1.A.46 The Anion Channel-forming Bestrophin (Bestrophin) Family
The bestrophins comprise a large family of Ca2+-regulated homo-tetrameric anion (chloride and bicarbonate; Qu et al., 2006; Bharill et al., 2014) channels found in animals, plants, fungi and bacteria (Sun et al., 2002; Hagen et al., 2005). Four bestrophins (VMD1-4) are encoded in the human genome; 4 in Drosophila melanogaster and 24 in Caenorhabditis elegans. Bestrophin-1 (VMD2 gene product) is the autosomal dominant vitelliform macular dystrophy protein or the Best disease protein (Burgess et al., 2008; Yu et al., 2008). The genetic defect causes loss of central vision and defects in the retinal pigment epithelium. The 585 aa VMD2 exhibits two strongly hydrophobic peaks in the N-terminal 100 residues, two moderately hydrophobic peaks centered at residues 150 and 200, respectively, and two more strongly hydrophobic peaks between residues 220 and 300. The remainder of the protein is strongly hydrophilic. Analyses suggest that the N- and C-termini are in the cytoplasm with three extracytoplasmic loops, suggesting a 4 TMS topological model with the moderately hydrophobic regions possibly dipping into the membrane (Tsunenari et al., 2003). hBest1 and sphingomyelin are miscible in surface films, and this property is a prerequisite for interaction with membrane domains (Mladenov et al. 2020).
Using single-molecule subunit analysis, Bharill et al. 2014 found that human Best1, 2, 3 and 4 each preferentially self-assembles into a homotetrameric channel. Thus, despite considerable conservation among human Bests, hBest1 has little or no interaction with other hBests or mTMEM16A. The domain responsible for assembly specificity was identified, and it also plays a role in channel function. Several human diseases are due to mutations in the members of this family (Stöhr et al. 2005).
Bestrophins can function both as Cl- channels and as regulators of voltage-gated Ca2+ channels. The founding member, human bestrophin-1 (hBest1), is responsible for a dominantly inherited, juvenile-onset form of macular degeneration called Best vitelliform macular dystrophy. Mutations in hBest1 have also been associated with a small fraction of adult-onset macular dystrophies. It is proposed that dysfunction of bestrophin results in abnormal fluid and ion transport by the retinal pigment epithelium, resulting in a weakened interface between the retinal pigment epithelium and photoreceptors (Hartzell et al., 2008). There is compelling evidence that bestrophins are Cl- channels, but bestrophins remain enigmatic because it is not clear that the Cl- channel function can explain Best disease. In addition to functioning as a Cl- channel, hBest1 also regulates voltage-gated Ca2+ channels. Some bestrophins are activated by increases in intracellular Ca2+ concentration, but whether bestrophins are the molecular counterpart of Ca2+-activated Cl- channels remains in doubt. Bestrophins are also regulated by cell volume and may be members of the volume-regulated anion channel family (Hartzell et al., 2008).
The best disease-linked Cl- channel hBest1 regulates Ca V 1 (L-type) Ca2+ channels via src-homology-binding domains (Yu et al., 2008). It probably interacts with the Ca(V)beta subunit, altering channel availability. This novel function provides a possible mechanism for the role of hBest1 in macular degeneration (Yu et al., 2008). Bestrophin is activated by Ca2+ which interacts with a C-terminal domain (EF1) to gate the channel. Ca2+ binding to EF1 activates the channel in a process that requires the acidic domain (293-308) and another regulatory domain (350-390). Many of the approximately 100 disease-causing mutations in hBest1 are located in this region, the Ca2+ sensing domain (Xiao et al., 2008). Human disease-causing mutations in the N- and C-termini of hBest1 disrupt an N-C-terminal interaction and channel function of bestrophin 1 (Qu et al., 2009).
The Best1 channel activity is regulated by ceramide and phosphorylation. Protein kinase C (PKC) phosphorylates (serine 358) in hBest1 for sustained channel function. Channel activity is maintained by PKC activators, protein phosphatase inhibitors, or pseudo-phosphorylation by substitution of glutamic acid for serine 358 ()Xiao et al., 2009. Ceramide accumulation during early stages of retinopathy inhibits hBest1 function, leading to abnormal fluid transport across the retina, and enhanced inflammation.
Multiple members of the Bestrophin family are found in mammals, insects and C. elegans. At least twenty paralogues are encoded in the C. elegans genome. Different functionally characterized bestrophins (2 from humans, one from Drosophila and one from C. elegans) produce chloride conductances with distinctive I-V relationships and ion selectivities (Hagen et al., 2005). The ion selectivity of VMD1 is; SCN-≥I-≥NO3->Br->Cl->HCO3- (Yu et al., 2006).
Some bestrophins are much larger (~900 residues) than VMD2, while some are much smaller (~280 residues). For example, a C. elegans homologue (Q17851) is 884 residues long and exhibits repeated elements as well as at least 8 strongly hydrophobic putative TMSs. Each of the 4 pairs of TMSs are centered at positions 60, 150, 400 and 700 in the protein. Distant homologues in E. coli (YneE; P76146) and Salmonella typhi (Q8Z706) are 315-321 aas long and exhibit a hydropathy plot similar to the first 300 residues of VMD2. Thus, the proteins in the Bestrophin family are not uniform in size or topology (Hagen et al., 2005).
