ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites

ToxR, a Vibrio cholerae transmembrane one-component signal transduction factor, lies within a regulatory cascade that results in the expression of ToxT, toxin coregulated pilus, and cholera toxin. While ToxR has been extensively studied for its ability to activate or repress various genes in V. cholerae, here we present the crystal structures of the ToxR cytoplasmic domain bound to DNA at the toxT and ompU promoters. The structures confirm some predicted interactions, yet reveal other unexpected promoter interactions with implications for other potential regulatory roles for ToxR. We show that ToxR is a versatile virulence regulator that recognizes diverse and extensive, eukaryotic-like regulatory DNA sequences, that relies more on DNA structural elements than specific sequences for binding. Using this topological DNA recognition mechanism, ToxR can bind both in tandem and in a twofold inverted-repeat-driven manner. Its regulatory action is based on coordinated multiple binding to promoter regions near the transcription start site, which can remove the repressing H-NS proteins and prepares the DNA for optimal interaction with the RNA polymerase.

Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein

DNA replication is essential to all living organisms as it ensures the fidelity of genetic material for the next generation of dividing cells. One of the simplest replication initiation mechanisms is the rolling circle replication. In the streptococcal plasmid pMV158, which confers antibiotic resistance to tetracycline, replication initiation is catalysed by RepB protein. The RepB N-terminal domain or origin binding domain binds to the recognition sequence (bind locus) of the double-strand origin of replication and cleaves one DNA strand at a specific site within the nic locus. Using biochemical and crystallographic analyses, here we show how the origin binding domain recognises and binds to the bind locus using structural elements removed from the active site, namely the recognition α helix, and a β-strand that organises upon binding. A new hexameric structure of full-length RepB that highlights the great flexibility of this protein is presented, which could account for its ability to perform different tasks, namely bind to two distinct loci and cleave one strand of DNA at the plasmid origin.

Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404

Severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) pose a threat to global public health. The 3C-like main protease (M^pro), which presents structural similarity with the active site domain of enterovirus 3C protease, is one of the best-characterized drug targets of these viruses. Here we studied the antiviral activity of the orally bioavailable enterovirus protease inhibitor AG7404 against SARS-CoV-1 and SARS-CoV-2 from a structural, biochemical, and cellular perspective, comparing it with the related molecule rupintrivir (AG7800). Crystallographic structures of AG7404 in complex with SARS-CoV-1 M^pro and SARS-CoV-2 M^pro and of rupintrivir in complex with SARS-CoV-2 M^pro were solved, revealing that all protein residues interacting with the inhibitors are conserved between the two proteins. A detailed analysis of protein-inhibitor interactions indicates that AG7404 has a better fit to the active site of the target protease than rupintrivir. This observation was further confirmed by biochemical FRET assays showing IC₅₀ values of 47 μM and 101 μM for AG7404 and rupintrivir, respectively, in the case of SARS-CoV-2 M^pro. Equivalent IC₅₀ values for SARS-CoV-1 also revealed greater inhibitory capacity of AG7404, with a value of 29 μM vs. 66 μM for rupintrivir. Finally, the antiviral activity of the two inhibitors against SARS-CoV-2 was confirmed in a human cell culture model of SARS-CoV-2 infection, although rupintrivir showed a higher potency and selectivity index in this assay.

[Continuous Glucose Monitoring. Which is the evidence in Children?]

Diabetes Technology refers to the software or hardware that is designed to facilitate and improve the quality of life of the patient with diabetes Mellitus. A non-systematic literature search was carried out which included articles in English and Spanish about the use of continuous glucose monitoring (CGM) in pediatric patients with Type 1 diabetes Mellitus. This review summarizes the performance of the CGM, its accuracy, and classification. A chronological synthesis of the general evidence up to June 2020 was done including both adult and pediatric studies. Aspects of metabolic control were specified on the use of real-time and intermittent / flash CGM, such as reduction of HbA1c levels, reduction in frequency and severity of hypoglycemia, decrease in episodes of ketoacidosis and well being, and variables such as the Frequency of CGM use, which have been related to the improvement of the objectives of diabetes control. This review presents a chronological summary of the evidence for flash glucose monitoring in studies where only pediatric population is included and provides an account of diabetes technology recommendations that apply to pediatric population from the Ame rican Diabetes Association 2020 guideline, the International Society for Pediatric and Adolescent Diabetes 2018 recommendations.

