The Structure of a Biologically Active Influenza Virus Ribonucleoprotein Complex

The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles (RNPs), which are responsible for virus transcription and replication. Despite their importance, information about the structure of these RNPs is scarce. We have determined the three-dimensional structure of a biologically active recombinant RNP by cryo-electron microscopy. The structure shows a nonameric nucleoprotein ring (at 12 Å resolution) with two monomers connected to the polymerase complex (at 18 Å resolution). Docking the atomic structures of the nucleoprotein and polymerase domains, as well as mutational analyses, has allowed us to define the interactions between the functional elements of the RNP and to propose the location of the viral RNA. Our results provide the first model for a functional negative-stranded RNA virus ribonucleoprotein complex. The structure reported here will serve as a framework to generate a quasi-atomic model of the molecular machine responsible for viral RNA synthesis and to test new models for virus RNA replication and transcription

Ultrastructural and functional analyses of recombinant influenza virus ribonucleoproteins suggest dimerization of nucleoprotein during virus amplification

8 pages, 7 figures.-- PMID: 10590102 [PubMed].-- PMCID: PMC111524.Full-text version available Open Access at PebMed Central: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10590102Influenza virus ribonucleoproteins (RNPs) were reconstituted in vivo from cloned cDNAs expressing the three polymerase subunits, the nucleoprotein (NP), and short template RNAs. The structure of purified RNPs was studied by electron microscopy and image processing. Circular and elliptic structures were obtained in which the NP and the polymerase complex could be defined. Comparison of the structure of RNPs of various lengths indicated that each NP monomer interacts with approximately 24 nucleotides. The analysis of the amplification of RNPs with different lengths showed that those with the highest replication efficiency contained an even number of NP monomers, suggesting that the NP is incorporated as dimers into newly synthesized RNPs.J. Ortega was a fellow of Instituto de Estudios Turolenses. This work was supported by Programa Sectorial de Promoción General del Conocimiento (grants PB97-1160 and PB96-0818).Peer reviewe

Globular Aggregates Stemming from the Self-Assembly of an Amphiphilic N-Annulated Perylene Bisimide in Aqueous Media

Herein, we describe the synthesis of highly emissive amphiphilic N-annulated PBI 1 decorated with oligo ethylene glycol (OEG) side chains. These polar side chains allow the straightforward solubility of 1 in solvents of different polarity such as water, iPrOH, dioxane, or chloroform. Compound 1 self-assembles in aqueous media by π-stacking of the aromatic units and van der Waals interactions, favored by the hydrophobic effect. The hypo- and hypsochromic effect observed in the UV-Vis spectra of 1 in water in comparison to chloroform is diagnostic of H-type aggregation. Solvent denaturation experiments allow deriving the free Gibbs energy for the self-assembly process in aqueous media and the factor m that is indicative of the influence exerted by a good solvent in the stability of the final aggregates. The ability of compound 1 to self-assemble in water yields globular aggregates that have been visualized by TEM imaging.Depto. de Química OrgánicaFac. de Ciencias QuímicasTRUEMCIUComunidad de Madridpu

Changes in microtubule protofilament number induced by Taxol binding to an easily accessible site. Internal microtubule dynamics

9 p.-7 fig.-2 tab.We have investigated the accessibility of the Taxol-binding site and the effects of Taxol binding on the structures of assembled microtubules. Taxol and docetaxel readily bind to and dissociate from microtubules, reaching 95% ligand exchange equilibrium in less than 3 min under our solution conditions (microtubules were previously assembled from GTP-tubulin, GTP-tubulin and microtubule-associated proteins, or GDP-tubulin and taxoid). Microtubules assembled from purified tubulin with Taxol are known to have typically one protofilament less than with the analogue docetaxel and control microtubules. Surprisingly, Taxol binding and exchange induce changes in the structure of preformed microtubules in a relatively short time scale. Cryoelectron microscopy shows changes toward the protofilament number distribution characteristic of Taxol or docetaxel, with a half-time of approximately 0.5 min, employing GDP-tubulin-taxoid microtubules. Correspondingly, synchrotron x-ray solution scattering shows a reduction in the mean microtubule diameter upon Taxol binding to microtubules assembled from GTP-tubulin in glycerol-containing buffer, with a structural relaxation half-time of approximately 1 min. These results imply that microtubules can exchange protofilaments upon Taxol binding, due to internal dynamics along the microtubule wall. The simplest interpretation of the relatively fast taxoid exchange observed and labeling of cellular microtubules with fluorescent taxoids, is that the Taxol-binding site is at the outer microtubule surface. On the contrary, if Taxol binds at the microtubule lumen in agreement with the electron crystallographic structure of tubulin dimers, our results suggest that the inside of microtubules is easily accessible from the outer solution. Large pores or moving lattice defects in microtubules might facilitate the binding of taxoids, as well as of possible endogenous cellular ligands of the inner microtubule wall.This work was supported in part by Dirección General de Enseñanza Superior Grant PB95-0116, the European Union Large Installations Program, Katholieke Universiteit Leuven Grant OT/93/20,and Nationale Funds voor Wetenschappelijk Onderzoek-Vlaanderen Grant 2.0163.94.Peer reviewe

