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91.
The effects of plastocyanin on photophosphorylation 总被引:4,自引:0,他引:4
92.
Laboratory evaluation of a two-stage treatment system for TCE cometabolism by a methane-oxidizing mixed culture 总被引:1,自引:0,他引:1
The objective of this research was to evaluate several factors affecting the performance of a two-stage treatment system employing methane-oxidizing bacteria for trichloroethylene (TCE) biodegradation. The system consists of a completely mixed growth reactor and a plug-flow transformation reactor in which the TCE is cometabolized. Laboratory studies were conducted with continuous growth reactors and batch experiments simulating transformation reactor conditions. Performance was characterized in terms of TCE transformation capacity (T(C), g TCE/g cells), transformation yield (T(Y), g TCE/g CH(4)), and the rate coefficient ratio k(TCE)/K(S,TCE) (L/mg-d). The growth reactor variables studied were solids retention time (SRT) and nutrient nitrogen (N) concentration. Formate and methane were evaluated as potential transformation reactor amendments. Comparison of cultures from 2- and 8-day SRT (nitrogen-limited) growth reactors indicated that there was no significant effect of growth reactor SRT or nitrogen availability on T(C) or T(Y), but N-limited conditions yielded higher k(TCE)/K(S,TCE). The TCE cometabolic activity of the 8-day SRT, N-limited growth reactor culture varied significantly during a 7-year period of operation. The T(C) and T(Y) of the resting cells increased gradually to levels a factor of 2 higher than the initial values. The reasons for this increase are unknown. Formate addition to the transformation reactor gave higher T(C) and T(Y) for 2-day SRT growth reactor conditions and significantly lower T(C), T(Y), and k(TCE)/K(S,TCE) for 8-day SRT N-limited conditions. Methane addition to the transformation reactor inhibited TCE cometabolism at low TCE concentrations and enhanced TCE cometabolism at high TCE concentrations, indicating that the TCE cometabolism in the presence of methane does not follow simple competitive inhibition kinetics. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 650-659, 1997. 相似文献
93.
Microbial Succession during a Field Evaluation of Phenol and Toluene as the Primary Substrates for Trichloroethene Cometabolism 总被引:1,自引:0,他引:1
Fries MR Hopkins GD McCarty PL Forney LJ Tiedje JM 《Applied and environmental microbiology》1997,63(4):1515-1522
Microbial community composition and succession were studied in an aquifer that was amended with phenol, toluene, and chlorinated aliphatic hydrocarbons to evaluate the effectiveness of these aromatic substrates for stimulating trichloroethene (TCE) bioremediation. Samples were taken after the previous year's field studies, which used phenol as the primary substrate, and after three successive monthly treatments of phenol plus 1,1-dichloroethene (1,1-DCE) plus TCE, phenol plus TCE, and toluene plus TCE. Dominant eubacteria in the community were assessed after each of the four treatments by characterizing isolates from the most dilute most-probable-number tubes and by extracting DNA from aquifer samples. The succession of dominant phenol- and toluene-degrading strains was evaluated by genomic fingerprinting, cellular fatty acid methyl ester (FAME) analysis, and amplified ribosomal DNA restriction analysis (ARDRA). 1,1-DCE was found to drastically reduce microbial growth and species richness, which corresponded to the reduction in bioremediation effectiveness noted previously for this treatment (G. D. Hopkins and P. L. McCarty, Environ. Sci. Technol. 29:1628-1637, 1995). Only a few gram-positive isolates could be obtained after treatment with 1,1-DCE, and these were not seen after any other treatments. Microbial densities returned to their original levels following the subsequent phenol-TCE treatment, but the original species richness was not restored until after the subsequent toluene-TCE treatment. Genomic fingerprinting and FAME analysis indicated that six of the seven originally dominant microbial groups were still dominant after the last treatment, indicating that the community is quite resilient to toxic disturbance by 1,1-DCE. FAME analysis indicated that six microbial taxa were dominant: three members of the (beta) subclass of the class Proteobacteria (Comamonas-Variovorax, Azoarcus, and Burkholderia) and three gram-positive groups (Bacillus, Nocardia, and an unidentified group). ARDRA revealed that the dominant community members were stable during the three nontoxic treatments and that virtually all of the bands could be accounted for by isolates from five of the dominant taxa, indicating that the isolation protocol used likely recovered most of the dominant members of this community. 相似文献
94.
