In-silico Characterization of Flower Development Associated Mikc Type Mads Box Gene in Petunia (Petunia Hybrida)

Abstract

Petunia (Petunia hybrida) is an ornamental plant belongs to the Solanaceae family which includes other well known species such as Solanum tuberosum, Lycopersicon esculentum, Capsicum annuum and Nicotiana tabacum. Transcription factors are proteins involved in the process of converting or transcribing, DNA into RNA. MADS-box have ~60 Amino acid DNA binding domain and classified as TFs family known to plays significant role during the development of floral organs in plants. The name MADS-Box was proposed by Schwarz-Sommer and colleagues and derives from the initials of the first four cloned genes MCM1 in yeast, AGAMOUS in Arabidopsis, DEFICIENS in snapdragon, and SERUM RESPONSE FACTOR in human. The MADS-box gene family characterized by a conserved ~58 Amino acid domain, can be divided into two lineages, type I and type II. Plant type I MADS-domain genes can be further subdivided into three groups: (Mα, Mβ and Mγ) based solely on phylogenetic criteria while, in the case of Type II genes, MIKCC and MIKC*group genes are distinguished by different lengths of their encoded K-domains and also on phylogenetic criteria. Here, we performed in-silico characterization of MIKC Type MADS Box PhFBP26 and PhFBPP29 genes based on MSA, Phylogeny, Exon/intron structure, Conserved Motifs and Protein structure using in silico approach. Multiple sequence alignment analysis of PhFBP26 and PhFBP29 proteins indicated that both genes shared highly conserved signature domain of their family MADS-box and K-box domain. Furthermore, phylogeny analysis helped to find the evolutionary related genes in Arabidopsis, Potato, Tobacco, and Tomato, revealed that both PhFBP26 and PhFBP29 genes are close to AtAGL8 and their homolog in other analysed plant species. Gene structure analysis of PhFBP26 and PhFBP29 from CDS and genomic region revealed the presence of large Intron and small exon region. The protein motifs prediction analysis by MEME-Suite confirmed the presence of conserved MADS box family signature domain along with other protein motifs. The 3-D proteins structure modeling of petunia hybrida (PhFBP26 and PhFBP29) MADS box proteins were computed by PHYRE2 showed α-helix region 57% and 51% respectively and both α-helix and β-sheet of proteins. The computational analysis of PhFBP26 and PhFBP29 proteins modelled structure revealed the high conservance, good alignment with other reported template, low to average mutational sensitivity, good order of folding and significant protein pocket in active site.