title: Whole genome transcriptome analysis of rice seedling reveals alterations in Ca(2+) ion signaling and homeostasis in response to Ca(2+) deficiency.
abstract: Ca(2+) is an essential inorganic macronutrient, involved in regulating major physiological processes in plants. It has been well established as a second messenger and is predominantly stored in the cell wall, endoplasmic reticulum, mitochondria and vacuoles. In the cytosol, the concentration of this ion is maintained at nano-molar range. Upon requirement, Ca(2+) is released from intra-cellular as well as extracellular compartments such as organelles and cell wall. In this study, we report for the first time, a whole genome transcriptome response to short (5 D) and long (14 D) term Ca(2+) starvation and restoration in rice. Our results manifest that short and long term Ca(2+) starvation involves a very different response in gene expression with respect to both the number and function of genes involved. A larger number of genes were up- or down-regulated after 14 D (5588 genes) than after 5 D (798 genes) of Ca(2+) starvation. The functional classification of these genes indicated their connection with various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. The results obtained here will enable to understand how changes in Ca(2+) concentration or availability are interpreted into adaptive responses in plants.
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India. Electronic address: alkashankar06@gmail.com.
authors.forename: Alka
authors.initials: A
authors.lastname: Shankar
authors.affiliation: Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India. Electronic address: ashish@barc.gov.in.
authors.forename: Ashish Kumar
authors.initials: AK
authors.lastname: Srivastava
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India. Electronic address: akhilesh_du@yahoo.co.in.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Yadav
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India. Electronic address: mannsharma.pmb@gmail.com.
authors.forename: Manisha
authors.initials: M
authors.lastname: Sharma
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India. Electronic address: amitap04@gmail.com.
authors.forename: Amita
authors.initials: A
authors.lastname: Pandey
authors.affiliation: Radioanalytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India. Electronic address: vvraut@barc.gov.in.
authors.forename: Vaibhavi V
authors.initials: VV
authors.lastname: Raut
authors.affiliation: Radioanalytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India. Electronic address: mkdas@barc.gov.in.
authors.forename: Mirnal K
authors.initials: MK
authors.lastname: Das
authors.affiliation: Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India. Electronic address: prasanna@barc.gov.in.
authors.forename: Penna
authors.initials: P
authors.lastname: Suprasanna
authors.affiliation: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India. Electronic address: gkpandey@south.du.ac.in.
authors.forename: Girdhar K
authors.initials: GK
authors.lastname: Pandey
mesh_terms: D017360:Arabidopsis / Q000254:growth & development / Q000378:metabolism; D002118:Calcium / Q000172:deficiency / Q000378:metabolism; D020013:Calcium Signaling; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D007477:Ions / Q000737:chemistry; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010940:Plant Proteins / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D036226:Seedlings / Q000254:growth & development / Q000378:metabolism
chemical_list: D007477:Ions; D010940:Plant Proteins; D002118:Calcium
keywords: Ca(2+) deficiency; Gene expression; Signal transduction; Starvation; Transcriptome analysis