AUTHOR=Pal Parul , Modi Malvika , Ravichandran Shashank , Yennamalli Ragothaman M. , Priyadarshini Richa 

TITLE=DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.733344

DOI=10.3389/fmicb.2021.733344

ISSN=1664-302X

ABSTRACT=<p>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 <italic>Borrelia burgdorferi</italic>, belonging to YbaB/EbfC family of NAPs capable of binding and altering DNA conformation. YbaB, an ortholog of EbfC found in <italic>Escherichia coli</italic> and <italic>Haemophilus influenzae</italic>, 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 <italic>Caulobacter crescentus. C. crescentus</italic> has one YbaB/EbfC family gene annotated in the genome (YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub>) and it shares 41% sequence identity with YbaB/EbfC family NAPs. Computational modeling revealed tweezer-like structure of YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub>, a characteristic of YbaB/EbfC family of NAPs. N-terminal–CFP tagged YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub> localized with the nucleoid and is able to compact DNA. Unlike <italic>B. burgdorferi</italic> EbfC protein, YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub> protein is a non-specific DNA-binding protein in <italic>C. crescentus</italic>. Moreover, YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub> shields DNA against enzymatic degradation. Collectively, our findings reveal that YbaB<sub><italic>C</italic></sub><sub><italic>c</italic></sub> is a small histone-like protein and may play a role in bacterial chromosome structuring and gene regulation in <italic>C. crescentus.</italic></p>