Transitioning a cardiovascular health and rehabilitation programme to a virtual platform during covid 19

Funding Acknowledgements

Type of funding sources: None.

OnBehalf

Our Hearts Our Minds

Purpose

Can a virtual cardiovascular prevention and rehabilitation programme be as effective as face-to-face programme.

Background

The Our Hearts Our Minds (OHOM) prevention and rehabilitation programme rapidly transitioned to a virtual platform in the covid era.  Here we compare if a virtual programme potentially could offer the same standard of the nursing intervention (education, smoking cessation, medical risk factor management and psychosocial health) as the previous face to face programme

Methods

Both the initial assessment (IA) and end of programme (EOP) assessments were conducted via telephone/video as per patient preference. The following measures were recorded at both time points (home blood pressure (BP) monitors were provided)

Smoking (self report) BP/Heart rate, Lipids/HbA1c (facilitated by phlebotomy hub), cardio protective drugs (doses, adherence), Hospital Anxiety and Depression score, EuroQoL

Nursing Intervention Smoking cessation counselling and pharmacotherapy where appropriate

Weekly meeting with cardiologist to optimise BP and lipid management and up titration cardio protective drugs

Bimonthly virtual coaching consultation for monitoring/goal resetting

Bimonthly group video education sessions

Results

From April to November 2020, of the 432 referrals received 400 were eligible with 377 accepting the offer of an IA (94% response rate). 262 have had an IA with the remaining 115 awaiting an assessment date.  Of the completed IA’s 257 were willing to attend the programme (98% uptake).  120 had been offered an end of programme assessment with 114 attending (96% of those offered). The results for the virtual programme were then compared to the same period one year previously when the programme was fully face to face and are outlined in the table below.

The comparison of results delivered via remote delivery are remarkably similar to those achieved in the previous year delivered via face to face.

Conclusion

Initial data has shown that virtual delivery of the nursing component of the OHOM prevention/rehabilitation programme was highly acceptable to patients and was as effective as that of the traditional face to face service.

Table 1 below exhibits the clinical and patient-reported outcomes.

Ecological and economic effects of COVID-19 in marine fisheries from the Northwestern Mediterranean Sea

The SARS-CoV-2 coronavirus pandemic starting at the end of 2019 impacted many human activities. We analysed the abrupt reduction in fishing pressure of the mixed small-scale and industrial fisheries in the Catalan Sea, Spanish Mediterranean, and resulting ecological and economic impacts during the first half of 2020. We used detailed fisheries data on fishing effort, landings, revenues, landings per unit of effort (LPUE) and revenues per unit of effort from January to June 2020, and complemented it with the outcomes of a marine ecosystem model. We analysed data from 2017 to 2019 and compared these to 2020 to characterise changes in the fishing activity from before (January-February) to during (March-May) the lockdown. Fishing effort during the lockdown dropped by 34%, landings were down by 49% and revenues declined by 39% in comparison with the same period in 2017-2019. LPUEs did not show significant changes during the lockdown, with the exception of shrimp species, especially the deep-water rose shrimp, which significantly increased in LPUE during March-May. These increases may reflect positive effects of reduced fishing on fast-growing species. Positive effects mostly disappeared in June 2020 with the relaxation of the lockdown. In agreement, the ecological simulations projected slight short-term increases of biomass for fast-growing, small-sized organisms during 2020, which quickly vanished when fishing resumed, and which had no detectable ecosystem effects. Three additional alternative ecological simulations illustrated that to substantially recover commercial species and ensure ecosystem sustainability in the study area, a sustained and notable reduction of fishing activity would be needed.

Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.

Lamotrigine induced Brugada-pattern in a patient with genetic epilepsy associated with a novel variant in SCN9A

BACKGROUND

A 30-year-old man presented with intellectual disability associated with epilepsy. The epilepsy was initially treated with sodium valproate and since he was 28 years-old with lamotrigine. With the addition of lamotrigine, a pattern of Brugada syndrome appeared on the electrocardiogram. The family history was positive for epilepsy from the motheŕs side, who had never been treated with lamotrigine.

OBJECTIVE

Determine the genetic cause of the intellectual disability, epilepsy and Brugada syndrome of the patient and try to establish a possible correlation between the genetic background and the Brugada syndrome pattern under lamotrigine treatment.

METHODS

A standard karyotype, array comparative genomic hybridization and two different NGS panels have done to the index case to identify the genetic causes of the intellectual disability, epilepsy and Brugada syndrome pattern.

