The socioeconomic epidemiology of inherited retinal diseases in Portugal.

BACKGROUND: Inherited retinal diseases (IRDs) are a group of rare degenerative disorders of the retina that can lead to blindness from birth to late middle age. Knowing the target population and its resources is essential to better plan support measures. The aim of this study was to evaluate the socioeconomic characteristics of regions in Portugal where IRD patients reside to inform the planning of vision aid and rehabilitation intervention measures. RESULTS: This study included 1082 patients from 973 families, aged 3 to 92 years, with a mean age of 44.8 ± 18.1 years. Patients living with an IRD were identified in 190 of the 308 municipalities. According to this study, the estimated IRD prevalence in Portugal was 10.4 per 100,000 inhabitants, and by municipalities, it ranged from 0 to 131.2 per 100,000 inhabitants. Overall, regions with a higher prevalence of IRD have a lower population density (r=-0.371, p < 0.001), a higher illiteracy rate (r = 0.404, p < 0.001) and an overall older population (r = 0.475, p < 0.001). Additionally, there is a lower proportion of doctor per capita (r = 0.350, p < 0.001), higher social security pensions beneficiaries (r = 0.439, p < 0.001), worse water quality for human consumption (r=-0.194, p = 0.008), fewer audiences at the cinema (r=-0.315, p < 0.001) and lower proportion of foreign guests in tourist accommodations (r=-0.287, p < 0.001). CONCLUSION: The number of identified patients with IRD varied between regions. Using data from national statistics (PORDATA), we observed differences in socioeconomic characteristics between regions. Multiple targeted aid strategies can be developed to ensure that all IRD patients are granted full clinical and socioeconomic support.

Charles Bonnet syndrome in age-related macular degeneration - prevalence and clinical features in a Portuguese population / Síndrome de Charles Bonnet na degeneração macular relacionada à idade - prevalência e características clínicas numa população portuguesa

ABSTRACT Objective: Age-related macular degeneration (AMD) is the most prevalent cause of irreversible visual loss in the developed world. In late stages, it may lead to extremely low visual acuities, especially when associated with geographic atrophy or choroidal neovascularization. According to recent literature, Charles Bonnet syndrome (CBS) may be a rather common feature of late AMD. Methods: One hundred patients with late-stage age-related macular degeneration were actively asked whether they had symptoms of Charles Bonnet syndrome. Those that answered positively underwent a comprehensive questionnaire about the details of the visual hallucinations. Results: The following factors were significantly associated with Charles Bonnet syndrome: older age (+6.3 years; p=0.003), lower visual acuity in the better eye (Charles Bonnet Syndrome Group: 0.11; Non-Charles Bonnet Syndrome Group: 0.42; p=0.005) and female sex (Charles Bonnet Syndrome Group: 88%; Non-Charles Bonnet Syndrome Group: 43%; p=0.02). The visual hallucinations occurred mainly straight ahead (n=5), once per day (n=4), at no particular time (n=6), lasted some minutes (n=5), and disappeared after blinking (n=3) or looking away (n=3). The majority of patients lived alone (n=7), had not told anyone about the hallucinations (n=6), and associated the episodes with severe distress (n=5). Conclusion: Charles Bonnet syndrome was fairly prevalent in this late-stage age-related macular degeneration population. Our sample shows the importance of directly asking subjects about Charles Bonnet syndrome since they are often reluctant to admit to having visual hallucinations. Reassurance about its benignity is crucial to improve their quality of life.

