Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria

DciA Helicase Operators Exhibit Diversity across Bacterial Phyla

Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli and Bacillus subtilis. In particular, most bacteria do not encode the helicase-loading proteins that are essential in E. coli and B. subtilis for DNA replication. Instead, most bacteria encode a DciA homolog that likely constitutes the predominant mechanism of helicase operation in bacteria. However, it is still unknown how DciA structure and function compare across diverse phyla that encode DciA proteins. In this study, we performed computational evolutionary analyses to uncover tremendous diversity among DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.

Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri

The intracellular bacterial pathogen Listeria monocytogenes can breach protective barriers in the pregnant host, allowing the colonization of the placenta in pregnant people and resulting in numerous adverse pregnancy outcomes. Previous studies aimed at delineating the mechanisms behind placental colonization of L. monocytogenes identified a key virulence factor, internalin P (InlP). The internalin family of proteins has been studied extensively due to their conservation in the genus Listeria and their contribution to virulence and pathogenicity in L. monocytogenes. Still, many questions remain regarding the evolution of internalins and their potential roles in non-pathogenic Listeria. Our work addresses this gap in knowledge by (1) identifying additional InlP homologs in Listeria, including L. ivanovii, L. seeligeri, L. innocua, and L. costaricensis, and (2) characterizing these homologs using computational evolutionary methods to compare their primary sequences, domain architectures, and structural models. Together, our findings contribute to the field by providing insights into the evolution of one key member of the internalin family, as well as serving as a catalyst for future studies of InlP and its role in Listeria pathogenesis.

Cross-database integration using evolution and machine learning to identify multiscale molecular building blocks for antibiotic resistance

MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny

Studying proteins through the lens of evolution can help identify conserved features and lineage-specific variants, and potentially, their functions. MolEvolvR ( is a web-app that enables researchers to run a …

Computational approaches to study molecular pathogenesis and intervention of infectious diseases

MolEvolvR: A webapp for characterizing proteins using molecular evolution and phylogeny

Studying how bacterial pathogenic proteins evolve can help identify lineage-specific and pathogen-specific signatures and variants, and consequently, their functions. We have developed a streamlined computational approach for characterizing the …

MolEvolvR: Web-app and R-package for characterizing proteins using molecular evolution and phylogeny

Molecular evolution and phylogeny can provide key insights into pathogenic protein families. Studying how these proteins evolve across bacterial lineages can help identify lineage-specific and pathogen-specific signatures and variants, and …

Using a computational molecular evolution and phylogeny to study pathogenic proteins

Background: Studying bacterial physiology, adaptation, and pathogenicity through the lens of evolution requires delineating the phylogenetic history of bacterial proteins and genomes. Moreover, delineating this history of proteins is best done at all …

S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens