DNA elements responsive to auxin

Phylogenetic evidence of allopatric speciation of bradyrhizobia nodulating cowpea (Vigna unguiculata L. walp) in South African and Mozambican soils

The legume host and soil environment play a major role in establishing effective symbiosis with diverse rhizobia for plant growth promotion and nodule formation. The aim of this study was to assess the morpho-physiology, distribution and phylogenetic position of rhizobia nodulating cowpea from South Africa and Mozambique. The results showed that the isolates were highly diverse in their appearance on yeast mannitol agar plates. The isolates tested also showed an ability to produce IAA at concentrations ranging from 0.64 to 56.46 μg.ml⁻¹ and to solubilise phosphorus at levels from 0 to 3.55 index. Canonical correspondence analysis showed that soil pH and mineral nutrients significantly influenced bradyrhizobial distribution. Analysis of BOX-PCR placed the isolates in eight major clusters with 0.01 to 1.00 similarity coefficient which resulted in 45 unique BOX-types. Phylogenetic analyses based on 16S rRNA, atpD, glnII, gyrB and recA gene sequences showed distinct novel evolutionary lineages within the genus Bradyrhizobium, with some of them being closely related to Bradyrhizobium kavangense, B. subterraneum and B. pachyrhizi. Furthermore, symbiotic gene phylogenies suggested that the isolates’ sym loci probably relates to the isolates’ geographical origin. The results indicated that geographical origin did affect the isolates’ phylogenetic placement and could be the basis for allopatric speciation

Three BnaIAA7 homologs are involved in auxin/brassinosteroid-mediated plant morphogenesis in rapeseed (Brassica napus L.)

BnaIAA7 crosstalk with BR signaling is mediated by the interaction between BnaARF8 and BnaBZR1 to regulate rapeseed plant morphogenesis. Auxin (indole-3-acetic acid, IAA) and brassinosteroids (BRs) are essential regulators of plant morphogenesis. However, their roles in rapeseed have not been reported. Here, we identified an extremely dwarf1 (ed1) mutant of rapeseed that displays reduced stature, short hypocotyls, as well as wavy and curled leaves. We isolated ED1 by map-based cloning, and found that it encodes a protein homologous to AtIAA7. ED1 acts as a repressor of IAA signaling, and IAA induces its degradation through its degron motif. A genomic-synteny analysis revealed that ED1 has four homologs in rapeseed, but two were not expressed. Analyses of transcriptomes and of various mutant BnaIAA7s in transgenic plants revealed that the three expressed BnaIAA7 homologs had diverse expression patterns. ED1/BnaC05.IAA7 predominantly functioned in stem elongation, BnaA05.IAA7 was essential for reproduction, while BnaA03.IAA7 had the potential to reduce plant height. Physical interaction assays revealed that the three BnaIAA7 homologs interacted in different ways with BnaTIRs/AFBs and BnaARFs, which may regulate the development of specific organs. Furthermore, BnaARF8 could directly interact with the BnaIAA7s and BnaBZR1. We propose that BnaIAA7s interact with BR signaling via BnaARF8 and BnaBZR1 to regulate stem elongation in rapeseed.

Auxin signaling: a big question to be addressed by small molecules

Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.

Structural Biology of Nuclear Auxin Action

Auxin coordinates plant development largely via hierarchical control of gene expression. During the past decades, the study of early auxin genes paired with the power of Arabidopsis genetics have unraveled key nuclear components and molecular interactions that perceive the hormone and activate primary response genes. Recent research in the realm of structural biology allowed unprecedented insight into: (i) the recognition of auxin-responsive DNA elements by auxin transcription factors; (ii) the inactivation of those auxin response factors by early auxin-inducible repressors; and (iii) the activation of target genes by auxin-triggered repressor degradation. The biophysical studies reviewed here provide an impetus for elucidating the molecular determinants of the intricate interactions between core components of the nuclear auxin response module.

Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii

Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.

