The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation

Yeast Cadmium Factor-1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4Å and 4.0Å in distinct inward-facing open conformations capturing a previously unobserved ordered state of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the lasso domain. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide long-sought after insights into how R-domains control ABCC transporter activity.

Role of Protein Kinase A-Mediated Phosphorylation in CFTR Channel Activity Regulation

Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel expressed on the apical membrane of epithelial cells, where it plays a pivotal role in chloride transport and overall tissue homeostasis. CFTR constitutes a unique member of the ATP-binding cassette transporter superfamily, due to its distinctive cytosolic regulatory (R) domain carrying multiple phosphorylation sites that allow the tight regulation of channel activity and gating. Mutations in the CFTR gene cause cystic fibrosis, the most common lethal autosomal genetic disease in the Caucasian population. In recent years, major efforts have led to the development of CFTR modulators, small molecules targeting the underlying genetic defect of CF and ultimately rescuing the function of the mutant channel. Recent evidence has highlighted that this class of drugs could also impact on the phosphorylation of the R domain of the channel by protein kinase A (PKA), a key regulatory mechanism that is altered in various CFTR mutants. Therefore, the aim of this review is to summarize the current knowledge on the regulation of the CFTR by PKA-mediated phosphorylation and to provide insights into the different factors that modulate this essential CFTR modification. Finally, the discussion will focus on the impact of CF mutations on PKA-mediated CFTR regulation, as well as on how small molecule CFTR regulators and PKA interact to rescue dysfunctional channels.

Central sensitization, illness perception and obesity should be considered when interpreting disease activity in axial spondyloarthritis

Objectives Many patients with axial spondyloarthritis (axSpA) report persistent pain even when treated with anti-inflammatory agents. Our aim was to explore the presence of central sensitization (CS) and different types of illness perceptions in patients with axSpA, and to assess their associations with disease activity assessments. Methods Consecutive outpatients from the Groningen Leeuwarden Axial Spondyloarthritis (GLAS) cohort were included. Besides standardized assessments, patients filled out the Central Sensitization Inventory (CSI), Illness Perception Questionnaire (IPQ-R) and Pain Catastrophizing Scale (PCS). Univariable and multivariable linear regression analyses were used to investigate the association between questionnaire scores, patient characteristics and disease activity assessments ASDASCRP, BASDAI and CRP. Results We included 182 patients with a mean symptom duration of 21.6 years. Mean ASDASCRP was 2.1, mean BASDAI 3.9, and median CRP 2.9. Mean CSI score was 37.8 (scale 0–100) and 45% of patients scored ≥40, indicating a high probability of CS. CSI score, IPQ-R domain identity (number of symptoms the patient attributes to their illness), and IPQ-R domain treatment control (perceived treatment efficacy), and obesity were significantly and independently associated with both ASDASCRP and BASDAI, explaining a substantial proportion of variation in these disease activity scores (R2=0.35 and R2=0.47, respectively). Only obesity was also independently associated with CRP. Conclusion CS may be common in patients with long-term axSpA. CS, as well as specific illness perceptions and obesity were all independently associated with the widely used (partially) patient-reported disease activity assessments ASDASCRP and BASDAI. Treating physicians should take this into account in the follow-up and treatment of their patients.

Simple binding of protein kinase A prior to phosphorylation allows CFTR anion channels to be opened by nucleotides

The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel is essential for epithelial salt–water balance. CFTR mutations cause cystic fibrosis, a lethal incurable disease. In cells CFTR is activated through the cAMP signaling pathway, overstimulation of which during cholera leads to CFTR-mediated intestinal salt–water loss. Channel activation is achieved by phosphorylation of its regulatory (R) domain by cAMP-dependent protein kinase catalytic subunit (PKA). Here we show using two independent approaches––an ATP analog that can drive CFTR channel gating but is unsuitable for phosphotransfer by PKA, and CFTR mutants lacking phosphorylatable serines––that PKA efficiently opens CFTR channels through simple binding, under conditions that preclude phosphorylation. Unlike when phosphorylation happens, CFTR activation by PKA binding is completely reversible. Thus, PKA binding promotes release of the unphosphorylated R domain from its inhibitory position, causing full channel activation, whereas phosphorylation serves only to maintain channel activity beyond termination of the PKA signal. The results suggest two levels of CFTR regulation in cells: irreversible through phosphorylation, and reversible through R-domain binding to PKA––and possibly also to other members of a large network of proteins known to interact with the channel.

