The molecular evolution of function in the CFTR chloride channel

Abstract

The ATP-binding cassette (ABC) transporter superfamily includes many proteins of clinical relevance, with genes expressed in all domains of life. Although most members use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes, the cystic fibrosis transmembrane conductance regulator (CFTR) is the only known animal ABC transporter that functions primarily as an ion channel. Defects in CFTR, which is closely related to ABCC subfamily members that bear function as bona fide transporters, underlie the lethal genetic disease cystic fibrosis. This article seeks to integrate structural, functional, and genomic data to begin to answer the critical question of how the function of CFTR evolved to exhibit regulated channel activity. We highlight several examples wherein preexisting features in ABCC transporters were functionally leveraged as is, or altered by molecular evolution, to ultimately support channel function. This includes features that may underlie (1) construction of an anionic channel pore from an anionic substrate transport pathway, (2) establishment and tuning of phosphoregulation, and (3) optimization of channel function by specialized ligand–channel interactions. We also discuss how divergence and conservation may help elucidate the pharmacology of important CFTR modulators.

Real-time observation of functional specialization among phosphorylation sites in CFTR

“…It specifically lacks the conserved hydrophobic residues that usually follow the phosphorylated serine in so-called “strong” PKA consensus sites and instead bears a glutamine and glutamate, both unfavored in the motif (Phosphosite Plus v. 6.6.0.2). An alignment of orthologous R domain sequences around S813 reveal that it is highly conserved among jawed vertebrates but absent in sea lamprey, suggesting it may have emerged relatively late in evolution ( Infield et al, 2021 ). However, this late emergence does not explain its lack of optimization, for example, S700 was also absent in lamprey but is fully optimized in mammals ( Infield et al, 2021 ).…”

“…An alignment of orthologous R domain sequences around S813 reveal that it is highly conserved among jawed vertebrates but absent in sea lamprey, suggesting it may have emerged relatively late in evolution ( Infield et al, 2021 ). However, this late emergence does not explain its lack of optimization, for example, S700 was also absent in lamprey but is fully optimized in mammals ( Infield et al, 2021 ).…”

Permissive and nonpermissive channel closings in CFTR revealed by a factor graph inference algorithm

“…(The states are labeled so that the first letter indicates whether the channel is closed [C] or open [O].) Beginning with C1a, with a single ATP bound at the first ATP binding site, which is incapable of hydrolysis ( 30 ), the reversible transition to C1b occurs when a second ATP binds so that both binding sites are occupied. Because this step involves ATP binding, the rate depends on the concentration of ATP.…”

Molecular mechanisms of cystic fibrosis – how mutations lead to misfunction and guide therapy

“…The CFTR (ABCC7) protein is a member of the ABC transporter superfamily, which evolved toward the specific function of a phosphorylation-activated and ATP-gated ion channel [ 24 ]. Accordingly, as supported first by theoretical studies [ 25–30 ] and afterwards demonstrated by experimental 3D structures [ 31–35 ], CFTR shares many features of ABC transporters but exhibits specific characteristics ( Figure 1 B).…”

“…An additional original feature of CFTR, which is also found in other members of the ABC-C family such as MRP1, SUR1 and SUR2, is a significant divergence in the ATP-binding site 1 motif, formed by the NBD1 Walker A, Walker B and H-loop and by the NBD2 ABC signature and D-loop [ 24 ]. These non-canonical features are responsible for increased affinity for ATP and slowed ATP hydrolysis at this site [ 57 , 58 ], which is also covered by large regulatory insertion (RI), bearing a phosphorylation site.…”