Tim Ulmasov

Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements.

A highly active synthetic auxin response element (AuxRE), referred to as DR5, was created by performing site-directed mutations in a natural composite AuxRE found in the soybean GH3 promoter. DR5 consisted of tandem direct repeats of 11 bp that included the auxin-responsive TGTCTC element. The DR5 AuxRE showed greater auxin responsiveness than a natural composite AuxRE and the GH3 promoter when assayed by transient expression in carrot protoplasts or in stably transformed Arabidopsis seedlings, and it provides a useful reporter gene for studying auxin-responsive transcription in wild-type plants and mutants. An auxin response transcription factor, ARF1, bound with specificity to the DR5 AuxRE in vitro and interacted with Aux/IAA proteins in a yeast two-hybrid system. Cotransfection experiments with natural and synthetic AuxRE reporter genes and effector genes encoding Aux/IAA proteins showed that overexpression of Aux/IAA proteins in carrot protoplasts resulted in specific repression of TGTCTC AuxRE reporter gene expression.

Soybean GH3 promoter contains multiple auxin-inducible elements.

The soybean GH3 gene is transcriptionally induced in a wide variety of tissues and organs within minutes after auxin application. To determine the sequence elements that confer auxin inducibility to the GH3 promoter, we used gel mobility shift assays, methylation interference, deletion analysis, linker scanning, site-directed mutagenesis, and gain-of-function analysis with a minimal cauliflower mosaic virus 35S promoter. We identified at least three sequence elements within the GH3 promoter that are auxin inducible and can function independently of one another. Two of these elements are found in a 76-bp fragment, and these consist of two independent 25- and 32-bp auxin-inducible elements. Both of these 25- and 32-bp auxin-inducible elements contain the sequence TGTCTC just upstream of an AATAAG. An additional auxin-inducible element was found upstream of the 76-bp auxin-inducible fragment; this can function independently of the 76-bp fragment. Two TGA-box or Hex-like elements (TGACGTAA and TGACGTGGC) in the promoter, which are strong binding sites for proteins in plant nuclear extracts, may also elevate the level of auxin inducibility of the GH3 promoter. The multiple auxin-inducible elements within the GH3 promoter contribute incrementally to the overall level of auxin induction observed with this promoter.

THE ARF FAMILY OF TRANSCRIPTION FACTORS AND THEIR ROLE IN PLANT HORMONE-RESPONSIVE TRANSCRIPTION

Abstract. Auxin response factors or ARFs are a recently discovered family of transcription factors that bind with specificity to auxin response elements (AuxREs) in promoters of primary or early auxin-responsive genes. ARFs have an amino-terminal DNA-binding domain related to the carboxyl-terminal DNA-binding domain in the maize transactivator VIVIPAROUS1. All but one ARF identified to date contain a carboxyl-terminal protein-protein interaction domain that forms a putative amphipathic α-helix. A similar carboxyl-terminal protein-protein interaction domain is found in the Aux/IAA class of auxin-inducible proteins. Some ARFs contain transcriptional activation domains, while others contain repression domains. ARFs appear to play a pivotal role in auxin-regulated gene expression of primary response genes.

The soybean GH2/4 gene that encodes a glutathione S-transferase has a promoter that is activated by a wide range of chemical agents.

Transcriptional activation of the soybean (Glycine max) GH2/4 gene (also referred to as Gmhsp26-A) and increase in abundance of the GH2/4 mRNA (also referred to as pCE54) have been previously shown to occur following treatment of soybean seedlings with auxins, nonauxin analogs, heavy metals, and a variety of other agents. To determine whether the GH2/4 promoter is responsive to an array of different agents, we have analyzed the inducibility of the GH2/4 promoter fused to the [beta]-glucuronidase reporter gene in transgenic tobacco (Nicotiana tabacum) plants. We have shown that a wide variety of chemical agents induce this promoter in a tissue-specific and concentration-dependent manner. In addition, we have used an affinity-purified antibody raised against recombinant GH2/4 protein to show that the GH2/4 protein increases in response to auxin application and is localized in the cytosol of soybean cells. Recombinant GH2/4 protein can be purified to homogeneity on a glutathione-agarose resin, and the purified protein has glutathione S-transferase activity when assayed with the substrate 1-chloro-2,4-dinitrobenzene.

The ocs element in the soybean GH2/4 promoter is activated by both active and inactive auxin and salicylic acid analogues

The octopine synthase (ocs or ocs-like) element has been previously reported to be responsive to the plant hormones, auxin, salicylic acid, and methyl jasmonate. Using transient assays with carrot protoplasts, we have demonstrated that an ocs element from the soybean auxin-inducible GH2/4 promoter is not only activated by strong auxins (i.e, 2,4-dichlorophenoxyacetic acid, 2,4,5-trichlorophenoxyacetic acid, α-naphthalene acetic acid) and salicylic acid, but also by weak auxin analogues (β-naphthalene acetic acid), inactive auxin analogs (i.e., 2,3-dichlorophenoxyacetic acid, 2,4,6-trichlorophenoxyacetic acid), and inactive salicylic acid analogs (3-hydroxybenzoic acid and 4-hydroxybenzoic acid). Our results indicate that the ocs element in the GH2/4 promoter is not selectively induced by plant hormones and might function similarly to tandem AP-1 sites in some animal glutathione S-transferase (GST) genes. The ocs element, like the AP-1 sites in animal GST promoters, may be induced not only by certain hormones but also by some non-hormonal stress-inducing or electrophilic agents.

