Research ArticleResearch Article

Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana

Paul J. Overvoorde, Yoko Okushima, José M. Alonso, April Chan, Charlie Chang, Joseph R. Ecker, Beth Hughes, Amy Liu, Courtney Onodera, Hong Quach, Alison Smith, Guixia Yu, Athanasios Theologis

Published December 2005. DOI: https://doi.org/10.1105/tpc.105.036723

Abstract

Auxin regulates various aspects of plant growth and development. The AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode short-lived transcriptional repressors that are targeted by the TRANSPORT INHIBITOR RESPONSE1/AUXIN RECEPTOR F-BOX proteins. The Aux/IAA proteins regulate auxin-mediated gene expression by interacting with members of the AUXIN RESPONSE FACTOR protein family. Aux/IAA function is poorly understood; herein, we report the identification and characterization of insertion mutants in 12 of the 29 Aux/IAA family members. The mutants show no visible developmental defects compared with the wild type. Double or triple mutants of closely related Aux/IAA genes, such as iaa8-1 iaa9-1 or iaa5-1 iaa6-1 iaa19-1, also exhibit wild-type phenotypes. Global gene expression analysis reveals that the molecular phenotypes of auxin-treated and untreated light-grown seedlings are unaffected in the iaa17-6 and iaa5-1 iaa6-1 iaa19-1 mutants. By contrast, similar analysis with the gain-of-function axr3-1/iaa17-1 mutant seedlings reveals dramatic changes in basal and auxin-induced gene expression compared with the wild type. Expression of several type-A ARABIDOPSIS RESPONSE REGULATOR genes and a number of genes involved in cell wall biosynthesis and degradation is repressed in axr3-1/iaa17-1. The data suggest extensive functional redundancy among Aux/IAA gene family members and that enhanced stability of the AXR3/IAA17 protein severely alters the molecular phenotype, resulting in developmental defects.

INTRODUCTION

The plant hormone auxin, typified by indole-3-acetic acid (IAA), regulates a variety of physiological processes, including apical dominance, tropic responses, lateral root formation, vascular differentiation, embryo patterning, and shoot elongation (Davies, 1995). Although auxin was the first plant hormone identified, insights into the molecular mechanism of auxin action is only recently beginning to emerge (Dharmasiri et al., 2005a, 2005b; Kepinski and Leyser, 2005). Auxin enhances the transcription of several classes of early genes, such as the Aux/IAA, Gretchen Hagen3 (GH3), and SMALL AUXIN UP RNA (SAUR) gene family members (Abel and Theologis, 1996). The central role of the Aux/IAA gene family members in auxin signaling has been suggested by molecular genetic and biochemical studies (Leyser, 2002; Woodward and Bartel, 2005).

The Aux/IAA genes were originally identified based on their rapid induction by auxin in etiolated soybean (Glycine max) and pea (Pisum sativum) tissues (Walker and Key, 1982; Theologis et al., 1985). Similar genes were subsequently isolated in a variety of plant species, including Arabidopsis thaliana, tomato (Lycopersicon esculentum), tobacco (Nicotiana tabacum), rice (Oryza sativa), and maize (Zea mays) (Reed, 2001). The Arabidopsis genome has 29 genes that encode putative Aux/IAA proteins (Arabidopsis Genome Initiative, 2000; Liscum and Reed, 2002; Remington et al., 2004). Auxin induces the expression of many, but not all, Aux/IAA gene family members. The Arabidopsis IAA1 through IAA14 and IAA19 genes are auxin inducible with varying induction kinetics, and their mRNA accumulation varies in different parts of the plant (Abel et al., 1995; Tatematsu et al., 2004). However, several Aux/IAA genes, including IAA17 and IAA28, show little or no response to exogenous auxin (Rogg et al., 2001; Tian et al., 2002; this study). The diversity in auxin responsiveness and tissue-specific expression among the various gene family members suggests that each member may have a distinct or overlapping function(s) during normal auxin responses required for plant development.

The Aux/IAA mRNAs are also rapidly induced by treatment with the protein synthesis inhibitor cycloheximide (Ballas et al., 1993; Abel et al., 1995; Koshiba et al., 1995). This observation led to the suggestion that auxin-mediated transcriptional activation might involve the removal of a short-lived transcriptional repressor (Theologis et al., 1985). Recent biochemical and genetic studies indicate that the Aux/IAA proteins are the postulated repressors of auxin-regulated transcriptional activation (Ulmasov et al., 1997b; Tiwari et al., 2001, 2003, 2004; Woodward and Bartel, 2005). The Aux/IAA genes encode short-lived nuclear proteins, and most of them contain four highly conserved domains (domain I, II, III, and IV) separated by variable regions (Abel et al., 1994, 1995; Reed, 2001). Each domain contributes to the functional properties of the protein. Domain I is responsible for the repressing activity of the proteins (Tiwari et al., 2004), whereas domain II confers instability to the proteins (Worley et al., 2000; Ouellet et al., 2001). Domains III and IV serve for homodimerization and heterodimerization with other Aux/IAA gene family members (Kim et al., 1997; Ouellet et al., 2001) as well as for heterodimerization with the AUXIN RESPONSE FACTORS (ARFs) (Ulmasov et al., 1997b; Ouellet et al., 2001).

The Aux/IAA proteins, while they do not bind to the auxin-responsive elements (AuxREs) directly, regulate auxin-mediated gene expression by controlling the activity of ARFs by protein–protein interactions (Ulmasov et al., 1997b; Tiwari et al., 2003). A typical ARF protein contains a B3-like DNA binding domain in its N terminus region and domains III and IV similar to those present in the Aux/IAAs in their C terminus region (Kim et al., 1997; Ulmasov et al., 1997a; Guilfoyle and Hagen, 2001). The ARF proteins bind to AuxREs in the promoter region of auxin-responsive genes, including Aux/IAAs, through their DNA binding domain (Ulmasov et al., 1997a, 1999b). The amino acid composition of their middle region determines whether an ARF protein is a transcriptional activator or repressor (Ulmasov et al., 1999a; Tiwari et al., 2003). These molecular observations suggest that the vast and diverse combinations of dimers among the Aux/IAA and ARF gene family members may regulate auxin-mediated gene expression in a cell- and tissue-specific manner (Abel et al., 1994; Kim et al., 1997; Kepinski and Leyser, 2002). The prospect arises that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins (Weijers and Jurgens, 2004; Weijers et al., 2005).

The molecular genetic and biochemical data indicate that rapid turnover of Aux/IAA proteins is required for normal auxin response. Significant advances toward linking Aux/IAA protein degradation and auxin signaling have been made. Auxin treatment increases the instability of the pea IAA6 (PSIAA6):luciferase (LUC) and Arabidopsis IAA1:LUC fusion proteins (Zenser et al., 2001, 2003), suggesting that auxin directly modulates the degradation rate of Aux/IAA proteins. Biochemical and genetic studies have shown that IAA7/AXR2 and IAA17/AXR3 proteins are targeted for ubiquitin-mediated proteolysis by the SCFTIR1 ubiquitin ligase complex. The interactions of IAA7/AXR2 and IAA17/AXR3 proteins with the SCFTIR1 complex involve domain II and occur in an auxin-dependent manner (Gray et al., 2001; Dharmasiri et al., 2003; Dharmasiri and Estelle, 2004; Kepinski and Leyser, 2004). Auxin directly binds to the TRANSPORT INHIBITOR RESPONSE1/AUXIN RECEPTOR F-BOX (TIR1/AFB) proteins, resulting in the degradation of the Aux/IAA proteins (Dharmasiri et al., 2005a, 2005b; Kepinski and Leyser, 2005). Therefore, stability of the Aux/IAA proteins is the central regulator of auxin signaling.

