Dataset Information

The Arabidopsis MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of E2Fa.

ABSTRACT: Seed size is the result of complex molecular networks controlling the development of the seed coat (of maternal origin) and the two fertilization products, the embryo and the endosperm. In this study we characterized the role of Arabidopsis thaliana MADS-domain transcription factor SEEDSTICK (STK) in seed size control. STK is known to regulate the differentiation of the seed coat as well as the structural and mechanical properties of cell walls in developing seeds. In particular, we further characterized stk mutant seeds. Genetic evidence (reciprocal crosses) of the inheritance of the small-seed phenotype, together with the provided analysis of cell division activity (flow cytometry), demonstrate that STK acts in the earlier phases of seed development as a maternal activator of growth. Moreover, we describe a molecular mechanism underlying this activity by reporting how STK positively regulates cell cycle progression via directly activating the expression of E2Fa, a key regulator of the cell cycle. Altogether, our results unveil a new genetic network active in the maternal control of seed size in Arabidopsis.

SUBMITTER: Paolo D

PROVIDER: S-EPMC7909557 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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The Arabidopsis MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of E2Fa.

Paolo Dario D Rotasperti Lisa L Schnittger Arp A Masiero Simona S Colombo Lucia L Mizzotti Chiara C

Plants (Basel, Switzerland) 20210120 2

Seed size is the result of complex molecular networks controlling the development of the seed coat (of maternal origin) and the two fertilization products, the embryo and the endosperm. In this study we characterized the role of Arabidopsis thaliana MADS-domain transcription factor SEEDSTICK (STK) in seed size control. STK is known to regulate the differentiation of the seed coat as well as the structural and mechanical properties of cell walls in developing seeds. In particular, we furth ...[more]

PMID: 33498552

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Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from the SEEDSTICK mutant in Arabidopsis with a wild type, to unveil the role of this transcription factor in seed development and decipher the impact of this factor in PAs metabolism Methods: Total RNA was extracted from two biological replicates from both wild-type and stk mutant inflorescences and siliques until 5 DAP with the Qiagen Kit according to the manufacturer's instructions. DNA contaminations were removed using the PROMEGA RQ1 RNase-Free DNase according to the manufacturer's instructions. RNA quality integrity was analyzed by electrophoresis gel and was validated on a Bioanalyzer 2100 (Aligent, Santa Clara, CA); RNA Integrity Number (RIN) values were greater than 7 for all the samples. In order to confirm that in stk mutant samples STK was not expressed, STK expression was checked by real time PCR with primer RT 780 (5’-TGCGATGCAGAAGTTGCGCTC-3’) and RT 781 (5’-AGTACGCGGCATTGATTTCTTG-3’). Sequencing libraries were prepared according to the manufacturer’s instructions by TruSeq RNA Sample Prep kit (Illumina Inc.) and sequenced on Illumina HiSeq2000 in one lane single-read 50bp. The processing of fluorescent images into sequences, base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8). Raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% bases with Q < 20. Finally, a quality control of the raw sequence data was performed using FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Results: A total of 102,278,242 reads passed a quality filter and 85% were mapped back to the Arabidopsis TAIR10 genome. Approximately 90% mapped uniquely to only one location and could be assigned to a single annotated TAIR10 gene. Normalization of expression values was performed using RPKM values. All other parameters were kept at default levels. The CLC Genomic Workbench was also further used to determine all differentially expressed transcripts found in each cDNA library. Baggerley's test and a FDR correction were used for statistical analysis of samples. Our analysis revealed that 156 genes were upregulated, whereas for 90 genes a reduction in their mRNA level was observed in the stk mutant when compared to wild-type . Data analysis revealed a significant enrichment for terms related to the phenylpropanoid metabolic process, flavonoid biosynthetic process as well as cellular amino acid derivative metabolic process. Conclusion: Our genome-wide transcriptomic analysis suggests that the ovule identity factor STK is involved in the regulation of several metabolic processes providing a strong connection between cell fate determination, development and metabolism. In particular we characterize, through phenotypic, genetic, biochemical and transcriptomic approaches, the role of STK in PAs biosynthesis. Our results indicate that STK exerts this role through the direct regulation of the gene encoding for BANYULS/ANTHOCYANIDIN REDUCTASE (BAN/ANR), which converts anthocyanidins into their corresponding 2,3-cis-flavan-3-ols. Our study also demonstrates that the levels of H3K9ac chromatin modification directly correlate with the active state of BAN in an STK-dependent way. This supports the theory that MADS-domain proteins control the expression of their target genes through the modification of the chromatin states. STK might recruit or negatively regulate histone modifying factors to control their activity. Moreover, we show that STK controls through a complex regulatory network not only directly BAN but also other regulators of this key gene in tannin production

Dataset Information

The Arabidopsis MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of E2Fa.

Publications

The <i>Arabidopsis</i> MADS-Domain Transcription Factor SEEDSTICK Controls Seed Size via Direct Activation of <i>E2Fa</i>.

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