Prefoldins contribute to maintaining the levels of the spliceosome LSM2–8 complex through Hsp90 in Arabidopsis

Although originally identified as the components of the complex aiding the cytosolic chaperonin CCT in the folding of actins and tubulins in the cytosol, prefoldins (PFDs) are emerging as novel regulators influencing gene expression in the nucleus. Work conducted mainly in yeast and animals showed that PFDs act as transcriptional regulators and participate in the nuclear proteostasis. To investigate new functions of PFDs, we performed a co-expression analysis in Arabidopsis thaliana. Results revealed co-expression between PFD and the Sm-like (LSM) genes, which encode the LSM2–8 spliceosome core complex, in this model organism. Here, we show that PFDs interact with and are required to maintain adequate levels of the LSM2–8 complex. Our data indicate that levels of the LSM8 protein, which defines and confers the functional specificity of the complex, are reduced in pfd mutants and in response to the Hsp90 inhibitor geldanamycin. We provide biochemical evidence showing that LSM8 is a client of Hsp90 and that PFD4 mediates the interaction between both proteins. Consistent with our results and with the role of the LSM2–8 complex in splicing through the stabilization of the U6 snRNA, pfd mutants showed reduced levels of this snRNA and altered pre-mRNA splicing patterns.Fil: Esteve Bruna, David. Universidad Politécnica de Valencia; EspañaFil: Carrasco López, Cristian. Consejo Superior de Investigaciones Científicas; EspañaFil: Blanco Touriñán, Noel. Universidad Politécnica de Valencia; EspañaFil: Iserte, Javier Alonso. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Calleja Cabrera, Julián. Universidad Politécnica de Valencia; EspañaFil: Perea Resa, Carlos. Consejo Superior de Investigaciones Científicas; EspañaFil: Úrbez, Cristina. Universidad Politécnica de Valencia; EspañaFil: Carrasco, Pedro. Universidad Politécnica de Valencia; EspañaFil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Blázquez, Miguel A.. Universidad Politécnica de Valencia; EspañaFil: Salinas, Julio. Consejo Superior de Investigaciones Científicas; EspañaFil: Alabadí, David. Universidad Politécnica de Valencia; Españ

MISTIC2: Comprehensive server to study coevolution in protein families

Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for structurally or functionally important sites. MISTIC is a server designed to assist users to calculate covariation in protein families and provide them with an interactive tool to visualize the results. Here, we present MISTIC2, an update to the previous server, that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA). The results visualization framework has been reworked for improved performance, compatibility and user experience. It includes a circos representation of the information contained in the alignment, an interactive covariation network, a 3D structure viewer and a sequence logo. Others components provide additional information such as residue annotations, a roc curve for assessing contact prediction, data tables and different ways of filtering the data and exporting figures. Comparison of different methods is easily done and scores combination is also possible. A newly implemented web service allows users to access MISTIC2 programmatically using an API to calculate covariation and retrieve results. MISTIC2 is available at: https://mistic2.leloir.org.ar.Fil: Colell, Eloy A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Iserte, Javier Alonso. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Marino Buslje, Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentin

Network dimensioning and base station on/off switching strategies for sustainable deployments in remote areas

This paper provides a methodology for the dimensioning of the access network in remote rural areas, considering the progressive introduction of cellular services in these regions. A 3G small cell (SC) network with one or several carriers deployed at the SC, fed with solar panels and connected to a backhaul with limited capacity is considered for the analysis. Because the backhaul may be inexistent or very expensive (e.g., satellite-based backhaul) the network design pursues the minimization of the required backhaul bandwidth. The required backhaul bandwidth and the required energy units (i.e., the size of the solar panels and the required number of batteries) are then obtained as an output of the dimensioning analysis. Both the backhaul minimization objective and the constraints associated with each of the carriers (low maximum radiated power and low number of users connected simultaneously) require a novel methodology compared to the classical dimensioning techniques. We also develop a procedure for switching on/off carriers in order to minimize the energy consumption without affecting the quality of service (QoS) perceived by the users. This technique allows reducing the required size of the energy units, which directly translates into a cost reduction. In the development of this on/off switching strategy, we first assume perfect knowledge of the traffic profile and later, we develop a robust Bayesian approach to account for possible error modeling in the traffic profile information.Peer ReviewedPostprint (published version

Antigen vehiculization particles based on the Z protein of Junin virus

Abstract Background Arenavirus matrix protein Z plays an important role in virus budding and is able to generate enveloped virus-like-particles (VLPs) in absence of any other viral proteins. In these VLPs, Z protein is associated to the plasma membrane inner surface by its myristoyl residue. Budding induction and vesicle formation properties can be exploited to generate enveloped VLPs platform. These structures can be designed to carry specific antigen in the inner side or on the surface of VLPs. Vaccines based on VLPs are a highly effective type of subunit vaccines that mimic the overall structure of virus particles in absence of viral nucleic acid, being noninfectious. In this work we assayed the capacity of Junin Z protein to produce VLPs carrying the green fluorescent protein (eGFP), as a model antigen. Results In this report the Junin Z protein ability to produce VLPs from 293T cells and its capacity to deliver a specific antigen (eGFP) fused to Z was evaluated. Confocal microscopy showed a particular membrane bending in cells expressing Z and a spot welded distribution in the cytoplasm. VLPs were detected by TEM (transmission electron microscopy) and were purified from cell supernatant. The proteinase protection assay demonstrated the VLPs integrity and the absence of degradation of the fused antigen, thus indicating its internal localization. Finally, immunization of mice with purified VLPs produced high titres of anti-eGFP antibodies compared to the controls. Conclusions It was proved that VLPs can be generated from cells transfected with a fusion Junin virus Z-eGFP protein in absence of any other viral protein, and the capacity of Z protein to support fusions at the C-terminal, without impairing its budding activity, allowing vehiculization of specific antigens into VLPs.</p