Gain-of-function mutations in several Aux/IAA genes, including shy2/iaa3 (Tian and Reed, 1999), shy1/iaa6 (Kim et al., 1996; Reed, 2001), axr2/iaa7 (Timpte et al., 1994; Nagpal et al., 2000), bdl/iaa12 (Hamann et al., 1999, 2002), solitary root (slr)/iaa14 (Fukaki et al., 2002), axr3/iaa17 (Leyser et al., 1996; Rouse et al., 1998), iaa18 (Reed, 2001), msg2/iaa19 (Tatematsu et al., 2004), and iaa28 (Rogg et al., 2001), have pleiotropic affects on plant growth. These mutants have been identified from a variety of developmental and auxin-specific genetic screens, and the changes in growth can be associated with decreased or increased auxin responses. For example, shy2-2/iaa3, axr2-1/iaa7, and iaa28-1 mutants show decreased apical dominance (Tian and Reed, 1999; Nagpal et al., 2000; Rogg et al., 2001), which is consistent with a reduced auxin response. By contrast, axr3-1/iaa17-1 mutant plants show increased apical dominance and increased adventitious rooting, suggesting an enhanced auxin response (Leyser et al., 1996). Each of the Aux/IAA gain-of-function mutants is caused by a single amino acid change in domain II of the corresponding Aux/IAA proteins. Mutations in domain II stabilize the Aux/IAA proteins. Mutant axr3-1/iaa17 protein has a sevenfold increased half-life compared with the wild-type version of the protein (Ouellet et al., 2001). Similarly, the shy2-2/iaa3 protein accumulates in the shy2-2/iaa3 mutant plants (Colon-Carmona et al., 2000). The increased protein level is thought to inhibit the activity of the ARF proteins by preventing them from binding to AuxREs (Tiwari et al., 2001, 2003, 2004; Kepinski and Leyser, 2002; Woodward and Bartel, 2005). The Aux/IAA gain-of-function mutations alter gene expression in untreated and auxin-treated plants. For example, the SAUR-AC1 transgene is ectopically expressed, and the auxin-mediated induction of several Aux/IAA genes is severely impaired in the axr3-1/iaa17-1 and axr2-1/iaa7 mutants (Abel et al., 1995; Leyser et al., 1996; Ouellet et al., 2001). Microarray analysis has shown that the auxin-mediated gene expression profile is globally altered in the shy2-2/iaa3 plants (Tian et al., 2002).

Here, we report the isolation and characterization of insertion mutants in the Aux/IAA genes. All the single mutants do not show obvious visible phenotypes. Construction of double (iaa8-1 iaa9-1) and triple (iaa5-1 iaa6-1 iaa19-1) mutants also failed to reveal visible phenotypes, suggesting a high degree of functional redundancy among the various gene family members. Consistent with these findings is the observation that the gene expression profiles of auxin-treated and untreated iaa17-6 and iaa5-1 iaa6-1 iaa19-1 mutant seedlings are similar to the treated or untreated wild-type plants. On the other hand, the gene expression profiles of the gain-of-function mutant axr3-1/iaa17-1 are altered by the mutation. These data suggest that the stabilized axr3/iaa17 protein functions as a repressor in auxin signaling even though some of the phenotypes of axr3-1/iaa17-1 are consistent with enhanced auxin responses (Leyser et al., 1996; Tiwari et al., 2001, 2003). Furthermore, the mutation also has global effects on non-auxin-regulated gene expression.

RESULTS

The Arabidopsis Aux/IAA Gene Family

The Arabidopsis genome contains 29 Aux/IAA genes scattered among the five chromosomes (Arabidopsis Genome Initiative, 2000, annotation version 5.0; Liscum and Reed, 2002; Figure 1A). The locations of the 10 previously described gain-of-function mutations, shy2/iaa3 (Tian and Reed, 1999), axr3/iaa17 (Leyser et al., 1996; Rouse et al., 1998), bdl/iaa12 (Hamann et al., 1999, 2002), iaa18 (Reed, 2001), shy1/iaa6 (Kim et al., 1996; Reed, 2001), msg2/iaa19 (Tatematsu et al., 2004), axr2/iaa7 (Nagpal et al., 2000), slr/iaa14 (Fukaki et al., 2002), axr5/iaa1 (Yang et al., 2004), and iaa28 (Rogg et al., 2001), are highlighted in Figure 1A. The IAA3/IAA17 and IAA1/IAA14 gene pairs are clustered on chromosomes I and IV, respectively. They have most likely risen during genome duplication and gene reshuffling (Blanc et al., 2000). The isolation of full-length open reading frames (ORFs) for all the gene family members except IAA15 (Figure 1B) demonstrates that all Aux/IAA genes are transcriptionally active (Figure 1B). IAA15 was previously thought to be a pseudogene (Abel et al., 1995); however, the amino acid alignment shown in Figure 2 shows that the predicted IAA15 protein (annotation version 5.0 of the Arabidopsis genome) contains all four conserved domains associated with the Aux/IAA proteins. Our efforts to isolate a full-length IAA15 ORF have been unsuccesful. This may be due to its low abundance mRNA or due to its expression in developmental stages other than those tested. The updated amino acid alignment shown in Figure 2 has been derived from full-length ORF cDNAs and reveals that not all the Aux/IAA proteins contain the four conserved domains I, II, III, and IV, a hallmark of these proteins (Abel et al., 1994; Reed, 2001). For example IAA10, IAA11, IAA20, and IAA29-34 do not contain the conserved amino acid residues in domain I shared by other members of the gene family. In addition domain II is quite different in IAA20, IAA30, IAA32, and IAA34. Domains I and II are divided into two subdomains in the IAA8/IAA9 and IAA10/IAA11 pairs, respectively, due to insertions of additional amino acid residues (Figure 2). Phylogenetic analysis shows that the Aux/IAA genes fall into 10 branches marked with different colors in Figure 1B. The Aux/IAA proteins vary widely in size, ranging from ∼18 (IAA31) to ∼36 kD (IAA9) (see Supplemental Table 1 online). Their isoelectric points also vary widely from 4.51 (IAA30) to 9.74 (IAA12) (see Supplemental Table 1 online). The amino acid identity among the various gene family members ranges from 83% (IAA20/IAA30 pair) to 10% (e.g., IAA8/IAA33 pair) as shown in Supplemental Table 2 online. The overall identity among the various proteins is low, even between members of the same phylogenetic branch (see Supplemental Table 2 online).

Figure 1.
Figure 1.

The Aux/IAA Gene Family of Arabidopsis.

(A) Chromosomal location of Aux/IAA genes. The locations of 29 putative Aux/IAA genes on the Arabidopsis chromosomes (I to V) are shown according to version 5.0 of the Arabidopsis genome annotation submitted to GenBank. Mutants that have been isolated in the Aux/IAA gene are shown on the left side of the chromosomes.

(B) Phylogenetic analysis. The gene names, accession numbers, protein IDs, and the accession numbers of the full-length ORFs used for this analysis are also shown. The full-length ORFs of IAA18, IAA19, IAA28, IAA29, IAA30, IAA31, IAA32, and IAA33 were constructed during this study.

Figure 2.
Figure 2.

Alignment of the Aux/IAA Proteins Reveals Several Highly Conserved Domains.

The deduced amino acid sequences of the Aux/IAA proteins were aligned using ClustalW (Thompson et al., 1994). The conserved domains I, II, III, and IV present in the Aux/IAA proteins are indicated at the top of the alignment. The sequences used in this analysis are the same as those used for constructing the phylogenetic tree shown in Figure 1B.