The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. 总被引:22,自引:4,他引:18
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The biochemical activities that underlie the genetically defined activator and repressor functions of the VIVIPAROUS1 (VP1) protein have resisted in vitro analysis. Here, we show that a glutathione S-transferase (GST) fusion protein, including only the highly conserved B3 domain of VP1, has a highly cooperative, sequence-specific DNA binding activity. GST fusion proteins that include larger regions of the VP1 protein have very low activity, indicating that removal of the flanking protein sequences is necessary to elicit DNA binding in vitro. DNA competition and DNase I footprinting analyses show that B3 binds specifically to the Sph element involved in VP1 activation of the C1 gene, whereas binding to the G-box-type VP1-responsive element is of low affinity and is nonspecific. Footprint analysis of the C1 promoter revealed that sequences flanking the core TCCATGCAT motif of Sph also contribute to the recognition of the Sph element in its native context. The salient features of the in vitro GST-B3 DNA interaction are in good agreement with the protein and DNA sequence requirements defined by the functional analyses of VP1 and VP1-responsive elements in maize cells. 相似文献
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Abstract— The metabolism of [14C]choline has been studied in the isolated perfused phrenic nerve-diaphragm of the rat. We obtained no evidence that acetylcholine was synthesized from labelled choline in this system. There was extensive incorporation of the choline into phosphatidylcholine and its precursors, cytidinediphosphocholine (CDP-choline) and phosphocholine. Autoradiographic studies indicated that the lipids of myelin sheaths and nerve endings were the primary sites labelled. 相似文献
99.
CAD/DFF40, the nuclease responsible for DNA fragmentation during apoptosis, exists as a heterodimeric complex with DFF45/ICAD. This study determines the molecular mechanisms of regulation of DFF40 via the chaperone and inhibition activities of DFF45. We analyze proteins corresponding to the fragments (D1, D2, and D3) of DFF45 generated by cleavage at the caspase consensus sites in DFF45. Either D1 or D2, as an isolated domain, is capable of inhibiting DFF40 nuclease activity while double domain fragments D1-2 and D2-3, as well as full-length DFF45, bind to DFF40 with high affinity and are much more effective inhibitors. The chaperone activity of DFF45 resides in part in its ability to maintain DFF40 as a soluble protein. In addition, D1 of DFF45 was found to be critical for the expression of active DFF40 in vivo, suggesting a role for DFF45 in binding nascent DFF40. 相似文献
100.
Daniel T. Infield Kerry M. Strickland Amit Gaggar Nael A. McCarty 《The Journal of general physiology》2021,153(12)
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.IntroductionThe ATP-binding cassette (ABC) transporter superfamily includes many members of clinical relevance, such as the multidrug resistance proteins (MRPs) and other proteins involved in generation of antibiotic resistance, transport of a wide variety of substrates in pathogenic bacteria, and transport of bile acids, lipids, and lipopolysaccharides (Ford and Beis, 2019; Jetter and Kullak-Ublick, 2020). ABC transporter genes encode the largest family of transmembrane (TM) proteins among living organisms (Briz et al., 2019) and are expressed in all domains of life (Ford and Beis, 2019; Holland et al., 2003). Either function or dysfunction of ABC transporters is implicated in development or treatment of cancer (Briz et al., 2019; Nobili et al., 2020), neurological disorders (Jha et al., 2019; Sumirtanurdin et al., 2019), detoxification (Briz et al., 2019), visual function (Garces et al., 2018), and, among many other clinical presentations (Moitra and Dean, 2011), in cystic fibrosis (CF; Riordan et al., 1989). In CF, mutations in the gene encoding CFTR lead to loss of anion transport in a wide variety of epithelial tissues (Csanády et al., 2019). In this review, we use the data generated from >30 yr of intensive structure-function study of CFTR and related proteins to propose and evaluate a potential route by which CFTR may have evolved unique function as a phosphorylation-regulated chloride channel. New insights are made possible by the advent of high-resolution cryo-EM structures of CFTR and the recent cloning and