Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools

Abstract

We have identified four novel repeats and two domains in cell surface proteins encoded by the Methanosarcina acetivorans genome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conserved sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat; (b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa residue LGFP repeat. The domains correspond to a certain number of aa residues in a protein sequence that do not comprise internal repeats. These correspond to: (a) a 200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss the occurrence of these repeats and domains in the different proteins and genomes analysed in this work.

Ideally glassy hydrogen-bonded networks

“…In fact, computer searches of genomes of the cell surface proteins of archaea and bacteria have identified many tandem repeats, including one in a single-stranded DNA-binding protein domain that was presumably present in the common ancestor to all three major branches of life, archaea, eukarya, and bacteria [34], with at least four tandem repeats (~ 100 amino acids). Several longer repeats (up to seven) have recently been found [35]. The adaptability of tandem repeats supports cooperative folding in multi-domain proteins [36] and favors evolutionary "agility" [37,38].…”

Cell surface proteins in archaeal and bacterial genomes comprising “LVIVD”, “RIVW” and “LGxL” tandem sequence repeats are predicted to fold as β-propeller

“…The identification of novel amino acid sequence repeats in cell surface proteins of M. acetivorans genome was performed using the RADAR program [33] and the detailed methodology is discussed elsewhere [9]. In the initial dataset, 45 proteins comprised LGxL repeats, 46 proteins comprised LVIVD repeats, and 54 proteins comprised RIVW repeats.…”

“…In our previous work [9], we identified four novel tandem repeats; LVIVD, RIVW, LGxL, LGFP and two new domains; DNRLRE and PEGA (represented as per their PROSITE pattern) in cell surface proteins of Methanosarcina acetivorans genome. These repeats and domains were also observed in other bacterial and archaeal genomes and they do not share significant similarity to proteins of known three-dimensional (3D) structure.…”

Genome Sequence and Characterization of the Tsukamurella Bacteriophage TPA2

“…The C terminus of the putative endolysin contains three conserved 54-amino-acid repeat sequences with identity to a repeat structure seen in the Corynebacterium glutamicum and Corynebacterium efficiens genomes. These repeats belong to the pfam08310 family and are hypothesized to anchor proteins into the bacterial cell wall (3).…”