PROSITE documentation PDOC52089

NtrC-type HTH DNA-binding domain profile

Transcription initiation is the most regulated step of gene expression and is essential for the cells response to environmental changes. Bacterial transcription initiation is regulated by a complex network of cell signalling pathways, which culminate in the recruitment of RNA polymerase (RNAP) to specific promoter regions by sigma factors and the formation of open promoter complexes. Sigma factors are directly responsible for promoter recognition, are the targets of transcription activator proteins and are required for DNA melting to make a transcription competent open promoter complex. Sigma-factors can be clustered into two structurally unrelated families: sigma(70) and sigma(54). Sigma(54) commonly regulates transcription of genes associated with processes that require a rapid response with a wide dynamic range, such as starvation responses, flagellar motility, protection from alkaline and high-pressure environments, and expression of virulence factors. Although all sigma factors play an analogous role in targeting promoters and regulating transcription, the mechanisms of the sigma(70) and sigma(54) classes are quite different. Transcriptionally competent open complex formation by the sigma(54) holoenzyme requires the actions of activators bound remotely upstream from the transcription start site. These activators, also called bacterial enhancer-binding proteins (bEBPs), belong to the AAA(+) (ATPase associated with diverse range of cellular activities) family and ATP hydrolysis by bEBPs is required for the isomerisation from the closed complex to the open complex. bEBPs are often made of three domains: an N-terminal regulatory domain, which can be the receiver domain of a two component phospho-relay system (R) (see <PDOC50110>), a central catalytic AAA(+) domain (C) (see <PDOC00579>) and a C-terminal helix-turn-helix DNA-binding domain (D or DBD), although there are some bEBPs without R or D domains. Typically, in the resting state, pairs of D domains bind to one or more upstream activating sequence (UAS) sites. The R domain typically serves as a constitutive inhibitor; upon receiving an activation signal inhibition is alleviated, and, with the help of integration host factor (IHF) to facilitate DNA looping, the AAA(+) domain is brought in close proximity in order to interact with sigma(54), promoter DNA and the RNAP to activate transcription [1,2].

The D domains from activators are typically composed of ~50 amino acids and all belong to the NtrC superfamily of helix-turn-helix (HTH) DNA-binding proteins. The NtrC-type HTH DNA-binding domain often binds to two high-affinity cooperative binding sites located ~100 bp upstream of the sigma(54)-binding site. The NtrC-type HTH DNA-binding domain consists of three well-defined α-helices: the dimerization helix, the first helix of the HTH, and the recognition helix, in keeping with general naming conventions for HTH proteins (see <PDB:4L5E>) [2,3,4,5].

The NtrC-type HTH DNA-binding domains are close homologs and evolutionary ancestors of the versatile DNA binding-and-bending protein, Fis (factor for inversion stimulation). Fis, which evolved from α proteobacterial NtrC by losing the regulatory and ATPase domains, is involved in a number of processes ranging from site-specific recombination, integration-excision reactions of phages, and negative transcriptional regulation to cell cycle timing in chromosome replication [2,4,5,6].

Some proteins known to contain a NtrC-type HTH DNA-binding domain:

• Bacterial nitrogen regulatory protein C (NtrC), a enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism.
• Bacterial anaerobic nitric oxide reductase transcription regulator (NorR).
• Bacterial tyrosine repressor (TyrR), a transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids.
• Bacterial acetoin catabolism regulatory protein (AcoR).
• Aromatoleum aromaticum EbN1 p-ethylphenol regulator EtpR.
• γ-proteobacterial factor for inversion stimulation (Fis), a multifunctional DNA-binding protein involved in many site-specific recombination events, regulation of gene expression and oriC-directed initiation of chromosomal replication.

The profile we developed covers the entire NtrC-type HTH domain.