CFTR gene and protein

The CFTR (Cystic Fibrosis Transmembrane Conductance Regulator, OMIM #602421) gene was identified in 1989 (Kerem et al., 1989; Riordan et al., 1989; Rommens et al., 1989). It was the first successful example of positional cloning and haplotype mapping of a rare disease, followed by a combination of chromosome jumping and walking to find the gene. The final proof that the gene responsible for cystic fibrosis had been identified was the discovery of the disease-causing variation 'ΔF508' [now named p.Phe508del], a 3-bp deletion in exon 10 [now exon 11] which results in the loss of a single amino acid (phenylalanine at codon 508). This mutant is present in approximately 70% of chromosomes from European descent.
Twenty-five years later, over 2,000 different variations have been described worldwide (CFMD; CFTR2).

CFTR gene

    The CFTR gene spans more than 197 kb (kilobases) on the long arm of chromosome 7 (7q31.2) (Tsui et al., 1985; Tsui and Dorfman, 2013) (position 117,470,772-117,668,665 on NC_000007.14 version) and contains 27 exons. With upstream and downstream regulatory elements required for proper gene expression, the transcription unit of CFTR encompasses approximately 216.7 kb.
    The CFTR gene shows a tissue-specific expression despite a promoter presenting similarities with housekeeping gene promoters (no TATA box, high GC content, binding sites for SP1). The CFTR promoter is also characterized by consensus binding sites for several transcription factors including CTCF, AP-1, GRE, CRE, C/RBP and Y-box proteins.


    The 6,132-nucleotides CFTR mRNA encodes a glycoprotein of 1,480 amino acids called 'Cystic Fibrosis Transmembrane conductance Regulator' (CFTR). The majority of transcripts are driven from the same promoter. However, there are transcripts with alternative splicing, resulting in skipping of different exons in a proportion of transcripts depending on tissues. The most striking example is the polypyrimidine track located within the acceptor splice site of intron 8 [now named intron 9]: the length of the T-track, which varies from five to nine Ts in the general population, influences the efficiency of exon 9 [now named exon 10] inclusion in the CFTR transcripts.

    Extracted from Claustres et al., 2005

CFTR protein

    The CFTR protein (Uniprot #P13569) is a member of the large adenosine triphosphate (ATP)-binding cassette (ABC) transporter family, especially subfamily C, member 7 (hence the other name of the CFTR gene is ABCC7) (Dean et al., 2001; Linsdell 2014). ABC transporters generally regulate trans-membrane transport of small molecules. However, CFTR is the only known member of the ABC family that acts as an ion channel that mediates the passive, electro-diffusional movement of Cl-, HCO3-, and other small anions across the cell membrane. As the typical ABC transporters architecture, CFTR is composed of two halves, each possessing: - a Trans-Membrane Domain (TMD) that consists of 6 membrane-spanning alpha-helices (TM1-6 or TM7-12) connected by extra- and intra-cellular loops. - a cytosolic Nucleotide-Binding Domain (NBD). NBD1 is defined as the sequence between residues 423 and 646, and NBD2 between residues 1210 and 1443. The two NBDs contain ATP binding sequences Walker A and Walker B. The two TMDs of CFTR form the channel pore. It is not known how many TMs contribute to the lining of the pore, although functional evidence suggests that TM1, TM6, TM11 and TM12 are major contributors. For example, variations in TM6 affect anion selectivity and conductance of the CFTR channel.

    The specificity of CFTR is an additional regulatory (R) region, which links together the two halves of the protein, as well as long N- and C-terminal extensions about 80 and 30 residues respectively (Hunt et al., 2013). The ~200-residues R domain appears relatively unstructured. It is highly charged and presents more than 10 potential Serine/Threonine phosphorylation sites (11 serines and 1 threonine ; Gadsby et al., en 1999). Phosphorylation and dephosphorylation of the R domain by protein kinases and phosphatases exert major control over chloride channel activity. The intracellular parts of CFTR (NBDs, R domain, N- and C-terminus, and four intracellular linkers of the trans-membrane helices) represent 80% of the total amino acid content of the protein.

    The locus and the CFTR protein (adapted from De Keukeleire, 2007)

    The structure of the human full-length CFTR has been determined, in the absence of ATP, by electron cryomicroscopy to 3.9 Å resolution. In the structure, the R domain is dephosphorylated and prevents NBD dimerization and the channel opening. Although the structure is in the inactive conformation (channel-closed), it provides a molecular understanding of many disease-causing mutations (Liu et al., 2017).

