Toward understanding transcriptional regulatory networks in abiotic stress responses and tolerance in rice

Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants

Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.

Recent advances in dissecting stress-regulatory crosstalk in rice

Biotic and abiotic stresses impose a serious limitation on crop productivity worldwide. Prior or simultaneous exposure to one type of stress often affects the plant response to other stresses, indicating extensive overlap and crosstalk between stress-response signaling pathways. Systems biology approaches that integrate large genomic and proteomic data sets have facilitated identification of candidate genes that govern this stress-regulatory crosstalk. Recently, we constructed a yeast two-hybrid map around three rice proteins that control the response to biotic and abiotic stresses, namely the immune receptor XA21, which confers resistance to the Gram-negative bacterium, Xanthomonas oryzae pv. oryzae; NH1, the rice ortholog of NPR1, a key regulator of systemic acquired resistance; and the ethylene-responsive transcription factor, SUB1A, which confers tolerance to submergence stress. These studies coupled with transcriptional profiling and co-expression analyses identified a suite of proteins that are positioned at the interface of biotic and abiotic stress responses, including mitogen-activated protein kinase 5 (OsMPK5), wall-associated kinase 25 (WAK25), sucrose non-fermenting-1-related protein kinase-1 (SnRK1), SUB1A binding protein 23 (SAB23), and several WRKY family transcription factors. Emerging evidence suggests that these genes orchestrate crosstalk between biotic and abiotic stresses through a variety of mechanisms, including regulation of cellular energy homeostasis and modification of synergistic and/or antagonistic interactions between the stress hormones salicylic acid, ethylene, jasmonic acid, and abscisic acid.

Identification of salt treated proteins in sorghum using gene ontology linkage

Sorghum bicolor (L.) is an important crop of arid and semi arid zones with most of its varieties tolerant to drought, heat and salt stress. Functional identification of many salt tolerant proteins has been reported in Arabidopsis, rice and other plants, however only little functional information has been predicted in sorghum till date. A 2-D gel electrophoresis based proteomic approach with MALDI-TOF mass spectrometer was utilized to analyze the salt stress response of sorghum. Major changes in protein complement were observed at 200 mM NaCl in hydroponic culture after 96 h of salt-stress. Highly expressed five proteins were excised for functional identification. We developed shortest path (SP) analysis based method on Gene Ontology (GO) hierarchy using sum of GO-term's semantic similarities. In this study, we observed that majority of expressed proteins belonged to the functional category of energy production and conversion, signal transduction mechanisms and ribosome maturation. These identified functions suggest a distinct mechanism of salt-stress adaptation in sorghum plant. The proposed method in this paper potentially has great importance to further understanding of newly identified proteins that can help in plant development.