View More View Less
  • 1 Central Agricultural University (Imphal), Umiam, Meghalaya 793103
Restricted access

Phosphorus deficiency adversely affects crop productivity. The mechanism of tolerance in plants is not well understood. The current study successfully annotated a set of highly significant (Log2 RPKM ≥3) nine novel sequences up-regulated in P deficient condition identified from a low P tolerant rice genotype. Sequence annotation identified two transcripts (Os01g37260 and Os02g11060) carrying known domains, F-box and WD, respectively. Multiple Expectation maximization for Motif Elicitation (MEME) revealed presence of conserved domains like D[LP][HY][CL]D[CM][DT]C[AP][DQ][IQ]C, [EH][DN]HN[HS] [ER][FY][EP]I[HN]H which might play a role in phosphorus deficiency tolerance. Analysis of the upstream regions indicated presence of stress responsive elements like E Box, ABRE, and MYBCORE suggesting regulation of the novel transcripts by DNA binding. Protein localization prediction tool suggests that these novel proteins might be targeted to nucleus, chloroplast and cell wall. Transcripts Os02g03640 and Os02g10250 revealed potential target sites for microRNA binding suggesting role of novel miRNAs in low phosphorus response. Our analysis suggests that an F-box protein, Os01g37260 (OSFBx14) might be a promising candidate gene playing a role in multiple abiotic stresses including P deficiency.

  • 1.

    Baker, S. S., Wilhelm, K. S., Thomashow, M. F. (1994) The 5’-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold, drought and ABA-regulated gene expression. Plant Mol Biol. 24, 701713.

    • Search Google Scholar
    • Export Citation
  • 2.

    Baranowskij, N., Frohberg, C., Prat, S., Willmitzer, L. (1994) A novel DNA binding protein with homology to Myb oncoproteins containing only one repeat can function as a transcriptional activator. EMBO J. 13, 53835392.

    • Search Google Scholar
    • Export Citation
  • 3.

    Castle, J. C. (2011) SNPs occur in regions with less genomic sequence conservation. PLoS ONE 6, 112.

  • 4.

    Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B. H., Hong, X., Agarwal, M., Zhu, J. K. (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 10431054.

    • Search Google Scholar
    • Export Citation
  • 5.

    Chou, K. C., Shen, H. B. (2010) Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE 5, e11335.

    • Search Google Scholar
    • Export Citation
  • 6.

    Cordell, D., Drangert, J., White, S. (2009) The story of phosphorus: Global food security and food for thought. Glob. Environ. Change 19, 292305.

    • Search Google Scholar
    • Export Citation
  • 7.

    Dkhar, F., Rai, M., Tyagi, W. (2014) Looking beyond PsTOL1: marker development for two rice genes showing differential expression in P deficient conditions. J. Genet. 93, 573577.

    • Search Google Scholar
    • Export Citation
  • 8.

    Filichkin, S. A., Leonard, J. M., Monteros, A., Liu, P. P., Nonogaki, H. (2004) A novel endobetamannanase gene in tomato LeMAN5 is associated with anther and pollen development. Plant Physiol. 134, 10801087.

    • Search Google Scholar
    • Export Citation
  • 9.

    Hartmann, U., Sagasser, M., Mehrtens, F., Stracke, R., Weisshaar, B. (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3- MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol. Biol. 57, 155171.

    • Search Google Scholar
    • Export Citation
  • 10.

    Kaplan, B., Davydov, O., Knight, H., Galon, Y., Knight, M. R., Fluhr, R. (2006) From rapid transcriptome changes induced by cytosolic Ca2+ transients reveal ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis. Plant Cell 18, 27332748.

    • Search Google Scholar
    • Export Citation
  • 11.

    Kirk, G. J. D., Du, L. V. (1997) Changes in rice root architecture, porosity, and oxygen and proton release under phosphorus deficiency. New Phytol. 135, 191200.

    • Search Google Scholar
    • Export Citation
  • 12.

    Kochian, L. (2012) Rooting for more phosphorus. Nature 488, 466467.

  • 13.

    Kyte, J., Doolittle, R. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105113.

  • 14.

    Mavrodi, D. V., Peever, T. L., Mavrodi, O. V., Parejko, J. A., Raaijmakers, J. M., Lemanceau, P., Mazurier, S., Heide, L., Blankenfeldt, W., Weller, D. M., Thomashow, L. S. (2010) Diversity and evolution of the phenazine biosynthesis pathway. Appl. Environ. Microbiol. 76, 866879.

    • Search Google Scholar
    • Export Citation
  • 15.

    Pant, B. D., Buhtz, A., Kehr, J., Scheible, W. (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J. 53, 731738.

    • Search Google Scholar
    • Export Citation
  • 16.

    Planchias, S., Samland, A. K., Murray, J. A. H. (2004) Differential stability of Arabidopsis D-type cyclins: CYCD3;1 is a highly unstable protein degraded by a proteasome-dependent mechanism. Plant J. 38, 616625.

    • Search Google Scholar
    • Export Citation
  • 17.

    Qin, F., Sakuma, Y., Li, J., Liu, Q., Li, Y. Q., Shinozaki, K., Yamaguchi-Shinozaki, K. (2004) Cloning and functional analysis of a novel DREB1/CBF transcription factor involved in cold-responsive gene expression in Zea mays L. Plant Cell Physiol. 45, 10421052.

    • Search Google Scholar
    • Export Citation
  • 18.

    Raghothama, K. G. (1999) Phosphate acquisition. Annu. Rev. Plant. Physiol. 50, 665693.

  • 19.

    Secco, D., Jabnoune, M., Walker, H. Wu, P., Shou, H., Poirier, Y., Whelan, J. (2013) Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. Plant Cell 25, 42854304.

    • Search Google Scholar
    • Export Citation
  • 20.

    Todaka, D., Nakashima, K., Shinozaki, K., Yamaguchi-Shinozaki, K. (2012) Towards understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice. Rice 5, 19.

    • Search Google Scholar
    • Export Citation
  • 21.

    Tuteja, N. (2007) Abscisic acid and abiotic stress signaling. Plant Signal. Behav. 2, 135138.

  • 22.

    Tyagi, W., Rai, M. (2017) Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance. Protoplasma 254, 725736.

    • Search Google Scholar
    • Export Citation
  • 23.

    Xue, G. P. (2002) Characterisation of the DNA-binding profile of barley HvCBF1 using an enzymatic method for rapid, quantitative and high-throughput analysis of the DNA-binding activity. Nucleic Acids Res. 30, 77.

    • Search Google Scholar
    • Export Citation
  • 24.

    Yang, A., Dai, X., Zhang, W. A. (2012) R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J. of Exp. Bot. 63, 25412556.

    • Search Google Scholar
    • Export Citation
  • 25.

    Yu, S., Ligang, C., Liping, Z., Diqiu, Y. (2010) Overexpression of OsWRKY72 gene interferes in the abscisic acid signal and auxin transport pathway of Arabidopsis. J. Biosci. 35, 45971.

    • Search Google Scholar
    • Export Citation
  • 26.

    Yumnam, J. S., Rai, M., Tyagi, W. (2015) Allele mining across two low-P tolerant genes PSTOL1 and PupK20-2 reveals novel haplotypes in rice genotypes adapted to acidic soils. Plant Genet. Resour. 1, 19.

    • Search Google Scholar
    • Export Citation
  • 27.

    Zhang, Z. L., Xie, Z., Zou, X., Casaretto, J., Ho, T. H., Shen, Q. J. (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol. 134, 15001513.

    • Search Google Scholar
    • Export Citation