Auxin-induced changes in the patterns of protein synthesis in soybean hypocotyl

The patterns of protein synthesis in elongating and mature (basal) sections of soybean hypocotyl were examined after incubation in a medium containing auxin (auxin-treated) or a medium lacking auxin (untreated). The hypocotyl sections (1.2 cm) were labeled with [(35)S]methionine, and polypeptide patterns were analyzed by one- and two-dimensional polyacrylamide gel electrophoresis. Auxin treatment altered the pattern of protein synthesis in both elongating and basal soybean hypocotyl sections. Excision of terminal segments from incubated sections was required to clearly observe auxin-induced changes in the synthesis of polypeptides. Polypeptides synthesized in terminal segments, possibly in response to wounding, can mask subtle changes in the spectrum of polypeptides synthesized in response to auxin. Cytokinin treatment caused a decrease in [(35)S]methionine incorporation into polypeptides and altered the pattern of protein synthesis in untreated and auxin-treated elongating hypocotyl sections.

AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin

Aux/IAA genes are early auxin response genes that encode short-lived nuclear proteins with four conserved domains, referred to as I, II, III, and IV. Arabidopsis Aux/IAA proteins repressed transcription on auxin-responsive reporter genes in protoplast transfection assays. Mutations in domain II resulted in increased repression, whereas mutations in domains I and III partially relieved repression. Aux/IAA proteins fused to a heterologous DNA binding domain were targeted to promoters of constitutively expressed reporter genes and actively repressed transcription in an auxin-responsive and dose-dependent manner. In comparison with an unfused luciferase protein, luciferase fused to Aux/IAA proteins displayed less luciferase activity, which further decreased in the presence of auxin in transfected protoplasts. Domain II mutations increased and domain I mutations decreased luciferase activity with the fusion proteins. These results suggested that Aux/IAA proteins function as active repressors by dimerizing with auxin response factors bound to auxin response elements and that early auxin response genes are regulated by auxin-modulated stabilities of Aux/IAA proteins.

AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin

Aux/IAA genes are early auxin response genes that encode short-lived nuclear proteins with four conserved domains, referred to as I, II, III, and IV. Arabidopsis Aux/IAA proteins repressed transcription on auxin-responsive reporter genes in protoplast transfection assays. Mutations in domain II resulted in increased repression, whereas mutations in domains I and III partially relieved repression. Aux/IAA proteins fused to a heterologous DNA binding domain were targeted to promoters of constitutively expressed reporter genes and actively repressed transcription in an auxin-responsive and dose-dependent manner. In comparison with an unfused luciferase protein, luciferase fused to Aux/IAA proteins displayed less luciferase activity, which further decreased in the presence of auxin in transfected protoplasts. Domain II mutations increased and domain I mutations decreased luciferase activity with the fusion proteins. These results suggested that Aux/IAA proteins function as active repressors by dimerizing with auxin response factors bound to auxin response elements and that early auxin response genes are regulated by auxin-modulated stabilities of Aux/IAA proteins.

Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression

A mutant screen was conducted in Arabidopsis that was based on deregulated expression of auxin-responsive transgenes. Two different tightly regulated (i.e., very low expression in the absence of auxin treatment and very high expression after exogenous auxin treatment) auxin-responsive promoters were used to drive the expression of both a beta-glucuronidase (GUS) reporter gene and a hygromycin phosphotransferase (HPH)-selectable marker gene. This screen yielded several mutants, and five of the mutations (axe1-1 to axe1-5) mapped to the same locus on chromosome 5. A map-based cloning approach was used to locate the axe1 mutations in an Arabidopsis RPD3-like histone deacetylase gene, referred to as HDA6. The axe1 mutant plants displayed increased expression of the GUS and HPH transgenes in the absence of auxin treatment and increased auxin-inducible expression of the transgenes compared with nonmutant control plants. None of a variety of endogenous, natural auxin-inducible genes in the mutant plants were upregulated like the transgenes, however. Results of treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine suggest that the axe1 mutations affect transgene silencing; however, histone deacetylase inhibitors had no affect on transgene silencing in mutant or control plants. The specific effect of AtHDA6 mutations on the auxin-responsive transgenes implicates this RPD3-like histone deacetylase as playing a role in transgene silencing. Furthermore, the effect of AtHDA6 on transgene silencing may be independent of its histone deacetylase activity.

Dimerization and DNA binding of auxin response factors

Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC auxin response elements (AuxREs) found in promoters of primary/early auxin response genes. ARFs are encoded by a multi-gene family, consisting of more than 10 genes. Ten ARFs have been analyzed by Northern analysis and were found to be expressed in all major plant organs and suspension culture cells of Arabidopsis. The predicted amino acid sequences indicate that the 10 ARFs contain a novel amino-terminal DNA binding domain and a carboxyl-terminal dimerization domain, with the exception of ARF3 which lacks this dimerization domain. All ARFs tested bind with specificity to the TGTCTC AuxRE, but there are subtle variations in the sequence requirements at positions 5 (T) and 6 (C) of the AuxRE. While the amino-terminal domain of about 350 amino acids is sufficient for binding ARF1 to TGTCTC AuxREs, this domain is not sufficient for the binding of some other ARFs to palindromic AuxREs. Our results suggest that ARFs must form dimers on palindromic TGTCTC AuxREs to bind stably, and this dimerization may be facilitated by conserved motifs found in ARF carboxyl-terminal domains. Dimerization in at least some cases may dictate which ARF(s) are targeted to AuxREs.

