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Histidine kinase and response regulator genes as they relate to salinity tolerance in rice

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Abstract

We have previously shown that Oryza sativa L. Pokkali maintains higher levels of transcripts under non-saline conditions, which are otherwise induced under salinity in the sensitive genotype—IR64. We wanted to test this hypothesis of differential gene regulation further, within the members of a given stress responsive gene family, which share significant structural and functional similarities. For this purpose, we chose to work on the two-component system (TCS family) which plays an important role in stress perception and signal transduction under hormonal, abiotic stress, light and developmental regulation. We present data to show that all members of TCS family, including sensory histidine kinases, phosphotransfer proteins and response regulators, are having differential transcript abundance (under both non-stress and salinity stress conditions) in contrasting rice genotypes. Further, under non-stress conditions, transcript abundance for all TCS members (except RR21) was found to be higher in the salt-tolerant genotype—Pokkali. TCS transcripts are otherwise induced by salinity stress to a relatively higher level in the sensitive cultivar IR64. A few of these members were also found to be localised within important salinity-related quantitative trait loci identified earlier. Based on the above findings, we propose that the TCS members may have a significant role in salinity tolerance in rice and can serve as useful ‘candidate genes’ for raising salinity-tolerant crop plants.

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Fig. 1

Abbreviations

TCS:

Two-component system

HK:

Histidine kinase

HPT:

Phosphotransfer protein

RR:

Response regulator

QTL:

Quantitative trait loci

RFLP:

Restriction fragment length polymorphism

References

  • Grefen C, Harter K (2004) Plant two-component systems: principles, functions, complexity and cross talk. Planta 219:733–742

    Article  PubMed  CAS  Google Scholar 

  • Hwang I, Chen HC, Sheen J (2002) Two-component signal transduction pathways in Arabidopsis. Plant Physiol 129:500–515

    Article  PubMed  CAS  Google Scholar 

  • Ismail AM, Heuer S, Thomson MJ, Wissuwa M (2007) Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol Biol 65:547–570

    Article  PubMed  CAS  Google Scholar 

  • Jain M, Tyagi AK, Khurana JP (2006) Molecular characterization and differential expression of cytokinin-responsive type-A response regulator in rice (Oryza sativa). BMC Plant Biol 6:1

    Article  PubMed  Google Scholar 

  • Jain M, Tyagi AK, Khurana JP (2008) Differential gene expression of rice two-component signaling elements during reproductive development and regulation by abiotic stress. Funct Integr Genomics 8:175–180

    Article  PubMed  CAS  Google Scholar 

  • Kakimoto T (2003) Perception and signal transduction of cytokinins. Annu Rev Plant Biol 54:605–627

    Article  PubMed  CAS  Google Scholar 

  • Kumar G, Purty RS, Sharma MP, Singla-Pareek SL, Pareek A (2009) Physiological responses among Brassica species under salinity stress show strong correlation with transcript abundance for SOS pathway-related genes. J Plant Physiol 166:507–520

    Google Scholar 

  • Kumari S, Panjabi Nee Sabharwal V, Kushwaha HR, Sopory SK, Singla-Pareek SL, Pareek A (2009a) Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. Funct Integr Genomics 9:109–123

    Article  PubMed  CAS  Google Scholar 

  • Kumari S, Singh P, Singla-Pareek SL, Pareek A (2009b) Heterologous expression of a salinity and developmentally regulated rice cyclophilin gene (OsCyp2) in E. coli and S. cerevisiae confers tolerance towards multiple abiotic stresses. Mol Biotechnol. doi:10.1007/s12033-009-9153-0

  • Leung H (2008) Stressed genomics-bringing relief to rice fields. Curr Opin Plant Biol 11:201–208

    PubMed  CAS  Google Scholar 

  • Lohrmann J, Harter K (2002) Plant two-component signaling systems and the role of response regulators. Plant Physiol 128:363–369

    Article  PubMed  CAS  Google Scholar 

  • Li WX, Oono Y, Zhu J, He XJ, Wu JM, Lida K, Lu XY, Cui X, Jin H, Zhu J-K (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post-transcriptionally to promote drought resistance. Plant Cell 8:2238–2251

    Google Scholar 

  • Ma S, Bohnert HJ (2007) Integration of Arabidopsis thaliana stress-related profiles, promoter structures, and cell specific expression. Genome Biol 8:R49

    Article  PubMed  Google Scholar 

  • Mentzen WI, Wurtele ES (2008) Regulon organization of Arabidopsis. BMC Plant Biol 8:99. doi:10.1186/1471-2229-8-99

