Variations in amino acid composition in bacterial single stranded DNA–binding proteins correlate with GC content

Abstract

Background and purpose

SSB proteins are essential for the maintenance of the genome in all domains of life. Most bacterial SSBs are active as homotetramers. Each monomer comprises N-terminal domain (OB-fold) which is responsible for ssDNA binding and a disordered C-terminal domain (Ct) with a conserved acidic tail responsible for protein interactions.

The variations in these essential proteins prompted us to conduct in silico analyses of the aa composition and properties of two distinct SSB domains in relation to bacterial GC content.

Materials and methods

SSB sequences were collected from genomes covering a wide range of GC content from 14 bacterial phyla. The maximum-likelihood (ML) trees were constructed for SSB sequences and corresponding 16S rRNA genes. The aa contents of OB folds and Ct domains were subsequently analysed. 

Results

We showed that SSB proteins followed predicted amino acid (aa) composition as a function of genomic GC content. However, two distinct domains of SSB exhibit significant differences to the expected aa composition. Variations in aa proportion were more prominent in Ct domains. Elevated accumulation of Gly (up to 60 %) and Pro (up to 24 %), significant drop in the proportion of basic Lys and reduction in hydrophobic Leu, Ile and Val were identified in Ct domains of SSBs from high GC genomes. Consequently, this influences the biochemical properties of Ct domains.

Conclusions

Based on this comparative study of SSBs we conclude that genomic GC content and two distinct domains with different functional roles participate in shaping aa composition of SSB proteins.