characterization of the evolutionarily oldest known orthologue of CFTR, from sea lamprey (Lp-CFTR; see below), which exhibits many functional differences from the human CFTR orthologue (hCFTR; Cui et al., 2019a).Overview of CFTRCFTR is a Cl−/HCO3− channel whose dysfunction directly leads to CF, the most common life-shortening genetic disease among Caucasians, affecting ∼80,000 individuals worldwide (Riordan et al., 1989; https://cftr2.org/mutations_history). The role of CFTR has been well characterized in airway, intestine, and sweat gland epithelial cells (Buchwald et al., 1991; Gonska et al., 2009; Haq et al., 2016; Quinton et al., 2012; Quinton, 2007; Trezíse and Buchwald, 1991), where the anionic flux mediated by the protein contributes to water secretion and regulation of pH (Pezzulo et al., 2012; Rowe et al., 2014). CFTR also functions in several nonepithelial cell types (Cook et al., 2016; Edlund et al., 2014; Gao and Su, 2015; Guo et al., 2014; Norez et al., 2014; Pohl et al., 2014; Schulz and Tümmler, 2016; Su et al., 2011), including in the brain (Ballerini et al., 2002; Guo et al., 2009; Hincke et al., 1995; Johannesson et al., 1997; Mulberg et al., 1995; Mulberg et al., 1998; Parkerson and Sontheimer, 2004; Pfister et al., 2015; Plog et al., 2010; Weyler et al., 1999). Several hundred disease-causing mutations have been identified in the CFTR gene. For a subset of these mutations, four small-molecule modulator therapeutics from Vertex Pharmaceuticals, Inc. that increase the surface expression or activity of CFTR have been approved for clinical use. The first approved drug, VX-770 (ivacaftor), is a gating potentiator that increases function of certain CFTR mutants (Cui et al., 2019b; Sosnay et al., 2013; Van Goor et al., 2009; Van Goor et al., 2014; Yu et al., 2012). A better understanding of these drugs and their binding sites may aid in refining the next class of therapeutics.ABC transporters use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes (Rees et al., 2009). There are seven subfamilies of mammalian ABC transporters (ABCA, ABCB, ABCC,… ABCG), of which the E and F subfamilies do not bear actual transport function (Dean et al., 2001; Ford and Beis, 2019). A new classification of the ABC transporter superfamily that is based on the transmembrane domain (TMD) fold has recently been suggested (Thomas et al., 2020). CFTR is denoted ABCC7 and a member of type IV, respectively, according to these two classification schemes. CFTR bears ATPase activity like that of other ABCC subfamily members (Li et al., 1996; Stratford et al., 2007; Jordan et al., 2008), but biophysical methods have firmly established that CFTR functions as a phosphorylation-activated and ATP-gated ion channel (Anderson et al., 1991a; Anderson et al., 1991b; Bear et al., 1992; Berger et al., 1991; Sheppard et al., 1993), whereas its closest ABCC relatives function as multispecific exporters of organic anions (Jordan et al., 2008). CFTR may directly mediate the flux of glutathione (Gao et al., 1999; Kogan et al., 2003; Linsdell and Hanrahan, 1998), although CFTR-mediated active transport has not been shown, to our knowledge. Glutathione is transported by close ABCC relatives ABCC1/MRP1 (Mao et al., 1999) and ABCC4/MRP4 (Choi et al., 2001; Ko et al., 2002; Kogan et al., 2003; Ritter et al., 2005; Serrano et al., 2006); previous analysis has identified ABCC4 as CFTR’s closest relative (Jordan et al., 2008; see also Cui et al., 2019a). The domain organization of CFTR is similar to that of its closest relatives, the “short transporters” of the ABCC subfamily (Jordan et al., 2008; Ford and Beis, 2019; Srikant and Gaudet, 2019), with two nucleotide-binding domains (NBDs) that function in ATP binding and hydrolysis, and two TMDs, each containing six TM helices that comprise the substrate transport pathway (Fig. 1). However, unique to CFTR is an intracellular regulatory (R) domain that contains multiple consensus sites for phosphorylation by PKA (Sebastian et al., 2013).Open in a separate windowFigure 1.Domain architecture of CFTR. (A) Five functional domains: TMD1, NBD1, R domain with multiple phosphorylation sites, TMD2, and NBD2. Each TMD includes six transmembrane helices, numbered 1–12. The N-terminus includes the lasso motif (shown in pink), whereas the C-terminus includes a PDZ binding domain motif (yellow). (B) hCFTR from cryo-EM structure (PDB accession no. 6MSM). The R domain is not shown, because