Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing

Background: The phytohormone auxin is involved in a wide range of developmental processes and auxin signaling is known to modulate the expression of target genes via two types of transcriptional regulators, namely, Aux/IAA and Auxin Response Factors (ARF). ARFs play a major role in transcriptional activation or repression through direct binding to the promoter of auxin-responsive genes. The present study aims at gaining better insight on distinctive structural and functional features among ARF proteins. Results: Building on the most updated tomato (Solanum lycopersicon) reference genome sequence, a comprehensive set of ARF genes was identified, extending the total number of family members to 22. Upon correction of structural annotation inconsistencies, renaming the tomato ARF family members provided a consensus nomenclature for all ARF genes across plant species. In silico search predicted the presence of putative target site for small interfering RNAs within twelve Sl-ARFs while sequence analysis of the 59-leader sequences revealed the presence of potential small uORF regulatory elements. Functional characterization carried out by transactivation assay partitioned tomato ARFs into repressors and activators of auxin-dependent gene transcription. Expression studies identified tomato ARFs potentially involved in the fruit set process. Genome-wide expression profiling using RNA-seq revealed that at least one third of the gene family members display alternative splicing mode of regulation during the flower to fruit transition. Moreover, the regulation of several tomato ARF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signaling pathways of these two hormones. Conclusion: All together, the data bring new insight on the complexity of the expression control of Sl-ARF genes at the transcriptional and post-transcriptional levels supporting the hypothesis that these transcriptional mediators might represent one of the main components that enable auxin to regulate a wide range of physiological processes in a highly specific and coordinated manner

Induction of gibberellin 20-oxidases and repression of gibberellin 2β-oxidases in unfertilized ovaries of entire tomato mutant, leads to accumulation of active gibberellins and parthenocarpic fruit formation

In tomato (Solanum lycopersicum L.), auxin and gibberellins (GAs) cross-talk plays an important role during fruit-set. The entire tomato mutant has been previously reported to carry a deletion in the coding region of the SlIAA9 gene, a member of the auxin signal repressor family Aux/IAA. In this paper, we examined the role of ENTIRE gene in controlling GAs metabolism and directing spontaneous fruit initiation and early ovary growth. It was shown that, similarly to pollinated fruits, facultative parthenocarpy in entire depends on active GA metabolism, since fruit growth is suppressed when GA biosynthesis is blocked. Analysis of endogenous GAs during the first 10 days after flower emasculation revealed that entire fruits accumulated higher amounts of active GAs (GA1 and GA3) in comparison to wild type pollinated fruits, suggesting that a different GA homeostasis regulation occurs. Transcript analysis of the main GA biosynthesis genes showed that differently from unpollinated and non parthenocarpic wild type ovaries, in entire active GA flux modulation is regulated by the activation of SlGA20ox1 and SlGA20ox2 and also by a marked reduction of GA catabolism (reduced transcription of GA 2β-oxidase genes) during the early fruit expansion phase.Fil: Mignolli, Francesco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Vidoz, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias; ArgentinaFil: Mariotti, Lorenzo. Università degli Studi di Pisa; ItaliaFil: Lombardi, Lara. Università degli Studi di Pisa; ItaliaFil: Picciarelli, Piero. Università degli Studi di Pisa; Itali

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

Cell-type transcriptome profiling greatly elucidate organismal development. Here, the authors report a spatiotemporally resolved comprehensive transcriptome analysis of tomato fruit ontogeny and suggest a new model of fruit maturation which initiates in internal tissues then radiates outwards