Coexistence of multivalent and monovalent TCRs explains high sensitivity and wide range of response

A long-standing paradox in the study of T cell antigen recognition is that of the high specificity–low affinity T cell receptor (TCR)–major histocompatibility complex peptide (MHCp) interaction. The existence of multivalent TCRs could resolve this paradox because they can simultaneously improve the avidity observed for monovalent interactions and allow for cooperative effects. We have studied the stoichiometry of the TCR by Blue Native–polyacrylamide gel electrophoresis and found that the TCR exists as a mixture of monovalent (αβγɛδɛζζ) and multivalent complexes with two or more ligand-binding TCRα/β subunits. The coexistence of monovalent and multivalent complexes was confirmed by electron microscopy after label fracture of intact T cells, thus ruling out any possible artifact caused by detergent solubilization. We found that although only the multivalent complexes become phosphorylated at low antigen doses, both multivalent and monovalent TCRs are phosphorylated at higher doses. Thus, the multivalent TCRs could be responsible for sensing low concentrations of antigen, whereas the monovalent TCRs could be responsible for dose-response effects at high concentrations, conditions in which the multivalent TCRs are saturated. Thus, besides resolving TCR stoichiometry, these data can explain how T cells respond to a wide range of MHCp concentrations while maintaining high sensitivity

The chaperonin CCT inhibits assembly of α-synuclein amyloid fibrils by a specific, conformation-dependent interaction

The eukaryotic chaperonin CCT (chaperonin containing TCP-1) uses cavities built into its double-ring structure to encapsulate and to assist folding of a large subset of proteins. CCT can inhibit amyloid fibre assembly and toxicity of the polyQ extended mutant of huntingtin, the protein responsible for Huntington's disease. This raises the possibility that CCT modulates other amyloidopathies, a still-unaddressed question. We show here that CCT inhibits amyloid fibre assembly of α-synuclein A53T, one of the mutants responsible for Parkinson's disease. We evaluated fibrillation blockade in α-synuclein A53T deletion mutants and CCT interactions of full-length A53T in distinct oligomeric states to define an inhibition mechanism specific for α-synuclein. CCT interferes with fibre assembly by interaction of its CCT and CCT 3 subunits with the A53T central hydrophobic region (NAC). This interaction is specific to NAC conformation, as it is produced once soluble α-synuclein A53T oligomers form and blocks the reaction before fibres begin to grow. Finally, we show that this association inhibits α-synuclein A53T oligomer toxicity in neuroblastoma cells. In summary, our results and those for huntingtin suggest that CCT is a general modulator of amyloidogenesis via a specific mechanism.Ministerio de Economía RYC- 2011-08746 , RTC-2015-3309-1 y BFU2016-75984Ministerio de Salud CP10/00527Comunidad de Madrid S2013/MIT-280

Truncation-Driven Lateral Association of α-Synuclein Hinders Amyloid Clearance by the Hsp70-Based Disaggregase

The aggregation of α-synuclein is the hallmark of a collective of neurodegenerative disorders known as synucleinopathies. The tendency to aggregate of this protein, the toxicity of its aggregation intermediates and the ability of the cellular protein quality control system to clear these intermediates seems to be regulated, among other factors, by post-translational modifications (PTMs). Among these modifications, we consider herein proteolysis at both the N- and C-terminal regions of α-synuclein as a factor that could modulate disassembly of toxic amyloids by the human disaggregase, a combination of the chaperones Hsc70, DnaJB1 and Apg2. We find that, in contrast to aggregates of the protein lacking the N-terminus, which can be solubilized as efficiently as those of the WT protein, the deletion of the C-terminal domain, either in a recombinant context or as a consequence of calpain treatment, impaired Hsc70-mediated amyloid disassembly. Progressive removal of the negative charges at the C-terminal region induces lateral association of fibrils and type B* oligomers, precluding chaperone action. We propose that truncation-driven aggregate clumping impairs the mechanical action of chaperones, which includes fast protofilament unzipping coupled to depolymerization. Inhibition of the chaperone-mediated clearance of C-truncated species could explain their exacerbated toxicity and higher propensity to deposit found in vivo.This work was supported by grants PID2019-111068GB-I00 (to A.M.) (AEI/FEDER, UE) and PID2019-105872GB-I00 (to J.M.V.) (AEI/FEDER, UE) from the Ministry of Science and Innovation and by the Basque Government (grant IT1201-19 to AM). The Centro Nacional de Biotecnología (CNB) is a Severo Ochoa Center of Excellence (MINECO award SEV 2017-0712). N.O. holds a contract funded by Fundacion Biofisika Bizkaia. Acknowledgment

