title: Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.
abstract: Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival.
authors.affiliation: Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Subramanian
authors.affiliation: Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India. Electronic address: rr.sarkar@ncl.res.in.
authors.forename: Ram Rup
authors.initials: RR
authors.lastname: Sarkar
mesh_terms: D000595:Amino Acid Sequence; D001482:Base Composition; D003062:Codon; D019143:Evolution, Molecular; D007891:Leishmania / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D009690:Nucleic Acid Conformation; D015800:Protozoan Proteins / Q000032:analysis*; D012333:RNA, Messenger / Q000737:chemistry*; D016053:RNA, Protozoan / Q000737:chemistry*; D013045:Species Specificity; D014351:Trypanosomatina / Q000235:genetics* / Q000378:metabolism
chemical_list: D003062:Codon; D015800:Protozoan Proteins; D012333:RNA, Messenger; D016053:RNA, Protozoan
keywords: Amino acid bias; Base composition; Codon usage bias; Leishmania; Mutation; Selection bias; Species specificity