In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn ( Zea mays L. )

Abstract

Carotenoids, a diverse group of colorful pigments, contribute to the development, light harvesting and photoprotection in plants as well as human health. Due to the interesting properties of carotenoids, enhanced carotenoid biosynthesis has been of ongoing interest. Recent advances in computational biology and bioinformatics make it more feasible to understand the transcriptional regulatory network underlying carotenoid biosynthesis.Studies on carotenoid biosynthesis in corn (Zea mays L.) have indicated the pivotal role of the phytoene synthase gene PSY1 (accession: GRMZM2G300348) in endosperm color and carotenoid accumulation in corn kernels.Computational approaches such as Genomatix, PlantPAN, PlantCARE, PlantTFDB and IGDE6 have been used for promoter prediction, regulatory features and transcription factor identification, as well as pairwise promoter comparisons. Four transcripts have been identified for the PSY1 gene. Based on Genomatix and PlantPAN, the promoter predicted for GRMZM2G300348_T01 was different from that predicted for the other three transcripts (GRMZM2G300348_T02, GRMZM2G300348_T03 and GRMZM2G300348_T04). The results indicated that the promoter of GRMZM2G300348_T01 has more diverse motifs involved in hormonal/environmental stress responses. The most significant result obtained from this study is the discovery of two transcription factors belonging to the HB family that are co-expressed with all four transcripts of PSY1 under environmental stresses. It is, therefore, likely that these transcription factors may act as critical regulators of PSY1 gene expression in corn. Identification of the proteins acting upstream of PSY1 within corn will shed light on the fine tuning of PSY1 expression regulation. Such an understanding would also contribute to metabolic engineering aimed at enhanced carotenoid biosynthesis.

Multi-species transcriptome analyses for the regulation of crocins biosynthesis in Crocus

“…Homeobox-protein 2 (HB-2) is a regulator that processes light signals from phytochromes to alter morphogenesis during shade avoidance responses, and its overexpression causes long hypocotyls and reduced leaf expansion, as observed in etiolated seedlings [69]. In maize, rice and Arabidopsis , this TF is co-expressed with PSY1 [70]. ICE1 encodes a MYC-type bHLH transcription factor directly implicated in the major cold acclimation pathway [71].…”

Maize leaves drought-responsive genes revealed by comparative transcriptome of two cultivars during the filling stage

“…Maize proteins encoded by AP2/ERF TFs can regulate a multitude of transcriptional programs to potentially participate in a variety of stress responses [33]. HB family also has abundant coding DEGs, which have been reported in the study of carotenoids, a diverse group of colorful pigments, contribute to the development in plants [34]. The gene of MYB family in wheat overexpression experiment has shown that it positively regulates plant response to drought stress [35].…”