In silico identification of cis-regulatory elements in folate biosynthesis and 1C metabolism genes in plants

Abstract

Folates (vitamin B9) are enzyme cofactors required for all organisms for one-carbon (1C) transfer reactions. A deficiency of these nutrients can lead to several health problems. Since humans are not natural producers of folates, the intake of these nutrients from plants is vital for human nutrition. Several techniques that involve the genetic modification of organisms have proved to be effective for the fortify plants with essential macronutrients. However, to achieve this, it is necessary to elucidate the metabolic control in plant systems. Although the genes involved in folate biosynthesis and 1C metabolism in plants are known, the mechanisms of transcriptional regulation have not yet been explored. This project focuses on discovering cis-regulatory DNA elements (motifs) using computational data analysis to provide insights regarding the regulation of folate biosynthesis in plants. For this, we first collected a compendium of known genes related to folate biosynthesis. Then, a database comprising the DNA promoter regions of folate biosynthesis and 1C metabolism genes in 19 different plant species was built and analyzed using different motif discovery algorithms. Afterward, the discovered motifs were tested for statistical significance and further associated with their putative biological role using other bioinformatics tools. A total of 149 statistically significant motifs (p < .05) were discovered in 18 of 19 species using the GimmeMotifs ensemble algorithm. These motifs were represented in 104 different regulatory networks built automatically from co-expression clusters obtained from each plant species. The results from this work could provide an insight into the transcriptional regulation of the folate biosynthesis pathway in plants. Furthermore, the elements found could be used for research in gene editing techniques to produce biofortified crops.