Bestrophin calcium-activated chloride channels (CaCCs) regulate the flow of chloride and other monovalent anions across cellular membranes in response to intracellular calcium (Ca2+) levels. Mutations in bestrophin 1 (BEST1) cause certain eye diseases. Kane Dickson et al. 2014 presented X-ray structures of chicken BEST1-Fab complexes, at 2.85 Å resolution, with permeant anions and Ca2+. The eukaryotic BEST1 channel recapitulates CaCC function in liposomes and is formed from a pentameric assembly of subunits. Ca2+ binds to the channel's large cytosolic region. A single ion pore, approximately 95 Å in length, is located along the central axis and contains at least 15 binding sites for anions. A hydrophobic neck within the pore probably forms the gate. Phenylalanine residues within it may coordinate permeating anions via anion-π interactions. Conformational changes observed near the 'Ca2+ clasp' hint at the mechanism of Ca2+-dependent gating. Disease-causing mutations are prevalent within the gating apparatus (Dickson et al. 2014).
The bestrophin family of calcium (Ca2+)-activated chloride (Cl-) channels, which mediate the influx and efflux of monovalent anions in response to the levels of intracellular Ca2+, comprises four members in mammals (bestrophin 1-4). Owji et al. 2020 reported cryo-EM structures of bovine bestrophin-2 (bBest2) bound and unbound by Ca2+ at 2.4- and 2.2-Å resolution, respectively. The bBest2 structure highlights four previously underappreciated pore-lining residues specifically conserved in Best2 but not in Best1, illustrating the differences between these paralogs. Structure-inspired electrophysiological analysis revealed that, although the channel is sensitive to Ca2+, it has substantial Ca2+-independent activity for Cl-, reflecting the opening at the cytoplasmic restriction of the ion conducting pathway, even when Ca2+ is absent. Moreover, the ion selectivity of bBest2 is controlled by multiple residues, including those involved in gating (Owji et al. 2020).
The reaction catalyzed by functionally characterized members of the Bestrophin family is:
Anions (out) ⇌ anions (in)
Bestrophin-1 (Best1) anion channel; VMD2 gene product (NO3- > I- > Br- > Cl-; PNO3-/PCl- = 5.8) (Sun et al., 2002). Regulated by ceramide-induced dephosphorylation (Xiao et al., 2009). Best1 mediates fast and slow glutamate release in astrocytes upon GPCR activation (Woo et al. 2012). Progressive posterior chorioretinal changes occur over time in the initial ADVIRC proband, leading to visual loss. The causative mutation is in the transmembrane domain of BEST1 (Chen et al. 2016). Autosomal dominant vitreoretinochoroidopathy (ADVIRC), caused by mutation in BEST-1, is a rare, early-onset retinal dystrophy characterised by distinct bands of circumferential pigmentary degeneration in the peripheral retina accompanied by developmental eye defects. It is an ion channel in the basolateral membrane of retinal pigment epithelial (RPE) cells. In patients, BEST1 is expressed at the basolateral membrane and the apical membrane. PolarProtPred is a program for predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning (Dobson et al. 2021). During human eye development, BEST1 is expressed more abundantly in peripheral RPE compared to central RPE and is also expressed in cells of the developing retina. Higher levels of mislocalised BEST1 expression in the periphery, from an early developmental stage, may provide the mechanism that leads to the distinct clinical phenotype observed in ADVIRC patients (Carter et al. 2016). Binding of Ca2+ induces conformational changes in the secondary structure leading to assembly of monomers and changes in molecular and macro-organization (Mladenova et al. 2016). BEST1 gene mutations are associated with at least two different forms of macular dystrophy (Chibani et al. 2019). intermolecular protein-lipid interactions may account for the conformational dynamics of hBest1 and its biological function as a multimeric ion channel (Videv et al. 2021). hBest1 is expressed in the retinal pigment epithelium, and mutations in the BEST1 gene cause ocular degenerative diseases colectivelly referred to as "bestrophinopathies". Videv et al. 2021 reviewed the current understanding of hBest1 surface organization, interactions with membrane lipids in model membranes, and its association with microdomains of cellular membranes.
Animals, plants, fungi, bacteria
Bestrophin-1 of Homo sapiens (O76090)
Bestrophin-2 anion channel, BEST2 or VMD2L1 (PNO3-/PCl- = 2.7) (Sun et al., 2002). It also transports bicarbonate (HCO3-) (Qu and Hartzell 2008). The mouse orthologue is swell-insensitive, but the first 64 aas of Bestrophin 1 of Drosophila melanogaster allowed it to mediate cell swelling in response to hypo-osmotic stress (Stotz and Clapham 2012). BEST2 and BEST4 are expressed in colonic goblet cells (Ito et al. 2013). The structure of bovine BEST2 has been determined, and differences with BEST1 have been noted (Owji et al. 2020).
