Abstract
RuvB, a member of AAA+ (ATPases Associated with diverse cellular Activities) superfamily of proteins, is essential, highly conserved and multifunctional in nature as it is involved in DNA damage repair, mitotic assembly, switching of histone variants and assembly of telomerase core complex. RuvB family is widely studied in various systems such as Escherichia coli, yeast, human, Drosophila, Plasmodium falciparum and mouse, but not well studied in plants. We have studied the transcript level of rice homologue of RuvB gene (OsRuvBL1a) under various abiotic stress conditions, and the results suggest that it is upregulated under salinity, cold and heat stress. Therefore, the OsRuvBL1a protein was characterized using in silico and biochemical approaches. In silico study confirmed the presence of all the four characteristic motifs of AAA+ superfamily—Walker A, Walker B, Sensor I and Sensor II. Structurally, OsRuvBL1a is similar to RuvB1 from Chaetomium thermophilum. The purified recombinant OsRuvBL1a protein shows unique DNA-independent ATPase activity. Using site-directed mutagenesis, the importance of two conserved motifs (Walker B and Sensor I) in ATPase activity has been also reported with mutants D302N and N332H. The OsRuvBL1a protein unwinds the duplex DNA in the 3′ to 5′ direction. The presence of unique DNA-independent ATPase and DNA unwinding activities of OsRuvBL1a protein and upregulation of its transcript under abiotic stress conditions suggest its involvement in multiple cellular pathways. The first detailed characterization of plant RuvBL1a in this study may provide important contribution in exploiting the role of RuvB for developing the stress tolerant plants of agricultural importance.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abdel-Monem M, Durwald H, Hoffmann-Berling H (1976) Enzymic unwinding of DNA. 2. Chain separation by an ATP-dependent DNA unwinding enzyme. Eur J Biochem 65:441–449
Ahmad M, Tuteja R (2012) Plasmodium falciparum RuvB proteins. Commun Integr Biol 5:350–361. https://doi.org/10.4161/cib.20005
Ahmad M, Tuteja R (2013) Plasmodium falciparum RuvB1 is an active DNA helicase and translocates in the 5′-3′ direction. Gene 515:99–109. https://doi.org/10.1016/j.gene.2012.11.020
Ahmad M, Afrin F, Tuteja R (2013) Identification of R2TP complex of Leishmania donovani and Plasmodium falciparum using genome wide in-silico analysis. Commun Integr Biol 6:e26005. https://doi.org/10.4161/cib.26005
Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201. https://doi.org/10.1093/bioinformatics/bti770
Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27:343–350. https://doi.org/10.1093/bioinformatics/btq662
Besche H, Tamura N, Tamura T, Zwickl P (2004) Mutational analysis of conserved AAA+ residues in the archaeal Lon protease from Thermoplasma acidophilum. FEBS Lett 574:161–166. https://doi.org/10.1016/j.febslet.2004.08.021
Biasini M et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258. https://doi.org/10.1093/nar/gku340
Bideshi DK, Federici BA (2000) DNA-independent ATPase activity of the Trichoplusiani granulovirus DNA helicase. J Gen virol 81:1601–1604. https://doi.org/10.1099/0022-1317-81-6-1601
Boo K et al (2015) Pontin functions as an essential coactivator for Oct4-dependent lincRNA expression in mouse embryonic stem cells. Nat Commun 6:6810. https://doi.org/10.1038/ncomms7810
Choi J, Heo K, An W (2009) Cooperative action of TIP48 and TIP49 in H2A.Z exchange catalyzed by acetylation of nucleosomal H2A. Nucleic Acids Res 37:5993–6007. https://doi.org/10.1093/nar/gkp660
Choudhury NR, Malik PS, Singh DK, Islam MN, Kaliappan K, Mukherjee SK (2006) The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase. Nucleic Acids Res 34:6362–6377. https://doi.org/10.1093/nar/gkl903
