The linker region of AraC protein

Abstract

AraC protein, a transcriptional regulator of the L-arabinose operon in Escherichia coli, is dimeric. Each monomer consists of a domain for DNA binding plus transcription activation and a domain for dimerization plus arabinose binding. These are connected to one another by a linker region of at least 5 amino acids. Here we have addressed the question of whether any of the amino acids in the linker region play active, specific, and crucial structural roles or whether these amino acids merely serve as passive spacers between the functional domains. We found that all but one of the linker amino acids can be changed to other amino acids individually and in small groups without substantially affecting the ability of AraC protein to activate transcription when arabinose is present. When, however, the entire linker region is replaced with linker sequences from other proteins, the functioning of AraC is impaired.

In Vivo DNA-Binding and Oligomerization Properties of the Shigella flexneri AraC-Like Transcriptional Regulator VirF as Identified by Random and Site-Specific Mutagenesis

“…As no other VirF mutation studied here abolished expression of the protein (data not shown), it is likely that the S150A mutation makes the protein sensitive to proteolysis at the exposed linker region rather than having a severe effect on translation. The linker region of VirF is rich in amino acid side chains such as alanine and serine that permit protein flexibility, and although the A154T mutation may restrict this slightly, its relatively mild effect is consistent with the hypothesis that the amino acids in the linker do not contribute critically to protein function and with the observation that the corresponding linker region in AraC is generally amenable to mutagenesis (5).…”

“…The best studied is the Escherichia coli AraC protein, which controls expression of the genes necessary for uptake and catabolism of arabinose (reviewed in reference 25). AraC is composed of an amino-terminal domain that includes the dimerization and arabinose-binding regions (26,27), a carboxy-terminal domain that contains two potential helix-turnhelix (HTH) motifs for sequence-specific DNA recognition and binding, and a linker region which connects the two functionally distinct domains (5). In contrast to family members involved in the utilization of sugars, the class of AraC proteins involved in stress response such as MarA, Rob, and SoxS are monomers (12).…”

Active Role of the Interdomain Linker of AraC

“…Our new results are somewhat surprising, in light of the earlier work on AraC (7,9). Previously, it was found that the interdomain linker was relatively tolerant to amino acid substitutions.…”

Mutagenesis of the Rns regulator of enterotoxigenic Escherichia coli reveals roles for a linker sequence and two helix–turn–helix motifs

“…It is postulated that this area of Rns forms, or is part of, a flexible interdomain linker that is necessary to correctly orientate the N-and C-terminal regions of the protein to enable them to participate in their functional roles. The NACRS sequence of Rns has some features in common with the flexible linkers of the AraC, RhaR and RhaS proteins (Eustance & Schleif, 1996;Kolin et al, 2007). The activity of other AraC-like proteins may also depend on the presence of a central disordered/flexible connecting sequence.…”