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First published online August 4, 2006; 10.1104/pp.106.086371

Plant Physiology 142:380-397 (2006)
© 2006 American Society of Plant Biologists

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GENOME ANALYSIS

Whole-Genome Analysis of Oryza sativa Reveals Similar Architecture of Two-Component Signaling Machinery with Arabidopsis1,[W]

Ashwani Pareek2,*, Anupama Singh2, Manoj Kumar, Hemant R. Kushwaha, Andrew M. Lynn and Sneh L. Singla-Pareek

Stress Physiology and Molecular Biology Laboratory, School of Life Sciences (A.P., M.K.), and Centre for Computational Biology and Bioinformatics (A.S., H.R.K., A.M.L.), Jawaharlal Nehru University, New Delhi 110067, India; and Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India (S.L.S-P.)

The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants.

1 This work was supported by the Government of India (Department of Science and Technology and Department of Biotechnology), by the International Foundation for Science (Sweden), by the International Atomic Energy Agency (Austria), and by the Council of Scientific and Industrial Research, India (Junior Research Fellowship to A.S.).

2 These authors contributed equally to the paper.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Ashwani Pareek (ashwanip{at}mail.jnu.ac.in).

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.086371

* Corresponding author; e-mail ashwanip{at}mail.jnu.ac.in; fax 91–11–26704504.

Received July 5, 2006; accepted July 24, 2006; published August 4, 2006.




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