Improving interpretability of individual Diabetes Symptom Checklist-Revised (DSC-R) scores: the role of patient characteristics

IntroductionThe Diabetes Symptom Checklist-Revised (DSC-R) is a well-validated patient-reported outcome designed to assess symptom burden in persons with type 2 diabetes mellitus (T2DM) across eight domains. The DSC-R has so far primarily been used in research settings. With the aim to make the DSC-R applicable in clinical practice by improving its interpretability, we sought to identify patient characteristics associated with DSC-R (domain) scores as a first initiative toward reference values.Research design and methodsWe used baseline data from two large observational studies to select patient characteristics significantly associated with DSC-R domain and total scores. Multivariable Tobit analyses with the backward procedure per (domain) score were performed.ResultsData from 1531 participants with T2DM were included. On a 0–100 scale, the median DSC-R total score was 15.88 (7.06–29.41), with domain scores ranging from 5.00 (0.00–22.50) (pain) to 35.00 (10.00–60.00) (fatigue). Low well-being status was most profoundly associated with higher scores across all domains. Persons with one or more complication, as well as one or more symptomatic hypoglycemic episode during the past 3 months, scored higher on (almost) all domains and the total scale.ConclusionsComplications, symptomatic hypoglycemia, and low well-being are important characteristics to take into account when using the DSC-R in individual patients. Further validation of our findings is warranted in diverse patient populations.

Protein kinase A phosphorylation potentiates cystic fibrosis transmembrane conductance regulator gating by relieving autoinhibition on the stimulatory C terminus of the regulatory domain

Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel activated by protein kinase A (PKA) phosphorylation on the regulatory (R) domain. Phosphorylation at several R domain residues stimulates ATP-dependent channel openings and closings, termed channel gating. To explore the protein segment responsible for channel potentiation and PKA-dependent activation, deletion mutations were constructed by removing one to three protein segments of the R domain including residues 708–759 (ΔR708–759), R760–783, and R784–835, each of which contains one or two PKA phosphorylation sites. Deletion of R708–759 or R760–783 had little effect on CFTR gating, whereas all mutations lacking R784–835 reduced CFTR activity by decreasing the mean burst duration and increasing the interburst interval (IBI). The data suggest that R784–835 plays a major role in stimulating CFTR gating. For ATP-associated regulation, ΔR784–835 had minor impact on gating potentiation by 2′dATP, CaATP, and pyrophosphate. Interestingly, introducing a phosphorylated peptide matching R809–835 shortened the IBI of ΔR708–835-CFTR. Consistently, ΔR815–835, but not ΔR784–814, enhanced IBI, whereas both reduced mean burst duration. These data suggest that the entirety of R784–835 is required for stabilizing the open state of CFTR; however, R815–835, through interactions with the channel, is dominant for enhancing the opening rate. Of note, PKA markedly decreased the IBI of ΔR708–783-CFTR. Conversely, the IBI of ΔR708–814–CFTR was short and PKA-independent. These data reveal that for stimulating CFTR gating, PKA phosphorylation may relieve R784–814–mediated autoinhibition that prevents IBI shortening by R815–835. This mechanism may elucidate how the R domain potentiates channel gating and may unveil CFTR stimulation by other protein kinases.

