Abstract
RCD1 protein confers multiple stress tolerance to plant, while playing in it developmental roles as well. After an extensive characterization of its gene in A. thaliana, role of its orthologues under varying stresses have also been characterized in rice, wheat and tomato plants. RCD1 of A. thaliana with its rice homologue has been found consensually involved in providing plant tolerance against oxidative and osmotic stresses; however, its stress-tolerance roles under other environmental stresses seem rather contrasting. This is also the case with the expression profile, primary protein structure and binding affinities of these two homologues. Such differences in behaviours of the RCD1 homologues raises need to study their evolutionary status, in an effort to infer relative conservation of their functions. To elucidate this pattern, available RCD1 homologues have been subjected to Maximum Parsimony and Bayesian Inference-based analysis in this research. Conservation status of the SRO1/RCD1 type-specific WWE domain has also been explored using the available sequences in online databases along with the WWE-encoding sequences obtained in sugarcane, wheat and rice using single set of primers designed on conserved flanking regions. Results suggest a high conservation of these homologues within plant families, suggesting family-specific conservation of their functionalities in demonstrating stress responses.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Ahlfors R., Lang S., Overmyer K., Jaspers P., Brosche M., Tauriainen A., Kollist H., Tuominen H., Belles-Boix E., Piippo M., Inze D., Palva E.T. & Kangasjarvi J. 2004. Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses. Plant Cell. 16: 1925–1937.
Anjum S., Raza S., Azhar A. & Qamarunnisa S. 2015. Bnsro 1: A new homologue of Arabidopsis thaliana rcd1 from Brassica napus. Biologia 70: 588–598.
Aravind L. 2001. The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation. Trends Biochem. Sci. 26: 273–275.
Babajani G., Effendy J. & Plant A.L. 2009. Sl-SROl increases salt tolerance and is a member of the radical-induced cell death 1-similar to RCD1 gene family of tomato. Plant Sci. 176: 214–222.
Bloomster T., Salojärvi J., Sipari N., Brosché M., Ahlfors R., Keinänen M., Overmeyer K. & Kangasjärvi J. 2011. Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis. Plant Physiol. 157: 1866–1883.
Boscaiu M., Donat P., Linares J. & Vicente O. 2012. Stresstolerant wild plants: a source of knowledge and biotechnological tools for the genetic improvement of stress tolerance in crop plants. Not. Bot. Horti. Agrobo. 40: 323–327.
Boyer J.S. 1982. Plant productivity and environment. Science 218: 443–448.
Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16: 10881–10890.
Citarelli M., Teotia S. & Lamb R.S. 2010. Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. BMC Evol. Biol. 10: 308.
D’Amours D., Desnoyers S., DaSilva I. & Poirier G. 1999. Poly (ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem. J. 342: 249–268.
Darriba D., Taboada G.L., Doallo R. & Posada D. 2012. ”jModel- Test 2: more models, new heuristics and parallel computing”. Nat. Methods 9: 772.
deCastro E., Sigrist C.J., Gattiker A., Bulliard V., Langendijk-Genevaux P.S., Gasteiger E., Bairoch A. & Hulo N. 2006. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 34: 362–365.
Doyle J.J. & Doyle J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11–15.
Drummond A.J. & Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
Fujibe T., Saji H., Arakawa K., Yabe N., Takeuchi Y. & Yamamoto K.T. 2004. A methyl viologen resistant mutant of Arabidopsis, which is allelic to ozone-sensitive rcd1, is tolerant to supplemental ultraviolet-B irradiation. Plant Physiol. 134: 275–285.
Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D. & Bairoch A. 2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31: 3784–3788.
Goodstein D.M., Shu S., Howson R., Neupane R., Hayes R.D., Fazo J., Mitros T., Dirks W., Hellsten U. & Putnam N. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: 1178–1186.
Hofmann K. & Bucher P. 1996. The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. Trends Biochem. Sci. 21: 172–173.
Jaspers P., Blomster T., Brosche M., Saloja J., Ahlfors R., Vainonen J.P., Reddy A.R., Immink R., Angenent G., Turck F., Overmyer K. & Kangasjärvi J. 2009. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. Plant J. 60: 268–279.
Jaspers P., Brosché M., Overmyer K. & Kangasjärvi J. 2010a. The transcription factor interacting protein RCD1 contains a novel conserved domain. Plant Signal. Behav. 5: 78–80.
Jaspers P., Overmyer K., Wrzaczek M., Vainonen J.P., Blomster T., Salojärvi J., Ramesha A.R. & Kangasjärvi J. 2010b. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics 11: 170.
