Abstract
Nucleoid-associated proteins (NAPs) or histone-like proteins (HLPs) are DNA-binding proteins present in bacteria that play an important role in nucleoid architecture and gene regulation. NAPs affect bacterial nucleoid organization via DNA bending, bridging, or forming aggregates. EbfC is a nucleoid-associated protein identified first in Borrelia burgdorferi, belonging to YbaB/EbfC family of NAPs capable of binding and altering DNA conformation. YbaB, an ortholog of EbfC found in Escherichia coli and Haemophilus influenzae, also acts as a transcriptional regulator. YbaB has a novel tweezer-like structure and binds DNA as homodimers. The homologs of YbaB are found in almost all bacterial species, suggesting a conserved function, yet the physiological role of YbaB protein in many bacteria is not well understood. In this study, we characterized the YbaB/EbfC family DNA-binding protein in Caulobacter crescentus. C. crescentus has one YbaB/EbfC family gene annotated in the genome (YbaBCc) and it shares 41% sequence identity with YbaB/EbfC family NAPs. Computational modeling revealed tweezer-like structure of YbaBCc, a characteristic of YbaB/EbfC family of NAPs. N-terminal–CFP tagged YbaBCc localized with the nucleoid and is able to compact DNA. Unlike B. burgdorferi EbfC protein, YbaBCc protein is a non-specific DNA-binding protein in C. crescentus. Moreover, YbaBCc shields DNA against enzymatic degradation. Collectively, our findings reveal that YbaBCc is a small histone-like protein and may play a role in bacterial chromosome structuring and gene regulation in C. crescentus.
Highlights
Similar to eukaryotic organisms, bacteria pack their genetic material in a very small space
EbfC family proteins from Borrelia burgdorferi (EbfC)/YbaB family of Nucleoid-associated proteins (NAPs) colocalize with the nucleoid and probably play a role in structuring of the bacterial chromosome (Jutras et al, 2012; Wang et al, 2012)
NAPs are involved in global gene expression by making alterations in DNA structure or by interactions with transcriptional machinery
Summary
Bacteria pack their genetic material in a very small space. DNA-binding proteins known as nucleoid-associated proteins (NAPs) play a crucial role in nucleoid structuring and controlling gene expression. NAPs are referred to as histonelike proteins (HLPs), they are functionally very distinct from eukaryotic histones. Bacterial cells contain a wide variety of NAPs and their expression in the cell varies with growth phase of the culture. NAPs are small, basic proteins that can have the ability to bind to DNA, either as monomers, dimers, or tetramers or in complex with other DNA modulating proteins The DNA binding occurs either through direct physical interaction or indirectly via binding with other accessory proteins (Dorman, 2014)
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