SUMMARYThe transcription factor ABA INSENSITIVE 4 (ABI4), discovered nearly 10 years ago, plays a central role in a variety of functions in plants, including sugar responses. However, not until very recently has its mechanism of action begun to be elucidated. Modulating gene expression is one of the primary mechanisms of sugar regulation in plants. Nevertheless, the transcription factors involved in regulating sugar responses and their role(s) during the signal transduction cascade remain poorly defined. In this paper we analyzed the participation of ABI4, as it is one of the main transcription factors implicated in glucose signaling during early seedling development. Our studies show that ABI4 is an essential activator of its own expression during development, in ABA signaling and in sugar responses. It is also important for the glucose-mediated expression of the genes ABI5 and SBE2.2. We demonstrate that ABI4 binds directly to the promoter region of all three genes and activates their expression in vivo through at CE1-like element. Previous studies found that ABI4 also functions as a transcriptional repressor of sugar-regulated genes, therefore this transcription factor is a versatile protein with dual functions for modulating gene expression.

Mutant characterization has demonstrated that ABI4 (Abscisic Acid [ABA] Insensitive 4), ABI5 (ABA Insensitive 5), and CTR1 (Constitutive Triple Response 1) genes play an important role in the sugar signaling response in plants. The present study shows that the transcripts of these three genes are modulated by glucose (Glc) independently of the developmental arrest caused by high Glc concentrations. ABI4 and ABI5 transcripts accumulate in response to sugars, whereas the CTR1 transcript is transiently reduced followed by a rapid recovery. The results of our kinetic studies on gene expression indicate that ABI4, ABI5, and CTR1 are regulated by multiple signals including Glc, osmotic stress, and ABA. However, the differential expression profiles caused by these treatments suggest that distinct signaling pathways are used for each signal. ABI4 and ABI5 response to the Glc analog 2-deoxy-Glc supports this conclusion. Glc regulation of ABI4 and CTR1 transcripts is dependent on the developmental stage. Finally, the Glc-mediated regulation of ABI4 and ABI5 is affected in mutants displaying Glc-insensitive phenotypes such as gins, abas, abi4, abi5, and ctr1 but not in abi1-1, abi2-1, and abi3-1, which do not show a Glc-insensitive phenotype. The capacity of transcription factors, like the ones analyzed in this work, to be regulated by a variety of signals might contribute to the ability of plants to respond in a flexible and integral way to continuous changes in the internal and external environment.

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BackgroundThe molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized.ResultsTo identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription.ConclusionsOur results demonstrate the feasibility of assigning molecular function to proteins of unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3853-9) contains supplementary material, which is available to authorized users.