Structural Mechanism for Cargo Recognition by the Retromer Complex.

Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and underlie some forms of Alzheimer's disease and Parkinson's disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.

TOR complex 1 negatively regulates NDR kinase Cbk1 to control cell separation in budding yeast.

The target of rapamycin (TOR) signalling pathway plays a key role in the coordination between cellular growth and the cell cycle machinery in eukaryotes. The underlying molecular mechanisms by which TOR might regulate events after anaphase remain unknown. We show for the first time that one of the 2 TOR complexes in budding yeast, TORC1, blocks the separation of cells following cytokinesis by phosphorylation of a member of the NDR (nuclear Dbf2-related) protein-kinase family, the protein Cbk1. We observe that TORC1 alters the phosphorylation pattern of Cbk1 and we identify a residue within Cbk1 activation loop, T574, for which a phosphomimetic substitution makes Cbk1 catalytically inactive and, indeed, reproduces TORC1 control over cell separation. In addition, we identify the exocyst component Sec3 as a key substrate of Cbk1, since Sec3 activates the SNARE complex to promote membrane fusion. TORC1 activity ultimately compromises the interaction between Sec3 and a t-SNARE component. Our data indicate that TORC1 negatively regulates cell separation in budding yeast by participating in Cbk1 phosphorylation, which in turn controls the fusion of secretory vesicles transporting hydrolase at the site of division.

The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair.

The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP-dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA-binding activity. The results suggest that MR is an ATP-controlled transient molecular clamp at DNA double-strand breaks.

Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model.

Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.

Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases.

Hyperthermophilic ('superheat-loving') archaea found in high-temperature environments such as Pyrobaculum aerophilum contain multicopper oxidases (MCOs) with remarkable efficiency for oxidizing cuprous and ferrous ions. In this work, directed evolution was used to expand the substrate specificity of P. aerophilum McoP for organic substrates. Six rounds of error-prone PCR and DNA shuffling followed by high-throughput screening lead to the identification of a hit variant with a 220-fold increased efficiency (kcat/Km) than the wild-type for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) without compromising its intrinsic activity for metal ions. The analysis of the X-ray crystal structure reveals four proximal mutations close to the T1Cu active site. One of these mutations is within the 23-residues loop that occludes this site, a distinctive feature of prokaryotic MCOs. The increased flexibility of this loop results in an enlarged tunnel and one additional pocket that facilitates bulky substrate-enzyme interactions. These findings underscore the synergy between mutations that modulate the dynamics of the active-site loop enabling enhanced catalytic function. This study highlights the potential of targeting loops close to the T1Cu for engineering improvements suitable for biotechnological applications.

Rationally Guided Improvement of NOV1 Dioxygenase for the Conversion of Lignin-Derived Isoeugenol to Vanillin.

Biocatalysis is a key tool in both green chemistry and biorefinery fields. NOV1 is a dioxygenase that catalyzes the one-step, coenzyme-free oxidation of isoeugenol into vanillin and holds enormous biotechnological potential for the complete valorization of lignin as a sustainable starting material for biobased chemicals, polymers, and materials. This study integrates computational, kinetic, structural, and biophysical approaches to characterize a new NOV1 variant featuring improved activity and stability compared to those of the wild type. The S283F replacement results in a 2-fold increased turnover rate (kcat) for isoeugenol and a 4-fold higher catalytic efficiency (kcat/Km) for molecular oxygen compared to those of the wild type. Furthermore, the variant exhibits a half-life that is 20-fold higher than that of the wild type, which most likely relates to the enhanced stabilization of the iron cofactor in the active site. Molecular dynamics supports this view, revealing that the S283F replacement decreases the optimal pKa and favors conformations of the iron-coordinating histidines compatible with an increased level of binding to iron. Importantly, whole cells containing the S283F variant catalyze the conversion of ≤100 mM isoeugenol to vanillin, yielding >99% molar conversion yields within 24 h. This integrative strategy provided a new enzyme for biotechnological applications and mechanistic insights that will facilitate the future design of robust and efficient biocatalysts.

Geo-Spatial Economic Assessment of the Potential Development of Bioenergy Combined with Direct Air Carbon Capture (BEDAC) in the USA.