Activation and repression of transcription by auxin-response factors

Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs), which are found in promoters of primary/early auxin-response genes. Nine different ARFs have been analyzed for their capacity to activate or repress transcription in transient expression assays employing auxin-responsive GUS reporter genes. One ARF appears to act as a repressor. Four ARFs function as activators and contain glutamine-rich activation domains. To achieve transcriptional activation on TGTCTC AuxREs in transient expression assays, ARFs require a conserved dimerization domain found in both ARF and Aux/IAA proteins, but they do not absolutely require their DNA-binding domains. Our results suggest that ARFs can activate or repress transcription by binding to AuxREs directly and that selected ARFs, when overexpressed, may potentiate activation further by associating with an endogenous transcription factor(s) (e.g., an ARF) that is bound to AuxREs. Transfection experiments suggest that TGTCTC AuxREs are occupied regardless of the auxin status in cells and that these occupied AuxREs are activated when exogenous auxin is applied to cells or when ARF activators are overexpressed. The results provide new insight into mechanisms involved with auxin regulation of primary/early-response genes.

Arabidopsis thaliana RNA polymerase II subunits related to yeast and human RPB5

Arabidopsis thaliana contains at least four genes that are predicted to encode polypeptides related to the RPB5 subunit found in yeast and human RNA polymerase II. This subunit has been shown to be the largest subunit common to yeast RNA polymerases I, II, and III (RPABC27). More than one of these genes is expressed in Arabidopsis suspension culture cells, but only one of the encoded polypeptides is found in purified RNA polymerases II and III. This polypeptide has a predicted pI of 9.6, matches 14 of 16 amino acids in the amino terminus of cauliflower RPB5 that was microsequenced, and shows 42 and 53% amino acid sequence identity with the yeast and human RPB5 subunits, respectively.

The ARF family of transcription factors and their role in plant hormone-responsive transcription

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 alpha-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.

Two small subunits in Arabidopsis RNA polymerase II are related to yeast RPB4 and RPB7 and interact with one another

An Arabidopsis cDNA (AtRPB15.9) that encoded a protein related to the RPB4 subunit in yeast RNA polymerase II was cloned. The predicted molecular mass of 15.9 kDa for the AtRPB15.9 protein was significantly smaller than 25 kDa for yeast RBP4. In SDS-PAGE, AtRPB15.9 migrated as the seventh or eighth largest subunit (i.e. apparent molecular mass of 14-15 kDa) in Arabidopsis RNA polymerase II, whereas RPB4 migrates as the fourth largest subunit (i.e. apparent molecular mass of 32 kDa) in yeast RNA polymerase II. Unlike yeast RPB4 and RPB7, which dissociate from RNA polymerase II under mildly denaturing conditions, plant subunits related to RPB4 and RPB7 are more stably associated with the enzyme. Recombinant AtRPB15.9 formed stable complexes with AtRPB19.5 (i.e. a subunit related to yeast RPB7) in vitro as did recombinant yeast RPB4 and RPB7 subunits. Stable heterodimers were also formed between AtRPB15. 9 and yeast RPB7 and between yeast RPB4 and AtRPB19.5.

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.

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.

A G-Box-Binding Protein from Soybean Binds to the E1 Auxin-Response Element in the Soybean GH3 Promoter and Contains a Proline-Rich Repression Domain

The E1 promoter fragment (-249 to -203) is one of three auxin-response elements (AuxREs) in the soybean (Glycine max L.) GH3 promoter (Z.-B. Liu, T. Ulmasov, X. Shi, G. Hagen, T.J. Guilfoyle [1994] Plant Cell 6: 645-657). Results presented here further characterize and delimit the AuxRE within the E1 fragment. The E1 fragment functioned as an AuxRE in transgenic tobacco (Nicotiana tabacum L.) plants, as well as in transfected protoplasts. The AuxRE within E1 contains a G-box, and this G-box was used to clone a G-box-binding factor (GBF) from soybean (SGBF-2). This 45-kD GBF contains an N-terminal proline-rich domain and a C-terminal basic/leucine zipper DNA-binding domain. Gel-mobility shift assays were used to characterize the binding specificity of SGBF-2. Antiserum raised against recombinant SGBF-2 was used to further characterize SGBF-2 and antigenically related GBFs in soybean nuclear extracts. Co-transfection assays with effector and reporter plasmids in carrot (Daucus carota L.) protoplasts indicated that the N-terminal proline-rich domain of SGBF-2 functioned as a repression domain in both basal and auxin-inducible transcription.

ARF1, a transcription factor that binds to auxin response elements

The plant hormone auxin regulates plant physiology by modulating the interaction of transcription factors with auxin response elements (AuxREs) of the affected genes. A transcription factor, Auxin Response Factor 1 (ARF1), that binds to the sequence TGTCTC in AuxREs was cloned from Arabidopsis by using a yeast one-hybrid system. ARF1 has an amino-terminal DNA-binding domain related to the carboxyl terminus of the maize transactivator Viviparous-1. Sequence requirements for ARF1 binding in vitro are identical to those that confer auxin responsiveness in vivo. The carboxyl terminus of ARF1 contains two motifs found in the Aux/IAA class of proteins and appears to mediate protein-protein interactions.

