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[Background and Objectives]: To conduct a genetic and molecular functional study of a family with members affected of hereditary spastic paraplegia (HSP) of unknown origin and carrying a novel pathogenic vaccinia-related kinase 1 (VRK1) variant., [Methods]: Whole-exome sequencing was performed in 2 patients, and their parents diagnosed with HSP. The novel VRK1 variant was detected by whole-exome sequencing, molecularly modeled and biochemically characterized in kinase assays. Functionally, we studied the role of this VRK1 variant in DNA damage response and its effect on the assembly of Cajal bodies (CBs)., [Results]: We have identified a very rare homozygous variant VRK1-D263G with a neurologic phenotype associated with HSP and moderate intellectual disability. The molecular modeling of this VRK1 variant protein predicted an alteration in the folding of a loop that interferes with the access to the kinase catalytic site. The VRK1-D263G variant is kinase inactive and does not phosphorylate histones H2AX and H3, transcription factors activating transcription factor 2 and p53, coilin needed for assembly of CBs, and p53 binding protein 1, a DNA repair protein. Functionally, this VRK1 variant protein impairs CB formation and the DNA damage response., [Discussion]: This report expands the neurologic spectrum of neuromotor syndromes associated with a new and rare VRK1 variant, representing a novel pathogenic participant in complicated HSP and demonstrates that CBs and the DNA damage response are impaired in these patients., P. M-G. was supported by Ministerio de Educación-FPU predoctoral fellowship (FPU16/01883). This work was funded by grants from Agencia Estatal de Investigaci´on/ Ministerio de Ciencia e Innovaci´on (PID2019-105610RBI00) and Consejería de Educación-Junta de Castilla y León (CSI264P20) to P.A.L. Agencia Estatal de Investigaci´onMinisterio de Ciencia, Innovaci´on y Universidades (RTC2017-6494-1 and RTI2018-094434-B-I00) and European Commission project “CONNECT-JPIAMR Virtual Research Institute” to P.G-P. The Instituto de Biolog´ıa Molecular y Celular del Cancer is funded by a grant from Junta de Castilla y León-FEDER (CLC-2017-01).

Complex neurodevelopmental syndromes frequently have an unknown etiology, in which genetic factors play a pathogenic role. This study utilizes whole-exome sequencing (WES) to examine four members of a family with a son presenting, since birth, with epileptic-like crises, combined with cerebral palsy, severe neuromotor and developmental delay, dystonic tetraparexia, axonal motor affectation, and hyper-excitability of unknown origin. The WES study detected within the patient a de novo heterozygous in-frame duplication of thirty-six nucleotides within exon 7 of the human KCNQ2 gene. This insertion duplicates the first twelve amino acids of the calmodulin binding site I. Molecular dynamics simulations of this KCNQ2 peptide duplication, modelled on the 3D structure of the KCNQ2 protein, suggest that the duplication may lead to the dysregulation of calcium inhibition of this protein function., Agencia Estatal de Investigación-Ministerio de Economía y Competitividad-FEDER-Fondo Social Europeo (SAF2016-75744-R, PID2019-105610RB-I00) and Consejería de Educación-Junta de Castilla y León (CLC-2017-01 and UIC-258) to P.A.L. Ministerio de Economía, Industria y Competitividad (CTQ2015-68756-R, BFU2015-66910-R) to A.V. Ministerio de Economía y Competitividad-Fondo Social Europeo Grant from Instituto de Salud Carlos III-Fondo Social Europeo (PI16/01920) to R. G-S. Agencia Estatal de Investigación-Ministerio de Economía y Competitividad-FEDER-Fondo Social Europeo (RTC-2017-6494-1 and RTI2018-094434-B-I00) to P. G-P. Financial support of the Departament de Salut de la Generalitat de Catalunya-URDCat Project (SLT002/16/00174)

The RNase II family of ribonucleases is ubiquitous and critical for RNA metabolism. The rnb500 allele has been widely used for over 30 years; however, the underlying genetic changes which result in RNase II thermolabile activity remain unknown. Here, we combine molecular and biophysical studies to carry out an in vivo and in vitro investigation of RNase II mutation(s) that confer the rnb500 phenotype. Our findings indicate that RNase II thermolability is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. These findings have important implications for the design of temperature-sensitive variants of other RNase II enzymes, namely those with yet unknown functions.

© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.. The cell division protein FtsZ assembles in vitro by a mechanism of cooperative association dependent on GTP, monovalent cations, and Mg2+. We have analyzed the GTPase activity and assembly dynamics of Streptococcus pneumoniae FtsZ (Spn-FtsZ). SpnFtsZ assembled in an apparently cooperative process, with a higher critical concentration than values reported for other FtsZ proteins. It sedimented in the presence of GTP as a high molecular mass polymer with a well defined size and tended to form double-stranded filaments in electron microscope preparations. GTPase activity depended on K+ and Mg2+ and was inhibited by Na+. GTP hydrolysis exhibited a delay that included a lag phase followed by a GTP hydrolysis activation step, until reaction reached the GTPase rate. The lag phase was not found in polymer assembly, suggesting a transition from an initial non-GTP-hydrolyzing polymer that switches to a GTP-hydrolyzing polymer, supporting models that explain FtsZ polymer cooperativity., Spanish Government GrantsBIO2011-28941-C03 (to G. R. and C. A.) and BIO2011-28941-C01; Torres Quevedo Program Grant PTQ-11-05049 to Biomol Informatics S.L.

Mitochondrial HMG-CoA synthase deficiency is a rare inherited metabolic disorder that affects ketone-body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycaemia, dicarboxylic aciduria, and in severe cases, coma. This deficiency may have been under-diagnosed owing to the absence of specific clinical and biochemical markers, limitations in liver biopsy and the lack of an effective method of expression and enzyme assay for verifying the mutations found. To date, eight patients have been reported with nine allelic variants of the HMGCS2 gene. We present a new method of enzyme expression and a modification of the activity assay that allows, for first time, the functional study of missense mutations found in patients with this deficiency. Four of the missense mutations (p.V54M, p.R188H, p.G212R and p.G388R) did not produce proteins that could have been detected in soluble form by western blot; three produced a total loss of activity (p.Y167C, p.M307T and p.R500H) and one, variant p.F174L, gave an enzyme with a catalytic efficiency of 11.5%. This indicates that the deficiency may occur with partial loss of activity of enzyme. In addition, we describe a new patient with this deficiency, in which we detected the missense allelic variant, c.1162G>A (p.G388R) and the nonsense variant c.1270C>T (p.R424X). © 2013 Elsevier Masson SAS., Diputación General de Aragón (DGA) (Grupo Consolidado B20); European Social Fund (“Construyendo Europa desde Aragón”); Spanish Ministry of Education and Science (SAF2004-06843-C03); Spanish Ministerio de Ciencia and Ministerio de Economía y Competitividad (SAF2007-61926, IPT2011-0964-900000, SAF2011-13156-E); Spanish Instituto de Salud Carlos III (CIBER Fisiopatología de la Obesidad y Nutrición); European Commission (FP7 HEALTH-F3-2009-223431, EU project “Divinocell”, FP7 HEALTH-2011-278603; EU project “Dorian”); European Social Fund

The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the ¿head¿ structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer., MINECO (contracts IPT2011-0964-900000 and SAF2011-13156-E to P.G-P and projects MAT2014-59966-R and “María de Maeztu” Programme for Units of Excellence in R&D; MDM-2014-0377, to J.O.); the Spanish Ministry of Health -ISCIII-Fondo de Investigación Sanitaria (FIS) (Ref.#PI15/00707, to F.J.R. and J.P.) and the Diputación General de Aragón (Grupo Consolidado B20; European Social Fund “Construyendo Europa desde Aragón”, to J.P.).

