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

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.

The Consistent Tick-Vertebrate Infectious Cycle of the Lyme Disease Spirochete Enables Borrelia burgdorferi To Control Protein Expression by Monitoring Its Physiological Status

“…Almost all known species of eubacteria encode a well-conserved homolog of EbfC, which has also been referred to as “ORF-12” or “YbaB” ( 132 – 137 ). We and others subsequently examined several EbfC homologs and determined that they, too, bind DNA ( 134 , 135 ).…”

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

“…The α1 region was also conserved in some groups, but this region appears to be less conserved than the other two. Interestingly, the α2-helix is believed to be the region directly interacting with DNA, at least in Caulobacter crescentus [ 47 ]. Notably, the β1/β2/β3 region is composed of amino acids with either hydrophobic side chains or small side chains.…”

“…Thus far, all the data indicate that EbfC/YbaB could be grouped into a family of DNA-binding proteins. The members of this family are encoded by a broad range of bacteria [ 27 , 30 , 34 , 35 , 47 , 49 , 53 , 54 , 55 ]. Interestingly, a chloroplast-localised protein encoded by a gene ( lta1 ) that controls the tiller angle and gravity response in rice and has homologs in other plants presents a conserved YbaB DNA-binding domain [ 56 ].…”

“…The DNA binding ability of EbfC/YbaB has been demonstrated in B. burgdorferi , H. influenzae , E. coli , Deinococcus radiodurans , and C. crescentus [ 28 , 30 , 34 , 47 , 55 ]. In B. burgdorferi , EbfC has been shown to bind to DNA as a homodimer, but other organised structures can also be formed [ 28 , 29 ].…”

“…The truncated YbaB protein could not form stable protein–DNA complexes, indicating that this domain is essential for DNA-binding activity. Its removal leads to the loss of double-stranded DNA-binding activity in C. crescentus [ 47 ].…”