it is intrinsically unstructured.The opening of CFTR may be simplified to involve three sequential steps that have been uncovered via a combination of functional and structural data. First, PKA binds to (Mihályi et al., 2020) and phosphorylates (Rich et al., 1991) the aforementioned R domain, which results in loss of inhibitory interactions between that domain and the rest of the channel protein. Second, ATP binds to two sites at the interface of the cytoplasmic NBDs, which promotes a stable NBD dimer (Mense et al., 2006; Vergani et al., 2005). Finally, the wave of conformational changes associated with ATP-induced dimerization of the NBDs is transmitted to the pore domain, resulting in pore opening (Rahman et al., 2013; Simhaev et al., 2017; Sorum et al., 2015; Strickland et al., 2019). In related ABC exporters, ATP-dependent dimerization of the NBDs drives an overall transition from inward- to outward-facing conformation of the TMDs; this function was coopted by CFTR to drive ATP-induced channel opening (Fig. 2). At the level of individual residues, there is high conservation with transporters among amino acids in CFTR that are proposed to stabilize the inward-facing (closed) conformation in the absence of ATP (Wang et al., 2010; Wei et al., 2014; Wei et al., 2016), suggesting conservation of motifs integral to energetic signaling (Wang et al., 2014b; Wei et al., 2014; Wei et al., 2016). The close proximity of intracellular loops 2 and 4 (ICL2 and ICL4, respectively; Doshi et al., 2013; Wang et al., 2014b), constriction of the intracellular vestibule (Bai et al., 2011), and dilation of the extracellular vestibule, relative to the closed state, are all associated with channel opening (Beck et al., 2008; Infield et al., 2016; Norimatsu et al., 2012b; Rahman et al., 2013; Strickland et al., 2019). The CFTR pore opens in stages, requiring the sequential breaking and forming of intraprotein residue–residue interactions (Cui et al., 2013, 2014; Rahman et al., 2013), resulting in two subconductance states in addition to the full-conductance state (Gunderson and Kopito, 1995; Zhang et al., 2005a; Zhang et al., 2005b; Fig. 3). Using a particularly informative cysteine mutant at the outer vestibule, R334C-CFTR, the McCarty laboratory found that transitions between these subconductance states are highly dependent upon experimental conditions; for example, closing transitions almost always start from the s2 state in the presence of ATP, and transitions from s2 to f never occur in channels bound with the poorly hydrolyzable ATP analogue AMP-PNP (see also Langron et al., 2018), suggesting that this transition requires hydrolysis of nucleotide at the NBDs (Zhang et al., 2005a; Zhang et al., 2005b). Subconductance states are evident in recordings of WT CFTR from membrane patches and planar lipid bilayers, depending on experimental conditions, indicating that these represent inherent steps in gating of the channel pore (Gunderson and Kopito, 1995). In WT-hCFTR, this open pore is quite stable and does not close until ATP is hydrolyzed at the NBDs (Baukrowitz et al., 1994). Note that because CFTR displays three types of gating in one channel (phosphorylation-mediated, ligand-mediated, and pore-mediated gating), it serves as an exemplary target for studying the evolution of functional mechanisms within a single membrane protein.Open in a separate windowFigure 2.Hypothesis for emergence of channel function in CFTR. Modification of ATP-dependent transport activity in ABC transporters led to channel behavior, coopting the conformational changes necessary for unidirectional substrate transport in common ABC transporter systems. CFTR evolved features that break the alternating access cycle (solid-line arrows), enabling it to be open at both ends (box). Color scheme for major domains (again, lacking the R domain) is the same as in Fig. 1.Open in a separate windowFigure 3.Gating scheme for CFTR. Prephosphorylated channels are shown in the membrane (gray slab) with two TMDs (brown and dark blue) and two NBDs (green and light blue), with ATP (red circle) and ADP (yellow circle). ATP-dependent gating is shown as including NBD-mediated gating steps leading to pore gating between conductance levels. Here, we do not distinguish between s1 and s2 subconductance levels, because s1→s2 occurs very rapidly in WT-hCFTR.Natural history of the CFTR channel in vertebratesGiven the structural conservation among CFTR and ABC