Efficient nonenzymatic cyclization and domain shuffling drive pyrrolopyrazine diversity from truncated variants of a fungal NRPS

Nonribosomal peptide synthetases (NRPSs) generate the core peptide scaffolds of many natural products. These include small cyclic dipeptides such as the insect feeding deterrent peramine, which is a pyrrolopyrazine (PPZ) produced by grass-endophyticEpichloëfungi. Biosynthesis of peramine is catalyzed by the 2-module NRPS, PpzA-1, which has a C-terminal reductase (R) domain that is required for reductive release and cyclization of the NRPS-tethered dipeptidyl-thioester intermediate. However, some PpzA variants lack this R domain due to insertion of a transposable element into the 3′ end ofppzA. We demonstrate here that these truncated PpzA variants utilize nonenzymatic cyclization of the dipeptidyl thioester to a 2,5-diketopiperazine (DKP) to synthesize a range of novel PPZ products. Truncation of the R domain is sufficient to subfunctionalize PpzA-1 into a dedicated DKP synthetase, exemplified by the truncated variant, PpzA-2, which has also evolved altered substrate specificity and reducedN-methyltransferase activity relative to PpzA-1. Further allelic diversity has been generated by recombination-mediated domain shuffling betweenppzA-1andppzA-2, resulting in theppzA-3andppzA-4alleles, each of which encodes synthesis of a unique PPZ metabolite. This research establishes that efficient NRPS-catalyzed DKP biosynthesis can occur in vivo through nonenzymatic dipeptidyl cyclization and presents a remarkably clean example of NRPS evolution through recombinant exchange of functionally divergent domains. This work highlights that allelic variants of a single NRPS can result in a surprising level of secondary metabolite diversity comparable to that observed for some gene clusters.

Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes

ABSTRACT Members of the Tombusviridae family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the Tombusviridae family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the “arm” region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the Tombusviridae viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus Aureusvirus) and red clover necrotic mosaic virus (RCNMV; genus Dianthovirus) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the Tombusviridae family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell. IMPORTANCE Members of the Tombusviridae family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the “arm,” seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.

Distinct psychopathology profiles in patients with epileptic seizures compared to non-epileptic psychogenic seizures

ObjectiveSimilarities in clinical presentations between epileptic seizures (ES) and psychogenic non-epileptic seizures (PNES) produces a risk of misdiagnosis. Video-EEG monitoring (VEM) is the diagnostic gold standard, but involves significant cost and time commitment, suggesting a need for efficient screening tools.Methods628 patients were recruited from an inpatient VEM unit; 293 patients with ES, 158 with PNES, 31 both ES and PNES, and 146 non-diagnostic. Patients completed the SCL-90-R, a standardised 90-item psychopathology instrument. Bayesian linear models were computed to investigate whether SCL-90-R domain scores or the overall psychopathology factor p differed between groups. Receiver operating characteristic (ROC) curves were computed to investigate the PNES classification accuracy of each domain score and p. A machine learning algorithm was also used to determine which subset of SCL-90-R items produced the greatest classification accuracy.ResultsEvidence was found for elevated scores in PNES compared to ES groups in the symptom domains of anxiety (b = 0.47, 95%HDI = [0.10, 0.80]), phobic anxiety (b = 1.32, 95%HDI = [0.98, 1.69]), somatisation (b = 0.84, 95%HDI = [0.49, 1.20]), and the general psychopathology factor p (b = 1.35, 95%HDI = [0.86, 1.82]). Of the SCL-90-R domain scores, somatisation produced the highest classification accuracy (AUC = 0.74, 95%CI = [0.69, 0.79]). The genetic algorithm produced a 6-item subset from the SCL-90-R, which produced comparable classification accuracy to the somatisation scores (AUC = 0.73, 95%CI = [0.64, 0.82]).SignificanceCompared to patients with ES, patients with PNES report greater symptoms of somatisation, general anxiety, and phobic anxiety against a background of generally elevated psychopathology. While self-reported psychopathology scores are not accurate enough for diagnosis in isolation, elevated psychopathology in these domains should raise the suspicion of PNES in clinical settings.