MobiDB: 10 years of intrinsically disordered proteins

: The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from the literature and from experimental evidence along with predictions for all known protein sequences. MobiDB generates new knowledge and captures the functional significance of disordered regions by processing and combining complementary sources of information. Since its first release 10 years ago, the MobiDB database has evolved in order to improve the quality and coverage of protein disorder annotations and its accessibility. MobiDB has now reached its maturity in terms of data standardization and visualization. Here, we present a new release which focuses on the optimization of user experience and database content. The major advances compared to the previous version are the integration of AlphaFoldDB predictions and the re-implementation of the homology transfer pipeline, which expands manually curated annotations by two orders of magnitude. Finally, the entry page has been restyled in order to provide an overview of the available annotations along with two separate views that highlight structural disorder evidence and functions associated with different binding modes

Exploring Genomic, Geographic and Virulence Interactions among Epidemic and Non-Epidemic St. Louis Encephalitis Virus (Flavivirus) Strains

<div><p><i>St</i>. <i>Louis encephalitis virus</i> (SLEV) is a re-emerging arbovirus in South America. In 2005, an encephalitis outbreak caused by SLEV was reported in Argentina. The reason for the outbreak remains unknown, but may have been related to virological factors, changes in vectors populations, avian amplifying hosts, and/or environmental conditions. The main goal of this study was to characterize the complete genome of epidemic and non-epidemic SLEV strains from Argentina. Seventeen amino acid changes were detected; ten were non-conservative and located in proteins E, NS1, NS3 and NS5. Phylogenetic analysis showed two major clades based on geography: the North America and northern Central America (NAnCA) clade and the South America and southern Central America (SAsCA) clade. Interestingly, the presence of SAsCA genotype V SLEV strains in the NAnCA clade was reported in California, Florida and Texas, overlapping with known bird migration flyways. This work represents the first step in understanding the molecular mechanisms underlying virulence and biological variation among SLEV strains.</p></div

Amino acid differences between epidemic (Ep) and non-epidemic (NEp) SLEV strains and the polyprotein conservation profile.

<p>The horizontal bar represents the SLEV polyprotein. (<b>A).</b> Black vertical lines represent residues (in one letter code) that differed between strains studied (CbaAr-4005 (Ep) and 79V-2533 (NEp)). In grey, the non-conservative changes and their respective individual protein positions are highlighted. (<b>B).</b> Polyprotein homology profile for all studied SLEV strains. The light pink areas show the more conserved regions while in the less conserved zones are in blue. (<b>C).</b> Individual protein homology profile for all studied SLEV strains. The Y axis shows the Relative Homology (RH) between 0 and 1 while the X axis shows the residue position. In each protein profile, the zones that show an RH value lower than 0.8 are boxed.</p

St. Louis encephalitis virus strains and their biological features.

<p>^<b>¥</b> Pathogenicity feature observed in swiss albino mice or monkeys according to cited literature.</p><p>^<b>±</b>Viremia observed in subcutaneously inoculated birds (house sparrows/chicks).</p><p>^A[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136316#pone.0136316.ref023" target="_blank">23</a>];</p><p>^B[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136316#pone.0136316.ref024" target="_blank">24</a>];</p><p>^C[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136316#pone.0136316.ref012" target="_blank">12</a>];</p><p>^D[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136316#pone.0136316.ref025" target="_blank">25</a>].</p><p>n.d.: No data available.</p><p>St. Louis encephalitis virus strains and their biological features.</p

Predicted secondary structures for 5′UTR and 3′UTR of a NEp SLEV strain.

<p>For both ends, the conserved sequences (grey shadowed and boxed) and structures being comparison with DENV2 are shown [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136316#pone.0136316.ref016" target="_blank">16</a>]. The conserved residues in the alignment are shadowed. (<b>A).</b> 5′UTR scheme, where structures of Stem Loop A (SLA), Stem Loop B (SLB), capsid hairpin (cHP), and the 5′ upstream AUG region (5′UAR), and 5′ conserved sequence (5′CS) are shown. (<b>B).</b> 3′UTR scheme, showing the Stem Loop (SL), Short Stem Loop (SSL), the Pseudoknot 1 and 2 (PSK1 and PSK2), Variable Region, the 3′ upstream AUG region (3′UAR) sequences, the 3′ conserved sequence (3′CS), and the repeated conserved sequences 1 and 2 (RCS1 and RCS2).</p