Isolation of Aux/IAA T-DNA Insertion Mutants

We initiated this project using a PCR-based screening approach to identify T-DNA insertion mutants for a large number of Aux/IAA genes. A total of 80,000 T-DNA insertion lines in the Columbia (Col) ecotype were initially screened, and 11 lines were identified (Alonso et al., 2003). Subsequently, the laboratory participated in generating the Garlic lines in collaboration with the former Torrey Mesa Research Institute, and one additional line was isolated (Sessions et al., 2002). A dSpm insertion line for IAA5 was also identified (Tissier et al., 1999). Taken together during the last 6 years, we identified 13 T-DNA insertion lines located between the start and stop codons of 12 Aux/IAA genes. Figure 3 and Supplemental Table 3 online provide a summary of all the mutants isolated and characterized during the course of this study. A recent search at the Salk T-DNA express line collection (http://signal.salk.edu/cgi-bin/tdnaexpress) reveals that there are additional T-DNA insertion lines in the coding regions of IAA5, IAA7, IAA11, IAA15, IAA17, IAA18, IAA28, IAA29, IAA30, IAA33, and IAA34, but the analysis and characterization of these lines has not been completed during this study. All the lines have been backcrossed at least once and partially characterized phenotypically. We plan to deposit all the lines in the Arabidopsis Biological Resource Center (http://www.biosci.ohio-state.edu/∼plantbio/Facilities/abrc/abrchome.htm) for further molecular and phenotypic characterization by the community.

Figure 3.
Figure 3.

Location of T-DNA or dSpm Insertions in the Aux/IAA Gene Family Members.

Boxes represent exons. Insertions with gray triangles denote lines whose characterization has been completed. Insertions with white triangles denote lines not characterized.

Phenotypes of Insertion Mutants

Figure 4 compares 6-week-old mature wild-type plants (Col) with each of the insertion lines. All the mutants fail to show an obvious visible phenotype during growth and development (Figure 4). These observations suggest that highly similar proteins encoded by one or more members of the Aux/IAA gene family are capable of performing overlapping functions during plant growth and development. The most evolutionarily linked genes would encode the most similar proteins and might also contain similar cis-regulatory elements. Therefore, the most closely related Aux/IAA genes would be good candidates to encode proteins in the appropriate cells for compensating the loss of an individual gene family member. It is also possible that a more distantly related member of the gene family whose expression pattern overlaps with that of the disrupted gene may encode a protein that performs the functions of the missing protein.

Figure 4.
Figure 4.

Growth Phenotype of Insertion Mutants of Various Aux/IAA Gene Family Members.

Three wild-type (left) and three mutant plants (right) were grown simultaneously and are shown for each line. White dots indicate the boundaries between the wild-type and the mutant plants.

To explore the extent of functional redundancy among the various gene family members, we constructed double and triple mutant plants of closely related Aux/IAA gene family members, for example, IAA8/IAA9 or IAA5/IAA6/IAA19 subfamilies (see Figure 1B). If closely related proteins are responsible for compensating for the loss of a single Aux/IAA protein, lines containing double and triple gene disruptions should reveal the overlapping functions during growth. Surprisingly, the iaa8-1 iaa9-1, iaa5-1 iaa6-1, iaa5-1 iaa19-1, and iaa6-1 iaa19-1 double mutants and the iaa5-1 iaa6-1 iaa19-1 triple mutant grow and develop like the wild-type plants under greenhouse conditions (Figures 5A to 5C). Furthermore, the roots of the iaa5-1 iaa6-1 iaa19-1 triple mutant show wild-type sensitivity to increasing concentrations of exogenous IAA, indicating that the auxin response of the root tissue is not affected by the removal of these three genes (Figure 5D). The findings are surprising because among the three Aux/IAA genes used to construct the triple mutant, at least IAA5 and IAA6 share similar expression patterns in terms of tissue specificity, kinetics of auxin-mediated induction, and auxin dose–response curves (Abel et al., 1995). In addition, the phenotypes of gain-of-function mutants of SHY1/IAA6 and MSG2/IAA19 suggest that they may participate in a light signaling pathway and differential growth response that is mediated by auxin, respectively (Kim et al., 1996; Tatematsu et al., 2004).

Figure 5.
Figure 5.

Phenotypes of iaa8 iaa9 Double and iaa5 iaa6 iaa19 Triple Mutants during Developmental Stages.

(A) Four-week-old soil-grown plants of the wild type and the iaa8-1 iaa9-1 double mutant.

(B) Four-week-old soil-grown plants of the wild type or the iaa5-1 iaa6-1, iaa5-1 iaa19-1, and iaa6-1 iaa19-1 double mutants.

(C) Four-week-old soil-grown plants of the wild type and the iaa5-1 iaa6-1 iaa19-1 triple mutant.

(D) Root growth inhibition assay of wild-type and iaa5-1 iaa6-1 iaa19-1 triple mutant seedlings. Four-day-old seedlings were transferred to medium containing the indicated concentrations of IAA, and the increase in root length was measured after 5 d. Root length is shown as a percentage of the root length in the absence of auxin. Each point represents the average of at least 10 seedlings. Bars represent se.

The double and triple mutants have been deposited with the ABRC (http://www.biosci.ohio-state.edu/∼plantbio/Facilities/abrc/abrchome.htm) and the Nottingham Arabidopsis Stock Centre (http://arabidopsis.info/).

Global Gene Expression Analysis

Although the single, double, and triple Aux/IAA mutants do not show any detectable phenotypic differences, it is possible that the loss of Aux/IAA gene function affects global gene expression. This prompted us to perform microarray analysis with one single loss-of-function mutant (iaa17-6), one single gain-of-function mutant (axr3-1/iaa17-1), and the triple mutant (iaa5-1 iaa6-1 iaa19-1; note the three genes of the mutant form a distinct clade on the phylogenetic tree; Figure 1B). We chose iaa17-6 as the representative of the single mutants because the AXR3/IAA17 gene and its mutant alleles have been well characterized (Leyser et al., 1996; Rouse et al., 1998; Gray et al., 2001; Ouellet et al., 2001). We identified and characterized two independent T-DNA insertion alleles for AXR3/IAA17, iaa17-5, and iaa17-6 (Figure 3); both of them failed to show an obvious growth phenotype (Figure 4). The T-DNA of the iaa17-5 allele is located in the first intron (Figure 3). RT-PCR analysis revealed that a properly processed AXR3/IAA17 transcript was still made in the plants homozygous for the iaa17-5 insertion, suggesting that the T-DNA insertion may be removed by splicing (data not shown). By contrast, RT-PCR analysis with RNA from iaa17-6 plants showed no detectable transcript for this gene (data not shown).

Effect of Mutations on Global Gene Expression in Auxin-Treated Seedlings

Light-grown seedlings of wild-type, iaa17-6, axr3-1/iaa17-1, and iaa5-1 iaa6-1 iaa19-1 were treated for 2 h with the carrier solvent ethanol (control sample) or 5 μM IAA (auxin-treated sample). Each experiment was performed in triplicate, and total RNA was independently isolated to generate biotin-labeled complementary RNA (cRNA) for hybridization (see Methods). The data were then subjected to a set of statistical analyses that consider signal strength and variance within and among the biological replicates (see Methods). Figure 6 shows the scatterplots (M-A plots; Dudiot et al., 2002) representing the auxin-regulated transcriptional profiles of wild-type, iaa17-6, iaa5-1 iaa6-1 iaa19-1, and axr3-1/iaa17-1 mutants. A cursory examination of the scatterplots indicates that the wild-type gene expression profile is globally altered by exogenous auxin treatment. However, the loss of IAA17 and IAA5/IAA6/IAA19 genes do not cause changes in auxin-induced gene expression, suggesting that the gene regulation response to exogenous auxin is intact in these two mutants. However, there is a reduced level of scattering in the expression profile of the axr3-1/iaa17-1 mutant seedlings (Figure 6), indicating that auxin-mediated gene expression is altered by this gain-of-function mutation. This is consistent with the reduced auxin sensitivity and the altered growth habit seen in axr3-1/iaa17-1 plants (Leyser et al., 1996).