    Structure of the complete human CFTR by cryo-EM to 3.9 Å resolution

The CFTR gene is expressed in the epithelial cells of a variety of tissues and organs including lungs, intestine, pancreas, salivary glands, kidney, reproductive tract and some parts of the human brain (Guo et al., 2009, Marcorelles et al., 2014).
The journey of the CFTR protein from gene transcription to cell membrane takes it through multiple interactions with proteins of several cellular compartments where it must pass stringent quality control. In the nucleus, the CFTR gene is transcribed into pre-mRNA. Then, the splicing process removes intronic regions and assembles the 27 exons to produce the CFTR mRNA. Mature mRNAs are translated by the ribosomes of the endoplasmic reticulum (ER) into a nascent polypeptide chain (at a translation rate of about 2.7 residues per second, synthesis of the full-length CFTR takes approximately 9 min).
Further protein maturation, necessary for the complex and multi-step protein folding process, occurs within the ER lipid bilayer (core glycosylations). Properly folded CFTR molecules leave the ER through coat protein complex II, are escorted by cytoplasmic chaperone proteins to the Golgi apparatus for final conversion to a mature protein (complex glycosylations). From the Golgi, clathrin-coated vesicles shuttle mature CFTR to the apical membrane of epithelial cells where it regulates trans-epithelial salt and water movement.

As most other plasma membrane proteins, the turnover of CFTR is estimated as 10% per minute, and its half-life is about 12h. Plasma membrane quality control involves recognition by chaperon Hsc70, ubiquitinization, and internalization within endosomes, where CFTR is either committed to recycling back to the plasma membrane, or to degradation.
Biosynthesis and processing of CFTR (from Molinski et al., 2012)

Note: it has been demonstrated that CFTR biogenesis is highly efficient in epithelial cells endogenously expressing CFTR (Varga et al., 2004). However, in heterologous overexpression systems (i.e. plasmids for in vitro studies), it has been repeatedly reported that CFTR folding and processing are quite inefficient, leading to the degradation of a large proportion of wild-type CFTR molecules before reaching the plasma membrane (40-70% in the literature).
CFTR plays a critical role in maintaining trans-epithelial osmotic balance at the apical surface of epithelia. Although CFTR is not the only chloride channel, it is the major secretion pathway of chloride ions (Cl-). In the airways, CFTR expression is the highest in distal regions of the sub-mucosal glands, where fluid secretion hydrates the mucus and helps to expel it to the airway surface.
The human CFTR chloride channel exhibits a low single-channel conductance.

The opening of the CFTR channel is gated by mechanical reorientation of the NBDs upon ATP binding at their interface. This conformational rearrangement leads to a structure called 'ATP-sandwich dimer' or 'head-to-tail' NBD dimer: two Mg-ATP molecules are bound at the inter-NBD interface, between Walker A and B sequences of one NBD and LSGGQ “ABC signature sequence” of the other NBD. Phosphorylation of the R domain by PKA (protein kinase A) facilitates tight structural interactions between the two NBDs. The conformational rearrangements are propagated to the TMDs then opening the channel pore. Hydrolysis of ATP causes destabilization of the NBD dimer. Sequential release of inorganic phosphate (Pi) and ADP resets the protein to its ground state. For review, see Hunt et al,. 2013 - Cystic Fibrosis Transmembrance Conductance Regulator (ABCC7) structure (Cold Spring Harbor Perspectives in Medicine).

In addition to its well-established ion channel function, the CFTR has been proposed to have many other roles and to impact, either directly or indirectly, other cellular proteins and functions. CFTR plays an important role in the transcellular secretion of bicarbonate (HCO3-), an alkalising agent crucial for pH buffering (Ishiguro et al., 2009). CFTR is involved in the regulation of other channels (epithelial sodium channel ENaC, chloride channel ORCC, potassium channel ROMK…). Other cell functions are modulated by CFTR including intravesicular acidification, activation of lysosomal enzymes, endocytic cycling, gap junction communication, chemokine production and activation…

CFTR, a multifunctional protein

Functional insufficiency of mutated CFTR or absence of CFTR protein result in perturbation of fluid and electrolyte transport across epithelia, and therefore alter both composition and quantity of epithelial fluids, such as mucus, sweat and digestive fluids, giving rise to CF or CFTR-RDs symptoms.

Defective or absent CFTR cause an imbalance between anion secretion and ENaC-mediated Na+ absorption, leading to fluid hyperabsorption and subsequent epithelial surface dehydration, which in turn, result in abnormal mucus with altered pH/electrolyte composition and increased polymeric mucin concentration. A cascade of events occurs including mucus obstruction, infection and inflammation in all epithelia affected by impaired surface hydration. In CF lung disease, mucociliary clearance is impaired, mucus is abnormally thick and the normal cilia movement is lost. Static mucus then becomes a niche for pathogens, including Pseudomonas aeruginosa. Chronic inflammation, increased production of cytokines and accumulation of neutrophils lead to lung tissue damage and remodeling.