RNase II and RNase R are the two E. coli exoribonucleases that belong to the RNase II super family of enzymes. They degrade RNA hydrolytically in the 3′ to 5′ direction in a processive and sequence independent manner. However, while RNase R is capable of degrading structured RNAs, the RNase II activity is impaired by dsRNAs. The final end-product of these two enzymes is also different, being 4 nt for RNase II and 2 nt for RNase R. RNase II and RNase R share structural properties, including 60% of amino acid sequence similarity and have a similar modular domain organization: two N-terminal cold shock domains (CSD1 and CSD2), one central RNB catalytic domain, and one C-terminal S1 domain. We have constructed hybrid proteins by swapping the domains between RNase II and RNase R to determine which are the responsible for the differences observed between RNase R and RNase II. The results obtained show that the S1 and RNB domains from RNase R in an RNase II context allow the degradation of double-stranded substrates and the appearance of the 2 nt long end-product. Moreover, the degradation of structured RNAs becomes tail-independent when the RNB domain from RNase R is no longer associated with the RNA binding domains (CSD and S1) of the genuine protein. Finally, we show that the RNase R C-terminal Lysine-rich region is involved in the degradation of double-stranded substrates in an RNase II context, probably by unwinding the substrate before it enters into the catalytic cavity. Proteins 2011; © 2011 Wiley-Liss, Inc.

RNase II is the prototype of a ubiquitous family of enzymes that are crucial for RNA metabolism. In Escherichia coli this protein is a single-stranded-specific 3′-exoribonuclease with a modular organization of four functional domains. In eukaryotes, the RNase II homologue Rrp44 (also known as Dis3) is the catalytic subunit of the exosome, an exoribonuclease complex essential for RNA processing and decay. In this work we have performed a functional characterization of several highly conserved residues located in the RNase II catalytic domain to address their precise role in the RNase II activity. We have constructed a number of RNase II mutants and compared their activity and RNA binding to the wild type using different single- or double-stranded substrates. The results presented in this study substantially improve the RNase II model for RNA degradation. We have identified the residues that are responsible for the discrimination of cleavage of RNA versus DNA. We also show that the Arg-500 residue present in the RNase II active site is crucial for activity but not for RNA binding. The most prominent finding presented is the extraordinary catalysis observed in the E542A mutant that turns RNase II into a “super-enzyme.”

Bacterial cell division occurs through the formation of a protein ring (division ring) at the site of division, with FtsZ being its main component in most bacteria. FtsZ is the prokaryotic ortholog of eukaryotic tubulin; it shares GTPase activity properties and the ability to polymerize in vitro. To study the mechanism of action of FtsZ, we used molecular dynamics simulations of the behavior of the FtsZ dimer in the presence of GTP–Mg2+ and monovalent cations. The presence of a K+ ion at the GTP binding site allows the positioning of one water molecule that interacts with catalytic residues Asp235 and Asp238, which are also involved in the coordination sphere of K+. This arrangement might favor dimer stability and GTP hydrolysis. Contrary to this, Na+ destabilizes the dimer and does not allow the positioning of the catalytic water molecule. Protonation of the GTP gamma-phosphate, simulating low pH, excludes both monovalent cations and the catalytic water molecule from the GTP binding site and stabilizes the dimer. These molecular dynamics predictions were contrasted experimentally by analyzing the GTPase and polymerization activities of purified Methanococcus jannaschii and Escherichia coli FtsZ proteins in vitro., This study was supported by the Spanish Ministerio de Educación y Ciencia through grants SAF2007-61926 (to P.G.-P.) and BIO2005-02194 (to M.V.); by CIBER Fisiopatología de la Obesidad y Nutrición, an initiative of Instituto de Salud Carlos III (to P.G.-P.); by the Comunidad de Madrid through grant S-BIO-0260/2006-COMBACT (to P. G-P., J. Mingorance, and M.V.); and by the European Union through grant FP7-223431 (EU “Divinocell” project; to P.G.-P. and M.V.). Financial support from the “Fundación Ramón Areces” to CBMSO is also acknowledged. J. Mingorance was a recipient of a Ramón y Cajal fellowship financed by the European Social Fund and the Ministerio de Educación y Ciencia. A.I.R. was a recipient of an I3P contract from the Spanish Council for Scientific Research.We also thank “Centro de Cálculo Científico” (CCCUAM) for computational support. Work at Biomol- Informatics SL was partially financed by the European Social Fund

Chaperones, a group of proteins that assist the folding of other proteins, seem to work in a coordinated manner. Two major chaperone families are heat-shock protein families Hsp60 and Hsp70. Here we show for the first time the formation of a stable complex between chaperonin-containing TCP-1 (CCT) and Hsc70, two eukaryotic representatives of these chaperone families. This interaction takes place between the apical domain of the CCT beta subunit and the nucleotide binding domain of Hsc70, and may serve to deliver the unfolded substrate from Hsc70 to the substrate binding region of CCT. We also show that a similar interaction does not occur between their prokaryotic counterparts GroEL and DnaK, suggesting that in eukarya the two types of chaperones have evolved to a concerted action that makes the folding task more efficient.

