Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins

Abstract

Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.

cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans

“…DdrI was able to form a stable complex with consensus CRP target DNA ( Fig. 3D ), which is consistent with previous structural, genetic, and in silico studies ( 10 , 11 ). On the other hand, DdrI also interacted with a variant of this sequence containing an RDRM-mimic in the presence of Mn 2+ , but with a much lower binding affinity in vitro (Fig.…”

“…The coil-to-helix transition of the C-helix is the key structural feature distinguishing between active and inactive ecCRP structures ( 10 , 11 ). Thus, the fully folded C-helix of apo DdrI led us to suspect that our DdrI without cAMP binding represents the active CRP form.…”

“…E. coli CRP (ecCRP) was the first transcription factor with a crystal structure available and serves as a model for biochemical and structural analyses ( 9 – 11 ). ecCRP exists as a dimer with each protomer containing an N-terminal domain and a C-terminal domain.…”

The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell

“…In many cAMP-regulated proteins, binding of cAMP to the β-barrel domain results in a conformational change that is propagated throughout the protein or complex to regulate the activity of a distal functional domain. In the dimeric Ec CAP for example, cAMP binding induces a conformational change that stabilizes a central coiled-coil helical domain and re-orients the DNA-binding domains to enable stable interaction with double-stranded DNA 46,47 . Instead of an extended α-helix able to form a coiled-coil, as found in Ec CAP, the C-terminus of monomeric Sg Enc CBD contains a long disordered loop that is unresolved in our cryo-EM density (Supplementary Fig.…”

The second messenger c-di-AMP controls natural competence via ComFB signaling protein

“…Likewise, the mycobacterial transcription factor DarR, which is regulated by c-di-AMP-binding, was found to be regulated as well through cAMP-binding (Schumacher et al 2023). Additionally, crosstalk between cyclic guanosine and adenosine second messengers is also known, as the CRP-Fnr transcription factors are known to bind both cAMP and cGMP, being only active in the cAMP-bound form in E. coli , while both cyclic nucleotides mediate the CRP activation in Sinorhizobium meliloti (Krol et al 2023; Werel et al 2023). Furthermore, both of cAMP and cGMP were found also to bind and modulate the activity of the AphA phosphatase in E. coli and Haemophilus influenzae (Kronborg & Zhang 2023).…”