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Genome-wide identification of the auxin/indole-3-acetic acid (Aux/IAA) gene family in pepper, its characterisation, and comprehensive expression profiling under environmental and phytohormones stress.

ABSTRACT: Auxin is an essential phytohormone that plays a crucial role in the growth and development of plants in stressful environments. Here, we analysed the auxin/indole-3-acetic acid (Aux/IAA) gene family, which produces auxin in pepper, and succeeded in identifying 27 putative members containing four conserved domains (I. II. III and IV) in their protein sequences. Sequence analysis, chromosomal mapping and motif prediction of all identified CaAux/IAA genes were performed. It was observed that these genes contained four conserved motifs divided into nine different groups and distributed across nine chromosomes in pepper plants. RNA-seq analysis revealed the organ specific expression of many CaAux/IAA genes. However, the majority of genes were expressed with high expression levels in the early stages of fruit development. However, the maximum expression level of the CA03g34540 gene was observed in the breaker stage. Moreover, thirteen CaAux/IAA genes were labelled as early responsive genes to various phytohormone and abiotic stresses. Furthermore, RNA-seq analysis in response to pathogen inoculation (PepMoV, TMV strains P0/P1, and Phytophthora capsici) showed distinct expression profiles of all identified genes, suggesting the diverse expression nature of genes under these stress conditions. Overall, this study provides insight into the dynamic response of CaAux/IAA genes under environmental and phytohormones stress conditions, providing bases to further explore the importance of these genes through mutant/transgenic analysis in pepper.

SUBMITTER: Waseem M

PROVIDER: S-EPMC6089902 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.).

Project description:Aux/IAA genes are early auxin-responsive genes and essential for auxin signaling transduction. There is little information about Aux/IAAs in the agriculturally important cereal, barley. Using in silico method, we identified and subsequently characterized 36 Aux/IAAs from the barley genome. Based on their genomic sequences and the phylogenic relationship with Arabidopsis and rice Aux/IAA, the 36 HvIAAs were categorized into two major groups and 14 subgroups. The indication of the presence or absence of these domains for the biological functions and acting mechanisms was discussed. The cis-element distributions in HvIAA promoters suggests that the HvIAAs expressions may not only regulated by auxin (the presence of AuxREs and TGA-element) but also by other hormones and developmental and environmental cues. We then studied the HvIAAs expression in response to NAA (1-Naphthaleneacetic acid) using quantitative real-time PCR (qRT-PCR). Like the promoter analysis, only 14 HvIAAs were upregulated by NAA over two-fold at 4 h. HvIAAs were clustered into three groups based on the spatiotemporal expression data. We confirmed by qRT-PCR that most HvIAAs, especially HvIAA3, HvIAA7, HvIAA8, HvIAA18, HvIAA24 and HvIAA34, are expressed in the developing barley spike compared within seedling, suggesting their roles in regulating spike development. Taken together, our data provide a foundation for further revealing the biological function of these HvIAAs.

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Project description:The plant hormone auxin can regulate gene expression by destabilizing members of the Aux/IAA family of transcriptional repressors. Auxin-induced Aux/IAA degradation requires the protein-ubiquitin ligase SCF(TIR1), with auxin acting to enhance the interaction between the Aux/IAAs and SCF(TIR1). SKP1, Cullin, and an F-box-containing protein (SCF)-mediated degradation is an important component of many eukaryotic signaling pathways. In all known cases to date, the interaction between the targets and their cognate SCFs is regulated by signal-induced modification of the target. The mechanism by which auxin promotes the interaction between SCF(TIR1) and Aux/IAAs is not understood, but current hypotheses propose auxin-induced phosphorylation, hydroxylation, or proline isomerization of the Aux/IAAs. We found no evidence to support these hypotheses or indeed that auxin induces any stable modification of Aux/IAAs to increase their affinity for SCF(TIR1). Instead, we present data suggesting that auxin promotes the SCF(TIR1)-Aux/IAA interaction by affecting the SCF component, TIR1, or proteins tightly associated with it.

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