Reconstitution of yeast and Arabidopsis RNA polymerase alpha-like subunit heterodimers

Two subunits of about 36-44 kDa and 13-19 kDa in the eukaryotic nuclear RNA polymerases share limited amino acid sequence similarity to the alpha subunit in Escherichia coli RNA polymerase. The alpha subunit in the prokaryotic enzyme has a stoichiometry of 2, but the stoichiometry of the alpha-like subunits in the eukaryotic enzymes is not entirely clear. To gain insight into the subunit stoichiometry and assembly pathway for eukaryotic RNA polymerases, in vitro reconstitution experiments have been carried out with recombinant alpha-like subunits from yeast and plant RNA polymerase II. The large and small alpha-like subunits from each species formed stable heterodimers in vitro, but neither the large or small alpha-like subunits formed stable homodimers. Furthermore, mixed heterodimers were formed between corresponding subunits of yeast and plants, but were not formed between corresponding subunits in different RNA polymerases from the same species. Our results suggest that RNA polymerase II alpha-like heterodimers may be the equivalent of alpha homodimers found in E. coli RNA polymerase.

A 14-kDa Arabidopsis thaliana RNA polymerase III subunit contains two alpha-motifs flanked by a highly charged C terminus

We have sequenced a cDNA and a gene, AtRPC14, from Arabidopsis thaliana (At) (ecotype Columbia) that encode a protein related to the yeast RNA polymerases (Pol) I and III subunits, yAC19. Polyclonal antibodies raised against the recombinant At polypeptide (AtC14) bind to the Pol I and/or III subunits of about 13-15 kDa, but do not bind to any Pol II subunit in Pol purified from cauliflower, wheat or At. The amino acid (aa) sequence derived from the AtRPC14 cDNA and genomic clones consists of 122 aa, as compared to the 142 aa in the yeast yAC19 subunit and 143 aa in a putative Caenorhabditis elegans CeAC16 subunit. AtC14, yAC19 and CeAC16 contain a conserved sequence of about 85 aa which is related to two motifs in the alpha subunit of Escherichia coli (Ec) Pol. AtC14 lacks a highly charged N terminus of about 50 aa found in both yAC19 and CeAC16, but has a highly charged C terminus of about 30 aa not found in yAC19 and CeAC16.

Association between 36- and 13.6-kDa alpha-like subunits of Arabidopsis thaliana RNA polymerase II

Two subunits in RNA polymerase II (e.g. RPB3 and RPB11 in yeast) and two subunits common to RNA polymerases I and III (e.g. AC40 and AC19 in yeast) contain one or two motifs related to the alpha subunit in prokaryotic RNA polymerases. We have sequenced two different cDNAs (AtRPB36a and AtRPB36b), the two corresponding genes from Arabidopsis thaliana that are homologs of yeast RPB3, and an Arabidopsis cDNA (AtRPB13.6) that is a homolog of yeast RPB11. The B36a subunit is the predominant B36 subunit associated with RNA polymerase II purified from Arabidopsis suspension culture cells, and this subunit has a stoichiometry of about 1. Results from protein association assays showed that the B36a and B36b subunits did not associate, but each of these subunits did associate with the B13.6 subunit in vivo and in vitro. Two motifs in the B36b subunit related to the prokaryotic alpha subunit were shown to be required for the in vitro interactions with the B13.6 subunit. Our results suggest that the B36 and B13.6 subunits associate to form heterodimers in Arabidopsis RNA polymerase II like the AC40 and AC19 heterodimers reported for yeast RNA polymerases I and III but unlike the B44 homodimers reported for yeast RNA polymerase II.

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.

Auxin regulated gene expression and gravitropism in plants

Transcription of two gene families, SAURs and GH3, in soybean has been shown to be specifically induced by the plant hormone auxin. The SAUR mRNAs have been shown to accumulate on the lower half and disappear from the upper half of soybean hypocotyls during gravitropic curvature. The SAUR and GH3 promoters have been fused to the beta-glucuronidase (GUS) reporter gene and shown to be specifically induced by auxins in transgenic tobacco plants. Histochemical staining and quantitative GUS assays indicate that these auxin inducible promoters are activated on the lower half of transgenic tobacco stems undergoing gravitropic curvature. The auxin transport inhibitors, TIBA and NPA, block both gravitropic curvature and the activation of the auxin responsive promoters in transgenic tobacco stems. The auxin responsive elements (AuxREs) within the SAUR and GH3 promoters have been identified, and these AuxREs are likely to be the elements that are responsible for the increased expression of the SAUR and GH3 genes during gravitropism.

Composite structure of auxin response elements

The auxin-responsive soybean GH3 gene promoter is composed of multiple auxin response elements (AuxREs), and each AuxRE contributes incrementally to the strong auxin inducibility to the promoter. Two independent AuxREs of 25 bp (D1) and 32 bp (D4) contain the sequence TGTCTC. Results presented here show that the TGTCTC element in D1 and D4 is required but not sufficient for auxin inducibility in carrot protoplast transient expression assays. Additional nucleotides upstream of TGTCTC are also required for auxin inducibility. These upstream sequences showed constitutive activity and no auxin inducibility when part or all of the TGTCTC element was mutated or deleted. In D1, the constitutive element overlaps the 5' portion of TGTCTC; in D4, the constitutive element is separated from TGTCTC. An 11-bp element in D1, CCTCGTGTCTC, conferred auxin inducibility to a minimal cauliflower mosaic virus 35S promoter in transgenic tobacco seedlings as well as in carrot protoplasts (i.e., transient expression assays). Both constitutive elements bound specifically to plant nuclear proteins, and the constitutive element in D1 bound to a recombinant soybean basic leucine zipper transcription factor with G-box specificity. To demonstrate further the composite nature of AuxREs and the ability of the TGTCTC element to confer auxin inducibility, we created a novel AuxRE by placing a yeast GAL4 DNA binding site adjacent to the TGTCTC element. Expression of a GAL4-c-Rel transactivator in the presence of this novel AuxRE resulted in auxin-inducible expression. Our results indicate that at least some AuxREs have a composite structure consisting of a constitutive element adjacent to a conserved TGTCTC element that confers auxin inducibility.