α,γ-Peptide nanotube templating of one-dimensional parallel fullerene arrangements

(Figure Presented) The formation and full characterization of single self-assembling α,γ-peptide nanotubes (α,γ-SPNs) is described. The introduction of C60 into cyclic peptides allows the preparation of supramolecular 1D fullerene arrangements induced by peptide nanotube formation under appropriate conditions. © 2009 American Chemical Society.This work was supported by the Spanish Ministry of Education and Science and the ERDF [SAF2007-61015 and Consolider Ingenio 2010 (CSD2007-00006)] and the Xunta de Galicia (GRC2006/ 132, PGIDIT06PXIB209018PR, PGIDIT08CSA047209PR, and R2006/ 124). The work by J.M.V. and J.L.C. was supported by Grants BFU2007- 62382/BMC from the Spanish MEC (J.M.V.) and S-0505/MAT/0283 from the Madrid Regional Government (J.M.V. and J.L.C.). C.R. and R.J.B. thank the Spanish MEC for their FPU Fellowships. We also thank Dr. Carmen Serra (Nanotechnology and Surface Analysis Service at C.A.C.T.I., University of Vigo) for her help with STM. We also thank Dowpharma for their kind gift of ENZA enzymes used in the preparation of D-Boc-γ-Acp-OH.Peer reviewe

Modulation of the chaperone DnaK allosterism by the nucleotide exchange factor GrpE

10 p.-6 fig.Hsp70 chaperones comprise two domains, the nucleotide-binding domain (Hsp70NBD), responsible for structural and functional changes in the chaperone, and the substrate-binding domain (Hsp70SBD), involved in substrate interaction. Substrate binding and release in Hsp70 is controlled by the nucleotide state of DnaKNBD, with ATP inducing the open, substrate-receptive DnaKSBD conformation, whereas ADP forces its closure. DnaK cycles between the two conformations through interaction with two cofactors, the Hsp40 co-chaperones (DnaJ in Escherichia coli) induce the ADP state, and the nucleotide exchange factors (GrpE in E. coli) induce the ATP state. X-ray crystallography showed that the GrpE dimer is a nucleotide exchange factor that works by interaction of one of its monomers with DnaKNBD. DnaKSBD location in this complex is debated; there is evidence that it interacts with the GrpE N-terminal disordered region, far from DnaKNBD. Although we confirmed this interaction using biochemical and biophysical techniques, our EM-based three-dimensional reconstruction of the DnaK-GrpE complex located DnaKSBD near DnaKNBD. This apparent discrepancy between the functional and structural results is explained by our finding that the tail region of the GrpE dimer in the DnaK-GrpE complex bends and its tip contacts DnaKSBD, whereas the DnaKNBD-DnaKSBD linker contacts the GrpE helical region. We suggest that these interactions define a more complex role for GrpE in the control of DnaK function.This work was supported in part by Spanish Ministry of Economy and Innovation Grants BFU2013-44202 (to J. M. V.), SAF2011-22988 (to O. L.), and BFU2013-47059 (to A. M.), Madrid Regional Government Grants S2013/MIT-2807 (to J. M. V.) and S2010/BMD-2316 (to O. L.), and Basque Government Grant IT709-13 (to A. M.).Peer reviewe

Strawberry GRN forever: insights into the transcriptional regulatory network controlling strawberry fruit ripening and quality

Ripening is a critical step for the development of flavor quality in fruits. This character has significantly declined in many fleshy fruits over recent decades. This is particularly significant in strawberry (Fragaria × ananassa), where current cultivars are derived from a narrow germplasm collection. Improving fruit quality requires two important breakthroughs: 1) a precise understanding of the fruit ripening process that will allow the targeting of relevant genes, and 2) the identification of novel alleles responsible for fruit quality traits. In our project, we aim at the identification and characterization of key transcription factors (TF) involved in fruit ripening regulation and their target genes, in order to infer the Gene Regulatory Network controlling this process. Among them, we have identified two TFs belonging to the NAC (FaRIF) and the BLH9 (FaRPL) family. Functional analyses establishing stable silencing and overexpression lines support that both TFs play a critical role in the regulation of fruit ripening and development. Furthermore, using a stage- and tissue-specific transcriptome analysis, we have identified TFs specifically expressed in the external layer of ripe receptacles of F. vesca fruits, which are involved in the regulation of wax and cuticle formation. Finally, we have implemented the use of the genome-editing tool CRISPR/Cas9 in the cultivated strawberry, which we expect to open opportunities for engineering this species to improve traits of economic importance