This study presents a geo-spatial and economic framework to localize future bioenergy power plants combined with direct air capture (BEDAC). This framework is applied to two regions in the USA to assess the optimal use of forest biomass and in situ carbon sequestration under three specific short-term sequestration targets. Results show that there are many locations that have both the necessary biomass and geology required for storage. The Southeast has greater potential for forestry biomass due to both the rate of growth and forested areas, but the sequestration potential is mostly limited to a CO2 solution in saline aquifers. The Pacific Northwest has more sequestration potential than the Southeast given the location of managed forests and storage sites in carbonate mineralization in bedrock. The two combined regions have a total potential sequestration of 9.3 GtCO2 for the next 20 years that can be achieved under an implicit carbon value of $249/tCO2.

Bronchobiliary fistula after stenting of biliary duct as the management of iatrogenic bile duct injury during elective cholecystectomy.

BACKGROUND: Bronchobiliary fistula is a rare and complex entity defined by an abnormal communication between the biliary and bronchial systems. The etiopathogenesis is not completely understood, but the most common factors implicated are hepatobiliary tumors, biliary obstruction, iatrogenic damage or trauma. METHODS: Here we present a case of a 69-year-old man that developed a bronchobiliary fistula and a pulmonary abscess after migration of a bile duct stent placed as part of the treatment of an iatrogenic bile duct injury that occurred during elective cholecystectomy. RESULTS: A conservative approach, that included broad-spectrum antibiotic, removal of the stent, and sphincterotomy, was enough for the closure of the fistula and resolution of the symptoms. CONCLUSION: We emphasize the importance of prompt recognition of this entity and a concerted therapeutic strategy to optimize the probability of success, avoiding the destructive consequences of the bile in the pulmonary parenchyma and septic complications.

Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD.

AMPylation, the post-translational modification with adenosine monophosphate (AMP), is catalyzed by effector proteins from a variety of pathogens. Legionella pneumophila is thus far the only known pathogen that, in addition to encoding an AMPylase (SidM/DrrA), also encodes a deAMPylase, called SidD, that reverses SidM-mediated AMPylation of the vesicle transport GTPase Rab1. DeAMPylation is catalyzed by the N-terminal phosphatase-like domain of SidD. Here, we determined the crystal structure of full length SidD including the uncharacterized C-terminal domain (CTD). A flexible loop rich in aromatic residues within the CTD was required to target SidD to model membranes in vitro and to the Golgi apparatus within mammalian cells. Deletion of the loop (Δloop) or substitution of its aromatic phenylalanine residues rendered SidD cytosolic, showing that the hydrophobic loop is the primary membrane-targeting determinant of SidD. Notably, deletion of the two terminal alpha helices resulted in a CTD variant incapable of discriminating between membranes of different composition. Moreover, a L. pneumophila strain producing SidDΔloop phenocopied a L. pneumophila ΔsidD strain during growth in mouse macrophages and displayed prolonged co-localization of AMPylated Rab1 with LCVs, thus revealing that membrane targeting of SidD via its CTD is a critical prerequisite for its ability to catalyze Rab1 deAMPylation during L. pneumophila infection.

Changes in food behavior during the first lockdown of COVID-19 pandemic: A multi-country study about changes in eating habits, motivations, and food-related behaviors.

The COVID-19 pandemic resulted in severe, unprecedented changes affecting the world population. Restrictions in mobility, social distancing measures, and the persistent social alarm, during the first period of pandemic, resulted in dramatic lifestyle changes and affected physical and psychological wellbeing on a global scale. An international research team was constituted to develop a study involving different countries about eating motivations, dietary habits and behaviors related with food intake, acquisition, and preparation. This study presents results of an online survey, carried out during the first lockdown, in 2020, assessing food-related behavior and how people perceived them to change, comparatively to the period preceding the COVID-19 outbreak. A total of 3332 responses, collected from 16 countries, were considered for analysis [72.8% in Europe, 12.8% in Africa, 2.2% in North America (USA) and 12.2% in South America]. Results suggest that the main motivations perceived to drive food intake were familiarity and liking. Two clusters were identified, based on food intake frequency, which were classified as "healthier" and "unhealthier". The former was constituted by individuals with higher scholarity level, to whom intake was more motivated by health, natural concerns, and weight control, and less by liking, pleasure or affect regulation. The second cluster was constituted by individuals with a higher proportion of male and intake more influenced by affect-related motivations. During this period, a generalized lower concern with the convenience attributes of foods was noted (namely, choice of processed products and fast-food meals), alongside an increase in time and efforts dedicated to home cooking. Understanding the main changes and their underlying motivations in a time of unprecedented crisis is of major importance, as it provides the scientific support that allows one to anticipate the implications for the future of the global food and nutrition system and, consequently, to take the appropriate action.