RESULTS

Genetic analyses in the family identified a de novo duplication of 1.3 Mb in 8p21.3 as well as two novel heterozygous rare variants in SCN9A and AKAP9 genes, both inherited from the mother.

CONCLUSION

We hypothesize that in this family the SCN9A variant was responsible for the epileptic syndrome. In addition, given that SCN9A is lightly expressed in the heart tissue, we postulate that this SCN9A variant, alone or in combination with AKAP9 variant, might be responsible for the Brugada pattern when challenged by lamotrigine.

Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism

Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.

tRNA deamination by ADAT requires substrate-specific recognition mechanisms and can be inhibited by tRFs

Adenosine deaminase acting on transfer RNA (ADAT) is an essential eukaryotic enzyme that catalyzes the deamination of adenosine to inosine at the first position of tRNA anticodons. Mammalian ADATs modify eight different tRNAs, having increased their substrate range from a bacterial ancestor that likely deaminated exclusively tRNA^Arg Here we investigate the recognition mechanisms of tRNA^Arg and tRNA^Ala by human ADAT to shed light on the process of substrate expansion that took place during the evolution of the enzyme. We show that tRNA recognition by human ADAT does not depend on conserved identity elements, but on the overall structural features of tRNA. We find that ancestral-like interactions are conserved for tRNA^Arg, while eukaryote-specific substrates use alternative mechanisms. These recognition studies show that human ADAT can be inhibited by tRNA fragments in vitro, including naturally occurring fragments involved in important regulatory pathways.

Future scenarios of marine resources and ecosystem conditions in the Eastern Mediterranean under the impacts of fishing, alien species and sea warming

Using a temporal-dynamic calibrated Ecosim food web model, we assess the effects of future changes on marine resources and ecosystem conditions of the Israeli Mediterranean continental shelf. This region has been intensely invaded by Indo-Pacific species. The region is exposed to extreme environmental conditions, is subjected to high rates of climate change and has experienced intense fishing pressure. We test the impacts of a new set of fishing regulations currently being implemented, a continued increase in sea temperatures following IPCC projections, and a continued increase in alien species biomass. We first investigate the impacts of the stressors separately, and then we combine them to evaluate their cumulative effects. Our results show overall potential future benefits of fishing effort reductions, and detrimental impacts of increasing sea temperature and increasing biomass of alien species. Cumulative scenarios suggest that the beneficial effects of fisheries reduction may be dampened by the impact of increasing sea temperature and alien species when acting together. These results illustrate the importance of including stressors other than fisheries, such as climate change and biological invasions, in an ecosystem-based management approach. These results support the need for reducing local and regional stressors, such as fishing and biological invasions, in order to promote resilience to sea warming.

Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase

Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.

Photo-identification as a tool to study small-spotted catshark Scyliorhinus canicula

Photo-identification (photo-ID) was tested as a means to identify individual small-spotted catsharks Scyliorhinus canicula. The spotting pattern of the caudal region of S. canicula was used for the tests and revealed that photo-ID is an efficient method to identify individuals. Photo-ID is logistically simple, making it a potential alternative to traditional tagging to provide information on the distribution patterns and population dynamics of S. canicula and related species.

Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE

Sulfur trafficking in living organisms relies on transpersulfuration reactions consisting in the enzyme-catalyzed transfer of S atoms via activated persulfidic S across protein-protein interfaces. The recent elucidation of the mechanistic basis for transpersulfuration in the CsdA-CsdE model system has paved the way for a better understanding of its role under oxidative stress. Herein we present the crystal structure of the oxidized, inactivated CsdE dimer at 2.4 Å resolution. The structure sheds light into the activation of the Cys61 nucleophile on its way from a solvent-secluded position in free CsdE to a fully extended conformation in the persulfurated CsdA-CsdE complex. Molecular dynamics simulations of available CsdE structures allow to delineate the sequence of conformational changes underwent by CsdE and to pinpoint the key role played by the deprotonation of the Cys61 thiol. The low-energy subunit orientation in the disulfide-bridged CsdE dimer demonstrates the likely physiologic relevance of this oxidative dead-end form of CsdE, suggesting that CsdE could act as a redox sensor in vivo.