Composite structure of auxin response elements

The auxin-responsive soybean GH3 gene promoter is composed of multiple auxin response elements (AuxREs), and each AuxRE contributes incrementally to the strong auxin inducibility to the promoter. Two independent AuxREs of 25 bp (D1) and 32 bp (D4) contain the sequence TGTCTC. Results presented here show that the TGTCTC element in D1 and D4 is required but not sufficient for auxin inducibility in carrot protoplast transient expression assays. Additional nucleotides upstream of TGTCTC are also required for auxin inducibility. These upstream sequences showed constitutive activity and no auxin inducibility when part or all of the TGTCTC element was mutated or deleted. In D1, the constitutive element overlaps the 5' portion of TGTCTC; in D4, the constitutive element is separated from TGTCTC. An 11-bp element in D1, CCTCGTGTCTC, conferred auxin inducibility to a minimal cauliflower mosaic virus 35S promoter in transgenic tobacco seedlings as well as in carrot protoplasts (i.e., transient expression assays). Both constitutive elements bound specifically to plant nuclear proteins, and the constitutive element in D1 bound to a recombinant soybean basic leucine zipper transcription factor with G-box specificity. To demonstrate further the composite nature of AuxREs and the ability of the TGTCTC element to confer auxin inducibility, we created a novel AuxRE by placing a yeast GAL4 DNA binding site adjacent to the TGTCTC element. Expression of a GAL4-c-Rel transactivator in the presence of this novel AuxRE resulted in auxin-inducible expression. Our results indicate that at least some AuxREs have a composite structure consisting of a constitutive element adjacent to a conserved TGTCTC element that confers auxin inducibility.

An auxin-inducible element in soybean SAUR promoters

The soybean SAUR (Small Auxin-Up RNA) genes are transcriptionally induced by exogenous auxins within a few minutes after hormone application. This response is specifically induced by auxins primarily in epidermal and cortical cells within elongation zones of hypocotyls and epicotyls. We have previously shown that an 832-bp soybean SAUR promoter/beta-glucuronidase (GUS) reporter gene fusion is responsive to auxin in transgenic tobacco plants (Y. Li, G. Hagen, T.J. Guilfoyle [1991] Plant Cell 3: 1167-1175). Similar results were obtained with an 868-bp SAUR 15A promoter-GUS reporter gene in transgenic tobacco (Y. Li, unpublished results). We have now analyzed a soybean SAUR 15A promoter in transgenic tobacco plants using 5' unidirectional deletions, internal deletions and mutations, and gain-of-function assays with a minimal cauliflower mosaic virus 35S promoter. Our results indicate that the distal upstream element/NdeI restriction endonuclease site element (NDE) (B.A. McClure, G. Hagen, C.S. Brown, M.A. Gee, T.J. Guilfoyle [1989] Plant Cell 1: 229-239) in the SAUR 15A promoter is necessary and sufficient for auxin induction. Our results also show that the 30-bp NDE portion of this element is responsible for most, if not all, of the auxin inducibility of the SAUR 15A promoter. The NDE contains two adjacent sequences, TGTCTC and GGTCCCAT, which have been previously identified as putative auxin-responsive elements. We propose that these elements might function independently or together, possibly with an additional element(s), to confer auxin inducibility to the SAUR promoters.

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 soybean SAUR open reading frame contains a cis element responsible for cycloheximide-induced mRNA accumulation

Little is known about how mRNA stability is regulated in higher plants. The SAURs (Small Auxin-Up RNAs) are a family of highly unstable mRNAs in soybean that rapidly increase in abundance after excised organs are treated with the plant hormone auxin. The SAURs are also induced by protein synthesis inhibitors, including cycloheximide, in the absence of auxin treatment and are superinduced when organs are treated with cycloheximide plus auxin. While the induction of SAURs is transcriptionally regulated by auxin, the induction by cycloheximide is posttranscriptional. Cycloheximide as well as other protein synthesis inhibitors appear to induce SAUR accumulation by increasing the stabilities of these mRNAs. To determine whether the 5'-untranslated region, the 3'-untranslated region, or the open reading frame of these unstable mRNAs is responsible for the cycloheximide inducibility, we have used chimeric genes in transgenic tobacco plants to test each of these mRNA regions. Our results show that the SAUR open reading frame within a chimeric mRNA confers cycloheximide inducibility in transgenic tobacco plants whereas chimeric mRNAs containing the SAUR 5'-untranslated region or 3'-untranslated region as isolated elements or in combination are not induced by cycloheximide. These results suggest that the SAUR open reading frame contains sequence elements that are involved in the stability of these mRNAs.

Sequence of the fifth largest subunit of RNA polymerase II from plants

An affinity-purified antibody raised against the fifth largest subunit of cauliflower (Brassica oleracea) RNA polymerase II was used to screen an expression library and isolate an Arabidopsis thaliana cDNA clone. This cDNA clone was used to isolate a soybean (Glycine max) cDNA clone, and both clones were sequenced. The open reading frames contain 176 amino acids and predict polypeptides of 19.5 and 19.6 kDa for Arabidopsis and soybean, respectively. The amino acid sequences of the Arabidopsis and soybean polypeptides are 91.5% identical. The fifth largest subunit in plant RNA polymerase II is present at unit stoichiometry in purified enzyme and does not dissociate from the holoenzyme during nondenaturing polyacrylamide gel electrophoresis. The gene encoding the 19.5-kDa subunit has been isolated and sequenced from Arabidopsis. The gene is single copy and contains five introns. The size of the mRNA encoding this RNA polymerase II subunit in Arabidopsis and soybean is approximately 1 kilobase. None of the published yeast or animal RNA polymerase subunit sequences show similarity to the fifth largest subunit in plants.