Hormonal regulation of tomato gibberellin 20-oxidase1 expressed in Arabidopsis

Gibberellin 20-oxidases, enzymes of gibberellin (GA) biosynthesis, play an important role in (GA) homeostasis. To investigate the regulation of tomato SlGA20ox1 expression, a genomic clone was isolated, its promoter transcriptionally fused to the GUS reporter gene, and the construct used to transform Arabidopsis. Expression was found in diverse vegetative (leaves and roots) and reproductive (flowers) organs. GUS staining was also localized in the columella of secondary roots. GA negative feed-back regulation of SlGA20ox1:GUS was shown to be active both in tomato and in transformed Arabidopsis. Auxin (indol-3-acetic acid, 2,4-dichlorophenoxyacetic acid and naphtaleneacetic acid), triiodobenzoic acid (an inhibitor of auxin transport) and benzyladenine (a cytokinin) treatment induced SlGA20ox1:GUS expression associated with increased auxin content and/or signaling, detected using DR5:GUS expression as a marker. Interestingly, SlGA20ox:GUS expression was induced by auxin and root excision in the hypocotyl, an organ not showing GUS staining in control seedlings. In etiolated seedlings, SlGA20ox1:GUS expression occurred in the elongating hypocotyl region of etiolated seedlings and was down-regulated upon transfer to light associated with decrease of growth rate elongation. Our results show that feed-back, auxin and light regulation of SlGA20ox1 expression depends on DNA elements contained within the first 834bp of the 5' upstream promoter region. Putative DNA regulatory sequences involved in negative feed-back regulation and auxin response were identified in that promoter.

Analysis of vascular development in the hydra sterol biosynthetic mutants of Arabidopsis

BACKGROUND

The control of vascular tissue development in plants is influenced by diverse hormonal signals, but their interactions during this process are not well understood. Wild-type sterol profiles are essential for growth, tissue patterning and signalling processes in plant development, and are required for regulated vascular patterning.

METHODOLOGY/PRINCIPAL FINDINGS

Here we investigate the roles of sterols in vascular tissue development, through an analysis of the Arabidopsis mutants hydra1 and fackel/hydra2, which are defective in the enzymes sterol isomerase and sterol C-14 reductase respectively. We show that defective vascular patterning in the shoot is associated with ectopic cell divisions. Expression of the auxin-regulated AtHB8 homeobox gene is disrupted in mutant embryos and seedlings, associated with variably incomplete vascular strand formation and duplication of the longitudinal axis. Misexpression of the auxin reporter proIAA2ratioGUS and mislocalization of PIN proteins occurs in the mutants. Introduction of the ethylene-insensitive ein2 mutation partially rescues defective cell division, localization of PIN proteins, and vascular strand development.

CONCLUSIONS

The results support a model in which sterols are required for correct auxin and ethylene crosstalk to regulate PIN localization, auxin distribution and AtHB8 expression, necessary for correct vascular development.

Mechanism of auxin-regulated gene expression in plants

Plant hormones control most aspects of the plant life cycle by regulating genome expression. Expression of auxin-responsive genes involves interactions among auxin-responsive DNA sequence elements, transcription factors and trans-acting transcriptional repressors. Transcriptional output from these auxin signaling complexes is regulated by proteasome-mediated degradation that is triggered by interaction with auxin receptor-E3 ubiquitin ligases such SCF(TIR1). Auxin signaling components are conserved throughout land plant evolution and have proliferated and specialized to control specific developmental processes.

A mutation in the anticodon of a single tRNAala is sufficient to confer auxin resistance in Arabidopsis

Auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. Here we report the isolation and molecular characterization of a novel auxin-resistant mutant in Arabidopsis (Arabidopsis thaliana). Like known mutated AUX/IAA transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, including apical hook deformation, defects in lateral root development, reduced stature, and homozygous lethality. This mutant showed the same sensitivity to the ethylene precursor 1-aminocyclopropane carboxylic acid as wild-type plants, and retained the ability to induce IAA19 expression in response to exogenously supplied indole-3-acetic acid. To our surprise, these phenotypes were not caused by a mutation in an AUX/IAA gene, but rather a mutation in a tRNA(ala) gene in which the anticodon was found changed from CGC to CAC. Such a change results in a tRNA that is charged with alanine but recognizes the second most highly used valine codon in Arabidopsis. Therefore, the observed phenotypes are likely the composite of stochastic mutations of many proteins, including downstream effectors.

AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator

AUXIN RESPONSE FACTORS (ARFs) regulate auxin-mediated transcriptional activation/repression. They are encoded by a gene family in Arabidopsis, and each member is thought to play a central role in various auxin-mediated developmental processes. We have characterized three arf2 mutant alleles, arf2-6, arf2-7 and arf2-8. The mutants exhibit pleiotropic developmental phenotypes, including large, dark green rosette leaves, delayed flowering, thick and long inflorescence, abnormal flower morphology and sterility in early formed flowers, large organ size and delayed senescence and abscission, compared with wild-type plants. In addition, arf2 mutant seedlings have elongated hypocotyls with enlarged cotyledons under various light conditions. The transcription of ACS2, ACS6 and ACS8 genes is impaired in the developing siliques of arf2-6. The phenotypes of all three alleles are similar to those of the loss-of-function mutants obtained by RNA interference or co-suppression. There is no significant effect of the mutation on global auxin-regulated gene expression in young seedlings, suggesting that ARF2 does not participate in auxin signaling at that particular developmental stage of the plant life cycle. Because ARF2 is thought to function as a transcriptional repressor, the prospect arises that its pleiotropic effects may be mediated by negatively modulating the transcription of downstream genes in signaling pathways that are involved in cell growth and senescence.

Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19

The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression. The biological function(s) of most ARFs is poorly understood. Here, we report the identification and characterization of T-DNA insertion lines for 18 of the 23 ARF gene family members in Arabidopsis thaliana. Most of the lines fail to show an obvious growth phenotype except of the previously identified arf2/hss, arf3/ett, arf5/mp, and arf7/nph4 mutants, suggesting that there are functional redundancies among the ARF proteins. Subsequently, we generated double mutants. arf7 arf19 has a strong auxin-related phenotype not observed in the arf7 and arf19 single mutants, including severely impaired lateral root formation and abnormal gravitropism in both hypocotyl and root. Global gene expression analysis revealed that auxin-induced gene expression is severely impaired in the arf7 single and arf7 arf19 double mutants. For example, the expression of several genes, such as those encoding members of LATERAL ORGAN BOUNDARIES domain proteins and AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE, are disrupted in the double mutant. The data suggest that the ARF7 and ARF19 proteins play essential roles in auxin-mediated plant development by regulating both unique and partially overlapping sets of target genes. These observations provide molecular insight into the unique and overlapping functions of ARF gene family members in Arabidopsis.

Transcriptional regulation of a pineapple polyphenol oxidase gene and its relationship to blackheart

Two genes encoding polyphenol oxidase (PPO) were isolated from pineapple (Ananas comosus[L.] Merr. cv. Smooth Cayenne). Sequence analyses showed that both contained a single intron and encoded typical chloroplast-localized PPO proteins, the sequences of which corresponded to two pineapple PPO cDNAs, PINPPO1 and PINPPO2, recently described by Stewart et al. (2001). Southern blot analyses suggested that pineapple contained only two PPO genes. Analysis of expression of PINPPO1 promoter GUS fusion constructs showed this promoter had a low basal activity and was cold- and wound-inducible, consistent with known mRNA expression profiles. Striking homologies to gibberellin response complexes (GARC) were observed in sequences of both the PINPPO1 and PINPPO2 promoters. Transient assays in mature pineapple fruit and stable expression in transgenic tobacco showed that PINPPO1 promoter-GUS fusions were indeed gibberellin (GA) responsive. A role for the element within the putative GARCs in mediating GA-responsiveness of the PINPPO1 promoter was confirmed by mutational analysis. PINPPO2 was also shown to be GA-responsive by RT-PCR analysis. Mutant PINPPO1 promoter-GUS fusion constructs, which were no longer GA-inducible, showed a delayed response to cold induction in pineapple fruit in transient assays, suggesting a role for GA in blackheart development. This was supported by observations that exogenous GA(3) treatment induced blackheart in the absence of chilling. Sequences showing homology to GARCs are also present in some PPO promoters in tomato, suggesting that GA regulates PPO expression in diverse species.

Cytokinin inhibits a subset of diageotropica-dependent primary auxin responses in tomato

Many aspects of plant development are regulated by antagonistic interactions between the plant hormones auxin and cytokinin, but the molecular mechanisms of this interaction are not understood. To test whether cytokinin controls plant development through inhibiting an early step in the auxin response pathway, we compared the effects of cytokinin with those of the dgt (diageotropica) mutation, which is known to block rapid auxin reactions of tomato (Lycopersicon esculentum) hypocotyls. Long-term cytokinin treatment of wild-type seedlings phenocopied morphological traits of dgt plants such as stunting of root and shoot growth, reduced elongation of internodes, reduced apical dominance, and reduced leaf size and complexity. Cytokinin treatment also inhibited rapid auxin responses in hypocotyl segments: auxin-stimulated elongation, H(+) secretion, and ethylene synthesis were all inhibited by cytokinin in wild-type hypocotyl segments, and thus mimicked the impaired auxin responsiveness found in dgt hypocotyls. However, cytokinin failed to inhibit auxin-induced LeSAUR gene expression, an auxin response that is affected by the dgt mutation. In addition, cytokinin treatment inhibited the auxin induction of only one of two 1-aminocyclopropane-1-carboxylic acid synthase genes that exhibited impaired auxin inducibility in dgt hypocotyls. Thus, cytokinin inhibited a subset of the auxin responses impaired in dgt hypocotyls, suggesting that cytokinin blocks at least one branch of the DGT-dependent auxin response pathway.