Dawid A, Croquette V, Grigoriev M, Heslot F (2004) Single-molecule study of RuvAB-mediated Holliday-junction migration. Proc Natl Acad Sci U S A 101:11611–11616. https://doi.org/10.1073/pnas.0404369101
Ducat D, Si K, Liu H, Yates JR, Zheng Y (2008) Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase pontin. Mol Biol Cell 19:3097–3110. https://doi.org/10.1091/mbc.e07-11-1202
Fritsch O, Benvenuto G, Bowler C, Molinier J, Hohn B (2004) The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol Cell 16:479–485. https://doi.org/10.1016/j.molcel.2004.09.034
Gartner W et al (2003) The ATP-dependent helicase RUVBL1/TIP49a associates with tubulin during mitosis. Cell Motil Cytoskeleton 56:79–93. https://doi.org/10.1002/cm.10136
Gonzales FA, Zanchin NIT, Luz JS, Oliveira CC (2005) Characterization of Saccharomyces cerevisiae Nop17p, a novel Nop58p-interacting protein that is involved in pre-rRNA processing. J Mol Biol 346:437–455. https://doi.org/10.1016/j.jmb.2004.11.071
Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM (1989) Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17:4713–4730
Greenleaf WB, Shen J, Gai D, Chen XS (2008) Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase. J Virol 82:6017–6023. https://doi.org/10.1128/JVI.00387-08
Gribun A, Cheung KL, Huen J, Ortega J, Houry WA (2008) Yeast Rvb1 and Rvb2 are ATP-dependent DNA helicases that form a heterohexameric complex. J Mol Biol 376:1320–1333. https://doi.org/10.1016/j.jmb.2007.12.049
Holt BF 3rd et al (2002) An evolutionarily conserved mediator of plant disease resistance gene function is required for normal Arabidopsis development. Dev Cell 2:807–817
Huang H, Zhao K, Arnett DR, Fanning E (2010) A specific docking site for DNA polymerase {alpha}-primase on the SV40 helicase is required for viral primosome activity, but helicase activity is dispensable. J Biol Chem 285:33475–33484. https://doi.org/10.1074/jbc.M110.156240
Ito K, Akiyama Y (2005) Cellular functions, mechanism of action, and regulation of FtsH protease. Annu Rev Microbiol 59:211–231. https://doi.org/10.1146/annurev.micro.59.030804.121316
Jayaraman A, Puranik S, Rai NK, Vidapu S, Sahu PP, Lata C, Prasad M (2008) cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.) Mol Biotechnol 40:241–251. https://doi.org/10.1007/s12033-008-9081-4
Jha S, Dutta A (2009) RVB1/RVB2: running rings around molecular biology. Mol Cell 34:521–533. https://doi.org/10.1016/j.molcel.2009.05.016
Jonsson ZO et al (2001) Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes. J Biol Chem 276:16279–16288. https://doi.org/10.1074/jbc.m011523200
Jonsson ZO, Jha S, Wohlschlegel JA, Dutta A (2004) Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol Cell 16:465–477. https://doi.org/10.1016/j.molcel.2004.09.033
Kanemaki M et al (1997) Molecular cloning of a rat 49-kDa TBP-interacting protein (TIP49) that is highly homologous to the bacterial RuvB. Biochem Biophys Res Commun 235:64–68. https://doi.org/10.1006/bbrc.1997.6729
Kanemaki M et al (1999) TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a. J Biol Chem 274:22437–22444
Lim CR, Kimata Y, Ohdate H, Kokubo T, Kikuchi N, Horigome T, Kohno K (2000) The Saccharomyces cerevisiae RuvB-like protein, Tih2p, is required for cell cycle progression and RNA polymerase II-directed transcription. J Biol Chem 275:22409–22417. https://doi.org/10.1074/jbc.m001031200
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCTmethod. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Lupas AN, Martin J (2002) AAA proteins. Curr Opin Struct Biol 12:746–753
