Biology subjects

Burke, J. T.

Publications and source records attributed to Burke, J. T..

3 recordsLinked to original sources

bioRxiv2022

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

Studying proteins through the lens of evolution can reveal features such as conserved domains, lineage-specific variants, and co-occurring domain architectures in phylogenetic context across all superkingdoms. MolEvolvR enables researchers to conduct such evolution-focused studies to generate testable hypotheses about protein function and evolution. MolEvolvR is a novel web-app allowing researchers to visualize the molecular evolution of their proteins of interest in a phylogenetic context across the tree of life. It accepts multiple input formats - protein/domain sequences, homologous proteins, or domain scans - and, using a general-purpose computational workflow, returns detailed homolog data and dynamic graphical summaries (e.g., phylogenetic trees, multiple sequence alignments, domain architectures, domain proximity networks, phyletic spreads, co-occurrence patterns across lineages). MolEvolvR performs domain-centric searches to capture remote homologs that are missed by full-length searches, integrates domain architecture evolution with phyletic distribution analyses, and provides evolutionary context visualizations that reveal lineage-specific adaptations versus those that are broadly conserved. Thus, MolEvolvR is a powerful, easy-to-use web interface for computational protein characterization. The web-app can be accessed here: https://jravilab.org/molevolvr.

genomics↗

bioRxiv2022

DciA helicase operators exhibit diversity across bacterial phyla

A fundamental requirement for life is the replication of an organisms DNA. Studies in Escherichia coli and Bacillus subtilis have set the paradigm for DNA replication in bacteria. During replication initiation in E. coli and B. subtilis, the replicative helicase is loaded onto the DNA at the origin of replication by an ATPase helicase loader. However, most bacteria do not encode homologs to the helicase loaders in E. coli and B. subtilis. Recent work has identified the DciA protein as a predicted helicase operator that may perform a function analogous to the helicase loaders in E. coli and B. subtilis. DciA proteins, which are defined by the presence of a DUF721 domain (termed the DciA domain herein), are conserved in most bacteria but have only been studied in mycobacteria and {gamma}-proteobacteria (Pseudomonas aeruginosa and Vibrio cholerae). Sequences outside of the DciA domain in Mycobacterium tuberculosis DciA are essential for protein function but are not conserved in the P. aeruginosa and V. cholerae homologs, raising questions regarding the conservation and evolution of DciA proteins across bacterial phyla. To comprehensively define the DciA protein family, we took a computational evolutionary approach and analyzed domain architectures and sequence properties of DciA-domain containing proteins across the tree of life. These analyses identified lineage-specific domain architectures amongst DciA homologs as well as broadly conserved sequence-structural motifs. The diversity of DciA proteins represents the evolution of helicase operation in bacterial DNA replication and highlights the need for phylum-specific analyses of this fundamental biological process. IMPORTANCEDespite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside of 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 perform computational evolutionary analyses to uncover tremendous diversity amongst DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.

microbiology↗

bioRxiv2022

Novel Internalin P homologs in Listeria

Listeria monocytogenes (Lm) is a bacterial pathogen that causes listeriosis in immunocompromised individuals, particularly pregnant women. Several virulence factors support the intracellular lifecycle of Lm and facilitate cell-to-cell spread, allowing it to occupy multiple niches within the host and cross protective barriers, including the placenta. One family of virulence factors, internalins, contributes to Lm pathogenicity by inducing specific uptake and conferring tissue tropism. Over 25 internalins have been identified thus far, but only a few have been extensively studied. Internalins contain leucine-rich repeat (LRR) domains which enable protein-protein interactions, allowing Lm to bind host proteins. Notably, other Listeria species express internalins but cannot colonize human hosts, prompting questions regarding the evolution of internalins within the genus Listeria. Internalin P (InlP) promotes placental colonization through interaction with the host protein afadin. Though prior studies of InlP have begun to elucidate its role in Lm pathogenesis, there remains a lack of information regarding homologs in other Listeria species. Here, we have used a computational evolutionary approach to identify InlP homologs in additional Listeria species. We found that L. ivanovii londoniensis (Liv) and L. seeligeri (Ls) encode InlP homologs. We also found InlP-like homologs in L. innocua and the recently identified species L. costaricensis. All newly identified homologs lack the full-length LRR6 and LRR7 domains found in Lms InlP. These findings inform on the evolution of one key Lm virulence factor, InlP, and serve as a springboard for future evolutionary studies of Lm pathogenesis as well as mechanistic studies of Listeria internalins. Impact StatementThe intracellular bacterial pathogen Listeria monocytogenes can breach protective barriers in the pregnant host, allowing for the colonization of the placenta in pregnant women 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 Listeria genus 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.

microbiology↗