RNase II is a key exoribonuclease involved in the maturation, turnover, and quality control of RNA. RNase II homologues are components of the exosome, a complex of exoribonucleases. The structure of RNase II unraveled crucial aspects of the mechanism of RNA degradation. Here we show that mutations in highly conserved residues at the active site affect the activity of the enzyme. Moreover, we have identified the residue that is responsible for setting the end product of RNase II. In addition, we present for the first time the models of two members of the RNase II family, RNase R from Escherichia coli and human Rrp44, also called Dis3. Our findings improve the present model for RNA degradation by the RNase II family of enzymes.

The oligomeric state and the hydrodynamic properties of human respiratory syncytial virus (HRSV) phosphoprotein (P), a known cofactor of the viral RNA-dependent RNA polymerase (L), and a trypsin-resistant fragment (X) that includes its oligomerization domain were analyzed by sedimentation equilibrium and velocity using analytical ultracentrifugation. The results obtained demonstrate that both P and fragment X are homotetrameric with elongated shapes, consistent with electron micrographs of the purified P protein in which thin rod-like molecules of ∼12.5 ± 1.0 nm in length were observed. A new chymotrypsin resistant fragment (Y*) included in fragment X has been identified and purified by gel filtration chromatography. Fragment Y* may represent a minimal version of the P oligomerization domain. Thermal denaturation curves based on circular dichroism data of P protein showed a complex behavior. In contrast, melting data generated for fragments X and particularly fragment Y* showed more homogeneous transitions indicative of simpler structures. A three-dimensional model of X and Y* fragments was built based on the atomic structure of the P oligomerization domain of the related Sendai virus, which is in good agreement with the experimental data. This model will be an useful tool to make rational mutations and test the role of specific amino acids in the oligomerization and functional properties of the HRSV P protein. Proteins 2008. © 2008 Wiley-Liss, Inc.

3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase adopts a (betaalpha)(8) TIM barrel structure with an additional beta9, alpha11 and alpha12 helices. Location of HMG part of the substrate has been suggested but the binding mode for the CoA moiety remains to be resolved. As mutation F305 fs(-2), which involves the last 21 residues of the protein, and mutation K48N caused 3-hydroxy-3-methylglutaric aciduria in two patients, we examined the role of the C-terminal end and Lys(48) in enzyme activity. Expression studies of various C-terminal-end-deleted and K48N-mutated proteins revealed that residues 311-313 (localized in the loop between alpha11 and alpha12 helices) and Lys(48) are essential for enzyme activity. An in silico docking model locating HMG-CoA on the surface of the enzyme implicates Asn(311) and Lys(313) in substrate binding by establishing multiple polar contacts with phosphate and ribose groups of adenosine, and Lys(48) by contacting the carboxyl group of the panthotenic acid moiety.

Ca2+ regulation of the Ca2+ binding mitochondrial carriers for aspartate/glutamate (AGCs) is provided by their N-terminal extensions, which face the intermembrane space. The two mammalian AGCs, aralar and citrin, are members of the malate-aspartate NADH shuttle. We report that their N-terminal extensions contain up to four pairs of EF-hand motifs plus a single vestigial EF-hand, and have no known homolog. Aralar and citrin contain one fully canonical EF-hand pair and aralar two additional half-pairs, in which a single EF-hand is predicted to bind Ca2+. Shuttle activity in brain or skeletal muscle mitochondria, which contain aralar as the major AGC, is activated by Ca2+ with S0.5 values of 280–350 nm; higher than those obtained in liver mitochondria (100–150 nm) that contain citrin as the major AGC. We have used aralar- and citrin-deficient mice to study the role of the two isoforms in heart, which expresses both AGCs. The S0.5 for Ca2+ activation of the shuttle in heart mitochondria is about 300 nm, and it remains essentially unchanged in citrin-deficient mice, although it undergoes a drastic reduction to about 100 nm in aralar-deficient mice. Therefore, aralar and citrin, when expressed as single isoforms in heart, confer differences in Ca2+ activation of shuttle activity, probably associated with their structural differences. In addition, the results reveal that the two AGCs fully account for shuttle activity in mouse heart mitochondria and that no other glutamate transporter can replace the AGCs in this pathway.

