EbfC (YbaB) Is a New Type of Bacterial Nucleoid-Associated Protein and a Global Regulator of Gene Expression in the Lyme Disease Spirochete

Abstract

Nearly every known species of Eubacteria encodes a homolog of the Borrelia burgdorferi EbfC DNA-binding protein. We now demonstrate that fluorescently tagged EbfC associates with B. burgdorferi nucleoids in vivo and that chromatin immunoprecipitation (ChIP) of wild-type EbfC showed it to bind in vivo to sites throughout the genome, two hallmarks of nucleoid-associated proteins. Comparative RNA sequencing (RNA-Seq) of a mutant B. burgdorferi strain that overexpresses EbfC indicated that approximately 4.5% of borrelial genes are significantly impacted by EbfC. The ebfC gene was highly expressed in rapidly growing bacteria, but ebfC mRNA was undetectable in stationary phase. Combined with previous data showing that EbfC induces bends in DNA, these results demonstrate that EbfC is a nucleoid-associated protein and lead to the hypothesis that B. burgdorferi utilizes cellular fluctuations in EbfC levels to globally control transcription of numerous genes. The ubiquity of EbfC proteins in Eubacteria suggests that these results apply to a wide range of pathogens and other bacteria.

BB0238, a Presumed Tetratricopeptide Repeat-Containing Protein, Is Required during Borrelia burgdorferi Mammalian Infection

“…6D). Prior studies showed that dbpBA transcription was elevated when ebfC was induced (48), and in agreement with these findings, DbpA production was higher in the samples from the IPTG-induced BbiEbfC cultures (Fig. 6D).…”

“…To date, only one other study that described differential regulation of bb0238 has been published. In this study, the authors detected an increase in bb0238 transcription by comparative RNA sequencing when the EbfC (YbaB) nucleoid-associated DNA-binding protein was overproduced (48). To confirm these results, the borrelial IPTG-inducible expression vector was adapted to express ebfC by replacing the rrp2 ORF in piRrp2(Kan) with the ebfC ORF to create pJSB499.…”

Borrelia burgdorferi cp32 BpaB Modulates Expression of the Prophage NucP Nuclease and SsbP Single-Stranded DNA-Binding Protein

“…Studies on the cellular effects of BpaB overproduction used B. burgdorferi strains KS50 and KS52, which are derivatives of B31 that carry pSZW53-4 or pBLS705, respectively (29,30). pBLS705 contains the lp56 bpaB (allele bpaB56) under the control of a TetR-repressible promoter, post (30,60).…”

Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis

“…Although YbaB itself is far from well characterized, it has been implicated in membrane biogenesis (Skretas and Georgiou, 2010): Coexpression of the native ybaB gene enhanced the accumulation of membraneintegrated heterologous proteins up to 10-fold in Escherichia coli. Although DNA binding activity has also been suggested for YbaB (Cooley et al, 2009;Jutras et al, 2012), the overall negative charge of STIC2 (charge at pH 7.0, -3.93; pI 4.95) and STCL (charge at pH 7.0, -1.94; pI 5.40) make this property seem unlikely. The crystal structure of YbaB shows a tweezer-like dimer formation (Lim et al, 2003), which based on homology modeling analysis is likely to be shared by STIC2 and STCL (Supplemental Figure 14) (Kelley et al, 2015).…”

“…Both ALB4 and ALB3 are members of the conserved Alb3/Oxa1/YidC family of protein insertases (Luirink et al, 2001;Kuhn et al, 2003;Yi and Dalbey, 2005). STIC2 is a homolog of bacterial ybaB, which encodes a protein implicated in membrane protein biogenesis (Skretas and Georgiou, 2010), as well as in DNA binding (Cooley et al, 2009;Jutras et al, 2012).…”