Real-Time Observation of "Soft" Magic-Size Clusters during Hydrolysis of the Model Metallodrug Bismuth Disalicylate.

Colloidal bismuth therapeutics have been used for hundreds of years, yet remain mysterious. Here we report an X-ray pair distribution function (PDF) study of the solvolysis of bismuth disalicylate, a model for the metallodrug bismuth subsalicylate (Pepto-Bismol). This reveals catalysis by traces of water, followed by multistep cluster growth. The ratio of the two major species, {Bi9O7} and {Bi38O44}, depends on exposure to air, time, and the solvent. The solution-phase cluster structures are of significantly higher symmetry in comparison to solid-state analogues, with reduced off-center Bi3+ displacements. This explains why such "magic-size" clusters can be both stable enough to crystallize and sufficiently labile for further growth.

The Area of Pressure-Induced Referred Pain Is Dependent on the Intensity of the Suprathreshold Stimulus: An Explorative Study.

OBJECTIVE: To investigate the pain referral area (number of pixels) and extent (vector length) as elicited from increasing intensities of pressure-induced pain at the shoulder. DESIGN: Cross-sectional design. SETTING: Clinical laboratory setting. PARTICIPANTS: Twenty-two healthy men and women participated in two experimental sessions. METHODS: Delayed onset of muscle soreness (DOMS) was induced in the dominant shoulder and assessed 24 hours later. Participants rated the level of DOMS on a 6-point Likert scale. Four different intensities (pressure pain threshold [PPT]+20%, PPT+30%, PPT+40%, and PPT+50%) were applied to the infraspinatus in a randomized, balanced fashion for 60 seconds from low to high intensity or vice versa. The resulting location, area, and extent of referred pain as drawn by the participants on a digital body chart were extracted and expressed in pixels. The extent of pain was defined as the vector length extending from the ipsilateral earlobe to the most distal location of the pain. RESULTS: The referred pain area from PPT+20% was smaller than PPT+30%, PPT+40%, and PPT+50%. The extent of referred pain did not differ between the pressure pain intensities. CONCLUSIONS: Pressure intensity at PPT+30%, but no more, produces the greatest referred pain area as compared with the traditional pressure intensity of PPT+20%. Thus, the intensity of PPT+30% may be ideal for exploring the mechanisms of referred pain. The extent of the pain represents an independent expression of the intensity of the provoking stimulus and may be more closely related to the location of the stimulus.

Multicomponent intervention provided by GPs to reduce cardiovascular risk factors: evaluation in an Italian large sample.

BACKGROUND: The cardiovascular risk increases in a multiplicative way when patients present more risk factors simultaneously. Moreover, the General Practitioners (GPs) play a crucial role in risk factors prevention and reduction. This work aimed to evaluate a multicomponent intervention in the Primary Care Department in an Italian Local Health Unit. METHODS: A pre-post study was conducted in Northern Italy (2018). Patients were eligible if: aged between 30 and 60 years, not chronic patients, not affected by hypertension or hypercholesterolaemia. The GPs assessed body mass index, hypertension, abdominal obesity, low-density lipoprotein (LDL) values, glycaemic values, smoking and exercise habit (T0). A counselling by GPs to at-risk patients and a multicomponent health education intervention were performed. Reassessment occurred after at least 3 months (T1). Main analyses were chi-squared tests for gender differences, McNemar or marginal homogeneity tests for changes in paired data (P < 0.05 as significant). RESULTS: Participants were 5828 at T0 (54.0% females) and 4953 at T1 (53.4% females). At T0, 99.1% presented at least one risk factor. Significant changes in paired data were reported for each risk factor. The greatest improvement frequencies occurred in glycaemia values (51.0%) and hypertension (45.6%), the lowest in abdominal obesity (3.7%). Some differences were recorded between genders, e.g. females reported higher improvement frequencies in hypertension (P = 0.001) and abdominal obesity (P < 0.001), whereas males in physical activity (P = 0.011) and LDL values (P = 0.032). CONCLUSION: The results showed significant changes for each risk factor, both for men and women. GPs and multicomponent educational interventions could play a key role in reducing cardiovascular risk factors.