Altered morphology in transgenic tobacco plants that overproduce cytokinins in specific tissues and organs

An auxin-inducible bidirectional promoter from the soybean SAUR gene locus was fused to a reporter gene in one direction and a cytokinin biosynthetic gene in the opposite direction and the expression of these fused genes was examined in transgenic tobacco. The Escherichia coli uidA gene, which encodes the enzyme beta-glucuronidase (GUS), was used as the reporter gene and the Agrobacterium tumefaciens ipt gene, which encodes the enzyme isopentenyl transferase, was used as the cytokinin biosynthetic gene. These constructs allowed the overproduction of cytokinins in tobacco in a tissue- and organ-specific manner. Localized overproduction of cytokinins was monitored using the GUS reporter gene and measured by an ELISA assay. The tissue- and organ-specific overproduction of cytokinins produced a number of morphological and physiological changes, including stunting, loss of apical dominance, reduction in root initiation and growth, either acceleration or prolonged delayed senescence in leaves depending on the growth conditions, adventitious shoot formation from unwounded leaf veins and petioles, altered nutrient distribution, and abnormal tissue development in stems. While some of these morphological changes result directly from the localized overproduction of cytokinins, other changes probably result from the mobilization of plant nutrients to tissues rich in cytokinins.

An Auxin-Responsive Promoter Is Differentially Induced by Auxin Gradients during Tropisms

We constructed a chimeric gene consisting of a soybean small auxin up RNA (SAUR) promoter and leader sequence fused to an Escherichia coli [beta]-glucuronidase (GUS) open reading frame and a 3[prime] untranslated nopaline synthase sequence from Agrobacterium tumefaciens. This chimeric gene was used to transform tobacco by Agrobacterium-mediated transformation. In R2 etiolated transgenic tobacco seedlings, GUS expression occurred primarily in elongation regions of hypocotyls and roots. In green plants, GUS was expressed primarily in the epidermis and cortex of stems and petioles, as well as in elongation regions of anther filaments in developing flowers. GUS expression was responsive to exogenous auxin in the range of 10-8 to 10-3 M. During gravitropism and phototropism, the GUS activity became greater on the more rapidly elongating side of tobacco stems. Auxin transport inhibitors and other manipulations that blocked gravitropism also blocked the asymmetric distribution of GUS activity in gravistimulated stems. Light treatment of dark-grown seedlings resulted in a rapid decrease in GUS activity. Light-induced decay in GUS activity was fully reversed by application of auxin. Taken together, our results add support for the formation of an asymmetric distribution of auxin at sites of action during tropism.

Auxin-induced expression of the soybean GH3 promoter in transgenic tobacco plants

The gene encoding the auxin-responsive GH3 mRNA (G. Hagen, A. Kleinschmidt, TJ. Guilfoyle, Planta 162: 147-153 (1984] from soybean was cloned, and its sequence and transcription initiation site were determined. The promoter of the GH3 gene has been fused to the open reading frame of the Escherichia coli uidA gene which encodes beta-glucuronidase (GUS). This fusion gene was introduced into tobacco via Agrobacterium tumefaciens-mediated transformation, and the expression of the gene was examined by fluorometric assay and histochemical staining of young R1 tobacco seedlings and mature plants. In transgenic tobacco plants that have not been exposed to exogenous auxin, expression of the fusion gene is largely restricted to roots of young green plants and developing floral organs, including ovules, developing seeds, and pollen, of mature plants. Application of exogenous auxin to tobacco seedlings or plant organs results in a greater than 50-fold increase in expression of GUS. Auxin-induced GUS expression is greatest in vascular tissue, but not restricted to this tissue. The auxin-deduced GUS expression was characterized for kinetics, auxin specificity and dose response.

Tissue-specific and organ-specific expression of soybean auxin-responsive transcripts GH3 and SAURs

We used in situ hybridization to localize two classes of auxin-regulated transcripts, GH3 and SAURs, within organs and tissues of soybean seedlings and flowers. GH3 transcripts occurred in the inner cortex and protoxylem ridges of roots and were expressed transiently during flower and pod development. SAUR transcripts were expressed in the epidermis, cortex, and starch sheath of epicotyls and immature hypocotyls. SAUR transcripts became more abundant on the bottom side of hypocotyls that were undergoing gravitropic curvature. SAURs were also expressed in developing xylem elements of the hypocotyl hook. When soybean organ sections were treated with 50 micromolar 2,4-dichlorophenoxyacetic acid (2,4-D), GH3 transcripts became more abundant in the vascular regions of all organs analyzed. High levels of GH3 transcripts were also found in developing palisade mesophyll cells of leaves, cotyledons, and flowers treated with 2,4-D. SAUR transcripts became more abundant in the epidermis, cortex, starch sheath, and pith of epicotyls and hypocotyls after 2,4-D treatment. Our results showed that a variety of tissues and cell types express auxin-responsive transcripts and that different tissues respond rapidly to exogenous auxin by expressing different hormone-responsive genes.