  • Mohammadi-Nejad G, Arzani A, Rezai AM, Singh RK, Gregorio GB (2008) Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL. Afr J Biotechnol 7:730–736

    Google Scholar 

  • Oka A, Sakai H, Iwakoshi S (2002) His-Asp phosphorelay signal transduction in higher plants: receptors and response regulators for cytokinin signaling in Arabidopsis thaliana. Gene Genet Syst 77:383–391

    Article  CAS  Google Scholar 

  • Pareek A, Singh A, Kumar M, Kushwaha H, Singla-Pareek S (2006) Whole genome analysis of Oryza sativa reveals similar architecture of two component signaling machinery with Arabidopsis. Plant Physiol 142:380–397

    Article  PubMed  CAS  Google Scholar 

  • Schaller GC, Doi K, Hwang I, Kieber JJ, Khurana JP, Kurata N, Mizuno T, Pareek A, Shiu SH, Wu P, Yip WK (2007) Nomenclature for two-component signaling elements of rice. Plant Physiol 143:555–557

    Article  PubMed  CAS  Google Scholar 

  • Singh RK, Gregario GB, Jain RK (2007) QTL mapping for salinity tolerance in rice. Physiol Mol Biol Plants 13:87–99

    CAS  Google Scholar 

  • Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835

    Article  PubMed  CAS  Google Scholar 

  • Wong CE, Li Y, Labbe A, Guevara D, Nuin P, Whitty B, Diaz C, Golding GB, Gray GR, Weretilnyk EA, Griffith M, Moffatt BA (2006) Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis. Plant Physiol 140:1437–1450

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This work was supported by research grants received from the International Atomic Energy Agency (Vienna), International Foundation for Science (Sweden), Department of Science and Technology, Government of India and Senior Research Fellowship (R. K.) from the University Grants Commission, Government of India. Authors would also like to thank Nausheen Tareen for helping in manuscript editing.

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Authors and Affiliations

  1. Stress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Ratna Karan & Ashwani Pareek

  2. Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India

    Sneh L. Singla-Pareek

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  1. Ratna Karan
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  2. Sneh L. Singla-Pareek
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  3. Ashwani Pareek
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Corresponding author

Correspondence to Ashwani Pareek.

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SUPPL Fig. 1

qRT-PCR analysis of TCS genes in contrasting rice genotypes under non-stress conditions. a Cartoon depicting the functioning of a hybrid type histidine kinase (TCS system) in eukaryotes. b Analysis of sensory HK genes expressed under non-stress conditions. c Analysis of HPT genes expressed under non-stress conditions. d Analysis of RR genes expressed under non-stress conditions. The values represented in each sample are the mean of two biological and three technical replicates, whilst bars indicate the standard error of triplicates. The expression of each TCS gene in control RNA samples of IR64 and Pokkali was normalised with the expression of internal control gene, actin (GIF 64.2 KB).

High resolution image file (TIFF 643 KB).

SUPPL Fig. 2

Fold increase of TCS transcripts in two contrasting genotypes of rice under salinity stress. a Fold change of sensory HK genes expressed during salinity stress condition by qRT-PCR. b Fold change of HPT genes expressed during salinity stress condition. c Fold change of RR genes differentially expressed during salinity stress condition. The mRNA levels for each gene in seedlings subjected to salinity stress were calculated relative to its expression in control seedlings using ΔΔCT method. The values represented are the mean of two biological and three technical replicates, whilst bars indicate the standard error of triplicates. The expression of each gene in the RNA samples was normalised with the expression of the internal control gene, actin (GIF 50.5KB).

High resolution image file (TIFF 563 KB).

SUPPL Fig. 3

Heat map display of TCS genes under control and salinity stress conditions in two contrasting genotypes of rice. a Heat map of sensory HKs, b heat map of HPTs and c heat map of RRs. IRC IR64 control, IRS salinity-stressed IR64, POKC Pokkali control, POKS salinity-stressed Pokkali. Normalised CT value of each sample with respect to actin was used for Heat map analysis (GIF 83.5 KB).

High resolution image file (TIFF 5.63 MB).

SUPPL Fig. 4

Histogram showing the distribution of sensory HKs, HPTs and RRs on various rice chromosomes (GIF 12.0 KB).

High resolution image file (TIFF 258 KB).

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Karan, R., Singla-Pareek, S.L. & Pareek, A. Histidine kinase and response regulator genes as they relate to salinity tolerance in rice. Funct Integr Genomics 9, 411–417 (2009). https://doi.org/10.1007/s10142-009-0119-x

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  • DOI: https://doi.org/10.1007/s10142-009-0119-x

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