Julia P.V., Pinja J., Michael W., Airi L., Ramesha A.R., Vaahtera L., Brosché M. & Kangasjärvi J. 2012. RCD1-DREB2A interaction in leaf senescence and stress responses in Arabidopsis thaliana. Biochem. J. 442: 573–581.
Katiyar-Agarwal S., Zhu J., Kim K., Agarwal M., Fu X., Huang A. & Zhu J.K. 2006. The plasma membrane Na+/H+ antiporter SOS1 interacts with RCD1 and functions in oxidative stress tolerance in Arabidopsis. Proc Natl. Acad. Sci. USA 103: 18816–18821.
Liu S., Wang M., Wei T., Meng C., Wang M. & Xia G. 2014. A wheat SIMILAR TO RCD-ONE gene enhances seedling growth and abiotic stress resistance by modulating redox homeostasis and maintaining genomic integrity. Plant Cell. 26: 164–180.
Marchler-Bauer A., Anderson J.B., Cherukuri P.F., De Weese-Scott C., Geer L.Y., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z. & et al. 2005. CDD: a Conserved Domain 650 B. Siddiqua et al. Database for protein classification. Nucleic Acids Res. 33: 192–196.
Overmyer K., Tuominen H., Kettunen R., Betz C., Langebartels C., Sandermann H., Kangasjärvi J. 2000. Ozone-sensitive Arabidopsis rcd1 mutant reveals opposite roles for ethylene and jasmonate signaling pathways in regulating superoxidedependent cell death. Plant Cell. 12: 1849–1862.
Posada D. & Buckley T. 2004. Model selection and model averaging in phylognetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53: 793–808.
Pruitt K.D., Tatusova T. & Maglott D.R. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35: 61–65.
Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., Ceric G. & Clements J. 2012. The Pfam protein families database. Nucleic Acids Res. 40: 290–301.
Rhee S.Y., Beavis W., Berardini T.Z., Chen G., Dixon D., Doyle A., Margarita Garcia-Hernandez M., Huala E., Lander G., Montoa M. & et al. 2003. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31: 224–228.
Rombel I.T., Sykes K.F., Rayner S. & Johnston S.A. 2002. ORFFINDER: a vector for high-throughput gene identification. Gene 282: 33–41.
Rouard M., Guignon V., Aluome C., Laporte M.A., Droc G., Walde C., Zmasek C.M., Perin C. & Conte M.G. 2011. Green- PhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res. 39: 1095–1102.
Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., McWilliam H., Remmert M., Söding J., Thompson J.D. & Higgins D.G. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7: 539.
Sigrist C.J., de Castro E., Cerutti L., Cuche B.A., Hulo N., Bridge A., Bougueleret L. & Xenarios I. 2013. New and continuing developments at PROSITE. Nucleic Acids Res. 41: 344–347.
Solcitis P.S. & Solcitis D.E. 2013. Angiosperm phylogeny: A framework for studies of genome evolution. Plant Genome Diversity Volume 2. Springer Vienna, pp. 1–11.
Swofford D.L. 2002. PAUP*: Phylogenetic analysis using parsimony (* and other methods). Version, 4.
Teotia S. & Lamb R.S. 2009. The paralogous genes RADICALINDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 have partially redundant functions during Arabidopsis development. Plant Physiol. 151: 180–198.
Thompson J.D., Higgins D.G. & Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
Untergrasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B.C., Remm M. & Rozen S.G. 2012. Primer3 — new capabilities and interfaces. Nucleic Acids Res. 40: 115.
You J., Zong W., Li X., Ning J., Hu H., Li X., Xiao J. & Xiong L. 2013a. The SNAC1-targeted gene OsSRO1c modulates stomatal closure and oxidative stress tolerance by regulating hydrogen peroxide in rice. J. Exp. Bot. 64: 569–583.
You J., Zong W., Du H., Hu H. & Xiong L. 2013b. A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. Plant Mol. Biol. 4: 693–705.
Zhu Y., Du B., Qian J., Zou B. & Hua J. 2013. Disease resistance gene-induced growth inhibition is enhanced by rcd1 independent of defense activation in Arabidopsis. Plant Physiol. 161: 2005–2013.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
11756_2016_7106642_MOESM1_ESM.pdf
Electronic supplementary material. The online version of this article (DOI: 10.1515/biolog-2016-0081) contains supplementary material, which is available to authorized users.
Rights and permissions
About this article
Cite this article
Siddiqua, B., Qamarunnisa, S. & Azhar, A. RCD1 homologues and their constituent WWE domain in plants: analysis of conservation through phylogeny methods. Biologia 71, 642–650 (2016). https://doi.org/10.1515/biolog-2016-0081
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1515/biolog-2016-0081