Induction and superinduction of auxin-responsive mRNAs with auxin and protein synthesis inhibitors

We have identified a class of small mRNAs (approximately 0.5 kilobases), referred to as small auxin-up RNAs (SAURs), that increases in abundance within minutes after auxin application to excised elongating hypocotyl sections of soybean. In this study, we present evidence that SAURs accumulate in the absence of auxin when protein synthesis is inhibited. Superinduction of SAURs occurs if the synthetic auxin 2,4-dichlorophenoxyacetic acid is added under conditions where protein synthesis is inhibited. Transcription run-on experiments with isolated nuclei show that, unlike 2,4-dichlorophenoxyacetic acid, protein synthesis inhibitors do not activate transcription of the SAUR genes. These results suggest that protein synthesis inhibitors act by stabilizing SAURs and that some labile protein(s) are involved in the rapid turnover of SAURs. This stabilization is not observed with GH3, another auxin-inducible mRNA. Whether induced with 2,4-dichlorophenoxyacetic acid or cycloheximide, SAURs are primarily expressed in epidermal and cortical cells of elongating hypocotyl sections, with little or no expression in vascular tissue. Unlike 2,4-dichlorophenoxyacetic acid-induced SAUR accumulation, the increase in abundance of SAURs induced by cycloheximide is transient, with a peak approximately 1 h after inhibitor addition. Complete inhibition of protein synthesis is not required for SAUR accumulation in the presence of protein synthesis inhibitors.

Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean

We have cloned and sequenced the gene encoding the largest subunit of RNA polymerase II (RPB1) from Arabidopsis thaliana and partially sequenced genes from soybean (Glycine max). We have also determined the nucleotide sequence for a number of cDNA clones which encode the carboxyl terminal domains (CTDs) of RNA polymerase II from both soybean and Arabidopsis. The Arabidopsis RPB1 gene encodes a polypeptide of approximately 205 kDa, consists of 12 exons, and encompasses more than 8 kb. Predicted amino acid sequence shows eight regions of similarity with the largest subunit of other prokaryotic and eukaryotic RNA polymerases, as well as a highly conserved CTD unique to RNA polymerase II. The CTDs in plants, like those in most other eukaryotes, consist of tandem heptapeptide repeats with the consensus amino acid sequence PTSPSYS. The portion of RPB1 which encodes the CTD in plants differs from that of RPB1 of animals and lower eukaryotes. All the plant genes examined contain 2-3 introns within the CTD encoding regions, and at least two plant genes contain an alternatively spliced intron in the 3' untranslated region. Several clustered amino acid substitutions in the CTD are conserved in the two plant species examined, but are not found in other eukaryotes. RPB1 is encoded by a multigene family in soybean, but a single gene encodes this subunit in Arabidopsis and most other eukaryotes.

A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase II

A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase IIA has been partially purified and characterized. The kinase has a native molecular weight of about 200 kilodaltons. This kinase utilizes Mg2+ and ATP and transfers about 20 phosphates to the heptapeptide repeats Pro-Thr-Ser-Pro-Ser-Tyr-Ser in the carboxyl-terminal domain of the 220-kilodalton subunit of soybean RNA polymerase II. This phosphorylation results in a mobility shift of the 220-kilodalton subunits of a variety of eukaryotic RNA polymerases to polypeptides ranging in size from greater than 220 kilodaltons to 240 kilodaltons on sodium dodecyl sulfate-polyacrylamide gels. The phosphorylation is highly specific to the heptapeptide repeats since a degraded subunit polypeptide of 180 kilodaltons that lacks the heptapeptide repeats is poorly phosphorylated. Synthetic heptapeptide repeat multimers inhibit the phosphorylation of the 220-kilodalton subunit.

Tissue print hybridization. A simple technique for detecting organ- and tissue-specific gene expression

We have used a new technique, which we call tissue print hybridization, to monitor organ- and tissue-specific expression of auxin-induced RNAs in soybean (Glycine max cv. Wayne) seedlings. This technique is modified from that originally published by Cassab and Varner (J Cell Biol 105: 2581-2588, 1987) for the localization of extensin protein in soybean seed using an antibody probe. We extended this original tissue print procedure by utilizing(35)S-labeled antisense RNAs for localization of specific RNAs immobilized on nylon membranes. We also employed modifications to improve the resolution of the autoradiographic images. We have used this technique to demonstrate the tissue-specific expression of auxin-regulated genes in elongating hypocotyl regions of etiolated soybean seedlings and the rapid turn-over of RNAs encoded by these genes during gravistimulation.

Transcription, organization, and sequence of an auxin-regulated gene cluster in soybean

We have characterized a soybean gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs). DNA sequencing of a portion of the locus reveals five homologous genes, spaced at intervals of about 1.25 kilobases and transcribed in alternate directions. At least three of the genes are transcriptionally regulated by auxin. An increase in the rate of transcription is detected 10 min after application of auxin to soybean elongating hypocotyl sections. Each of the genes contains an open reading frame that could encode a protein of 9 kilodaltons to 10.5 kilodaltons. Sequence comparisons among the five genes reveal several areas of high homology. Two regions of high homology begin about 250 base pairs upstream of the open reading frames and two regions of homology have been identified in sequences downstream of the open reading frames. One of the latter sequences occurs in the 3'-untranslated region of the RNAs. The other occurs far downstream, 618 base pairs to 741 base pairs from the stop codon. Conservation of these sequences among the five different genes suggests that they may be important for the regulation of expression of the genes.

