Evidence for directed evolution of larger size motif in Arabidopsis thaliana genome.
Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome.
Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India. rajmeh25@hotmail.com
Rajesh
R
Mehrotra
Amit
A
Yadav
Purva
P
Bhalothia
Ratna
R
Karan
Sandhya
S
Mehrotra
D000040:Abscisic Acid / Q000737:chemistry; D000465:Algorithms; D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D004268:DNA-Binding Proteins / Q000235:genetics; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D008027:Light; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D020156:Salicylic Acid / Q000737:chemistry
D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D000040:Abscisic Acid; D020156:Salicylic Acid