Auxin induces mitogenic activated protein kinase (MAPK) activation in roots of Arabidopsis seedlings

Genome analyses have shown that plants contain gene families encoding various components of mitogen-activated protein kinase (MAPK) signaling pathways. Previous reports have described the involvement of MAPK pathways in stress and pathogen responses of leaves and suspension-cultured cells. Here we show that auxin treatment of Arabidopsis roots transiently induced increases in protein kinase activity with characteristics of mammalian ERK-like MAPKs. The MAPK response we monitored was the result of hormonal action of biologically active auxin, rather than a stress response provoked by auxin-like compounds. Auxin-induced MAPK pathway signaling was distinguished genetically in the Arabidopsis auxin response mutant axr4, in which MAPK activation by auxin, but not by salt stress, was significantly impaired. Perturbation of MAPK signaling in roots using inhibitors of a mammalian MAPKK blocked auxin-activated transgene expression in BA3-GUS seedlings, while potentiating higher than normal levels of MAPK activation in response to auxin. Data presented here indicate that MAPK pathway signaling is positively involved in auxin response, and further suggest that interactions among MAPK signaling pathways in plants influence plant responses to auxin.

Auxin induces mitogenic activated protein kinase (MAPK) activation in roots of Arabidopsis seedlings

Genome analyses have shown that plants contain gene families encoding various components of mitogen-activated protein kinase (MAPK) signaling pathways. Previous reports have described the involvement of MAPK pathways in stress and pathogen responses of leaves and suspension-cultured cells. Here we show that auxin treatment of Arabidopsis roots transiently induced increases in protein kinase activity with characteristics of mammalian ERK-like MAPKs. The MAPK response we monitored was the result of hormonal action of biologically active auxin, rather than a stress response provoked by auxin-like compounds. Auxin-induced MAPK pathway signaling was distinguished genetically in the Arabidopsis auxin response mutant axr4, in which MAPK activation by auxin, but not by salt stress, was significantly impaired. Perturbation of MAPK signaling in roots using inhibitors of a mammalian MAPKK blocked auxin-activated transgene expression in BA3-GUS seedlings, while potentiating higher than normal levels of MAPK activation in response to auxin. Data presented here indicate that MAPK pathway signaling is positively involved in auxin response, and further suggest that interactions among MAPK signaling pathways in plants influence plant responses to auxin.

Cloning of an auxin-responsive 1-aminocyclopropane-1-carboxylate synthase gene (CMe-ACS2) from melon and the expression of ACS genes in etiolated melon seedlings and melon fruits

Two cDNA fragments (pCMe-ACS2 and 3) encoding auxin-responsive 1-aminocyclopropane-1-carboxylate synthase (ACS; EC.4.4.1.14) have been isolated from melon, and the expression patterns of the genes in etiolated melon seedlings and melon fruit have been determined by RT-PCR analysis. The deduced amino acid sequences of pCMe-ACS2 and 3 were homologous to those of AT-ACS6 and 4, which were auxin-responsive ACS genes of Arabidopsis. Both CMe-ACS2 and 3 were auxin-responsive ACS genes and their expressions in roots and hypocotyls were induced by treatment with indole acetic acid (IAA, 100 µM). The mRNA level of CMe-ACS2 in the fruit increased after pollination. Those of both CMe-ACS2 and 3 temporarily increased in the mesocarp tissues at the preclimacteric stage (from day 3 to day 5 after harvest) during ripening, while that of CMe-ACS3 was lower than that of CMe-ACS2. The increase in the mRNA level of CMe-ACS1 (wound- and ripening-induced gene, T. Miki, M. Yamamoto, N. Nakagawa, O. Ogura, H. Mori, H. Imaseki, T. Sato, Nucleotide sequence of a cDNA for 1-aminocyclopropane-1-carboxylate synthase from melon fruits, Plant Physiol. 107 (1995) 297-298.) in the mesocarp tissue was not observed until 5 days after harvest. A genomic DNA encoding CMe-ACS2 was isolated and its nucleotide sequence was determined. Nucleotide sequences resembling the auxin-responsive elements (AuxRE) D1 and D4 (the TGTCTC element) in the GH3 gene from soybean, and the auxin-responsive domain (AuxRD) B in PS-IAA4/5 from pea were found in the 5'-flanking region of the CMe-ACS2 gene.

EIR1, a root-specific protein involved in auxin transport, is required for gravitropism in Arabidopsis thaliana

The EIR1 gene of Arabidopsis is a member of a family of plant genes with similarities to bacterial membrane transporters. This gene is expressed only in the root, which is consistent with the phenotypes of the eir1 mutants-the roots are agravitropic and have a reduced sensitivity to ethylene. The roots of eir1 mutants are also insensitive to the excess auxin produced by alf1-1 and fail to induce an auxin-inducible gene in the expansion zone. Although they fail to respond to internally generated auxin, they respond normally to externally applied auxin. Expression of the EIR1 gene in Saccharomyces cerevisiae confers resistance to fluorinated indolic compounds. Taken together, these data suggest that the EIR1 protein has a root-specific role in the transport of auxin.