engleski

Bioinformatics analyses of IDL regions of eubacterial SSB proteins

Background: SSB (single-stranded DNA binding) proteins are indispensable for the cell survival in all kingdoms of life. These proteins have role in single-stranded DNA (ssDNA) protection during processes of DNA recombination, replication and repair. The eubacterial SSB proteins act as a homotetramers and display two distinct domains: N-terminal domain with a conserved oligonucleotide-oligosaccharide fold (OB-fold) responsible for ssDNA binding, and C-terminal domain (Ct). Ct-domain is intrinsically disordered (IDL) and play important role in mediating SSB-protein interactions. PXXP and GGX motives were found to be conserved within IDL regions of SSB proteins and possibly play role in its funcionality. Objectives: We have noticed that high GC actinobacterial SSB proteins have high glycine ratio in IDL regions and decided to investigate how composition of aminoacids varies in SSB protein OB fold and IDL region with an increase in GC content. Furthermore, we will inspect the conservation of PXXP and GGX elements in SSB proteins with respect to GC content. Methods: SSB sequences were collected from genomes covering a wide range of GC content from 14 bacterial phyla. The ML trees were constructed for SSB sequences and corresponding 16S rRNA genes. The aa content of OB folds and IDL regions were subsequently analysed. Variability and presence of PXXP and GGX motives within IDLs will be observed. Results: SSB protein sequence analysis suggested a correlation between aa composition and GC content. We will show how two distinct domains of SSB exhibit significant difference to the expected aa composition. In line with this, we will discuss the conservation of PXXP and GGX motives in SSBs with the respect to GC content.

SSB ; Streptomycetes ; IDL

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