SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing

The MADS Box Gene FBP2 Is Required for SEPALLATA Function in Petunia

The ABC model, which was accepted for almost a decade as a paradigm for flower development in angiosperms, has been subjected recently to a significant modification with the introduction of the new class of E-function genes. This function is required for the proper action of the B- and C-class homeotic proteins and is provided in Arabidopsis by the SEPALLATA1/2/3 MADS box transcription factors. A triple mutant in these partially redundant genes displays homeotic conversion of petals, stamens, and carpels into sepaloid organs and loss of determinacy in the center of the flower. A similar phenotype was obtained by cosuppression of the MADS box gene FBP2 in petunia. Here, we provide evidence that this phenotype is caused by the downregulation of both FBP2 and the paralog FBP5. Functional complementation of the sepallata mutant by FBP2 and our finding that the FBP2 protein forms multimeric complexes with other floral homeotic MADS box proteins indicate that FBP2 represents the same E function as SEP3 in Arabidopsis

Arabidopsis thaliana ambient temperature responsive lncRNAs

Background: Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. Results: Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis. Conclusion: A number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.</p

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genomewide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADSdomain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1–3) subclade. Furthermore, we demonstrate the potentia

Additional file 5: of Arabidopsis thaliana ambient temperature responsive lncRNAs

Figure S1. Temperature induced flowering for T-DNA insertion lines. Col-8 plants were used for comparison with AtLnc2 (A), AtLnc120 (B), and AtLnc1524 (D) T-DNA insertion lines, while wild-type and T-DNA carrying plants from segregating population were compared for AtLnc213 (C). The experiment was performed using four biological replicates with 13 plants per replicate for each genotype/condition. The T-DNA insertion did not affect temperature-induced flowering in any of these mutants since no significant difference was observed in the ratio of flowering time at the different temperatures between wild-type and mutant plants. (TIF 642 kb

Additional file 1: of Arabidopsis thaliana ambient temperature responsive lncRNAs

TableS1. LncRNAs annotation. List of lncRNAs retrieved in this study and corresponding identification in the Plant long non-coding RNA database (PlncDB) and Araport11. (XLSX 422 kb

Additional file 2: of Arabidopsis thaliana ambient temperature responsive lncRNAs

TableS2. List of lncRNAs located within a 5 kb region of a gene involved in flowering time regulation. (XLSX 15 kb

Additional file 8: of Arabidopsis thaliana ambient temperature responsive lncRNAs

Table S5. Arabidopsis thaliana genomic region with sequence homology to FLINC. (XLSX 11 kb

Additional file 6: of Arabidopsis thaliana ambient temperature responsive lncRNAs

Figure S2. A. FLINC location in the genome. B. FLINC expression in WT and flinc mutant plants. The graph shows the average of three biological replicates, each composed of a pool of 10 2 weeks-old plants. Plants were growing at 21 °C in long day conditions. Bars indicate SEM of the replicates. Plants with a T-DNA insertion in the lncRNA locus do not show detectable expression of the lncRNA transcript. C. At1g56233 expression in WT and flinc mutant plants. The graph shows the average of three biological replicates, each composed of a pool of 10 2 weeks-old plants. Plants were growing at 21 °C in long day conditions. Bars indicate SEM of the replicates. No significant difference in At1g56233 expression was observed in flinc, p-value equals 0.3439 according to the T-test. D. FLINC expression in WT and FLINC-OE plants. A pool of 10 2 weeks-old plants growing on selection medium at 21 °C in long day was used for the analysis. E. FLINC expression measured by qPCR in plants growing at 16 °C and 25 °C in long days. Expression is relative to the level at 16 °C. Bars indicate SEM of two biological replicates, each composed of a pool of seven plants. FLINC expression is significantly lower at 25 °C compared to 16 °C (p-value = 0.0467, Students’ t-test). F. FLINC expression during a 24 h time course in plants grown at 21 °C in long days. The graph shows the average of four biological replicates, each composed of a pool of 25 ten days-old plants. Plants were growing at 21 °C in long day conditions. Bars indicate SEM of the replicates. G. FLINC expression measured by qRT-PCR in different plant tissues. The graph shows the average of three biological replicates, each composed of a pool of 6 to 8 plants for all tissues, except for ‘siliques’ and ‘stems’, for which only two biological replicates were used. Bars indicate SEM between the replicates. Plants were growing at 21 °C in long day conditions. H. FLINC and AP1 expression measured by qPCR in rosettes during a development time course at 21 °C in long day conditions. The graph shows the average of three biological replicates, each composed of a pool of 6 to 8 plants. Bars indicate SEM between the replicates. (PDF 476 kb