Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa)

Abstract

Auxin exerts pleiotropic effects on plant growth and development by regulating the expression of early auxin-responsive genes of auxin/indoleacetic acid (Aux/IAA), small auxin-up RNA, and GH3 classes. These genes have been studied extensively in dicots like soybean and Arabidopsis. We had earlier characterized a cDNA of the first monocot member of Aux/IAA family from rice. The achievement of the large scale rice genome sequencing combined with the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encyclopedia provided us the opportunity to draw up the first comprehensive list of Aux/IAA genes in a monocot. By screening the available databases, we have identified 31 Aux/IAA genes having high sequence identity within the conserved domains I, II, III, and IV. The genomic organization as well as chromosomal location of all the Oryza sativa indoleacetic acid (OsIAA) genes is reported. The rice Aux/IAA proteins can be classified in two groups (A and B) on the basis of their phylogenetic relationship with Arabidopsis Aux/IAA proteins. An evolutionary pattern of the rice Aux/IAA genes has been discussed by analyzing their structure (exon/intron organization) and duplications. Interestingly, the duplication of rice Aux/IAA genes was found to be associated with chromosomal block duplication events in rice. The in-silico analysis has been complemented with real-time polymerase chain reaction analysis to quantify transcript levels of all Aux/IAA family members. OsIAA genes showed differential and overlapping organ-specific expression patterns in light- and dark-grown seedlings/plants. Although auxin enhanced the transcript abundance of most of the OsIAA genes, the effect was more pronounced on OsIAA9, 14, 19, 20, 24, and 31. These results provide a foundation for future studies on elucidating the precise role of rice Aux/IAA genes in early steps of auxin signal transduction.

RiceLHS1/OsMADS1Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways

“…S4, A and B; Supplemental Table S3) were affected. This was paralleled by elevated expression of a predicted C2 domain-containing OsARF-GAP (an ADP ribosylation GTPase activating protein) and of several Aux/IAA (for Auxin/indole-3-acetic acid) repressors of auxin-dependent gene expression (Jain et al, 2006;Supplemental Table S3). The deregulated expression of OsARF9, OsARF18, two ETTIN-like genes, OsETTIN1 and OsETTIN2, and two key signaling factors, OsPIN1 and OsARF-GAP, was validated by RT-qPCR (Fig.…”

Rice leaf inclination2, a VIN3-like protein, regulates leaf angle through modulating cell division of the collar

“…In addition, analysis of the expression of GA metabolismrelated genes OsGA2ox3 and OsGA20ox2 revealed increased GA biosynthesis in lc2-1 ( Figure 6C, left panel) [39] and hence a possibly suppressed GA signaling. Although LC2 is also induced by IAA, examination of the expression of IAA signaling-related genes OsIAA1, OsIAA9, and OsIAA24 revealed no obvious changes in lc2-1 ( Figure 6C, right panel [40]), suggesting that LC2 may not be involved in auxin signaling.…”

Modulating plant hormones by enzyme action

“…[18][19][20][21][22] In the genome of the model monocot Oryza sativa (rice) genome, there are 13 GH3 genes. 23 Transcripts have been detected, but not characterized, in other monocots, including wheat, maize, sorghum and barley. 18,23 In addition, GH3 genes are found in the gymnosperm Pinus pinaster and the moss Physomitrella patens.…”

“…23 Transcripts have been detected, but not characterized, in other monocots, including wheat, maize, sorghum and barley. 18,23 In addition, GH3 genes are found in the gymnosperm Pinus pinaster and the moss Physomitrella patens. [24][25][26] EST analysis suggests that GH3 genes are found across multiple plants, mosses and algae.…”

“…[24][25][26] EST analysis suggests that GH3 genes are found across multiple plants, mosses and algae. 18,23 Phylogenetic analysis of the GH3 families in Arabidopsis and rice show that these sequences fall into Figure 1. Pre-receptor enzyme action by GH3 enzymes.…”