The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins

Abstract

Evidence is presented that establishes a novel class of interdomain linkers, named Q-linkers, as a defined element of protein structure. Q-linkers occur at the boundaries of functionally distinct domains in a widespread set of bacterial regulatory and sensory transduction proteins, typified by the nitrogen regulatory proteins, NtrB, NtrC, NifA and NifL. Q-linkers are not strongly conserved in sequence in otherwise homologous proteins, are approximately 15-25 residues long and relatively rich in glutamine, arginine, glutamate, serine and proline, and are assigned as 'coil', with a very low probability of alpha or beta structure, by eight secondary structure prediction methods. Hydrophobic amino acids are spaced with a periodicity of approximately 4-5 residues in the C-terminal 15 residues of these sequences. A pattern discriminator is presented that incorporates these properties and is used to predict segments resembling Q-linkers in sequence databases. Insertions of four and eight amino acids, constructed in the Q-linker sequences of NtrC and NifA, were found to have no effect on the function of the proteins in signal transduction and transcriptional activation. However, when NtrC was expressed as two separate polypeptides, consisting of the domains normally joined by the Q-linker, the construct failed to function. These results suggest that the Q-linker serves a simple but essential role in tethering the structurally-distinct but interacting domains of the protein. Q-linkers are therefore potentially applicable as domain fusion junctions for engineered chimaeric multidomain proteins expressed in enteric bacterial systems.