An intron sense suppression construct targeting soybean FAD2-1 requires a double-stranded RNA-producing inverted repeat T-DNA insert.

We demonstrate that the transformation of soybean (Glycine max) with sense suppression constructs using intron sequences from the fatty acid oleyl Δ12 desaturase gene FAD2-1A leads to efficient and specific reduction of FAD2-1 transcripts in developing seeds, increased oleic acid, and decreased polyunsaturated fatty acids. The related FAD2-2 transcripts are only marginally affected. Despite screening a large number of independent transformants, no single-copy efficacious transformants could be found. Invariably, all the least complex transgenic loci have two T-DNA copies in an inverted repeat configuration, centered at the right borders. We show that this T-DNA configuration produces an inverted repeat transcript and that small interfering RNAs accumulate against the target sequence.

Use of Bacterial Quorum-Sensing Components to Regulate Gene Expression in Plants

We describe an efficient inducible system to regulate gene expression in plants based on quorum-sensing components found in Gram-negative bacteria such as Agrobacterium tumefaciens. These bacteria monitor their own population density by utilizing members of the N-acyl homoserine lactone family as inducers and a transcriptional activator as its receptor. In our study, we utilize the components from A. tumefaciens (i.e. 3-oxooctanyl-l-homoserine lactone [OOHL]) synthesized by the TraI protein and its receptor, TraR. When OOHL binds to TraR, it recognizes its specific cis-element, the tra box. We translationally fused the eukaryotic VP16 activation domain to the N terminus of TraR. In the presence of OOHL, the chimeric VP16:TraR transcriptional regulator induces reporter gene expression in moss (Physcomitrella patens), barley (Hordeum vulgare), and carrot (Daucus carota) cells, as well as in transgenic Arabidopsis (Arabidopsis thaliana) seedlings. The inducible system shows a low level of reporter gene expression in the absence of the inducer. Foliar application and a floating-leaf assay in the presence of the inducer shows a 30- and 200-fold induction, respectively. Induction by foliar application of the inducer to whole seedlings is achieved within 8 h. The VP16:TraR activator also shows specificity for binding to its cognate inducer, OOHL. Based on microarray analyses, endogenous gene expression is not significantly affected due to overexpression of the TraR protein or presence of OOHL in either wild-type or lactone-inducible transgenic plants.

Arabidopsis expresses two genes that encode polypeptides similar to the yeast RNA polymerase I and III AC40 subunit.

A 40-kDa subunit in eukaryotic RNA polymerases (Pol) I and III (e.g., yeast yAC40) is related in a part of its aa sequence to the alpha subunit of prokaryotic Pol and to a 35-44-kDa subunit in Pol II (e.g., yeast yB44). We have cloned two cDNAs, AtRPAC42 and AtRPAC43, from an Arabidopsis thaliana (At) (ecotype Columbia) lambda Yes expression library that encode Pol I and III subunits related to yAC40. The aa sequences derived from the cDNA clones were found to be 72% identical to each other and 40% identical to yeast Pol I and III subunits yAC40, but only 30% identical to yeast Pol II subunit yB44. While most other nuclear Pol genes identified to date are single-copy genes, two genes encode 42 and 43-kDa subunits of At Pol I and/or III. A 42-kDa subunit with identical mobility in SDS-PAGE to the aAC42 in vitro translated subunit is found in Pol III purified from At suspension culture cells.

Transcriptional regulation of auxin-responsive genes

We have identified, sequenced, and characterized a number of auxin-responsive genes and cDNAs from soybean (Guilfoyle et al., 1990). These include the genes that encode the mRNAs for GHI, GH2/4, GH3, and SAURs (Hagen et al., 1984; McClure and Guilfoyle, 1987). Nuclear run-on in vitro transcription assays have been used to show that all of these genes are transcriptionally activated within minutes after exogenous auxins are applied to excised, incubated plant organs or intact seedlings (Hagen and Guilfoyle, 1985; McClure et al., 1989). Tissue print and in situ hybridization assays have demonstrated that these auxin-responsive genes are expressed in organ-specific and tissuespecific manners (McClure and Guilfoyle, 1989a; Gee et al., 1991). With the exception of GH2/4, the genes are specifically induced by a variety of active auxins at concentrations ranging from 10-8 to 10-3 M. Below, we sununarize some recent results obtained with these auxin-responsive genes and their promoters.

Auxin-Regulated Gene Expression

A variety of auxin-responsive mRNAs have been identified and characterized (reviewed by Hagen, 1989 and Key, 1989). In a number of cases, the genes that encode these mRNAs have also been identified and sequenced (reviewed by Guilfoyle et al., 1993). The promoter elements that confer auxin-responsiveness are under investigation in several laboratories. Here, we summarize some of our recent results on auxin-responsive mRNAs in soybean and Arabidopsis, the genes that encode these mRNAs, and the auxin-inducible promoters.