EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes

Abstract

Genomic compaction is an essential characteristic of living organisms. Nucleoid-associated proteins (NAPs) are a group of small proteins that play crucial roles in chromosome architecture and affect DNA replication, transcription, and recombination by imposing topological alterations in genomic DNA, thereby modulating global gene expression. EbfC/YbaB was first described as a DNA-binding protein of Borrelia burgdorferi that regulates the expression of surface lipoproteins with roles in virulence. Further studies indicated that this protein binds specifically and non-specifically to DNA and colocalises with nucleoids in this bacterium. The data showed that this protein binds to DNA as a homodimer, although it can form other organised structures. Crystallography analysis indicated that the protein possesses domains responsible for protein–protein interactions and forms a “tweezer” structure probably involved in DNA binding. Moreover, sequence analysis revealed conserved motifs that may be associated with dimerisation. Structural analysis also showed that the tridimensional structure of EbfC/YbaB is highly conserved within the bacterial domain. The DNA-binding activity was observed in different bacterial species, suggesting that this protein can protect DNA during stress conditions. These findings indicate that EbfC/YbaB is a broadly distributed NAP. Here, we present a review of the existing data on this NAP.

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

“…S6 ). Sequence analysis reveal that the Dr_ebfC protein contains domains responsible for PPI and participates in DNA binding through the formation of a “tweezer-like” structure (29). To study the role of this protein in chromosomal organization, we constructed the dr_0199 deletion mutant in D. radiodurans .…”

“…EbfC ( erp -binding factor, chromosomal), also known as YbaB, is a less-studied NAP but widely distributed in prokaryotes (29). It was first discovered in Borrelia burgdorferi and characterized as a site-specific DNA binding protein (30).…”

Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5

“…The sequence for LysPMBT3 (UniProtKB: A0A2I6PHU80), from glycoside hydrolase family 19 (GH19), a SAR-endolysin from the glucosaminidase superfamily, was used as an outgroup to root the phylogenetic tree. The phylogenetic tree was reconstructed using MetaLogo version 1.1.3 [ 23 ], as previously described [ 24 ]. Multiple sequence alignment (MSA) was determined by mafft version 7.505 [ 25 ] and blast version 1.0 [ 26 ].…”

Borrelia burgdorferi DnaA and the Nucleoid-Associated Protein EbfC Coordinate Expression of the dnaX-ebfC Operon

“…EbfC is highly conserved across eubacteria, and its gene is typically the second gene in a bicistronic operon with dnaX , an essential component of the DNA Pol III HE ( 12 – 14 ). In the model organism Escherichia coli , dnaX codes for two subunits, the full-length Tau (τ) and shortened Gamma (γ), by translational frameshift ( 15 – 17 ).…”