Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B sub(12)-based photosensory regulator

• Published in: European biophysics journal 2013-06, Vol.42 (6), p.463-476
• Main Authors: Diez, Ana I, Ortiz-Guerrero, Juan Manuel, Ortega, Alvaro, Elias-Arnanz, Montserrat, Padmanabhan, S, Garcia de la Torre, Jose
• Format: Article
• Language: English
• Subjects: Absorbance; Thermus thermophilus
• ISSN: 0175-7571; 1432-1017
• DOI: 10.1007/s00249-013-0897-x

Thermus thermophilus transcriptional factor TtCarH belongs to a newly discovered class of photoreceptors that use 5'-deoxyadenosylcobalamin (AdoB sub(12)) as the light-sensing chromophore. Photoregulation relies on the repressor activity of AdoB sub(12)-bound oligomers in the dark, which light counteracts by oligomer disruption due to AdoB sub(12) photolysis. In this study, we investigated TtCarH self-association and binding to DNA in the dark and in the light using analytical ultracentrifugation (AUC) methods, both sedimentation velocity (SV) as well as equilibrium (SE). From a methodological point of view, this study shows that AUC can provide hydrodynamic insights in cases where light is a crucial determinant of solution properties. For the light-sensitive TtCarH, absorbance as well as interference AUC data yielded comparable results. Sedimentation coefficients and whole-body hydrodynamic analysis from SV experiments indicate that in solution apo-TtCarH and light-exposed AdoB sub(12)-TtCarH are predominantly aspherical, ellipsoidal monomers, in accord with SE data. By comparison, AdoB sub(12)-TtCarH exists as a more compact tetramer in the dark, with smaller forms such as dimers or monomers remaining undetected and low levels of larger oligomers appearing at higher protein concentrations. AUC analyses indicate that in the dark AdoB sub(12)-TtCarH associates as a tetramer with DNA but forms smaller complexes in the apo form or if exposed to light. The self-association and DNA-binding properties of TtCarH deduced from AUC are consistent with data from size-exclusion and DNA-binding gel-shift assays. AUC analyses together with hydrodynamic modeling provide insights into the AdoB sub(12)- and light-dependent self-association and DNA-binding of TtCarH.