Makino Y, Kanemaki M, Kurokawa Y, Koji T, Tamura T (1999) A rat RuvB-like protein, TIP49a, is a germ cell-enriched novel DNA helicase. J Biol Chem 274:15329–15335
March-Diaz R, Reyes JC (2009) The beauty of being a variant: H2A.Z and the SWR1 complex in plants. Mol Plant 2:565–577. https://doi.org/10.1093/mp/ssp019
Matias PM, Gorynia S, Donner P, Carrondo MA (2006) Crystal structure of the human AAA+ protein RuvBL1. J Biol Chem 281:38918–38929. https://doi.org/10.1074/jbc.M605625200
Mezard C, Davies AA, Stasiak A, West SC (1997) Biochemical properties of RuvBD113N: a mutation in helicase motif II of the RuvB hexamer affects DNA binding and ATPase activities. J Mol Biol 271:704–717. https://doi.org/10.1006/jmbi.1997.1225
Morrison AJ, Shen X (2009) Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. Nat Rev Mol Cell Biol 10:373–384. https://doi.org/10.1038/nrm2693
Mueller-Cajar O (2017) The diverse AAA+ machines that repair inhibited Rubisco active sites. Front Mol Biosci 4:31. https://doi.org/10.3389/fmolb.2017.00031
Nath M, Garg B, Sahoo RK, Tuteja N (2015) PDH45 overexpressing transgenic tobacco and rice plants provide salinity stress tolerance via less sodium accumulation. Plant Signal Behav 10:e992289. https://doi.org/10.4161/15592324.2014.992289
Petukhov M et al (2012) Large-scale conformational flexibility determines the properties of AAA+ TIP49 ATPases. Structure 20:1321–1331. https://doi.org/10.1016/j.str.2012.05.012
Pradhan A, Tuteja R (2007) Bipolar, dual Plasmodium falciparum helicase 45 expressed in the intraerythrocytic developmental cycle is required for parasite growth. J Mol Biol 373:268–281. https://doi.org/10.1016/j.jmb.2007.07.056
Puri T, Wendler P, Sigala B, Saibil H, Tsaneva IR (2007) Dodecameric structure and ATPase activity of the human TIP48/TIP49 complex. J Mol Biol 366:179–192. https://doi.org/10.1016/j.jmb.2006.11.030
Qiu XB et al (1998) An eukaryotic RuvB-like protein (RUVBL1) essential for growth. J Biol Chem 273:27786–27793
Rombel I, Peters-Wendisch P, Mesecar A, Thorgeirsson T, Shin YK, Kustu S (1999) MgATP binding and hydrolysis determinants of NtrC, a bacterial enhancer-binding protein. J Bacteriol 181:4628–4638
Rotanova TV, Botos I, Melnikov EE, Rasulova F, Gustchina A, Maurizi MR, Wlodawer A (2006) Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains. Protein Sci: Publ Protein Soc 15:1815–1828. https://doi.org/10.1110/ps.052069306
Sakato M, King SM (2004) Design and regulation of the AAA+ microtubule motor dynein. J Struct Biol 146:58–71. https://doi.org/10.1016/j.jsb.2003.09.026
Sanan-Mishra N, Pham XH, Sopory SK, Tuteja N (2005) Pea DNA helicase 45 overexpression in tobacco confers high salinity tolerance without affecting yield. Proc Natl Acad Sci U S A 102:509–514. https://doi.org/10.1073/pnas.0406485102
Schumacher J, Joly N, Rappas M, Zhang X, Buck M (2006) Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation. J Struct Biol 156:190–199. https://doi.org/10.1016/j.jsb.2006.01.006
Sigala B, Edwards M, Puri T, Tsaneva IR (2005) Relocalization of human chromatin remodeling cofactor TIP48 in mitosis. Exp Cell Res 310:357–369. https://doi.org/10.1016/j.yexcr.2005.07.030
Singleton MR, Dillingham MS, Wigley DB (2007) Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem 76:23–50. https://doi.org/10.1146/annurev.biochem.76.052305.115300
Smith DM, Benaroudj N, Goldberg A (2006) Proteasomes and their associated ATPases: a destructive combination. J Struct Biol 156:72–83. https://doi.org/10.1016/j.jsb.2006.04.012
Snider J, Thibault G, Houry WA (2008) The AAA+ superfamily of functionally diverse proteins. Genome Biol 9:216. https://doi.org/10.1186/gb-2008-9-4-216