Untangling surface oxygen exchange effects in YBa2Cu3O6+x thin films by electrical conductivity relaxation

The kinetics of oxygen incorporation (in-diffusion process) and excorporation (out-diffusion process), in YBa₂Cu₃O_6+x (YBCO) epitaxial thin films prepared using the chemical solution deposition (CSD) methodology by the trifluoroacetate route, was investigated by electrical conductivity relaxation measurements. We show that the oxygenation kinetics of YBCO films is limited by the surface exchange process of oxygen molecules prior to bulk diffusion into the films. The analysis of the temperature and oxygen partial pressure influence on the oxygenation kinetics has drawn a consistent picture of the oxygen surface exchange process enabling us to define the most likely rate determining step. We have also established a strategy to accelerate the oxygenation kinetics at low temperatures based on the catalytic influence of Ag coatings thus allowing us to decrease the oxygenation temperature in the YBCO thin films.

Neutrophil gelatinase-associated lipocalin is a biomarker of acute-on-chronic liver failure and prognosis in cirrhosis

BACKGROUND & AIMS

Acute-on-chronic liver failure (ACLF) is a syndrome that occurs in cirrhosis characterized by organ failure(s) and high mortality rate. There are no biomarkers of ACLF. The LCN2 gene and its product, neutrophil gelatinase-associated lipocalin (NGAL), are upregulated in experimental models of liver injury and cultured hepatocytes as a result of injury by toxins or proinflammatory cytokines, particularly Interleukin-6. The aim of this study was to investigate whether NGAL could be a biomarker of ACLF and whether LCN2 gene may be upregulated in the liver in ACLF.

METHODS

We analyzed urine and plasma NGAL levels in 716 patients hospitalized for complications of cirrhosis, 148 with ACLF. LCN2 expression was assessed in liver biopsies from 29 additional patients with decompensated cirrhosis with and without ACLF.

RESULTS

Urine NGAL was markedly increased in ACLF vs. no ACLF patients (108(35-400) vs. 29(12-73)μg/g creatinine; p<0.001) and was an independent predictive factor of ACLF; the independent association persisted after adjustment for kidney function or exclusion of variables present in ACLF definition. Urine NGAL was also an independent predictive factor of 28day transplant-free mortality together with MELD score and leukocyte count (AUROC 0.88(0.83-0.92)). Urine NGAL improved significantly the accuracy of MELD in predicting prognosis. The LCN2 gene was markedly upregulated in the liver of patients with ACLF. Gene expression correlated directly with serum bilirubin and INR (r=0.79; p<0.001 and r=0.67; p<0.001), MELD (r=0.68; p<0.001) and Interleukin-6 (r=0.65; p<0.001).

CONCLUSIONS

NGAL is a biomarker of ACLF and prognosis and correlates with liver failure and systemic inflammation. There is remarkable overexpression of LCN2 gene in the liver in ACLF syndrome.

LAY SUMMARY

Urine NGAL is a biomarker of acute-on-chronic liver failure (ACLF). NGAL is a protein that may be expressed in several tissues in response to injury. The protein is filtered by the kidneys due to its small size and can be measured in the urine. Ariza, Graupera and colleagues found in a series of 716 patients with cirrhosis that urine NGAL was markedly increased in patients with ACLF and correlated with prognosis. Moreover, gene coding NGAL was markedly overexpressed in the liver tissue in ACLF.

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.

The structure of the complex between α-tubulin, TBCE and TBCB reveals a tubulin dimer dissociation mechanism

Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation pathway is not clearly understood. Here, we carried out biochemical assays to dissect the role of the human TBCE and TBCB chaperones in α-tubulin-β-tubulin dissociation. We used electron microscopy and image processing to determine the three-dimensional structure of the human TBCE, TBCB and α-tubulin (αEB) complex, which is formed upon α-tubulin-β-tubulin heterodimer dissociation by the two chaperones. Docking the atomic structures of domains of these proteins, including the TBCE UBL domain, as we determined by X-ray crystallography, allowed description of the molecular architecture of the αEB complex. We found that heterodimer dissociation is an energy-independent process that takes place through a disruption of the α-tubulin-β-tubulin interface that is caused by a steric interaction between β-tubulin and the TBCE cytoskeleton-associated protein glycine-rich (CAP-Gly) and leucine-rich repeat (LRR) domains. The protruding arrangement of chaperone ubiquitin-like (UBL) domains in the αEB complex suggests that there is a direct interaction of this complex with the proteasome, thus mediating α-tubulin degradation.

Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli

In order to maintain proper cellular function, the metabolism of the bacterial microbiota presents several mechanisms oriented to keep a correctly balanced amino acid pool. Central components of these mechanisms are enzymes with alanine transaminase activity, pyridoxal 5′-phosphate-dependent enzymes that interconvert alanine and pyruvate, thereby allowing the precise control of alanine and glutamate concentrations, two of the most abundant amino acids in the cellular amino acid pool. Here we report the 2.11-Å crystal structure of full-length AlaA from the model organism Escherichia coli, a major bacterial alanine aminotransferase, and compare its overall structure and active site composition with detailed atomic models of two other bacterial enzymes capable of catalyzing this reaction in vivo, AlaC and valine-pyruvate aminotransferase (AvtA). Apart from a narrow entry channel to the active site, a feature of this new crystal structure is the role of an active site loop that closes in upon binding of substrate-mimicking molecules, and which has only been previously reported in a plant enzyme. Comparison of the available structures indicates that beyond superficial differences, alanine aminotransferases of diverse phylogenetic origins share a universal reaction mechanism that depends on an array of highly conserved amino acid residues and is similarly regulated by various unrelated motifs. Despite this unifying mechanism and regulation, growth competition experiments demonstrate that AlaA, AlaC and AvtA are not freely exchangeable in vivo, suggesting that their functional repertoire is not completely redundant thus providing an explanation for their independent evolutionary conservation.

Adnexal Glands Chemistry of Messor ebeninus Forel (Formicidae: Myrmicinae)

Anabasine is the major volatile product in the poison gland exudate of Messor ebeninus, acting as a defensive compound. Exudates of the poison gland also contain minor, yet unidentified, components that are possibly responsible for the alarm behavior that is also elicited by the venom.

Dufour’s gland secretion is characterized by aliphatic hydrocarbons of which 1-pentadecene predominates. Upon exposure to Dufour’s gland secretion the ants recruited to the emitting source, but did not exhibit any aggressive behavior. The possible concordant effects of both adnexal glands secretions is discussed.

Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors

Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.

Structure and non-structure of centrosomal proteins

Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

PhoB transcriptional activator binds hierarchically to pho box promoters

The PhoR-PhoB phosphorelay is a bacterial two-component system that activates the transcription of several genes involved in phosphate uptake and assimilation. The response begins with the autophosphorylation of the sensor kinase PhoR, which activates the response regulator PhoB. Upon binding to the pho box DNA sequence, PhoB recruits the RNA polymerase and thereby activates the transcription of specific genes. To unveil hitherto unknown molecular mechanisms along the activation pathway, we report biochemical data characterizing the PhoB binding to promoters containing multiple pho boxes and describe the crystal structure of two PhoB DNA-binding domains bound in tandem to a 26-mer DNA.

σ70 and PhoB activator: getting a better grip

Transcription factors modulate gene expression by distinct, barely understood mechanisms. The crystal structure of a bacterial transcription subcomplex comprising the effector domain of factor PhoB, its target DNA and the σ4 domain of the RNA polymerase σ70 subunit supports the notion that a stronger grip on the promoter-factor complex results in an enhanced RNAP architecture.

Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability

Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied on to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase in up to 800% in comparison with the generally accepted maximum of 30-40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent or the Sp parameter. Consequently, we argue that greater standardization should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.

Nanoscale strain-induced pair suppression as a vortex-pinning mechanism in high-temperature superconductors

Boosting large-scale superconductor applications require nanostructured conductors with artificial pinning centres immobilizing quantized vortices at high temperature and magnetic fields. Here we demonstrate a highly effective mechanism of artificial pinning centres in solution-derived high-temperature superconductor nanocomposites through generation of nanostrained regions where Cooper pair formation is suppressed. The nanostrained regions identified from transmission electron microscopy devise a very high concentration of partial dislocations associated with intergrowths generated between the randomly oriented nanodots and the epitaxial YBa(2)Cu(3)O(7) matrix. Consequently, an outstanding vortex-pinning enhancement correlated to the nanostrain is demonstrated for four types of randomly oriented nanodot, and a unique evolution towards an isotropic vortex-pinning behaviour, even in the effective anisotropy, is achieved as the nanostrain turns isotropic. We suggest a new vortex-pinning mechanism based on the bond-contraction pairing model, where pair formation is quenched under tensile strain, forming new and effective core-pinning regions.

Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93

Members of the Enterovirus genus of the Picornaviridae family are abundant, with common human pathogens that belong to the rhinovirus (HRV) and enterovirus (EV) species, including diverse echo-, coxsackie- and polioviruses. They cause a wide spectrum of clinical manifestations ranging from asymptomatic to severe diseases with neurological and/or cardiac manifestations. Pandemic outbreaks of EVs may be accompanied by meningitis and/or paralysis and can be fatal. However, no effective prophylaxis or antiviral treatment against most EVs is available. The EV RNA genome directs the synthesis of a single polyprotein that is autocatalytically processed into mature proteins at Gln↓Gly cleavage sites by the 3C protease (3C(pro)), which has narrow, conserved substrate specificity. These cleavages are essential for virus replication, making 3C(pro) an excellent target for antivirus drug development. In this study, we report the first determination of the crystal structure of 3C(pro) from an enterovirus B, EV-93, a recently identified pathogen, alone and in complex with the anti-HRV molecules compound 1 (AG7404) and rupintrivir (AG7088) at resolutions of 1.9, 1.3, and 1.5 Å, respectively. The EV-93 3C(pro) adopts a chymotrypsin-like fold with a canonically configured oxyanion hole and a substrate binding pocket similar to that of rhino-, coxsackie- and poliovirus 3C proteases. We show that compound 1 and rupintrivir are both active against EV-93 in infected cells and inhibit the proteolytic activity of EV-93 3C(pro) in vitro. These results provide a framework for further structure-guided optimization of the tested compounds to produce antiviral drugs against a broad range of EV species.

The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold

Background

Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the evolution of new functions consists of gene duplication followed by functional divergence. UlaG, a unique manganese-dependent metallo-β-lactamase (MBL) enzyme involved in L-ascorbate metabolism by commensal and symbiotic enterobacteria, provides a model for the study of the emergence of new catalytic activities from the modification of an ancient fold. Furthermore, UlaG is the founding member of the so-called UlaG-like (UlaGL) protein family, a recently established and poorly characterized family comprising divalent (and perhaps trivalent) metal-binding MBLs that catalyze transformations on phosphorylated sugars and nucleotides.

Results

Here we combined protein structure-guided and sequence-only molecular phylogenetic analyses to dissect the molecular evolution of UlaG and to study its phylogenomic distribution, its relatedness with present-day UlaGL protein sequences and functional conservation. Phylogenetic analyses indicate that UlaGL sequences are present in Bacteria and Archaea, with bona fide orthologs found mainly in mammalian and plant-associated Gram-negative and Gram-positive bacteria. The incongruence between the UlaGL tree and known species trees indicates exchange by HGT and suggests that the UlaGL-encoding genes provided a growth advantage under changing conditions. Our search for more distantly related protein sequences aided by structural homology has uncovered that UlaGL sequences have a common evolutionary origin with present-day RNA processing and metabolizing MBL enzymes widespread in Bacteria, Archaea, and Eukarya. This observation suggests an ancient origin for the UlaGL family within the broader trunk of the MBL superfamily by duplication, neofunctionalization and fixation.

Conclusions

Our results suggest that the forerunner of UlaG was present as an RNA metabolizing enzyme in the last common ancestor, and that the modern descendants of that ancestral gene have a wide phylogenetic distribution and functional roles. We propose that the UlaGL family evolved new metabolic roles among bacterial and possibly archeal phyla in the setting of a close association with metazoans, such as in the mammalian gastrointestinal tract or in animal and plant pathogens, as well as in environmental settings. Accordingly, the major evolutionary forces shaping the UlaGL family include vertical inheritance and lineage-specific duplication and acquisition of novel metabolic functions, followed by HGT and numerous lineage-specific gene loss events.

The structure of a transcription activation subcomplex reveals how σ(70) is recruited to PhoB promoters

PhoB is a two-component response regulator that activates transcription by interacting with the σ(70) subunit of the E. coli RNA polymerase in promoters in which the -35 σ(70)-recognition element is replaced by the pho box. The crystal structure of a transcription initiation subcomplex that includes the σ(4) domain of σ(70) fused with the RNA polymerase β subunit flap tip helix, the PhoB effector domain and the pho box DNA reveals how σ(4) recognizes the upstream pho box repeat. As with the -35 element, σ(4) achieves this recognition through the N-terminal portion of its DNA recognition helix, but contact with the DNA major groove is less extensive. Unexpectedly, the same recognition helix contacts the transactivation loop and helices α2 and α3 of PhoB. This result shows a simple and elegant mechanism for polymerase recruitment to pho box promoters in which the lost -35 element contacts are compensated by new ones with the activator. In addition, σ(4) is reoriented, thereby suggesting a remodelling mechanism for transcription initiation.