Abstract
The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.
Highlights
Transcription factors (TFs) are DNA-binding proteins that regulate gene expression at the level of mRNA transcription
Using the available data regarding correlations between different Arabidopsis genes, we constructed a network composed of the SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) genes and their co-expressed genes
The SPL gene family belongs to a group of plant-specific zinc finger protein genes that encodes plant-specific transcription factors
Summary
Transcription factors (TFs) are DNA-binding proteins that regulate gene expression at the level of mRNA transcription. As in all living organisms, transcription factors are an important level of gene regulation. Many families of transcription factors have been identified in plants. Analysis of the Arabidopsis genome reveals 29 classes of transcription factors, 16 of which appear to be unique to plants [1]. One of these contains a DNA binding domain referred to as the SQUAMOSA PROMOTER. BINDING PROTEIN (SBP) domain and is encoded by the SBP-box, a feature characteristic of the Arabidopsis SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family [2, 3]. The first SBP-domain proteins, which were isolated from snapdragon [4], showed in vitro binding to a sequence motif in the promoter region of the floral meristem identity gene SQUAMOSA [5]
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