Identification, cloning and characterization of sis7 and sis10 sugar-insensitive mutants of Arabidopsis

Abstract

Background: The levels of soluble sugars, such as glucose and sucrose, help regulate many plant metabolic, physiological and developmental processes. Genetic screens are helping identify some of the loci involved in plant sugar response and reveal extensive cross-talk between sugar and phytohormone response pathways.

Results: A forward genetic screen was performed to identify mutants with increased resistance to the inhibitory effects of high levels of exogenous sugars on early Arabidopsis seedling development. The positional cloning and characterization of two of these sugar insensitive (sis) mutants, both of which are also involved in abscisic acid (ABA) biosynthesis or response, are reported. Plants carrying mutations in SIS7/NCED3/STO1 or SIS10/ABI3 are resistant to the inhibitory effects of high levels of exogenous Glc and Suc. Quantitative RT-PCR analyses indicate transcriptional upregulation of ABA biosynthesis genes by high concentrations of Glc in wild-type germinating seeds. Gene expression profiling revealed that a significant number of genes that are expressed at lower levels in germinating sis7-1/nced3-4/sto1-4 seeds than in wild-type seeds are implicated in auxin biosynthesis or transport, suggesting cross-talk between ABA and auxin response pathways. The degree of sugar insensitivity of different sis10/abi3 mutant seedlings shows a strong positive correlation with their level of ABA insensitivity during seed germination.

Conclusion: Mutations in the SIS7/NCED3/STO1 gene, which is primarily required for ABA biosynthesis under drought conditions, confer a sugar-insensitive phenotype, indicating that a constitutive role in ABA biosynthesis is not necessary to confer sugar insensitivity. Findings presented here clearly demonstrate that mutations in ABI3 can confer a sugar-insensitive phenotype and help explain previous, mixed reports on this topic by showing that ABA and sugar insensitivity exhibit a strong positive correlation in different abi3 mutants. Expression profiling revealed a potentially novel regulation of auxin metabolism and transport in an ABA deficient mutant, sis7-1/nced3-4/sto1-4.

Figure 1

Mutations in SIS7 confer a sugar-insensitive phenotype. Col wild-type and sis7 seeds were stratified for 3 d and then sown on the indicated media and scored after 14 d at 22°C under continuous light. Data represent the means of three independent assays. The error bars indicate standard deviations. Asterisks indicate results where the mutant phenotype differed from the corresponding wild-type phenotype with a p-value of less than 0.05 according to a Student's t-test.

Figure 2

The sis7-1/sto1-4/nced3-4 mutation confers a subtle ABA-insensitive phenotype. Col wild-type and sis7-1/sto1-4/nced3-4 seeds were stratified for 3 d and then sown on media containing 1, 2 or 5 μM ABA and incubated at 25°C under continuous light conditions. Germination rates on minimal media were also checked and found to be consistently high, indicating a high rate of viability in the seeds used for these experiments (data not shown). Seed germination was scored at the indicated time points. Germination is defined as the emergence of the radicle from the seed coat. Data represent the means of three independent assays. The error bars represent standard deviations. The abi4-103/sis5-3 [16] seeds were included as a positive control.

Figure 3

The sis7-1/sto1-4/nced3-4 mutation confers a paclobutrazol-resistant phenotype. Col wild-type and sis7-1/sto1-4/nced3-4 seeds were stratified for 3 d and then sown on media containing 30, 60 or 240 μM paclobutrazol and incubated at 25°C under continuous light conditions. Germination rates on minimal media were also checked and found to be consistently high, indicating a high rate of viability in the seeds used for these experiments (data not shown). Seed germination was scored at the indicated time points. Germination is defined as the emergence of the radicle from the seed coat. Data represent the means of three independent assays. The error bars represent standard deviations. The spy-3 [36] seeds were included as a positive control.

Figure 4

Characterization of sis7 molecular lesions. (A) Mutations in SIS7/NCED3/STO1. The molecular lesions associated with the three sis7/nced3/sto1 mutants identified as part of this work are shown. Nucleotides are numbered with respect to the start codon. (B) SIS7 transcript levels in wild-type and sis7 plants. RT-PCR was used to amplify SIS7/NCED3/STO1 transcripts from 4-week old wild-type (Col) and sis7 mutant plants. 2 μL cDNA was used as a template for the first PCR reaction (35 cycles). ACTIN transcripts were amplified as a positive control.

Figure 5

Exogenous ABA causes sis7 mutants to exhibit approximately wild-type sugar sensitivity. Wild-type (Col) and mutant seeds were cold treated for 3 d and then sown on minimal media supplemented with 220 mM Glc, with or without 0.1 μM ABA. Additional mutants deficient in ABA biosynthesis (aba2-3) or ABA response (abi4-103) were included as controls. Percent seed germination, cotyledon expansion and true leaf formation were scored after an additional 14 d incubation under continuous light at 22°C. Data represent the means of three independent assays. The error bars represent standard deviations. Asterisks indicate results where the phenotype of one of the mutants differed from that of the wild type with a p-value of less than 0.05 according to a Student's t-test.