SMA-10 Is a Non-Canonical Member of the TGF-ß Sma/Mab Pathway and Immunity Regulator via the DAF-2 Insulin Receptor in Caenorhabditis elegans.

Transforming growth factor ß (TGF-ß) signalling pathways are highly conserved across metazoa and play essential roles not only during development but also in adult tissue maintenance. Alterations of these pathways usually result in a plethora of pathologies. In the nematode Caenorhabditis elegans, the TGF-ß Sma/Mab (small/male abnormal) pathway regulates various worm phenotypes such as body size, immune response, ageing, matricide and reproductive span. SMA-10 has been described as a positive modulator of worm body size through the TGF-ß Sma/Mab pathway. To better understand if SMA-10 is a core component of the pathway, we use gene epistatic analysis to assess the contribution of SMA-10 to various phenotypes regulated by TGF-ß Sma/Mab. We confirm that SMA-10 controls body size and find that it also affects the matricide and reproductive span of the nematodes. However, neither male tail formation (previously reported) nor ageing appeared altered. Lastly, although null sma-10 worms are more susceptible to Pseudomonas aeruginosa infections than wild-types, this response does not depend on TGF-ß Sma/Mab but on the insulin receptor DAF-2. We also show that the expression of sma-10 in either hypodermis or intestine fully rescues the wild-type immune response. Our results contribute to understanding the role of SMA-10 as a context-dependent component of TGF-ß Sma/Mab, and reveal a function of SMA-10 in immunity in association to the Insulin/insulin-like growth factor signalling (IIS) pathway.

Effects of Dry Needling on Biomechanical Properties of the Myofascial Trigger Points Measured by Myotonometry: A Randomized Controlled Trial.

OBJECTIVE: The purpose of the present study was to examine the effect of dry needling (DN) on the biomechanical properties of a latent medial myofascial trigger point (MTrP) of the soleus muscle compared with an adjacent point within the taut band (TB) measured by myotonometry. METHODS: Fifty asymptomatic volunteers were randomly assigned to an intervention group (n = 26) or control group (n = 24). One session of DN was performed in every group as follows: 10 needle insertions into the MTrP area (intervention group) or TB area (control group). Myotonometric measurements (frequency, decrement, and stiffness) were performed at baseline (pre-intervention) and after the intervention (post-intervention) in both locations (MTrP and TB areas). RESULTS: The results showed that stiffness outcome significantly decreased with a large effect size after DN in the MTrP when measured in the MTrP location (P = .002; d = 0.928) but not when measured in the TB location. In contrast, no significant changes were observed in any location when the TB was needled (P > .05). CONCLUSIONS: The findings suggest that only DN into the MTrP area was effective in decreasing stiffness outcome, therefore a specific puncture was needed to modify myofascial muscle stiffness.

Functional gastrointestinal disorders: real-life results of a multidisciplinary non-pharmacological approach based on group-consultations.

INTRODUCTION: functional gastrointestinal disorders are prevalent and resource consuming. The use of group-consultations in these diseases is limited and no specific multidisciplinary programs have been developed. METHODS: a multidisciplinary approach was used in patients with diverse functional gastrointestinal disorders attending group-consultations (group A). Five two-hour sessions were scheduled over a four-month period. Sessions consisted of a theoretical introduction (Pathophysiology, Low fodmap diet, Over the counter medications, Mediterranean diet, and Laughter therapy workshop) followed by relaxation techniques. This group was compared to a similar group of patients who received written information covering the topics discussed during the group-consultations (group B). Severity of digestive and psychological symptoms, use of drugs and adherence to the diet were the main outcomes measured. RESULTS: the mean age of participants was 43 (± 1.38) years, 78 % were female and 73 % had at least two functional gastrointestinal disorders. Sixty-two patients were included in group A and 17 in group B. The severity of gastrointestinal and psychological symptoms at baseline was similar in both groups. Globally, there was an improvement in all symptoms in both groups. The proportion of participants with severe baseline gastrointestinal symptoms or pathologic anxiety scores that showed improvement was significantly higher in group A (74 % vs 23 %, p = 0.005; 47 % vs 8 %, p = 0.02, respectively). Symptoms were reassessed at six and 12 months after the intervention in participants from group A who attended ≥ 80 % sessions and a sustained response was observed. CONCLUSIONS: group-consultations are useful and efficient to alleviate gastrointestinal and psychological symptoms in patients with functional gastrointestinal disorders.

Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8.

Recent reports indicate that the Type six secretion system exported effector 8 (Tse8) is a cytoactive effector secreted by the Type VI secretion system (T6SS) of the human pathogen Pseudomonas aeruginosa. The T6SS is a nanomachine that assembles inside of the bacteria and injects effectors/toxins into target cells, providing a fitness advantage over competing bacteria and facilitating host colonisation. Here we present the first crystal structure of Tse8 revealing that it conserves the architecture of the catalytic triad Lys84-transSer162-Ser186 that characterises members of the Amidase Signature superfamily. Furthermore, using binding affinity experiments, we show that the interaction of phenylmethylsulfonyl fluoride (PMSF) to Tse8 is dependent on the putative catalytic residue Ser186, providing support for its nucleophilic reactivity. This work thus demonstrates that Tse8 belongs to the Amidase Signature (AS) superfamily. Furthermore, it highlights Tse8 similarity to two family members: the Stenotrophomonas maltophilia Peptide Amidase and the Glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus.

RavN is a member of a previously unrecognized group of Legionella pneumophila E3 ubiquitin ligases.

The eukaryotic ubiquitylation machinery catalyzes the covalent attachment of the small protein modifier ubiquitin to cellular target proteins in order to alter their fate. Microbial pathogens exploit this post-translational modification process by encoding molecular mimics of E3 ubiquitin ligases, eukaryotic enzymes that catalyze the final step in the ubiquitylation cascade. Here, we show that the Legionella pneumophila effector protein RavN belongs to a growing class of bacterial proteins that mimic host cell E3 ligases to exploit the ubiquitylation pathway. The E3 ligase activity of RavN was located within its N-terminal region and was dependent upon interaction with a defined subset of E2 ubiquitin-conjugating enzymes. The crystal structure of the N-terminal region of RavN revealed a U-box-like motif that was only remotely similar to other U-box domains, indicating that RavN is an E3 ligase relic that has undergone significant evolutionary alteration. Substitution of residues within the predicted E2 binding interface rendered RavN inactive, indicating that, despite significant structural changes, the mode of E2 recognition has remained conserved. Using hidden Markov model-based secondary structure analyses, we identified and experimentally validated four additional L. pneumophila effectors that were not previously recognized to possess E3 ligase activity, including Lpg2452/SdcB, a new paralog of SidC. Our study provides strong evidence that L. pneumophila is dedicating a considerable fraction of its effector arsenal to the manipulation of the host ubiquitylation pathway.

Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.

Microbial pathogens employ sophisticated virulence strategies to cause infections in humans. The intracellular pathogen Legionella pneumophila encodes RidL to hijack the host scaffold protein VPS29, a component of retromer and retriever complexes critical for endosomal cargo recycling. Here, we determined the crystal structure of L. pneumophila RidL in complex with the human VPS29-VPS35 retromer subcomplex. A hairpin loop protruding from RidL inserts into a conserved pocket on VPS29 that is also used by cellular ligands, such as Tre-2/Bub2/Cdc16 domain family member 5 (TBC1D5) and VPS9-ankyrin repeat protein for VPS29 binding. Consistent with the idea of molecular mimicry in protein interactions, RidL outcompeted TBC1D5 for binding to VPS29. Furthermore, the interaction of RidL with retromer did not interfere with retromer dimerization but was essential for association of RidL with retromer-coated vacuolar and tubular endosomes. Our work thus provides structural and mechanistic evidence into how RidL is targeted to endosomal membranes.