exporters noted above, and functional conservation in terms of ATP dependence, how CFTR evolved to function as an anion channel regulating passive ionic diffusion has been an enduring question (Srikant, 2020; Srikant et al., 2020). Molecular evolution studies are facilitated by the availability of many orthologues for the protein/gene of interest, spanning as much of the evolutionary record as possible. Currently, ∼300 CFTR orthologues are included in GenBank/UniProt, although not all of these are represented by expressible cDNA clones. Until very recently, the oldest CFTR orthologue known was from the dogfish shark, arising ∼150 million yr ago (MYA; Fig. 4; Marshall et al., 1991); this orthologue bears functional characteristics similar to those of hCFTR. However, reasoning that the identification of an earlier CFTR orthologue with altered structure/function would provide novel insight into the evolution of epithelial anion transport, the Gaggar and McCarty laboratories recently led an effort to clone and characterize the Lp-CFTR (Cui et al., 2019a), which arose ∼550 MYA (Smith et al., 2013). The identification of a CFTR orthologue in the jawless vertebrates establishes that CFTR exists across all vertebrates, predating the divergence of jawed and jawless vertebrates at the end of the Cambrian Period ∼488 MYA. Sequence analysis indicates 46% sequence identity and 65% sequence similarity between Lp-CFTR and hCFTR, which is much lower than that among jawed vertebrate CFTRs (jv-CFTRs) and includes surprising divergence in functionally relevant motifs. Accordingly, Lp-CFTR differs from hCFTR in multiple functional characteristics (Fig. 4). Thus, it cannot be automatically assumed that every position in CFTR that is unique in sea lamprey represents transitional change in the development of regulated channel activity. A good example in this regard is that of F508 in hCFTR, which is conserved across multiple ABC proteins but is leucine in lamprey (Cui et al., 2019a). Sorum et al. (2017) showed that replacing F508 with L in hCFTR significantly reduced its open probability. All known CFTRs other than Lp-CFTR and all known human ABCCs have F at this position, where the aromatic side chain is necessary for stabilizing the outward-facing state (Cui et al., 2006), so finding that this is substituted by a nonaromatic side chain in Lp-CFTR is mechanistically interesting and may represent a species-specific adaptation (Cui et al., 2019a).Open in a separate windowFigure 4.Simplified and truncated evolutionary tree for vertebrates. Green, common vertebrate ancestor; blue, jawless vertebrates; red and yellow, jawed vertebrates; yellow, mammals. CFTR orthologues studied in functional assays are shown underlined. (The time domain in this figure is not implied.)Table 1.Comparison of features between human and lamprey orthologues, focusing on three major domains of function: channel behavior, regulation, and modulation
Open in a separate windowNPPB, 5-nitro-2-(3-phenyl-propylamino) benzoic acid. Related to Cui et al., 2019a.Below, we identify several potential routes by which CFTR evolved regulated channel behavior. We propose that many features shared among bona fide ABCC proteins and present in recent ABCC ancestors of CFTR provided a unique opportunity for emergence of novel channel function by incremental evolutionary changes.Molecular evolution of channel functionConstruction of an anionic pore from an anionic substrate pathwayBoth the passive conduction of anions by CFTR and the unidirectional transport of highly structurally diverse organic anions by its ABCC relatives (Sauna et al., 2004) is accomplished by pathways through the TMDs. Therefore, divergence in these pathways would be expected to most closely reflect the principal difference between channels and transporters: channels contain a pore that allows uninterrupted permeation across the plasma membrane, a violation of the “alternating access” mechanism of transporters (Fig. 2; Bai et al., 2011; Gadsby, 2009). This divergence would be accomplished by evolutionary changes distributed broadly through the TMDs, as suggested by a recent study of mutations that alter substrate specificity in a fungal pheromone transporter (Srikant and Gaudet, 2019; Srikant et al., 2020). In formation of the CFTR chloride channel, this would require both degradation of the “gates” seen in ABC transporters and stabilization of an open pore conformation (Bai et al., 