Animals, plants, fungi, bacteria
Bestrophin-2 of Homo sapiens (AAM76995)
Best3 of Mus musculus
Bestrophin1, isoform B. Identified as the Cl- (swell) channel that allows swelling in hypo-osmotic solutions (Stotz and Clapham 2012). Its N-terminal 64 aas are essential for swell activation.
Bestrophin1 of Drosophila melanogaster (B7Z0U6)
Bestrophin-1 (Best1) of 689 aas and 4 TMSs in a 2 + 2 arrangement. The x-ray structure has been determined at 2.85 Å resolution with permeant anions and Ca2+ bound (Kane Dickson et al. 2014). The channel is formed from a pentameric assembly of subunits. Ca2+ binds to the channel's large cytosolic region. A single ion pore, approximately 95 Å in length, is located along the central axis and contains at least 15 binding sites for anions. A hydrophobic neck within the pore probably forms the gate. Phenylalanine residues within it may coordinate permeating anions via anion-π interactions. Conformational changes observed near the 'Ca2+ clasp' hint at the mechanism of Ca2+-dependent gating (Kane Dickson et al. 2014).
Best1 of Gallus gallus (chicken)
Bestrophin-4, BEST4, Vmd2L2, of 473 aas and 7 TMSs. BEST2 and BEST4 are expressed in colonic goblet cells (Ito et al. 2013). Both proteins transport a variety of monovalent anions.
BEST4 of Homo sapiens
Bestrophin-3, BEST3, Vmd2L3 of 668 aas and 7 TMSs. It forms calcium-sensitive chloride channels permeable to monovalent anions including bicarbonate (Tsunenari et al. 2003). It's expression prevents ER-stress-induced cell death in renal peithelial cells (Lee et al. 2012). It is expressed in glial cells of the brain (Wang et al. 2019), and when mutant may cause mandibular prognathism (Kajii et al. 2019). Vitamin C induces expression (Wang et al. 2019).
BEST3 of Homo sapiens
Plasma membrane Ca2+-activated anion-selective channel, Best1 (AN2251) of 499 aas and 4 TMSs. Transports citrate, propionate, benzoate, and sorbate (Roberts et al., 2011).
Best1 of Aspergillus nidulans (Q5BB29)
Bestrophin homologue of 361 aas and 2 - 4 TMSs.
Best protein of Galdieria sulphuraria (Red alga)
Bestrophin homologue of 446 aas and ~ 4 TMSs.
Best protein of Volvox carteri
Uncharacterized protein of 396 aas with several TMSs, 2 - 4 TMSs near the N-terminus, and 2 - 3 TMSs near the C-terminus.
UP of Klebsormidium nitens
Fungal Best2 protein, AN6909 (Roberts et al., 2011) (29% identical to Best1 (TC# 1.A.46.2.1)).
Best2 of Aspergillus nidulans (Q5AXS1)
Bestrophin homologue of Cyanothece sp. PCC8801 (B7K217)
Bestrophin homologue of Bacillus cereus (C2UY63)
Bestrophin homologue of Bdellovibrio bacteriovorus (Q6MLK6)
Bestrophin homologue, YneE
YneE of E. coli (B2N0W4)
Chloroplast bestrophin homologue of 410 aas and 4 or 5 TMSs, VCCN1. Plants adjust photosynthetic light utilization by controlling electron transport and photoprotective mechanisms, and this involves the proton motive force (PMF) across the thylakoid membrane. VCCN1 is a voltage-dependent Cl- channel which localizes to the thylakoid membrane and fine-tunes the PMF by anion influx into the lumen during illumination, adjusting electron transport and photoprotective mechanisms (Herdean et al. 2016). The activity of AtVCCN1 accelerates the activation of photoprotective mechanisms on sudden shifts to high light. Thus, AtVCCN1 acts as an early component in the rapid adjustment of photosynthesis in variable light intensities.
Bestrophin homologue of Arabidopsis thaliana (Q9M2D2)
Functionally characterized bestrophin homologue, KpBEST, YneE or RFP-TM of 305 aas and 3 or 4 TMSs per subunit. KpBest is a pentamer that forms a five-helix transmembrane pore, closed by three rings of conserved hydrophobic residues, and has a cytoplasmic cavern with a restricted exit (Yang et al. 2014). From electrophysiological analysis of structure-inspired mutations in KpBest and hBest1, a sensitive control of ion selectivity was observed in the bestrophins, including reversal of anion/cation selectivity, and dramatic activation by mutations at the cytoplasmic exit. The wild type protein seems to be a cation (Na+) channel but the I66F mutation changed it into an anion (Cl-) channel (Yang et al. 2014). There are two constrictions in the channel, one provides the ion selectivity and the other serves as the gate.
KpBEST of Klebsiella pneumoniae
Uncharacterized protein of 895 aas and 10 TMSs in a 2 + 2 + 2 + 2 + 2 arrangement. There appear to be two full length repeats, each of 4 TMSs, plus and extra C-terminal two TMSs, all homologous to each other.
UP of Ostreococcus lucimarinus