Transcription, organization, and sequence of an auxin-regulated gene cluster in soybean

We have characterized a soybean gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs). DNA sequencing of a portion of the locus reveals five homologous genes, spaced at intervals of about 1.25 kilobases and transcribed in alternate directions. At least three of the genes are transcriptionally regulated by auxin. An increase in the rate of transcription is detected 10 min after application of auxin to soybean elongating hypocotyl sections. Each of the genes contains an open reading frame that could encode a protein of 9 kilodaltons to 10.5 kilodaltons. Sequence comparisons among the five genes reveal several areas of high homology. Two regions of high homology begin about 250 base pairs upstream of the open reading frames and two regions of homology have been identified in sequences downstream of the open reading frames. One of the latter sequences occurs in the 3'-untranslated region of the RNAs. The other occurs far downstream, 618 base pairs to 741 base pairs from the stop codon. Conservation of these sequences among the five different genes suggests that they may be important for the regulation of expression of the genes.

Regulation of expression of an auxin-induced soybean sequence by cadmium

An auxin-regulated soybean sequence has been characterized and shown to be induced by the heavy metals cadmium, silver, and copper. Cadmium induces the accumulation of two size classes of mRNA: a 1-kilobase (kb) RNA class, which is the same size as the RNA class induced by auxin, silver, and copper, and a 1.4-kb RNA class. DNA sequence analysis of cDNA clones and a soybean genomic fragment has shown the presence of an intron in this gene. A restriction fragment probe isolated from the intron segment hybridizes specifically to the 1.4-kb mRNA. The transcription rate of this sequence is rapidly increased following exposure of soybean primary leaves to cadmium, as assayed by nuclear run-off transcription experiments. These results suggest that cadmium not only induces the transcription of a specific soybean sequence, but interferes with the processing of the precursor mRNA, resulting in the accumulation of the 1.4-kb mRNA precursor species.

Synthesis of 5S rRNA and putative precursor tRNAs in nuclei isolated from wheat embryos

Nuclei isolated from wheat embryos synthesize 4.5S precursor tRNAs and 5S rRNA in vitro. The precursor tRNAs can be processed to 4S tRNAs. Transcription of the tRNA and 5S rRNA genes is carried out by endogenous RNA polymerase III, and addition of exogenous wheat RNA polymerase III results in increased transcription on these genes. A number of experimental results suggest that proper initiation and accurate transcription of the tRNA and 5S rRNA genes occurs with isolated wheat nuclei.

Rapid induction of selective transcription by auxins

Nuclei isolated from excised soybean plumules that were treated with 2,4-dichlorophenoxyacetic acid (2,4-D) were active in transcription of four auxin-regulated genes or DNA sequences, which have been described previously (G. Hagen, A. Kleinschmidt, and T. Guilfoyle, Planta 162:147-153, 1984). The rates of transcription of the auxin-responsive sequences were 10- to 100-fold greater with nuclei isolated from auxin-treated plumules than with those from untreated plumules. The transcriptional response was also observed with hypocotyls of intact soybean seedlings and hypocotyl sections, as well as with green bean and mung bean plumules that were treated with 2,4-D. Other auxins, including 2,4,5-trichlorophenoxyacetic acid, alpha-naphthaleneacetic acid, and indole-3-acetic acid, also induced the transcriptional response. Increased transcription rates were observed within 5 min after application of auxins to excised plumules, and half-maximal to maximal transcription rates were achieved by 15 min after application of auxins. As little as 10(-7) to 10(-8) M 2,4-D induced a transcriptional response, but maximal transcription rates were achieved at 10(-3) M 2,4-D. Brief treatment with the protein synthesis inhibitor cycloheximide did not inhibit the induction of transcription by auxins. These results clearly demonstrated that auxin-regulated gene expression is under rapid transcriptional control.

Immunological studies on plant DNA-dependent RNA polymerases with antibodies raised against individual subunits

Antibodies were raised against native soybean RNA polymerase II and individual subunits of RNA polymerase II purified from soybean, cauliflower, and wheat. These antibodies were used to study the immunological relationships of plant RNA polymerases I, II, and III at the subunit level. RNA polymerases I and II from soybean, I, II, and III from cauliflower and wheat, and II from turnip were purified to homogeneity, and enzyme subunits were separated on polyacrylamide gels containing sodium dodecyl sulfate. Separated RNA polymerase subunits were electrophoretically transferred to nitrocellulose, reacted with antibodies, and the immunoglobulin complexes were revealed by reaction with 125I-labeled Protein A. Antibodies directed against native soybean RNA polymerase II bind to all or most of the subunits of soybean and wheat RNA polymerase II and to the putative common subunits in RNA polymerases I and III. Antibodies directed against individual subunits of RNA polymerase II enzymes react specifically with the subunit to which the antibody was raised and to related or identical subunits in RNA polymerases I and III. These studies confirm the presence of common subunits in the three classes of nuclear RNA polymerase and provide information on analogous or related subunits within each class of enzyme purified from different plant species.

Size heterogeneity of the largest subunit of nuclear RNA polymerase II. An immunological analysis

Antibodies raised against the 180-kDa subunit of cauliflower RNA polymerase II bind selectively to the largest subunit of RNA polymerase II purified from a variety of plant species. The selective binding of this antibody to the largest RNA polymerase II subunit has allowed us to probe for the size of this subunit in crude cell extracts, in fractions containing partially purified RNA polymerase II, and in isolated nuclei. Fractions containing RNA polymerase II were subjected to electrophoresis in the presence of sodium dodecyl sulfate, blotted onto nitrocellulose, and blots were probed with antibody. Immunoglobulin complexes were revealed with 125I-Protein A. Published purification procedures result in rapid conversion of a 220-kDa subunit to a 180-kDa polypeptide, but purification at high pH (pH 9.0) retards this proteolysis. RNA polymerase II associated with isolated nuclei is largely protected from proteolytic degradation, and a 240-kDa polypeptide as well as a 220-kDa polypeptide can be detected. These results suggest that the 180-kDa subunit of RNA polymerase II arises artificially during cell lysis and enzyme purification, and that even the 220-kDa polypeptide may be a degradation product of a 240-kDa polypeptide in plants.