Figure 6.
Figure 6.

Global Gene Expression Profiling.

M-A plots (Dudiot et al., 2002) showing changes of auxin-mediated gene expression in the wild type, iaa17-6, axr3-1/iaa17-1, and iaa5-1 iaa6-1 iaa19-1. Each plot represents the log2 ratio of the average of the auxin-treated samples (I) to the control samples (C) [M = log2 (I/C)] versus overall average intensity [A = log2 √(I*C)] (Dudiot et al., 2002). The genes induced by auxin treatment (M > 1) are shown in red, and the genes repressed by auxin treatment (M < −1) are shown in green. The data were further analyzed for variance to extract the statistically valid auxin-regulated genes discussed in Tables 1 and 2 and Figure 8.

We identified a preliminary set of genes whose expression was affected at least twofold by auxin treatment using the log2 expression values from the robust multiarray analysis (RMA) output file (Irizarry et al., 2003). From this initial set of genes, we identified those genes whose expression pattern of expression was statistically significant (see Methods). As shown in Table 1, of the 22,800 genes analyzed, in wild-type seedlings only 168 genes were identified as auxin induced, and only 57 genes were identified as auxin-repressed genes. A complete list of all the auxin-regulated genes according to their functional classification can be found in Supplemental Tables 4 and 5 online. The lists include various classes of known auxin-regulated genes, such as Aux/IAA, GH3, SAUR, and 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE, consistent with similar studies reported previously (Tian et al., 2002; Pufky et al., 2003; Redman et al., 2004; Okushima et al., 2005).

View this table:
Table 1.

Summary of Genes with Impaired Auxin-Mediated Reguation in the Mutants

The question immediately arises as to whether the three mutants have a defective gene expression profile in the presence of exogenous auxin. We extracted the gene sets that were induced or repressed by auxin in the wild type and compared them with those extracted from auxin-treated mutants seedlings (iaa17-6, axr3-1/iaa17-1, and iaa5-1 iaa6-1 iaa19-1). We used fold change ratio of induction or repression levels between mutants and the wild type as criteria, with a cutoff fold change ratio value of ≥2. Almost all auxin-regulated genes respond normally to exogenous auxin treatment in the iaa17-6 and iaa5-1 iaa6-1 iaa19-1 mutants (see Table 1). This is consistent with the gene distribution observed by the scatterplot analyses (Figure 6). In fact, in the iaa17-6 seedlings, only one auxin-repressed gene (At5g47450), which encodes TIP2;3, shows a reduced level of auxin-regulated repression (Table 1). A small number (four genes) show reduced level of induction by auxin treatment in the iaa5-1 iaa6-1 iaa19-1 mutant (Table 1). Three of the four genes, IAA5, IAA6, and IAA19, are the inactivated genes in the mutant (Table 1; see Supplemental Figure 1 online). The fourth gene (At5g47450) encodes a protein of unknown function (Table 1). By contrast, in the axr3-1/iaa17-1 mutant, 77 (46%) of the 168 auxin-induced genes and 37 (65%) out of 57 auxin-repressed genes show impaired auxin-mediated regulation (Table 1; see Supplemental Tables 6 and 7 online). The mutation affects a group of auxin-regulated genes that encode proteins with diverse functions (Table 1; see Supplemental Tables 6 and 7 online). Among the 28 Aux/IAA genes present on the ATH1 GeneChip, only IAA1, IAA2, IAA4, IAA5, IAA6, IAA11, IAA13, IAA19, and IAA29 are auxin induced in wild-type seedlings (see Supplemental Figure 1 online). The axr3-1/iaa17-1 mutation impairs the auxin inducibility of three Aux/IAA genes, IAA5, IAA6, and IAA11 (see Supplemental Figure 1 online). The expression of IAA2 is not affected by the mutation (see Supplemental Figure 1 online). The remaining five auxin-inducible Aux/IAA genes (IAA1, IAA4, IAA13, IAA19, and IAA29) remain auxin inducible, but the amplitude of the response is dampened (see Supplemental Figure 1 online). Furthermore, the basal expression level of AXR2/IAA7 and AXR3/IAA17 is reduced in untreated axr3-1/iaa17-1 seedlings compared with the wild type (see Supplemental Figure 1 online).

Effect of the Mutations on Global Gene Expression in Non-Auxin-Treated Seedlings (Basal Expression)

To identify the genes affected by the mutants in the absence of exogenous auxin, we compared the gene expression profiles of each mutant with the wild-type profile in the absence of auxin treatment. Among the 22,810 genes, only 2/5 genes were induced and 4/1 genes were repressed in iaa17-6 and iaa5-1 iaa6-1 iaa19-1, respectively (Table 2). Given the small number of genes whose expression is altered in the untreated mutant seedlings, we conclude that the single and triple loss-of-function mutations do not affect their molecular phenotype. Numerous genes, however, are differentially expressed in untreated axr3-1/iaa17-1 seedlings compared with the wild type. Among the 22,810 genes, 108 and 78 genes are identified as repressed or induced genes in mock-treated axr3-1/iaa17-1 (Table 2). The mutation affects the expression of diverse classes of genes (Table 2). The genes are listed in Supplemental Tables 8 and 9 online. Among the 108 repressed genes in the axr3-1/iaa17-1 mutant (Table 2), 28 genes encode cell wall structural proteins and proteins involving cell wall degradation enzymes, including xyloglucan endotransglycosylases (XTHs), pectinmethylesterases (PMEs), expansins, extensins, Pro-rich proteins (PRPs), and arabinogalactan proteins (AGPs) (Table 3; see Supplemental Table 8 online). Their expression characteristics in the presence and absence of auxin are shown in Figure 7. In addition to the genes that encode cell wall–related proteins, the expression of several peroxidase genes is enhanced or repressed in untreated axr3-1/iaa17-1 seedlings (see Supplemental Figure 2 and Supplemental Tables 8 and 9 online). The class III plant peroxidases (POXs; EC 1.11.1.7) are encoded by 73 genes in Arabidopsis, and they have been named P1 to P73 (Tognolli et al., 2002). Among the 73 POX genes, eight of them (P2, P24, P35, P39, P44, P59, P60, and P73) show reduced expression in untreated axr3-1/iaa17-1 mutant seedlings compared with untreated wild-type seedlings, while two of them, P14 and P34, are upregulated (see Supplemental Table 9 online).

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Table 2.

Number of Genes with Repressed or Enhanced Expression in Mutants in the Absence of Exogenous Auxin

View this table:
Table 3.

Induced and Repressed Cell Wall–Related Genes in the axr3-l/iaal7-1 Mutant

Figure 7.
Figure 7.

Expression Characteristics of Cell Wall–Related Genes in Wild-Type, iaa17-6, axr3-1/iaa17-1, and iaa5-1 iaa6-1 iaa19-1 Seedlings.

Data represent the average relative expression intensity of control (open bars) or auxin-treated (gray bars) samples from triplicate experiments. See Methods for further details. Bars represent sd.