2011). The relationship between substrate binding and opening/closure of these gates, relevant to establishing the occluded state in transporters, may remain in CFTR in a vestigial state, as evidenced by reports that permeating anions may affect gating transitions (Sorum et al., 2015; Yeh et al., 2015; Zhang et al., 2000; Zhang et al., 2002).Understanding how the CFTR pore evolved requires the integration of functional and structural information. Early 2-D electron crystallography of hCFTR at low resolution (Rosenberg et al., 2004; Rosenberg et al., 2011) confirmed the general ABC-like architecture of CFTR predicted in the initial gene discovery study (Riordan et al., 1989). In addition, several homology models of CFTR were developed using structures of related ABC transporters as a template. These studies contributed to the understanding of the molecular interface encompassing the most common CF-causing mutation (ΔF508; Mornon et al., 2008; Serohijos et al., 2008), as well as several details relating to the conformational transitions underlying CFTR gating (Corradi et al., 2015; Dalton et al., 2012; Furukawa-Hagiya et al., 2013; Mornon et al., 2015; Mornon et al., 2009; Rahman et al., 2013; Strickland et al., 2019). However, the disparity between the wide variety of substrates of nonchannel ABC transporters and the chloride channel function of CFTR resulted in intrinsically limited confidence in these homology models, at least with respect to the TMDs.In the last 5 yr, eight structures of detergent-solubilized CFTR from three orthologues have been released from two laboratories in a large range of resolutions, all solved by single-particle cryo-EM (Fig. 5).Table 2.High-resolution CFTR structures to date
Open in a separate windowch, chicken; CHS, cholesteryl hemisuccinate; DMNG, decyl maltose neopentyl glycol; LMNG, lauryl maltose neopentyl glycol; zf, zebrafish.Open in a separate windowFigure 5.High-resolution structures of CFTR. See Liu et al., 2017; Zhang and Chen, 2016). Subsequently, the structures of phosphorylated, ATP-bound, hydrolysis-deficient mutants of zfCFTR and hCFTR in the outward-facing state were resolved at reported resolutions of 3.4 Å and 3.2 Å, respectively (Zhang et al., 2017; Zhang et al., 2018). In addition to revealing a structural motif unsuspected for CFTR—the lasso motif found in other ABCC transporters (e.g., SUR1, SUR2, MRP1) in which the N-terminus loops into the lipid bilayer (Fig. 1 A)—these CFTR structures exhibited TM helix positioning and secondary structure that may be unique to CFTR among the ABCs. Of note, TM7 and TM8 are rearranged such that the top-down TM helix symmetry of most ABC transporters is broken. There are also kinks in TM8 and TM5 helices in approximately the same vertical position. We note that two structures from recombinant thermostabilized chicken CFTR (chCFTR), one in dephosphorylated conditions with ATP present (resolution, 4.3 Å) and one in phosphorylated conditions with ATP present (resolution, 6.6 Å), show TM8 as fully helical and lack the rearrangement of TM7 and TM8, instead positioning TM7 nearly orthogonal to the fatty acid tails of the lipid bilayer (see Fig. 5; Fay et al., 2018).The positioning of TM8 in the Chen structures has been supported by functional evidence suggesting that some residues of TM8 line the CFTR channel pore (Negoda et al., 2019). The unwound portion of TM8 has been proposed by the Chen laboratory to underlie CFTR’s unique channel function (Liu et al., 2017), and molecular dynamics studies suggest that this unwinding would be maintained in a lipid bilayer (Corradi et al., 2018). The stability of this segment may be enhanced by interactions between R933, located at the intracellular boundary of the unwound portion of TM8, and E873, in TM7. In both the structures of closed hCFTR (Protein Data Bank [PDB] accession no. 5UAK) and nearly open hCFTR with ATP bound (PDB accession no. 6MSM), the oppositely charged ends of these residues essentially overlap. It is very interesting to note that R933 is conserved within CFTR and ABCC4 orthologues among both jawed and jawless vertebrates. However, E873 is conserved within jawed vertebrates but is Q in both Lp-CFTR and all ABCC4s, although this assignment must remain tentative due to the poor alignment between CFTR and ABCC4 sequences in TM7. Within the unwound stretch of TM8 itself, sequences are poorly conserved even within the CFTR and ABCC4 branches.Importantly, an