Figure 6

Quantitative RT-PCR analysis of ABA biosynthesis genes in sis7 and wild-type germinating seeds. Relative expression levels were measured by qRT-PCR in Col, sis7-1 and sis7-3 germinating seeds treated with 300 mM Glc or 300 mM sorbitol. Data were obtained from two biologically independent experiments and relative mRNA levels were determined by using UBQ6 as a reference. The relative mRNA level of each gene in sorbitol-treated Col was set to 100. Bars indicate standard deviations.

Figure 7

Functional categorization of genes mis-regulated in sis7-1 on 100 mM Glc. Affymetrix ATH1 GeneChips were used for transcriptional profiling of germinating sis7-1/nced3-4/sto1-4 and wild-type seeds. Col wild-type and sis7-1/nced3-4/sto1-4 seeds were sown on minimal media for 20 h and transferred to 100 mM Glc media for 13 h under continuous light. The Expressionist software package was used to identify genes with transcript levels that differ by at least two fold and with a p value of less than 0.05 when comparing the results of mutant versus wild-type samples. Using these cutoffs, the levels of 83 transcripts were found to be altered in sis7-1/nced3-4/sto1-4 versus wild-type seeds (Table 1). Functional categorization of these mis-regulated genes was performed using the GO (Gene Ontology) Annotations tool from TAIR [39]. Panel A shows the distribution of annotations for molecular function and panel B shows the distribution for annotations for biological process. Percentages were calculated as: (number of annotations to terms in this GOslim category/number of total annotations to terms in this ontology) × 100.

Figure 8

Quantitative RT-PCR analysis of auxin-related genes. Genes involved in auxin metabolism or transport were chosen for analysis. Relative expression levels of these genes were measured by qRT-PCR in wild-type Col, sis7-1 and sis7-3 germinating seeds treated with 100 mM Glc or 100 mM sorbitol. Data were obtained from two biologically independent experiments and relative mRNA levels were determined by using UBQ6 as a reference. The relative mRNA level of each gene in sorbitol-treated wild-type Col was set to 100. Bars indicate standard deviations.

Figure 9

sis7-1 exhibits increased root system size on sorbitol media. Wild-type Col and sis7-1 seedlings were grown for 12 d on vertically-oriented Petri plates containing the indicated media. Root systems of sis7-1 are less repressed by osmotica than are the root systems of wild-type seedlings.

Figure 10

Molecular lesions present in different abi3 mutants. Nucleotides are numbered with respect to the start codon. Exons are depicted with boxes and introns are depicted with single lines.

Figure 11

Suc-response assays of three abi3 mutants. Seeds were sown on media containing 300 mM Suc and incubated at 22°C for 14 d under 2200-3400 Lux continuous light prior to scoring. Seed germination, cotyledon expansion and true leaf formation were scored as previously described [16]. Error bars indicate standard deviations. Asterisks indicate results where the mutant phenotype differed from the corresponding wild-type phenotype with a p-value of less than 0.05 according to a Student's t-test.

Figure 12

Quantification of Suc and ABA insensitivity in nine abi3 mutants. (A) For Suc-response assays seeds were sown on media containing 270 or 320 mM Suc and incubated at 22°C for 14 d under 2200-3400 Lux continuous light prior to scoring. Seed germination, cotyledon expansion and true leaf formation were scored as previously described [16]. Error bars indicate standard deviations. Asterisks indicate results where the mutant phenotype differed from the corresponding wild-type phenotype with a p-value of less than 0.05 according to a Student's t-test. (B) For ABA response assays seeds were imbibed on media with the indicated ABA concentrations and scored for germination after 24, 48, 82 and 106 h. Seed germination is defined as the emergence of the radicle from the seed coat. Error bars indicate standard deviations. Asterisks indicate results where the mutant phenotype differed from the corresponding wild-type phenotype with a p-value of less than 0.05 according to a Student's t-test. (C) Regression analysis of data on Suc and ABA response assays reveals strong positive correlation between sugar- and ABA- insensitivity. Each data point on the scatterplot represents the percentage of normal shoot development (defined as seedlings with green expanded cotyledons) on Suc media and the percentage of seeds that germinated after 106 h on ABA media for each genotype. Correlation coefficients were calculated for two assay conditions: 1 μM ABA and 270 mM Suc representing relatively non-stringent assay conditions and 2 μM ABA and 320 mM Suc representing more stringent assay conditions.