RESUMO Objetivo: A doença macular ligada à idade (DMI) é a causa mais prevalente de perda visual irreversível nos países desenvolvidos. Em estadios avançados, esta doença pode levar a acuidades visuais extremamente baixas. De acordo com literatura recente, a Síndrome de Charles Bonnet (SCB) pode acontecer de forma relativamente comum na DMI tardia. Métodos: Cem doentes com degeneração macular da idade avançada foram interrogados ativamente sobre terem sintomas da síndrome de Charles Bonnet. Os que responderam de forma positiva foram submetidos a um questionário oral detalhado sobre os pormenores das alucinações visuais. Resultados: Os seguintes fatores foram significativamente associados à síndrome de Charles Bonnet: idade avançada (+6,3 anos; p=0,003), menor melhor acuidade visual corrigida no melhor olho (Grupo com Síndrome de Charles Bonnet: 0,11; Grupo sem Síndrome de Charles Bonnet: 0,42; p=0,005) e sexo feminino (Grupo com Síndrome de Charles Bonnet: 88%; Grupo sem Síndrome de Charles Bonnet: 43%; p=0,02). As alucinações visuais ocorriam principalmente em frente (n=5), uma vez por dia (n=4), em qualquer altura do dia (n=6), duravam alguns minutos (n=5) e desapareciam após pestanejo (n=3) ou desvio do olhar (n=3). A maioria dos doentes vivia sozinha (n=7), não tinha partilhado sua condição com ninguém (n=6) e associava os episódios a uma sensação angustiante (n=5). Conclusão: A síndrome de Charles Bonnet teve prevalência relativamente alta nessa população de degeneração macular da idade. Nossa amostra sublinha a importância de questionar diretamente sobre síndrome de Charles Bonnet, uma vez que os doentes se sentem muitas vezes relutantes em admitir alucinações visuais. A reafirmação da benignidade da situação é crucial para aumentar a qualidade de vida desses indivíduos.

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression.

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.

The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins.

RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2).

A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.

Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition.

The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap."

Structure-function studies of the staphylococcal methicillin resistance antirepressor MecR2.

Methicillin resistance in Staphylococcus aureus is elicited by the MecI-MecR1-MecA axis encoded by the mec locus. Recently, MecR2 was also identified as a regulator of mec through binding of the methicillin repressor, MecI. Here we show that plasmid-encoded full-length MecR2 restores resistance in a sensitive S. aureus mecR2 deletion mutant of the resistant strain N315. The crystal structure of MecR2 reveals an N-terminal DNA-binding domain, an intermediate scaffold domain, and a C-terminal dimerization domain that contributes to oligomerization. The protein shows structural similarity to ROK (repressors, open reading frames, and kinases) family proteins, which bind DNA and/or sugar molecules. We found that functional cell-based assays of three point mutants affecting residues participating in sugar binding in ROK proteins had no effect on the resistance phenotype. By contrast, MecR2 bound short double-stranded DNA oligonucleotides nonspecifically, and a deletion mutant affecting the N-terminal DNA-binding domain showed a certain effect on activity, thus contributing to resistance less than the wild-type protein. Similarly, a deletion mutant, in which a flexible segment of intermediate scaffold domain had been replaced by four glycines, significantly reduced MecR2 function, thus indicating that this domain may likewise be required for activity. Taken together, these results provide the structural basis for the activity of a methicillin antirepressor, MecR2, which would sequester MecI away from its cognate promoter region and facilitate its degradation.

Redefining the role of the ß-lactamase locus in methicillin-resistant Staphylococcus aureus: ß-lactamase regulators disrupt the MecI-mediated strong repression on mecA and optimize the phenotypic expression of resistance in strains with constitutive mecA expression.

In response to ß-lactam chemotherapy, Staphylococcus aureus has acquired two resistance determinants: blaZ, coding for ß-lactamase, which confers resistance to penicillins only, and mecA, coding for an extra cell wall cross-linking enzyme with reduced affinity for virtually all other ß-lactams. The transcriptional control of both resistance determinants is regulated by homologous repressors (BlaI and MecI, respectively) and sensor inducers (BlaR1 and MecR1, respectively). There is a cross-talk between the two regulatory systems, and it has been demonstrated that bla regulators stabilize the mecA acquisition. In a recent study, we have unexpectedly observed that in most MRSA strains, there was no significant change in the resistance phenotype upon the overexpression in trans of a MecI repressor, whereas in those few strains negative for the bla locus, there was a massive decrease of resistance (D. C. Oliveira and H. de Lencastre, PLoS One 6:e23287, 2011). Here, we demonstrate that, contrary to what is currently accepted, the bla regulatory system efficiently disrupts the strong MecI-mediated repression on mecA, enabling the optimal expression of resistance. This effect appears to be due to the formation of MecI::BlaI heterodimers that might bind less efficiently to the mecA promoter and become nonfunctional due to the proteolytic inactivation of the BlaI monomer. In addition, we have also observed that the presence of bla regulators may enhance dramatically the expression of ß-lactam resistance in MRSA strains with constitutive mecA expression, compensating for the fitness cost imposed by the large ß-lactamase plasmid. These observations point to important unrecognized roles of the bla locus for the expression of the methicillin-resistant S. aureus (MRSA) phenotype.

