title: Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.
abstract: Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.
authors: a Department of Biophysics Molecular Biology and Bioinformatics , University of Calcutta , Kolkata 700009 , India.|b Department of Biotechnology , The University of Burdwan , Golapbag, Burdwan 713104 , India.
authors: Sunil Kanti
authors: SK
authors: Mondal
authors: a Department of Biophysics Molecular Biology and Bioinformatics , University of Calcutta , Kolkata 700009 , India.
authors: Sudip
authors: S
authors: Kundu
authors: c Department of Statistics , The University of Burdwan , Golapbag, Burdwan 713104 , India.
authors: Rabindranath
authors: R
authors: Das
authors: d Department of Botany , The University of Burdwan , Golapbag, Burdwan 713104 , India.
authors: Sujit
authors: S
authors: Roy
mesh_terms: D000596:Amino Acids; D001419:Bacteria / Q000145:classification / Q000201:enzymology / Q000235:genetics; D001482:Base Composition; D003062:Codon; D019143:Evolution, Molecular; D015870:Gene Expression; D009591:Nitrogenase / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D000596:Amino Acids; D003062:Codon; D012336:RNA, Ribosomal, 16S; D009591:Nitrogenase
keywords: CAI; GC3%; nifD; nifH; nifK