Untreated axr3-1/iaa17-1 seedlings also show altered expression of genes that encode components of the cytokinin signal transduction pathway. Eleven type A ARABIDOPSIS RESPONSE REGULATORS (ARRs) have been identified in Arabidopsis (Hwang et al., 2002). Four of them, namely, ARR3 (At1g59940), ARR5 (At3g48100), ARR6 (At5g62920), and ARR7 (At1g19050), are repressed by the axr3-1/iaa17-1 mutation (Figure 8; see Supplemental Table 8 online). Although ARR4 (At1g10470) appears to be repressed in axr3-1/iaa17-1, this observation was not supported by our statistical analysis (Figure 8; see Supplemental Table 8 online). The expression of ARR8 (At2g41310) and ARR9 (At3g57040) is similar in the axr3-1/iaa17-1 and wild-type seedlings (Figure 8). The expression of these two genes is unaffected by cytokinin treatment (D'Agostino et al., 2000). The expression intensities of the remaining four ARR genes (ARR15, ARR16, ARR17, and ARR22) are similar to background level, indicating that these four genes are not expressed under our experimental conditions (data not shown).

Figure 8.
Figure 8.

The Expression of Several Type A ARR Genes Is Suppressed in axr3-1/iaa17-1 Seedlings.

Histograms show expression patterns of seven type A ARR genes in the wild type, iaa17-6, axr3-1/iaa17-1, and iaa5-1 iaa6-1 iaa19-1. Data represent the average relative expression intensity of control (open bars) or auxin-treated (gray bars) samples from triplicate experiments. The asterisks indicate genes whose expression is statistically different in wild-type (Col) and axr3-1/iaa17-1 seedlings. Bars represent sd.

Does the axr3-1/iaa17-1 Mutation Induce Auxin-Regulated Genes?

It has been suggested that the phenotype of the axr3-1/iaa17-1 plants is consistent with enhanced auxin responses (Leyser et al., 1996). The question then arises whether untreated axr3-1/iaa17-1 seedlings express auxin-regulated genes. In order to examine whether the expression profile of the axr3-1/iaa17-1 seedlings resembles wild-type seedlings treated with auxin, we compared the list of auxin-induced or repressed genes in the wild type with the list of induced or repressed genes in axr3-1/iaa17-1 in the absence of auxin treatment. We expect that if the axr3-1/iaa17-1 mutation causes enhanced auxin responses, auxin-induced genes should be enhanced in axr3-1/iaa17-1; likewise, auxin-repressed genes should be repressed in axr3-1/iaa17-1. Figure 9 shows the results of such a comparison. A very small number of genes (seven) are overlapping between auxin-induced genes in the wild type and enhanced genes in the axr3-1/iaa17-1 mutant (Figure 9A). Likewise, only six genes are overlapping among auxin-repressed genes in the wild type and repressed genes in axr3-1/iaa17-1 (Figure 9B). This relatively small overlap suggests that >90% (212 of 225 genes) of the auxin-regulated genes (induced and repressed; see Table 1) do not show increased or repressed expression in the axr3-1/iaa17-1 untreated seedlings. For example, previous reports indicated that the SAUR-AC1/AtSAUR-15 promoter driving β-glucuronidase is ectopically expressed in roots of the axr3-1/iaa17-1 seedlings (Leyser et al., 1996). In untreated wild-type and axr3-1/iaa17-1plants, the SAUR-AC1/AtSAUR-15 gene is similarly expressed, but its auxin induciblity is impaired in axr3-1/iaa17-1 seedlings (Figure 9E). Figures 9C and 9D show the expression characteristics of the overlapping set of genes. Their expression is auxin regulated in the wild type as well as in the two loss-of-function mutants iaa7-6 and iaa5-1 iaa6-1 iaa19-1. However, their expression in untreated axr3-1/iaa17-1 is similar to the auxin-treated wild-type seedlings. Among the 13 overlapping genes, the biological role of the myb-transcription factor, ATR1 (At5g60890), has been previously described. The expression of ATR1 is repressed by auxin, and its encoded protein functions as a positive regulator of ASA1 (At3g54640) and CYP79B2 (At4g39950) expression (Bender and Fink, 1998; Smolen and Bender, 2002). ASA1 encodes an enzyme that catalyzes the first step in Trp biosynthesis (Niyogi and Fink, 1992). CYP79B2 and a closely related gene, CYP79B3 (At2g22330), encode cytochrome P450 enzymes that are involved in converting Trp to indole-3-acetaldodoxime, the precursor of IAA (Zhao et al., 2002). Auxin-mediated repression of ATR1, therefore, appears to be a feedback mechanism, and the reduced level of ATR1 expression in the untreated axr3-1/iaa17-1 seedlings is consistent with the enhanced auxin response phenotypes seen in these plants.

Figure 9.
Figure 9.

Comparision of the Auxin-Regulated Genes in the Wild Type with the Genes Whose Expression Is Altered in axr3-1/iaa17-1 Seedlings.

(A) Venn diagram showing the number of overlapping and unique genes that are auxin induced in wild-type seedlings and whose expression is enhanced in control-treated axr3-1/iaa17-1 seedlings.

(B) Venn diagram showing the number of overlapping and unique genes that are downregulated by auxin treatment of wild-type seedlings and downregulated in control-treated axr3-1/iaa17-1 seedlings.

(C) Expression profiles of the seven overlapping genes whose expression is auxin induced in wild-type seedlings and enhanced in control axr3-1/iaa17-1 seedlings shown in (A). Data represent the average relative expression intensity of control (open bars) or auxin-treated (gray bars) seedlings from triplicate experiments. Bars represent sd.

(D) Expression profiles of the six overlapping genes whose expression is downregulated in wild-type seedlings and downregulated in control-treated axr3-1/iaa17-1 seedlings shown in (B).

(E) Expression characteristics of the SAUR-AC1 gene.

DISCUSSION

Functional Redundancy among the Aux/IAA Gene Family Members

The Aux/IAA proteins constitute a large family of plant-specific transcription factors that play a central role in auxin-regulated transcriptional activation/repression. According to the current view of auxin action, the Aux/IAAs are repressors of ARF activity. They are targeted by the TIR1/AFB receptors for proteolytic degradation, resulting in ARF-dependant transcriptional activation/repression of auxin-regulated gene expression, thereby modulating auxin-dependent growth and development (Woodward and Bartel, 2005). Thus far, gain-of-function mutations in 10 of 29 Arabidopsis Aux/IAA members have been described using forward genetics (i.e., iaa1/axr5, iaa3/shy2, iaa6/shy1, iaa7/axr2, iaa12/bdl, iaa14/slr, iaa17/axr3, iaa18, iaa19/msg2, and iaa28). Phenotypic analysis of the mutants reveals distinct and overlapping functions among the various members. For example, expression of the stabilized mutant form of iaa3/shy2 or iaa17/axr3 proteins from a heat shock promoter causes different effects on root hair development (Knox et al., 2003). The phenotype of the gain-of-function mutants can be mimicked by the expression of corresponding Aux/IAA proteins with the domain II mutation under the control of their own promoters (Fukaki et al., 2002, 2005; Weijers et al., 2005). Promoter-swapping experiments among IAA12/BDL, IAA13, and IAA3/SHY2 using stabilized forms of these proteins reveal distinct functions of these proteins during plant development, embryonic root formation, and seedling growth (Weijers et al., 2005). The functional difference of each Aux/IAA member may be due to its specific preference for a particular ARF partner.

Analysis of transgenic plants expressing stabilized mutant forms of Aux/IAA proteins can contribute to obtaining new insights into the function of the uncharacterized Aux/IAAs. However, since some of the effects of the gain-of-function mutations appear to be created by the ectopic accumulation of the mutant protein, the phenotypes are unlikely to accurately reflect the biological function of the corresponding Aux/IAA protein. It is possible that some of them may not be normally involved in auxin sensing at all, having auxin effects only in gain-of-function mutant states. Moreover, whether these proteins are positive or negative regulators of auxin responses cannot be inferred even if they are components of the auxin signaling apparatus. Thus, it is crucial to analyze the loss-of-function mutant phenotypes of these genes to elucidate their role in auxin signal transduction.