Tarique M, Ahmad M, Ansari A, Tuteja R (2013) Plasmodium falciparum DOZI, an RNA helicase interacts with eIF4E. Gene 522:46–59. https://doi.org/10.1016/j.gene.2013.03.063
Tsaneva IR, Muller B, West SC (1993) RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro. Proc Natl Acad Sci U S A 90:1315–1319
Tuteja N, Rahman K, Tuteja R, Falaschi A (1993) Human DNA helicase V, a novel DNA unwinding enzyme from HeLa cells. Nucl Acids Res 21:2323–2329. https://doi.org/10.1093/nar/21.10.2323
Tuteja N, Ahmad P, Panda BB, Tuteja R (2009) Genotoxic stress in plants: shedding light on DNA damage, repair and DNA repair helicases. Mutat Res 681:134–149. https://doi.org/10.1016/j.mrrev.2008.06.004
Tuteja N, Sahoo RK, Garg B, Tuteja R (2013) OsSUV3 dual helicase functions in salinity stress tolerance by maintaining photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. IR64). Plant J Cell Mol biol 76:115–127. https://doi.org/10.1111/tpj.12277
Tuteja N, Tarique M, Trivedi DK, Sahoo RK, Tuteja R (2015) Stress-induced Oryza sativa BAT1 dual helicase exhibits unique bipolar translocation. Protoplasma 252:1563–1574. https://doi.org/10.1007/s00709-015-0791-8
Venteicher AS, Meng Z, Mason PJ, Veenstra TD, Artandi SE (2008) Identification of ATPases pontin and reptin as telomerase components essential for holoenzyme assembly. Cell 132:945–957. https://doi.org/10.1016/j.cell.2008.01.019
Wang CW, Chen WC, Lin LJ, Lee CT, Tseng TH, Leu WM (2011) OIP30, a RuvB-like DNA helicase 2, is a potential substrate for the pollen-predominant OsCPK25/26 in rice. Plant Cell Physiol 52:1641–1656. https://doi.org/10.1093/pcp/pcr094
Watanabe YH, Motohashi K, Yoshida M (2002) Roles of the two ATP binding sites of ClpB from Thermus thermophilus. J Biol Chem 277:5804–5809. https://doi.org/10.1074/jbc.M109349200
Wood MA, McMahon SB, Cole MD (2000) An ATPase/helicase complex is an essential cofactor for oncogenic transformation by c-Myc. Mol Cell 5:321–330. https://doi.org/10.1016/s1097-2765(00)80427-x
Zhang P et al. (2017) The Rice AAA-ATPase OsFIGNL1 is essential for male meiosis Front Plant Sci 8 doi:https://doi.org/10.3389/fpls.2017.01639
Zhao R et al (2008) Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol 180:563–578. https://doi.org/10.1083/jcb.200709061
Zhou X, Zolotukhin I, Im DS, Muzyczka N (1999) Biochemical characterization of adeno-associated virus rep68 DNA helicase and ATPase activities. J Virol 73:1580–1590
Zolkiewski M (2006) A camel passes through the eye of a needle: protein unfolding activity of Clp ATPases. Mol Microbiol 61:1094–1100. https://doi.org/10.1111/j.1365-2958.2006.05309
Zylicz M, LeBowitz JH, McMacken R, Georgopoulos C (1983) The dnaK protein of Escherichia coli possesses an ATPase and autophosphorylating activity and is essential in an in vitro DNA replication system. Proc Natl Acad Sci U S A 80:6431–6435
Acknowledgements
We would like to thank Dr. Tarique Mohammad and Dr. Irum Rizvi for their helpful contribution on experiments.
Funding
The authors gratefully acknowledge financial support from the CSIR (Council of Scientific and Industrial Research) for this work. SS is a recipient of fellowship from the CSIR and NP is a recipient of fellowship from the DBT (Department of Biotechnology).
Author information
Authors and Affiliations
Corresponding author
Additional information
Handling Editor: Peter Nick
Electronic supplementary material
ESM 1
(PPTX 1236 kb)
Rights and permissions
About this article
Cite this article
Saifi, S.K., Passricha, N., Tuteja, R. et al. Stress-induced Oryza sativa RuvBL1a is DNA-independent ATPase and unwinds DNA duplex in 3′ to 5′ direction. Protoplasma 255, 669–684 (2018). https://doi.org/10.1007/s00709-017-1178-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00709-017-1178-9