Nuclei purified from cauliflower mosaic virus-infected turnip leaves contain subgenomic, covalently closed circular cauliflower mosaic virus DNAs

Nuclei isolated from cauliflower mosaic virus (CaMV) infected turnip leaves contain subgenomic CaMV DNA species in addition to the genome length CaMV DNA. These subgenomic CaMV DNA species are present as covalently closed circles (form I), relaxed circles (form II) and linear (form III) molecules. The subgenomic form I DNA species range in size from about 10% of genome length to nearly genome length. These subgenomic DNA species appear in tissue infected with cloned CaMV DNA, indicating that they arise rapidly and have not accumulated in the virus population from serial propagation of CaMV. No specific region of the CaMV genome appears to be preferentially deleted to form the subgenomic CaMV DNA species. At least three distinct subgenomic species appear to accumulate preferentially in nuclei isolated from infected tissue. Two of these abundant subgenomic CaMV DNA species are form I and the other one is form III. Some of the subgenomic CaMV DNA species appear to be minichromosomes.

A transcriptionally active, covalently closed minichromosome of cauliflower mosaic virus DNA isolated from infected turnip leaves

Purified nuclei from turnip leaves infected by cauliflower mosaic virus (CaMV) have been shown to contain a fraction of CaMV DNA that consists of covalently closed circular molecules; possesses a nucleosome structure, based on sensitivity to micrococcal nuclease; and contains nuclear RNA polymerase II that selectively transcribes the coding strand of CaMV DNA in vitro. Our results suggest that the transcriptionally active CaMV DNA is in the form of a minichromosome and that this DNA does not contain the site-specific discontinuities characteristic of the virion.

Auxin- and ethylene-induced changes in the population of translatable messenger RNA in Basal sections and intact soybean hypocotyl

In vitro translation products of polyadenylated RNA from untreated and auxin-treated basal sections of soybean (Glycine max var. Wayne) hypocotyl were analyzed by two-dimensional polyacrylamide gel electrophoresis. Within one hour of 2,4-dichlorophenoxyacetic acid treatment, the translatable messenger RNAs for at least twelve in vitro translation products are modulated upward. In vitro translation products of polyadenylated RNA from untreated, auxin-treated and Ethephon-treated intact soybean hypocotyl were also analyzed. Within two hours of treatment with either 2,4-dichlorophenoxyacetic acid or Ethephon, the translatable messenger RNAs for a group of high molecular weight in vitro translation products are modulated upward. There is a particular set of translatable messenger RNA, encoding in vitro translation products in the 24,000 to 32,000 molecular weight range, that is specifically modulated upward by auxin treatment in intact soybean hypocotyl and in hypocotyl sections.

Auxin-induced changes in the population of translatable messenger RNA in elongating sections of soybean hypocotyl

In vitro translation products of polyadenylated RNA from untreated and auxin-treated elongating sections of soybean (Glycine max var. Wayne) hypocotyl were analyzed by two-dimensional polyacrylamide gel electrophoresis. The levels of translatable messenger RNA for at least ten in vitro translation products are increased by auxin treatment. The induction by auxin occurs rapidly (within 15 minutes), and the amounts of the induced in vitro translation products increase with time of auxin treatment. Indoleacetic acid has the same effect on the population of translatable messenger RNA as 2,4-dichlorophenoxyacetic acid. The auxin-induced in vitro translation products disappear rapidly when Actinomycin D is present during the last two hours of a three-hour auxin treatment.

Auxin-induced changes in the population of translatable messenger RNA in elongating maize coleoptile sections

In-vitro translation products of polyadenylated RNA from untreated and indole-3-acetic acid (IAA)-treated elongating sections of maize (Zea mays L.) coleoptiles were analyzed by twodimensional polyacrylamide gel electrophoresis. Treatment with IAA results in an increased amount of at least four in-vitro translation products. The amounts of two of these translation products are increased within 10 min of IAA treatment.

Auxin-induced deoxyribonucleic acid dependent ribonucleic acid polymerase activities in mature soybean hypocotyl

When 3-day-old etiolated soybean seedlings are treated with the synthetic auxin, 2,4-dichlorophenoxyacetic acid, cells of the mature hypocotyl swell and proliferate abnormally. By 48 h after auxin application ribonucleic acid (RNA) polymerase I and II levels increase by about 10-20- and 6-fold, respectively, on a fresh weight tissue basis and about 3-6- and 2-fold, respectively, on a tissue deoxyribonucleic acid (DNA) basis. [35S]Methionine incorporation into RNA polymerase subunits suggests that this increase in levels of RNA polymerases results from de novo synthesis of the enzymes. No alteration in subunit structure or patterns of incorporation of [35S]methionine into RNA polymerase subunits is detected following auxin treatment. No differences in the phosphorylation patterns of RNA polymerase subunits are detected after hormone treatment. These results indicate that although the levels of RNA polymerases I and II may regulate, in part, the rates of transcription during physiological or developmental transitions, alteration or modification of RNA polymerase subunit structure does not appear to be involved in transcriptional regulation in the auxin-induced soybean hypocotyl.