We therefore attempted to identify and characterize loss-of-function mutants of Aux/IAA family members using a reverse genetics approach. Currently, the T-DNA or dSpm transposon insertion mutants for 18 out of 29 Aux/IAA genes are available (SIGnAL; http://signal.salk.edu/cgi-bin/tdnaexpress; Alonso et al., 2003). An initial characterization has been conducted for 12 Aux/IAA insertion alleles in this study, but all of them, including previously identified mutants, failed to show dramatic defects on plant development. In addition, the iaa8-1 iaa9-1 and iaa5-1 iaa6-1 iaa19-1 double and triple mutants, whose protein products are more closely related to each of these gene sets and produce distinct clades in the phylogenetic tree, also grow normally under greenhouse conditions. Global gene expression profiles of iaa17-6 single and iaa5-1 iaa6-1 iaa19-1 triple mutant seedlings are also almost the same as those of the wild-type seedlings treated with or without 5 μM IAA for 2 h. Although considering a small number of possible combinations, these observations suggest that the inactivation of single or triple Aux/IAA gene function(s) does not affect the auxin-mediated gene expression, suggesting a broad functional redundancy among the Aux/IAA gene family members. There is still a possibility that each single Aux/IAA insertional mutant and the double and triple mutants that we have described do have specific phenotypes but would warrant additional scrutiny to detect them. It has been previously reported that the loss-of-function mutants of iaa3/shy2 and iaa7/axr2 have subtle but significant phenotypes (Tian and Reed, 1999; Nagpal et al., 2000). Therefore, all our Aux/IAA insertional mutants may reveal specific phenotypes by meticulous and careful observations or by determining their sensitivity/resistance to chemical genetic screens and various environmental stresses.

The Aux/IAA family members with a high degree of similarity most likely compensate for the loss of one or more gene functions. However, given that we did not see obvious phenotypes with the iaa8-1 iaa9-1 double and iaa5-1 iaa6-1 iaa19-1 triple mutants, the compensatory function might be provided by family members that share a lower degree of similarity but whose expression profiles more closely correlate to those of the inactivated genes. An analysis of available microarray databases using the GENEVESTIGATOR program (http://www.genevestigator.ethz.ch; Zimmermann et al., 2004) shows that (1) each Aux/IAA gene is widely expressed during plant development, (2) each tissue expresses different sets of multiple Aux/IAA genes, and (3) each member has distinct expression profiles in terms of expression levels and specificity. Furthermore, cell type–specific microarray analysis reveals that each Aux/IAA member has different expression profiles in various types of root cells (Birnbaum et al., 2003; Weijers and Jurgens, 2004). For example, although IAA5, IAA6, and IAA19 share sequence similarity, their expression patterns show distinct tissue specificity. An alternative analysis using another database (http://www.atted.bio.titech.ac.jp/) also indicates that none of the three IAA genes (IAA5, IAA6, and IAA19) exhibit significant correlative expression profiles with each other, suggesting that these genes are not involved in the same biological pathways. These findings are consistent with the distinct type of defects caused by the gain-of-function mutations iaa6/shy1 and iaa19/msg2 during plant development (Reed, 2001; Liscum and Reed, 2002; Tatematsu et al., 2004). On the other hand, although IAA1 and IAA19 are relatively divergent members among the Aux/IAA family members, the phenotype of iaa19/msg2 is partially overlapping with that of iaa1/axr5 (Yang et al., 2004). Interestingly, the tissue-specific expression of IAA19 is partially but significantly correlated with that of IAA1 (http://www.atted.bio.titech.ac.jp/). It appears that the level and pattern of expression as well as the sequence similarity affect the phenotypes caused by the gain-of-function mutation of each Aux/IAA gene. The generation of double or higher-order loss-of-function mutants with family members whose expression pattern is similar may yield loss-of-function phenotypes.

While the results presented may be viewed as disappointing, they reveal important information about the function of these important proteins. Overlapping functions among gene family members have been recently unmasked in yeast from studies of the oxysterol binding protein (OSH) gene family (Beh et al., 2001). The Saccharomyces cerevisiae genome encodes seven OSH genes; a combination of genetics, genomics, and sterol lipid analysis was used to characterize OSH deletion mutants. All 127 combinations and permutations of OSH deletion alleles were constructed, and the results show that the loss of individual OSH genes does not alter growth (Beh et al., 2001). However, elimination of the entire OSH gene family is lethal (Beh et al., 2001). The findings suggest that each OSH gene performs a multitude of nonessential functions and contributes to a common essential function. The possibility exists that each member of the Aux/IAA gene family performs a plethora of nonessential functions, while contributing to one essential function by analogy with the yeast OSH gene family members. Since the OSH experiment cannot be duplicated for the Arabidopsis Aux/IAA family for obvious reasons, the question arises as to how to determine the function of each Aux/IAA gene. In the short term, the use of RNA interference technology to inactivate a large set of genes that share a common DNA sequence has the potential to provide useful information. In the long term, the development of gene transplacement in a cell- and tissue-specific manner in Arabidopsis has the potential to provide the answers to this difficult biological problem (Scherer and Davis, 1979).

Similar functional analysis with the ARF gene family members has also revealed functional redundancy among the ARF gene family members but not as severe as with that observed with the Aux/IAA family (Okushima et al., 2005). A number of single loss-of-function mutants have been isolated during the past 10 years, such as arf2/hss, arf3/ettin, arf5/mp, and arf7/nonphototropic hypocotyl4/msg1, which result in distinct developmental defects (Sessions et al., 1997; Hardtke and Berleth, 1998; Harper et al., 2000; Okushima et al., 2005). In addition, ARF double mutants have strong and visible phenotypes (Hardtke et al., 2004; Ellis et al., 2005; Okushima et al., 2005; Wang et al., 2005; Weijers et al., 2005; Wilmoth et al., 2005; H. Quach and A. Theologis, unpublished data). The higher degree of biological functional specificity among the ARF proteins may be due to their DNA binding specificity and tissue-specific expression. The Aux/IAAs, on the other hand, act as repressors of ARF function (Tiwari et al., 2001, 2003) and may be more promiscuous in order to tightly regulate ARF funtion.

The axr3/iaa17-3 Mutation and Its Effects on Global Gene Expression

The axr3-1/iaa17-1 mutation is a gain-of-function mutation that has pleiotropic effects on Arabidopsis growth and development (Leyser et al., 1996). Biochemical evidence indicates that the mutation increases the stability of the encoded protein (Ouellet et al., 2001). Based on the current model of auxin action, the stabilized protein acts as repressor of ARF activity. Protoplast transfection assays have shown that the overexpression of AXR3/IAA17 attenuates the auxin-dependent expression from a promoter that contains AuxREs because the protein acts as a repressor of ARF function (Tiwari et al., 2001, 2003). The axr3-1/iaa17-1 protein completely eliminates auxin-induced reporter gene expression (Tiwari et al., 2001, 2003). Consistent with this model, we found that the expression of 114 auxin-regulated genes is impaired in axr3-1/iaa17-1 (Table 1). Similarly, shy2-2/iaa3 affects auxin-regulated gene expression (Tian et al., 2002). Since different ARF proteins can activate or repress transcription, repressing their activity will result in altered auxin-regulated gene expression, thus leading to dramatic changes in growth and development in the axr3-1/iaa17-1 plants.

