Abstract
BackgroundAuxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes. So far, significant progress has been made toward the identification and characterization of auxin-response genes in several model plants, while no systematic analysis for these families was reported in cucumber (Cucumis sativus L.), a reference species for Cucurbitaceae crops. The comprehensive analyses will help design experiments for functional validation of their precise roles in plant development and stress responses.ResultsA genome-wide search for auxin-response gene homologues identified 16 auxin-response factors (ARFs), 27 auxin/indole acetic acids (Aux/IAAs), 10 Gretchen Hagen 3 (GH3s), 61 small auxin-up mRNAs (SAURs), and 39 lateral organ boundaries (LBDs) in cucumber. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of these five auxin-related family members. The distribution and density of auxin response-related genes on chromosomes were not uniform. Evolutionary analysis showed that the chromosomal segment duplications mainly contributed to the expansion of the CsARF, CsIAA, CsGH3, and CsLBD gene families. Quantitative real-time RT-PCR analysis demonstrated that many ARFs, AUX/IAAs, GH3s, SAURs, and LBD genes were expressed in diverse patterns within different organs/tissues and during different development stages. They were also implicated in IAA, methyl jasmonic acid, or salicylic acid response, which is consistent with the finding that a great number of diverse cis-elements are present in their promoter regions involving a variety of signaling transduction pathways.ConclusionGenome-wide comparative analysis of auxin response-related family genes and their expression analysis provide new evidence for the potential role of auxin in development and hormone response of plants. Our data imply that the auxin response genes may be involved in various vegetative and reproductive developmental processes. Furthermore, they will be involved in different signal pathways and may mediate the crosstalk between various hormone responses.
Highlights
Auxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes
We carried out a genome-wide survey of auxin response-related gene including auxin response factor (ARF), auxin/indoleacetic acid (Aux/IAA), Gretchen Hagen 3 (GH3), small auxin up mRNA (SAUR), and lateral organ boundaries (LBD) in cucumber (Cucumis sativus L.)
Quantitative real-time RT-PCR analysis showed that the CsARFs, CsAUX/IAAs, CsGH3s, CsSAURs, and CsLBDs genes were expressed in at least one of the cucumber organs or tissues
Summary
Auxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes. A typical ARF protein contains a conserved N-terminal B3-like DNA-binding domain (DBD) that regulates the expression of auxin response genes, a conserved C-terminal dimerization domain (CTD) that resembles domains III and IV in Aux/IAA proteins, and a variable middle region (MR) [10,11]. The N-terminal lateral organ boundaries (LOB) domain is approximately 100 amino acids in length [20] and typically contains three highly conservative regions, including C-domain, Gly-Ala-Ser (GAS) block, and predicted coiledcoil motif [20,21]. The C-domain contains four highly conserved cysteine (C) residues arranged in a CX2CX6CX3C motif, which is required for DNA binding. The predicted coiled-coil motif contains four perfectly conserved leucine residues in a LX6LX3LX6L spacing that is reminiscent of a leucine zipper and may provide protein interaction [22]
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