Proteolysis of mecA repressor is essential for expression of methicillin resistance by Staphylococcus aureus.

Recently, we have demonstrated that the cognate regulatory locus of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) is in fact a three-component system containing the novel mecR2 gene coding for an antirepressor. MecR2 interacts with the repressor MecI, disturbing its binding to the mecA promoter and fostering its proteolysis. Here, we engineered a point mutation in the putative cleavage site of MecI and demonstrated that MecI proteolysis is strictly required for the optimal expression of ß-lactam resistance.

The anti-repressor MecR2 promotes the proteolysis of the mecA repressor and enables optimal expression of ß-lactam resistance in MRSA.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen, which is cross-resistant to virtually all ß-lactam antibiotics. MRSA strains are defined by the presence of mecA gene. The transcription of mecA can be regulated by a sensor-inducer (MecR1) and a repressor (MecI), involving a unique series of proteolytic steps. The induction of mecA by MecR1 has been described as very inefficient and, as such, it is believed that optimal expression of ß-lactam resistance by MRSA requires a non-functional MecR1-MecI system. However, in a recent study, no correlation was found between the presence of functional MecR1-MecI and the level of ß-lactam resistance in a representative collection of epidemic MRSA strains. Here, we demonstrate that the mecA regulatory locus consists, in fact, of an unusual three-component arrangement containing, in addition to mecR1-mecI, the up to now unrecognized mecR2 gene coding for an anti-repressor. The MecR2 function is essential for the full induction of mecA expression, compensating for the inefficient induction of mecA by MecR1 and enabling optimal expression of ß-lactam resistance in MRSA strains with functional mecR1-mecI regulatory genes. Our data shows that MecR2 interacts directly with MecI, destabilizing its binding to the mecA promoter, which results in the repressor inactivation by proteolytic cleavage, presumably mediated by native cytoplasmatic proteases. These observations point to a revision of the current model for the transcriptional control of mecA and open new avenues for the design of alternative therapeutic strategies for the treatment of MRSA infections. Moreover, these findings also provide important insights into the complex evolutionary pathways of antibiotic resistance and molecular mechanisms of transcriptional regulation in bacteria.

Structural and functional analyses reveal that Staphylococcus aureus antibiotic resistance factor HmrA is a zinc-dependent endopeptidase.

HmrA is an antibiotic resistance factor of methicillin-resistant Staphylococcus aureus. Molecular analysis of this protein revealed that it is not a muramidase or ß-lactamase but a nonspecific double-zinc endopeptidase consisting of a catalytic domain and an inserted oligomerization domain, which probably undergo a relative interdomain hinge rotation upon substrate binding. The active-site cleft is located at the domain interface. Four HmrA protomers assemble to a large ∼170-kDa homotetrameric complex of 125 Å. All four active sites are fully accessible and ∼50-70 Å apart, far enough apart to act on a large meshwork substrate independently but simultaneously. In vivo studies with four S. aureus strains of variable resistance levels revealed that the extracellular addition of HmrA protects against loss of viability in the presence of oxacillin and that this protection depends on proteolytic activity. All of these results indicate that HmrA is a peptidase that participates in resistance mechanisms in vivo in the presence of ß-lactams. Furthermore, our results have implications for most S. aureus strains of known genomic sequences and several other cocci and bacilli, which harbor close orthologs. This suggests that HmrA may be a new widespread antibiotic resistance factor in bacteria.