The microarray data also reveal that although the auxin-mediated regulation of many auxin-induced and repressed genes is impaired in axr3-1/iaa17-1, the basal expression level of most of these auxin-regulated genes is similar in both the wild type and the axr3-1/iaa17-1 mutant (Figure 9). These findings are similar to the seemingly paradoxical observations made by Leyser et al. (1996) when this mutant was first characterized, as having reduced sensitivity to exogenous auxin as well as enhanced auxin-related phenotypes (such as strong apical dominance). Similarly, other gain-of-function mutants in Aux/IAA genes, such as slr1-1/iaa14, show phenotypes that reflect a reduced auxin response (e.g., no lateral roots) as well as enhanced auxin response (e.g., strong apical dominance; Fukaki et al., 2002). It appears that stabilized Aux/IAA proteins have the capacity to exert opposite effects on developmental events that are mediated by auxin.

The axr3-1/iaa17-1 mutation also affects the expression of a large number of non-auxin-regulated genes with diverse functions (Table 2). Among this class of genes, a large percentage encodes proteins involved in cell wall biosynthesis and degradation. Plant cell walls contain several classes of structural proteins, including extensins, PRPs, Gly-rich proteins, and AGPs (Showalter, 1993). These proteins form the proteoglycan backbone of the extracellular matrix. In addition, the plant cell wall contains many proteins that are involved in mediating cell elongation, including XTHs, PMEs, and expansins (Showalter, 1993). These cell wall structural proteins and enzymes are thought to be essential for cell elongation. For example, XTHs are involved in cell elongation by hydrolyzing the cell wall component, xyloglucan, and subsequent loosening of the cell wall (Rose et al., 2002). Among the seven XTH genes that were suppressed in the axr3-1/iaa17-1 mutant, At-XTH17 is expressed in the elongation and differentiating regions of the roots, and At-XTH20 is specifically expressed in the basal mature region of the roots (Vissenberg et al., 2005). Repression of these two XTH genes may be responsible for root growth inhibition in the axr3-1/iaa17-1 mutant. Alterations in cell wall expansion may account for the pleiotropic morphological phenotypes that include small and curled leaves, short inflorescence, and reduced root length observed in the mutant (Leyser et al., 1996). Furthermore, several POX genes are differentially expressed in the axr3-1/iaa17-1 mutant. Plant POXs appear to be involved in the event associated with cell wall construction, such as lignification and cross-linking of cell wall proteins, as well as auxin catabolism and stress response (Hiraga et al., 2001). Altered expression levels of several POX genes might also be associated with growth inhibition in the axr3-1/iaa17-1 mutant.

In addition to the altered expression of cell wall–associated proteins, the axr3-1/iaa17-1 seedlings show altered expression of genes that encode components of the cytokinin signal transduction pathway. Type A ARRs are rapidly and specifically induced by cytokinin treatment and are known as primary response genes for cytokinins (Brandstatter and Kieber, 1998; Imamura et al., 1998; D'Agostino et al., 2000). Since the expression levels of several type A ARRs, namely, ARR3, ARR5, ARR6, and ARR7, are suppressed in the axr3-1/iaa17-1 seedlings, it is likely that the cytokinin response or level of endogenous active cytokinin content is suppressed in the axr3-1/iaa17-1 mutant. The phenotypes of axr3-1/iaa17-1 can be partially rescued by cytokinin treatment (Leyser et al., 1996), and roots of axr3-1/iaa17-1 seedlings exhibit an altered response to exogenous cytokinin application as well as severe auxin resistance (Leyser et al., 1996). Although we have not determined the endogenous cytokinin content, the lower expression levels of type A ARR genes suggest that at least a downstream cytokinin signaling pathway(s) is impaired in the mutant. Because the axr3-1/iaa17-1 mutant has similar levels of free and conjugated IAA as the wild type (Leyser et al., 1996), it is likely that the normal ratio of auxin to cytokinin is impaired in this mutant, resulting in the severe morphological phenotypes associated with it (Leyser et al., 1996). It is of a great interest that inactivation of the cytokinin receptors enhances cytokinin content in Arabidopsis (T. Schmülling, personal communication). This suggests that the cytokinin sensing pathway communicates with the biosynthetic pathway. We also examined the expression profiles of the genes that encode enzymes involved in cytokinin biosynthesis and catabolism (e.g., isopentenyl transferases and cytokinin oxidases) in the axr3-1/iaa17-1 mutant, but they were not significantly different from those of the wild type (data not shown). AXR3/IAA17 may be involved in the crosstalk between cytokinin and auxin signaling (Swarup et al., 2002), and disrupting this communication results in the morphological and molecular phenotypes of the axr3-1/iaa17-1 mutant.

The genes discussed above in the gain-of-function mutant seemingly have been classified as non-auxin-regulated genes because their expression is not regulated by auxin in the wild-type control 7-d-old light-grown seedlings. Their expression may be unmasked, however, in the mutant seedlings because of the ectopic expression of the axr3-1/iaa17-1 protein, resulting in activation of expression of genes that are not regulated by auxin in the wild type at the particular developmental stage investigated in this study. The possibility exists that these genes are indeed auxin regulated in developmental stages other than the stage investigated in this study, or the axr3-1/iaa17-1 protein may have effects on other pathways and systems not mediated via the TIR1/AFB-Aux/IAA-ARF system (e.g., associating with other proteins affecting their function). The new equilibrium of gene expression established in the axr3-1/iaa17-1 background indicates that the Aux/IAA proteins may, in addition to serving as targets for TIR1/AFB receptors, mediate additional levels of gene expression, suggesting a broader role for these proteins in auxin signaling.

METHODS

Materials

All chemicals used for this study were ACS reagent grade or molecular biology grade. Oligonucleotides were purchased from Operon Technologies or synthesized in house with a Polyplex Oligonucleotide Synthesizer (GeneMachines).

Molecular Biology

Standard protocols were followed for DNA manipulations described by Sambrook et al. (1989). Standard protocols for DNA sequencing were used to confirm the accuracy of the DNA constructs.

Plant Growth Conditions

Arabidopsis thaliana ecotype Col was used throughout this study. Seeds were surface sterilized for 8 min in 5% sodium hypochlorite + 0.15% Tween-20, excessively rinsed in distilled water, and plated on 0.8% agar plates containing 0.5× Murashige and Skoog salts (Murashige and Skoog, 1962; Life Technologies) + 0.5 mM MES, pH 5.7, + 1% sucrose + 1× vitamin B5. The plates were incubated in the dark at 4°C for 2 d and were subsequently transferred to a 16-h-light/8-h-dark cycle at 22°C for light-grown seedlings or in the dark for etiolated seedlings. Mature plants were also grown under the light conditions mentioned above. The root auxin sensitivity assay was performed as follows: 4-d-old light-grown seedlings were transferred to vertically oriented agar plates containing appropriate concentrations of IAA. The root length was determined after an additional 5 d of growth. The root length was determined using the NIH Image 1.63 program (http://rsb.info.nih.gov/nih-image/download.html).

Phylogenetic Analysis

An unrooted dendogram was generated using ClustalW (Thompson et al., 1994). TreeView was used to generate the graphical output (Page, 1996). The numbers at the branching points (see Figure 1) indicate the percentage of times that each branch topology was found during bootstrap analysis (n = 1000).

