Proteome analysis reveals the influence of isoelectric point and amino acid usages on the lifestyle of nitrogen fixing microorganisms

Abstract

Biological nitrogen fixation is an important phenomenon in the ecosystem of our planet. Increasing number of complete proteomes for nitrogen fixing organisms has given scope to recognize characteristic features of protein functionality linked to nitrogen fixation and nature of the proteome. Physico-chemical aspects like isoelectric point (pI), protein energetic cost, aromaticity, hydropathicity and amino-acid adaptation index are significant in portraying the functions of microbes. The present work aims to recognize diversity in amino-acid usage patterns to understand the forces influencing them and to investigate association of pI with lifestyle of the organisms shaping its role in manipulating diversity across proteomes. Combination of <i style="mso-bidi-font-style:normal">in silico</i> tools like DAMBE and CodonW were used for comparative analysis of properties and amino acid usage. Distributions of pI across different COGs (Cluster of orthologous groups) were compared. Proteomes of nitrogen fixing organisms show diversity at the interspecific and intraspecific level with tri-modal distribution for pI. Nitrogen fixation related proteins are more acidic in contrast to whole proteomes. Analysis of pI across COGs throws light upon the variation and lifestyle of organisms and substantiates the role of pI as a molecular signature. Proteomes show a shift towards acidity and are influenced by habitat and environmental adaptations. Acidic residues in COG functional groups belonging to cellular processes (Cp), metabolism (Me) and information storage and processing (Isp) play a significant role in shaping proteomes of nitrogen fixers. Methanogens and aquatic free living nitrogen fixing organisms are more acidic than others. Higher amino acid adaptation index (AAAI) values of proteomes imply their better adaptability in shaping frequency of amino acids. Hydropathicity and aromaticity are relevant for evaluating amino acid usage in these organisms.