Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects

• Published in: Mitochondrial DNA. Part A. DNA mapping, sequencing, and analysis Vol. 29; no. 2; pp. 236 - 249
• Main Authors: Seddigh, Samin, Darabi, Maryam
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 17.02.2018
• Subjects: Bioinformatics; cytochrome b; hydropathy; tertiary structure; hydropathy; tertiary structure; Bioinformatics; cytochrome b
• ISSN: 2470-1394; 2470-1408
• DOI: 10.1080/24701394.2016.1275596

Cytochrome b (Cytb, EC 1.10. 2.2) is the only cytochrome coded by mitochondrial DNA and involved in electron transport in the mitochondrial respiratory chain. In this study, characterization of cytb protein was identified on fifty-four insect protein sequences, from different orders. According to the conserved motifs obtained with MEME and MAST tools, eight motifs were common to all insects. The structural and functional analyses of 16 selected insects from different orders were performed with ProtParam, Compute PI, SOPMA, SignalP 4.1, TMHMM 2.0, ProtScale and ProDom tools in the ExPASy database and DNASTAR 12.1 software. The tertiary structure of Drosophila melanogaster as a sample of insects was predicted by the Phyre2 and TM-score servers and their similarities were verified by SuperPose servers. The tertiary structures were predicted using the 'd1ppjc2' model (PDB accession code: 1ppj C). A phylogenetic tree was constructed with MEGA 6.06 software using the neighbour-joining method. According to the results, there is a high identity of cytb in different insects so that they should be derived from a common ancestor. In protein-protein interaction analysis with STRING 10.0, twenty-three enriched pathways of KEGG were identified in D. melanogaster and other species. The obtained data provided a background for bioinformatic studies of the function and evolution of other insects and organisms.