Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula.

Rui Liu,Zhenfei Guo,Shaoyun Lu

doi:10.3390/ijms221910494

Abstract

Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

Highlights

Indole-3-acetic (IAA) is the primary auxin in higher plants and regulates plant growth and development as well as responses to environmental stimuli [1,2]
The changes in auxin levels trigger downstream gene reprogramming through auxin response genes, such as the auxin/indole-3-acetic acid (Aux/IAA) family, the auxin response factor (ARF) family, and small auxin upregulated RNA (SAUR), and the auxin-responsive gretchen hagen 3 (GH3)
The IAA and ARF genes of Arabidopsis thaliana and soybean were used as query sequences to search for IAA and ARF genes in the genomes of M. truncatula

Summary

Introduction

Indole-3-acetic (IAA) is the primary auxin in higher plants and regulates plant growth and development as well as responses to environmental stimuli [1,2]. Aux/IAA proteins bind with ARFs for repressing activation of downstream auxin-responsive genes in the absence of auxin. Aux/IAA is ubiquitinated by interacting with TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB). Domain II is the auxin degron with a conserved “GWPPV” motif that directly interacts with SCFTIR1 (SKP1/Cullin/F-box protein complex containing the transport inhibitor response 1 protein) and is associated with the turnover of Aux/IAA proteins [8]. A carboxy-terminal PB1 (Phox and Bem 1) domain is contained within a region that was previously called domain III/IV and functions to interact with ARF. It is, involved in the regulation of ARF activity [9]. Aux/IAA family members are identified in other plants, such as tomato (Solanum lycopersicon), cucumber (Cucumis sativus), maize (Zea mays), and rice (Oryza sativa) [16,17,18,19]

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