DciA helicase operators exhibit diversity across bacterial phyla

Abstract

A fundamental requirement for life is replication of an organism's DNA. Studies in Escherichia coli and Bacillus subtilis have set the paradigm for how DNA replication occurs 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, raising the question of how helicase activity is facilitated in other bacteria during DNA replication initiation. 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 are defined by the presence of a DUF721 domain and are conserved in most bacteria. However, we find that the sequence conservation between DciA proteins across different phyla is very low. Therefore, to comprehensively define the DciA protein family, we took a computational evolutionary approach. These analyses identified diversity in sequence features and domain architectures amongst DciA homologs that were associated with specific phylogenetic lineages. The diversity of DciA proteins elucidated here represents the evolution of helicase operation in bacterial DNA replication, highlights the need for phyla-specific analyses of this fundamental biological process, and is an important example of how research in bacterial DNA replication is necessary in organisms beyond E. coli and B. subtilis.

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

“…The PSP system is a great use case to characterize using molecular evolution and phylogeny due to the variety of domain architectures, cellular localizations, and phyletic spreads of each of these protein families and operons. The PSP work, including this Lia operon use case, as well as other recent diverse biological applications [2][3][4][5][6][7][8][9][10][11] indicate that the MolEvolvR approach is invaluable in characterizing new protein families of interest in the context of evolution. Homolog data table with the best hits from all superkingdoms of life (queried across all RefSeq genomes).…”

“…This gap impedes identifying and characterizing the complete molecular systems involved in various critical cellular processes such as molecular pathogenesis, antibiotic resistance, or stress response. Several studies [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] have demonstrated the power of molecular evolution and phylogenetic analysis in determining molecular functions of such proteins. There are many individual tools [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] for protein sequence similarity searches or ortholog detection, delineating co-occurring domains (domain architectures), and building multiple sequence alignments and phylogenetic trees.…”

“…MolEvolvR is a generalized web-server of this web-app. To demonstrate its broad applicability, we have applied the approach underlying MolEvolvR to study several systems, including proteins/operons in zoonotic pathogens, e.g ., nutrient acquisition systems in Staphylococcus aureus 4,5 , novel phage defense system in Vibrio cholerae 6 , surface layer proteins in Bacillus anthracis 7 , helicase operators in bacteria 8 , and internalins in Listeria 9 .…”