open structure of CFTR with a fully conducting ion pore has yet to be published. Currently, all structures have been determined with CFTR in detergent; additional structures of CFTR in a lipidic environment may be needed to elucidate the fully conducting ion pathway as well as to understand the complex conformational transitions between open and closed states. Regardless of these considerations, these structures can certainly be used to spatially locate amino acids that have been implicated in CFTR channel function. In aid of this, significant effort has been expended to functionally map the chloride conduction pathway through CFTR. Many studies have mutated putative pore residues and characterized channel behavior and modulation (Linsdell et al., 1997; McCarty et al., 1993; McDonough et al., 1994; Tabcharani et al., 1997). To identify explicitly “pore-lining” residues, several groups have employed the substituted cysteine accessibility method. This approach probes the environment of specific residues by mutating them to cysteine and characterizing their reaction to sulfhydryl-specific chemicals (Karlin and Akabas, 1998).In the process of going through the channel to exit the cell, the chloride ion first encounters highly conserved basic residues in the ICLs, including K190, R248, R303, K370, R1030, K1041, and R1048. These residues are proposed to play roles in attracting chloride ions into the pore because charge-eliminating mutations reduce single-channel conductance (Aubin and Linsdell, 2006; El Hiani and Linsdell, 2015; Zhou et al., 2008). Considering that they mediate anion conduction, it is initially surprising that this group of residues is very highly conserved in transporter ABCCs: all seven residues analogous to those listed above are basic in ABCC4 and most (five of seven) are basic in ABCC5. To our knowledge, the effect of mutations at these positions on the function of ABCC4 or ABCC5 has not been directly tested. However, functional studies of MRP1 (ABCC1) have specifically implicated several basic residues in analogous regions in the binding of organic anionic substrates (Conseil et al., 2006; Haimeur et al., 2004) that are transported by the majority of ABCCs, including ABCC4 and ABCC5 (Jansen et al., 2015; Ritter et al., 2005). These data are intriguing because they suggest that one way in which CFTR evolved chloride channel activity was to use residues already functionally important in the transport of organic anionic substrates and repurpose them toward the novel function of conducting inorganic anions through the channel pore. In further support of this, several substrates of ABCC transporters inhibit CFTR by blocking the pore from the intracellular side (Linsdell and Hanrahan, 1999). Hence, these residues may contribute to a vestigial binding site for these substrates within CFTR. Another intriguing possibility is that ABCC4 and ABCC5 may allow the conductance of chloride along with their traditional substrates during transport, in a manner akin to the leak current associated with the function of neurotransmitter transporters (Fairman et al., 1995; Sonders and Amara, 1996; Wadiche et al., 1995). Such a substrate-induced current has not yet been measured from cells expressing ABCC4 or ABCC5, although this would be expected to be of very low amplitude (due to the slower nature of transporter function) and would likely be challenging to measure because substrate binds intracellularly in these proteins.As the chloride ion travels further up the CFTR pore toward the extracellular space, it encounters pore-lining residues contributed by TM helices 1, 5, 6, 8, 9, 11, and 12 (Alexander et al., 2009; Bai et al., 2010; Bai et al., 2011; Gao et al., 2013; McDonough et al., 1994; Wang et al., 2014a; Zhang and Hwang, 2015; Zhang et al., 2005b; Zhang et al., 2002). Fig. 6 A shows the nearly open structure of hCFTR, wherein we have highlighted residues shown by the substituted cysteine accessibility method to line the pore (Akabas, 1998; Alexander et al., 2009; Aubin and Linsdell, 2006; Bai et al., 2010; Bai et al., 2011; El Hiani and Linsdell, 2015; El Hiani et al., 2016; Fatehi and Linsdell, 2009; Gao et al., 2013; Liu et al., 2004; Negoda et al., 2019; Norimatsu et al., 2012a; Norimatsu et al., 2012b; Qian et al., 2011; Rubaiy and Linsdell, 2015; Serrano et al., 2006; Wang et al., 2011; Wang et al., 2014a; Zhang and Hwang, 2015; Zhou et al., 2008). Residues are colored