Diversification,phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize <Emphasis Type="Italic">ARF</Emphasis> genes

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.     

Auxin-related gene families in abiotic stress response in Sorghum bicolor

Sorghum, a C4 model plant, has been studied to develop an understanding of the molecular mechanism of resistance to stress. The auxin-response genes, auxin/indole-3-acetic acid (Aux/IAA), auxin-response factor (ARF), Gretchen Hagen3 (GH3), small auxin-up RNAs, and lateral organ boundaries (LBD), are involved in growth/development and stress/defense responses in Arabidopsis and rice, but they have not been studied in sorghum. In the present paper, the chromosome distribution, gene duplication, promoters, intron/exon, and phylogenic relationships of Aux/IAA, ARF, GH3, and LBD genes in sorghum are presented. Furthermore, real-time PCR analysis demonstrated these genes are differently expressed in leaf/root of sorghum and indicated the expression profile of these gene families under IAA, brassinosteroid (BR), salt, and drought treatments. The SbGH3 and SbLBD genes, expressed in low level under natural condition, were highly induced by salt and drought stress consistent with their products being involved in both abiotic stresses. Three genes, SbIAA1, SbGH3-13, and SbLBD32, were highly induced under all the four treatments, IAA, BR, salt, and drought. The analysis provided new evidence for role of auxin in stress response, implied there are cross talk between auxin, BR and abiotic stress signaling pathways.     

Mathematical Modelling of the <Emphasis Type="Italic">Aux/IAA</Emphasis> Negative Feedback Loop

The hormone auxin is implicated in regulating a diverse range of developmental processes in plants. Auxin acts in part by inducing the Aux/IAA genes. The associated pathway comprises multiple negative feedback loops (whereby Aux/IAA proteins can repress Aux/IAA genes) that are disrupted by auxin mediating the turnover of Aux/IAA protein. In this paper, we develop a mathematical model of a single Aux/IAA negative feedback loop in a population of identical cells. The model has a single steady-state. We explore parameter space to uncover a number of dynamical regimes. In particular, we identify the ratio between the Aux/IAA protein and mRNA turnover rates as a key parameter in the model. When this ratio is sufficiently small, the system can evolve to a stable limit cycle, corresponding to an oscillation in Aux/IAA expression levels. Otherwise, the steady-state is either a stable-node or a stable-spiral. These observations may shed light on recent experimental results.     

Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.)

The phytohormone auxin is important in various aspects of organism growth and development. Aux/IAA genes encoding short-lived nuclear proteins are responsive primarily to auxin induction. Despite their physiological importance, systematic analysis of Aux/IAA genes in maize have not yet been reported. In this paper, we presented the isolation and characterization of maize Aux/IAA genes in whole-genome scale. A total of 31 maize Aux/IAA genes (ZmIAA1 to ZmIAA31) were identified. ZmIAA genes are distributed in all the maize chromosomes except chromosome 2. Aux/IAA genes expand in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize Aux/IAA proteins share all the four conserved domains. Phylogenetic analysis indicated Aux/IAA family can be divided into seven subfamilies. Putative cis-acting regulatory DNA elements involved in auxin response, light signaling transduction and abiotic stress adaption were observed in the promoters of ZmIAA genes. Expression data mining suggested maize Aux/IAA genes have temporal and spatial expression pattern. Collectively, these results will provide molecular insights into the auxin metabolism, transport and signaling research.     

Genome-wide analysis of Aux/IAA genes in Vitis vinifera: cloning and expression profiling of a grape Aux/IAA gene in response to phytohormone and abiotic stresses

Auxin is one of the most important phytohormones involved in plant growth and development. Here, we identified a total of 26 Aux/IAA genes displaying high sequence identity within the conserved domains I, II, III, and IV by screening the grapevine genome proteome 12× database. The Vitis vinifera Aux/IAA proteins can be classified into two groups (A and B) on the basis of their phylogenetic relationships. A search for cis-regulatory elements in the promoter sequences of VvAux/IAA genes revealed that the majority of these proteins may be regulated by light, phytohormones, and abiotic stresses. We also report the isolation and expression analysis of the cDNA of VvAux/IAA4, the most highly expressed VvAux/IAA gene from V. vinifera cv. Sultanine, according to ESTs in the NCBI database. The VvAux/IAA4 gene contains a full-length open reading frame of 1,080 bp, and its predicted amino acid sequence is highly similar to those of Aux/IAA proteins from other plants, including the presence of an AuxIAA/ARF dimerization motif in the C-terminal region. The expression of VvAux/IAA4 was found to be elevated during berry development, and slowly decrease from the initiation of ripening to the overripening stage. VvAux/IAA4 was highly expressed in young leaves and roots, and expressed at low levels in pollen and tendrils. Finally, the expression of VvAux/IAA4 was rapidly induced in response to NAA treatment, but was decreased by salt, drought, and SA treatments. Our results provide evidence of crosstalk between phytohormone and abiotic stresses, and support a role for auxin in stress responses.     

植物Aux/IAA基因家族生物学功能研究进展

生长素是最重要的植物激素之一, 对植物生长发育起着关键调控作用。生长素作用于植物后, 早期生长素响应基因家族Aux/IAA、GH3和SAUR等被迅速诱导, 基因表达上调。其中Aux/IAA基因家族编码的蛋白一般由4个保守结构域组成, 结构域I具有抑制生长素信号下游基因表达的作用, 结构域II在生长素信号转导中主要被TIR1调控进而影响Aux/IAA的稳定性, 结构域III/IV通过与生长素响应因子ARF相互作用调控生长素信号。Aux/IAA基因家族在双子叶植物拟南芥(Arabidopsis thaliana)的器官发育、根形成、茎伸长和叶扩张等方面发挥重要作用; 在单子叶植物水稻(Oryza sativa)和小麦(Triticum aestivum)中, 主要影响根系发育和株型, 但大多数Aux/IAA基因的功能尚不清楚。该文主要从Aux/IAA蛋白的结构、功能和生长素信号转导途径方面综述Aux/IAA家族在拟南芥、禾谷类作物及其它植物中的研究进展, 以期为全面揭示Aux/IAA家族基因的生物学功能提供线索。