Comprehensive expression profiling reveals the possible involvement of Cullins in developmental and stress regulation in rice

Abstract

In eukaryotes, the Cullin proteins, particularly Cullin-4, are well-known for their role in mediating protein ubiquitination in combination with diverse cellular components that form complexes called E3 ligases or Cullin-RING Ligases (CRLs). In a genome-wide survey, we noticed that the Cullin gene family comprises thirteen genes including individual gene copies in rice. All the genes of the family were selected for a study on their in silico gene and protein properties, the presence of regulatory elements in their putative promoter regions, and their spatio-temporal and stress regulation. Native transcript profiling of Cullin genes in different tissues representing the major growth stages of rice revealed their involvement in the growth and development of the rice plant. Comprehensive transcript analysis under phytohormone- Abscisic acid (ABA), polyethylene glycol (PEG), salt and oxidative stress treatments indicated that all the genes are stress responsive with several of them exhibiting instant and significant up-regulation in their transcript levels. Many of them also showed an overlap in their transcript up-regulation in both shoot and root tissues under various stress treatments. Similarly, treatments with important rice pathogens, Xanthomonas oryzae and Rhizoctonia solani also up-regulated several of these Cullin genes. Among those that became highly up-regulated in all the abiotic and biotic stress treatments in both root and shoot tissues is Cullin-3c, while the transcript levels of Cullin-4 exhibited an upward trend in all the abiotic stress treatments. Collectively, our exploration of the transcript analysis of Cullin genes suggests a significant role for them in stress responsiveness and forms the first investigation that emphasizes the role of Cullins in relation to stress in rice.