Phylogenetic Approach for Inferring the Origin and Functional Evolution of Bacterial ADP-ribosylation Superfamily

Abstract

Bacterial ADP-ribosyltransferases (BADPRTs) are extensively contributed to determine the strain-specific virulence state and pathogenesis in human hosts. Understanding molecular evolution and functional diversity of the BADPRTs is an important standpoint to describe the fundamental behind in the vaccine designing for bacterial infections. In the present study, we have evaluated the origin and functional evolution of conserved domains within the BADPRTs by analyzing their sequence-function relationship. To represent the evolution history of BADPRTs, phylogenetic trees were constructed based on their protein sequence, structure and conserved domains using different evolutionary programs. Sequence divergence and genetic diversity were studied herein to deduce the functional evolution of conserved domains across the family and superfamily. The results of sequence similarity search have shown that three hypothetical proteins (above 90%) were identical to the members of BADPRTs and their functions were annotated by phylogenetic approach. Phylogenetic analysis of this study has revealed the family members of BADPRTs were phylogenetically related to one another, functionally diverged within the same family, and dispersed into closely related bacteria. The presence of core substitution pattern in the conserved domains would determine the family-specific function of BADPRTs. Functional diversity of the BADPRTs was exclusively distinguished by Darwinian positive selection (diphtheria toxin C and pertussis toxin S) and neutral selection (arginine ADP-ribosyltransferase, enterotoxin A and binary toxin A) acting on the existing domains. Many of the family members were sharing their sequence-specific features from members in the arginine ADP-ribosyltransferase family. Conservative functions of members in the BADPRTs have shown to be expanded only within closely related families, and retained as such in pathogenic bacteria by evolutionary process (domain duplication or recombination events). Hence, we conclude that evolutionary significance of the members in the BADPRTs would provide an insight for experimental set-up on site-directed mutagenesis and vaccine engineering.

Structural constraints-based evaluation of immunogenic avirulent toxins from Clostridium botulinum C2 and C3 toxins as subunit vaccines

“…Coevolution resulted from the first point mutation may sometimes bring instability in the amino acid network structure of C2 and C3 toxins (Chellapandi et al, 2013;Chellapandi, 2014;Prathiviraj et al, 2015). We found no structural fluctuations in R299K, R300K, E389Q of C2I, G305K, E399A of C2II and E156D, E156Q, Q211A of C3 upon point mutations.…”

“…Several evolutionary constraints observed to be acted on the structure-function link of bacterial ADP-ribosyltransferases, particularly C2 and C3 toxins (Chellapandi et al, 2013;Chellapandi, 2014;Prathiviraj et al, 2015). Our study intensively described various structural constraints in the experimental mutants showing avirulent potential on the targets.…”

“…Thus, site-directed mutagenesis experiments have been supported to define the functional roles of the critical residues in their structures and catalytic mechanisms. Evolutionary constraints in structure-function link were inferred to assess the avirulent states of some hypothetical proteins identical to this superfamily (Chellapandi et al, 2013;Chellapandi, 2014). An extensive study on structure-function integrity of mutant proteins is thus prerequisite determinants for the prioritization of immunotoxins.…”

<i>Mycobacterium bovis</i> BCG as a Delivery System for the <i>dtb</i> Gene Antigen from Diphtheria Toxin

“…DT is a polypeptide of 535 amino acids with a molecular weight of approximately 58.3 kDa, which is proteolytically cleaved after secretion into two fragments with distinct activities. The aminoterminal fragment A (DTA) is responsible for toxicity and the nontoxic carboxyl fragment (DTB) with 341 amino acids is responsible for adherence and internalization of the DT [8] [9].…”

Structure–function discrepancy inClostridium botulinumC3 toxin for its rational prioritization as a subunit vaccine

“…Evolutionary constraints imposing on sequence-structure-function relationship of its superfamily were studied to identify and evaluate the non-virulent mutants from the hypothetical proteins identical to ADP-ribosyltransferases (Chellapandi et al, 2013;Chellapandi, 2014). Amino acid exchange by point mutation and coevolution sites are the major constraints to decipher the structural and functional aspects of a protein family (Chakrabarti and Panchenko, 2010;Studer et al, 2013;Chellapandi, 2014).…”