Identification and Characterization of T-DNA Insertion Alleles

Screening for T-DNA Insertions

The identification of insertional mutants utilizes a PCR-based screen. For each gene, a forward primer annealing to 100 to 150 bp 5′ of the ATG and a reverse primer annealing to 100 to 150 bp 3′ of the translation stop codon were designed (see Supplemental Table 10 online). PCR amplification (35 cycles: 94°C for 15 s, 56°C for 15 s, and 72°C for 3 min) was performed, and the resulting PCR products were subjected to DNA gel blot analysis using radiolabeled Aux/IAA cDNA fragments as probes. The size of the genomic products ranged from 6 to 3.2 kb. Eight sets of DNA template derived from 10,000 plants each (80,000 lines total) were screened. Each set of template contained 40 tubes of DNA (10 each of DNA combined from column, row, plate, and individual superpools). Identification of an individual requires a PCR product in each of the four superpools. Using all combinations of forward and reverse primers with primers annealing to the left border and right border of the T-DNA, PCRs were run (4 × 40 × 8 = 1280 reactions per gene). All operations were adapted to a 384-well format, and handling of samples was performed with a BioMek robot. The products were analyzed by DNA gel blotting to allow increased sensitivity of detection and to assess the specificity of screening. Subsequent to this screen, two large databases containing sequence of DNA flanking T-DNA inserts in 100,000 and 20,000 independent lines have been screened in silico. Data for the 100,000 lines were generated in a collaboration of the University of California at Berkeley with the Torrey Mesa Research Institute, and the 20,000 lines have been obtained by SIGNAL (http://signal.salk.edu/cgi-bin/tdnaexpress).

Confirmation of T-DNA Lines

The nature and location of the T-DNA insertion was confirmed by sequencing PCR products. Once the location of the T-DNA insertion was confirmed, we designed gene-specific PCR primers that flank the T-DNA for use in a codominant genotyping analysis. By performing two sets of PCR, one using the gene-specific primer pair and the other using a gene-specific primer and the T-DNA border primer, we could determine whether the individual is homozygous for no T-DNA insertion, heterozygous for the T-DNA insertion, or homozygous for the T-DNA insertion.

Molecular Characterization of the T-DNA Lines

To determine the number of T-DNA inserts present in the lines, we compared the DNA gel blot hybridization patterns arising from sibling plants that were either homozygous for the T-DNA insertion or homozygous for no T-DNA. To remove additional T-DNA loci from the lines of interest, backcrosses to wild-type Col were performed and plants homozygous for the T-DNA insertion were again identified.

RNA Preparation and Microarray Hybridization

Surface-sterile seeds (1.8 mg) were germinated in 40 mL of liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16-h-light/8-h-dark cycle with gentle shaking (100 rpm). After a 7-d culture period, the seedlings were treated with 5 μM IAA (IAA treated) or ethanol (control) for 2 h. Total RNA was prepared using the RNAqueous RNA isolation kit with plant RNA isolation aid (Ambion). After LiCl precipitation, RNA was purified using RNeasy columns (Qiagen) and reprecipitated with LiCl. RNA pellets were washed with 70% ethanol (three times) and resuspended in diethyl pyrocarbonate–treated water. Five micrograms of total RNA was used for biotin-labeled cRNA probe synthesis. cRNA probe synthesis, hybridization, and washing and scanning and detection of array images were performed according to the manufacturer's protocols (Affymetrix). Twenty-four independent hybridization experiments (three independent biological replicates for eight different samples [two treatments × four genotypes]) were performed in this study.

Microarray Data Analysis

Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The cell intensity files (CEL files) were used for background correction and normalization using the log2 scale RMA procedure (Irizarry et al., 2003). The R environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2-converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal <5.64 (= log2 50) was considered as background; all signals <5.64 were converted to 5.64 prior to further analysis. The entire data set is provided in the supplemental data online and has been deposited in the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE629, GSM9595 to GSM9603, and GSM9605 to GSM9619.

We used an M-A plot (Dudiot et al., 2002) to display the data in Figure 6, where M = log2 I/C, where I = mean expression level for a gene in auxin-treated samples and C = mean expression level for the same gene in the control samples and A = log2 √(I*C).

To extract the genes differentially expressed between two treatments (auxin-treated/control) or two genotypes (iaa17-6/wild type, axr3-1/wild type, or iaa5-1 iaa6-1 iaa19-1/wild type), the expression values for each gene were averaged within each treatment/genotype. Then the fold change and the standard two-sample t statistic (Dudiot et al., 2002) were computed. A gene was considered differentially expressed if it was at least twofold upregulated or downregulated and the P value for its t statistic was <0.001. This strict criteria limits the type I family-wise error rate and allowed us to consider genes that demonstrated highly reliable auxin-mediated modulation. For comparative analysis, Venn diagrams were drawn using GeneSpring software package version 5.1 (Silicon Genetics). The entire data set is provided in the supplemental data online.

Accession Numbers

Sequence data from this article can be found in the GenBank/EMBL data libraries under the following accession numbers: AY669797 (At1g51950, IAA18), AY669798 (At3g15540, IAA19), AY669799 (At5g25890, IAA28), AY669800 (At4g32280, IAA29), AY669801 (At3g62100, IAA30), AY669802 (At3g17600, IAA31), AY669803 (At2g01200, IAA32), and AY669804 (At5g57420, IAA33). The microarray data have been deposited in the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE629, GSM9595 to GSM9603, and GSM9605 to GSM9619.

Supplemental Data

The following materials are available in the online version of this article.

  • Supplemental Table 1. Predicted Molecular Mass, Number of Amino Acids, and Isoelectric Points of the IAA Gene Family Members.

  • Supplemental Table 2. Amino Acid Sequence Comparison of the Arabidopsis IAA Proteins.

  • Supplemental Table 3. Summary of aux/iaa T-DNA Insertion Mutants Isolated in This Study.

  • Supplemental Table 4. List of Auxin-Induced Genes.

  • Supplemental Table 5. List of Auxin-Repressed Genes.

  • Supplemental Table 6. List of Genes with Reduced Induction in the axr3-1/iaa17-1 Mutant (among Auxin-Induced Genes).

  • Supplemental Table 7. List of Genes with Reduced Repression in the axr3-1/iaa17-1 Mutant (among Auxin-Repressed Genes).

  • Supplemental Table 8. List of Genes Repressed in the axr3-1/iaa17-1 Mutant.

  • Supplemental Table 9. List of Genes Induced in the axr3-1/iaa17-1 Mutant.

  • Supplemental Figure 1. Expression Characteristics of Several Aux/IAA Genes in Wild-Type, iaa17-6, axr3-1 iaa17-1, and iaa5-1 iaa6-1 iaa19-1 Seedlings.

  • Supplemental Figure 2. Expression of Peroxidase Genes in Wild-Type, iaa17-6, axr3-1 iaa17-1, and iaa5-1 iaa6-1 iaa19-1 Seedlings.

Acknowledgments

We thank T. Speed (University of California, Berkeley, CA) and J. Armstrong (Mendel Corp., Haywood, CA) for helpful discussions regarding microarray data analysis. We also thank D. Hantz for greenhouse work. This research was supported by National Institutes of Health Grant GM035447 to A.T.

Footnotes

  • The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Athanasios Theologis (theo{at}nature.berkeley.edu).

  • Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.105.036723.

  • ↵ [W] Online version contains Web-only data.

  • ↵1 These authors contributed equally to this work.

  • ↵2 Current address: Macalester College, St. Paul, MN 55105.

  • ↵3 Current address: Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0101, Japan.

  • ↵4 Current address: Department of Genetics, North Carolina State University, Raleigh, NC 27695.

  • Received August 3, 2005.
  • Revised September 26, 2005.
  • Accepted October 13, 2005.
  • Published November 11, 2005.

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Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana
Paul J. Overvoorde, Yoko Okushima, José M. Alonso, April Chan, Charlie Chang, Joseph R. Ecker, Beth Hughes, Amy Liu, Courtney Onodera, Hong Quach, Alison Smith, Guixia Yu, Athanasios Theologis
The Plant Cell Dec 2005, 17 (12) 3282-3300; DOI: 10.1105/tpc.105.036723
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