar Associated Protein (FAP174) orthologous to MYCBP-1, a protein that binds to organellar AKAPs and Myc onco-protein. An in silico analysis shows that the N-terminus of FAP174 is similar to those RII domain-containing proteins that have binding affinities to AKAPs. Binding of FAP174 was tested with the AKAP97/RSP3 using in vitro pull down assays; however, this binding was rather poor with AKAP97/RSP3. Antibodies were generated against FAP174 and the cellular localization was studied using Western blotting and immunoflourescence in wild type and various flagella mutants. We show that FAP174 localises to the central pair of the axoneme. Using overlay assays we show that FAP174 binds AKAP240 previously identified in the C2 portion of the central pair apparatus. Conclusion It appears that the flagella of Chlamydomonas reinhardtii contain proteins that bind to AKAPs and except for the D/D domain, lack the conventional a.a. stretches of PKA regulatory subunits (RSP7 and RSP11). We add FAP174 to this growing list. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0103-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Venkatramanan G Rao
- UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098, India
| | - Ruhi B Sarafdar
- UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098, India
| | - Twinkle S Chowdhury
- UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098, India
| | - Priyanka Sivadas
- Wehr Life Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Pinfen Yang
- Wehr Life Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Prabhakar M Dongre
- Department of Biophysics, University of Mumbai, Kalina campus, Santacruz (E), Mumbai, 400098, India
| | - Jacinta S D'Souza
- UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098, India.
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Gupta GD, Makde RD, Rao BJ, Kumar V. Crystal structures of Drosophila mutant translin and characterization of translin variants reveal the structural plasticity of translin proteins. FEBS J 2008; 275:4235-49. [PMID: 18647346 DOI: 10.1111/j.1742-4658.2008.06571.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Translin protein is highly conserved in eukaryotes. Human translin binds both ssDNA and RNA. Its nucleic acid binding site results from a combination of basic regions in the octameric structure. We report here the first biochemical characterization of wild-type Drosophila melanogaster (drosophila) translin and a chimeric translin, and present 3.5 A resolution crystal structures of drosophila P168S mutant translin from two crystal forms. The wild-type drosophila translin most likely exists as an octamer/decamer, and binds to the ssDNA Bcl-CL1 sequence. In contrast, ssDNA binding-incompetent drosophila P168S mutant translin exists as a tetramer. The structures of the mutant translin are identical in both crystal forms, and their C-terminal residues are disordered. The chimeric protein, possessing two nucleic acid binding motifs of drosophila translin, the C-terminal residues of human translin, and serine at position 168, attains the octameric state and binds to ssDNA. The present studies suggest that the oligomeric status of translin critically influences the DNA binding properties of translin proteins.
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Affiliation(s)
- Gagan D Gupta
- High Pressure Physics Division, Bhabha Atomic Research Centre, Mumbai, India
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Suseendranathan K, Sengupta K, Rikhy R, D'Souza JS, Kokkanti M, Kulkarni MG, Kamdar R, Changede R, Sinha R, Subramanian L, Singh K, Rodrigues V, Rao BJ. Expression pattern of Drosophila translin and behavioral analyses of the mutant. Eur J Cell Biol 2007; 86:173-86. [PMID: 17275950 DOI: 10.1016/j.ejcb.2006.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 10/21/2006] [Accepted: 11/01/2006] [Indexed: 11/29/2022] Open
Abstract
Translin is an evolutionarily conserved approximately 27-kDa protein that binds to specific DNA and RNA sequences and has diverse cellular functions. Here, we report the cloning and characterization of the translin orthologue from the fruit fly Drosophila melanogaster. Under protein-denaturing conditions, purified Drosophila translin exists as a mixture of dimers and monomers just like human translin. In contrast to human translin, the Drosophila translin dimers do not appear to be stabilized by disulfide interactions. Drosophila translin shows a ubiquitous cytoplasmic localization in early embryonal syncytial stage, with an enhanced staining in ventral neuroblasts at later stages (8-9), which are probably at metaphase. An elevated expression was seen in several other cell types, such as cells around the tracheal pits in the embryo and oenocytes in the third instar larva. RNA in situ hybridization showed an increased expression in the ventral midline cells of the larval brain, suggesting a neuronal expression, which was corroborated by protein immunostaining. In adult flies, Drosophila translin is localized in the brain neuronal cell bodies and in early spermatocytes. Interestingly, Drosophila translin mutants exhibit an impaired motor response which is sex specific. Taken together, the multiple cellular localizations, the high neuronal expression and the attendant locomotor defect of the Drosophila translin mutant suggest that Drosophila translin may have roles in neuronal development and behavior analogous to that of mouse translin.
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Affiliation(s)
- Kumud Suseendranathan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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Abstract
The vertebrate RNA and ssDNA-binding protein Translin has been suggested to function in a variety of cellular processes, including DNA damage response, RNA transport, and translational control. The Translin-associated factor X (Trax) interacts with Translin, and Trax protein stability depends on the presence of Translin. To determine the function of the Drosophila Translin and Trax, we generated a translin null mutant and isolated a trax nonsense mutation. translin and trax single and double mutants are viable, fertile, and phenotypically normal. Meiotic recombination rates and chromosome segregation are also not affected in translin and trax mutants. In addition, we found no evidence for an increased sensitivity for DNA double-strand damage in embryos and developing larvae. Together with the lack of evidence for their involvement in DNA double-strand break checkpoints, this argues against a critical role for Translin and Trax in sensing or repairing such DNA damage. However, Drosophila translin is essential for stabilizing the Translin interaction partner Trax, a function that is surprisingly conserved throughout evolution. Conversely, trax is not essential for Translin stability as trax mutants exhibit normal levels of Translin protein.
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Affiliation(s)
- Maike Claussen
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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