according to conservation between CFTR and ABCC4 (Jordan et al., 2008; dark blue, conserved; black, similar; magenta, divergent).Open in a separate windowFigure 6.Conservation with ABCC4 in residues lining the CFTR channel pore. (A) hCFTR structure (PDB accession no. 6MSM) in nearly open state, showing major domains, with sections of non–pore-lining helices removed in order to visualize the chloride ion permeation pathway. Dark blue residues, identical between jawed vertebrate consensus CFTR and ABCC4; black residues, biochemically similar; magenta, biochemically divergent. The highly divergent pore-lining TM6 is bounded in red. (B) hCFTR (PDB accession no. 6MSM) is again shown, highlighting a lateral portal proposed to enable unique chloride channel activity among ABCCs. Inset is a closeup view of a kink in TM6. P355 is conserved with ABCC4, whereas R352 and Q353 are divergent.Strikingly, the pore-lining residues of several TMs are highly conserved between CFTR and ABCC4; for example, in TM1, six of seven pore-lining residues in CFTR are identical in ABCC4. Regarding this conservation, TM6 (see region bounded in red in Fig. 6) is an outlier, both in terms of the number of biochemically divergent pore-lining residues and as calculated as a sum of the Grantham scores (incorporating differences in composition, polarity, and molecular volume; Grantham, 1974) to gauge evolutionary distance between consensus amino acids of CFTR and ABCC4 sequences from jawed vertebrates (Alexander et al., 2009; Bai et al., 2010; Norimatsu et al., 2012a), whereas residues F337 through V345 exhibit a helical pattern of modification by MTS reagents applied intracellularly (Bai et al., 2010; El Hiani and Linsdell, 2010). This also contrasts with better-conserved helices such as TM1 and TM11, wherein reactivity follows a helical periodicity (Region Residue numbers Aggregate Grantham scorea TM1 92, 95, 98, 102, 106, 107, 109 111 ICL1 186, 188, 189, 190, 32 TM3 191, 192, 193, 194, 195, 196, 197, 199, 200, 203, 205, 207, 211, 213, 215 532 ICL2 241, 243, 244, 248, 252, 299, 303, 142 TM5 306, 307, 310, 311, 326 209 TM6 331, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 344, 345, 348, 349, 352, 353, 355, 356, 360, 367, 370 1,389 TM8 913, 914, 917 327 ICL3 986, 988, 989, 990 0 TM9 993, 1000, 1003, 1008, 1009, 1010 361 ICL4 1030, 1041, 1048 0 TM11 1112, 1115, 1118 58 TM12 1127, 1129, 1131, 1132, 1134, 1135, 1137, 1138, 1139, 1140, 1141, 1142, 1144, 1145, 1147, 1148, 1150, 1152, 1156 561
Lp-CFTR | hCFTR | |
---|---|---|
Functional domain: channel behavior | ||
Open channel stability (open burst duration) | Low | High |
Frequency of subconductance states | High | Low |
Single-channel open conductance | Low | High |
Shape of I-V relationship | Rectified | Linear |
Sensitivity to (affinity for) ATP for channel opening | Very low | High |
Functional domain: regulation by phosphorylation | ||
Rate of activation by PKA-mediated phosphorylation | Low | High |
Number of predicted PKA sites in the R domain | 4 | 8 |
Functional domain: pharmacological modulation | ||
Effect of VX-770/ivacaftor (inhibition versus potentiation) | Small inhibition | Potentiation |
Inhibition by CFTRinh172 | Low | High |
Sensitivity to pore block by GlyH-101 | None | High |
Sensitivity to pore block by NPPB | Low | High |
Sensitivity to pore block by glibenclamide | Equal | Equal |
Protein | zfCFTR | hCFTR | zfCFTR | hCFTR | hCFTR | hCFTR | chCFTR | chCFTR |
---|---|---|---|---|---|---|---|---|
Orthologue | Zebrafish | Human | Zebrafish | Human | Human | Human | Chicken | Chicken |
Resolution | 3.7 Å | 3.9 Å | 3.4 Å | 3.2 Å | 3.3 Å | 3.2 Å | 4.3 Å | 6.6 Å |
Detergent | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (DMNG, digitonin) | Detergent (DMNG, digitonin) |
Mutation | – | – | E1372Q | E1371Q | E1371Q | E1371Q | ΔRI/1404S/1441X | ΔRI/1404S/1441X |
State | Closed, inward facing, dephosphorylated, apo-ATP | Closed, inward facing, dephosphorylated, apo-ATP | Closed, outward facing, phosphorylated, ATP-bound | Closed, outward facing, Phosphorylated, ATP-bound | Closed, outward facing, Phosphorylated, ATP-bound, VX-770-bound | Closed, outward facing, Phosphorylated, ATP-bound, GLPG1837-bound | Closed, inward facing, dephosphorylated, ATP-present | Closed, inward facing, phosphorylated, ATP-present |
PDB accession no. | 5UAR | 5UAK | 5W81 | 6MSM | 6O2P | 6O1V | 6D3R | 6D3S |
Year | 2016 | 2017 | 2017 | 2018 | 2019 | 2019 | 2018 | 2018 |