Prefoldin (PFD) is a molecular chaperone that stabilizes and then delivers unfolded proteins to a chaperonin for facilitated folding. The PFD hexamer has undergone an evolutionary change in subunit composition, from two PFDalpha and four PFDbeta subunits in archaea to six different subunits (two alpha-like and four beta-like subunits) in eukaryotes. Here, we show by electron microscopy that PFD from the archaeum Pyrococcus horikoshii (PhPFD) selectively uses an increasing number of subunits to interact with nonnative protein substrates of larger sizes. PhPFD stabilizes unfolded proteins by interacting with the distal regions of the chaperone tentacles, a mechanism different from that of eukaryotic PFD, which encapsulates its substrate inside the cavity. This suggests that although the fundamental functions of archaeal and eukaryal PFD are conserved, their mechanism of substrate interaction have diverged, potentially reflecting a narrower range of substrates stabilized by the eukaryotic PFD.

Chaperonins are large oligomers made up of two superimposed rings, each enclosing a cavity used for the folding of other proteins. Among the chaperonins, the eukaryotic cytosolic chaperonin CCT is the most complex, not only with regard to its subunit composition but also with respect to its function, still not well understood. Unlike the more well studied eubacterial chaperonin GroEL, which binds any protein that presents stretches of hydrophobic residues, CCT recognises in its substrates specific binding determinants and interacts with them through particular combinations of CCT subunits. Folding then occurs after the conformational changes induced in the chaperonin upon nucleotide binding have occurred, through a mechanism that, although still poorly defined, clearly differs from the one established for GroEL. Although CCT seems to be mainly involved in the folding of actin and tubulin, other substrates involved in various cellular roles are beginning to be characterised, including many WD40-repeat, 7-blade propeller proteins.

Carnitine palmitoyltransferase I (CPT I) and carnitine octanoyltransferase (COT) catalyze the conversion of long- and medium-chain acyl-CoA to acylcarnitines in the presence of carnitine. We propose a common three-dimensional structural model for the catalytic domain of both, based on fold identification for 200 amino acids surrounding the active site through a threading approach. The model is based on the three-dimensional structure of the rat enoyl-CoA hydratase, established by x-ray diffraction analysis. The study shows that the structural model of 200 amino acids of the catalytic site is practically identical in CPT I and COT with identical distribution of 4 β-sheets and 6 α-helices. Functional analysis of the model was done by site-directed mutagenesis. When the critical histidine residue 473 in CPT I (327 in COT), localized in the acyl-CoA pocket in the model, was mutated to alanine, the catalytic activity was abolished. Mutation of the conserved alanine residue to aspartic acid, A381D (in CPT I) and A238D (in COT), which are 92/89 amino acids far from the catalytic histidine, respectively (but very close to the acyl-CoA pocket in the structural model), decreased the activity by 86 and 80%, respectively. The Km for acyl-CoA increased 6–8-fold, whereas the Km for carnitine hardly changed. The inhibition of the mutant CPT I by malonyl-CoA was not altered. The structural model explains the loss of activity reported for the CPT I mutations R451A, W452A, D454G, W391A, del R395, P479L, and L484P, all of which occur in or near the modeled catalytic domain.

The influenza A virus NEP (NS2) protein is an structural component of the viral particle. To investigate whether this protein has an effect on viral RNA synthesis, we examined the expression of an influenza A virus-like chloramphenicol acetyltransferase (CAT) RNA in cells synthesizing the four influenza A virus core proteins (nucleoprotein, PB1, PB2, and PA) and NEP from recombinant plasmids. Influenza A virus NEP inhibited drastically, and in a dose-dependent manner, the level of CAT expression mediated by the recombinant influenza A virus polymerase. This inhibitory effect was not observed in an analogous artificial system in which expression of a synthetic CAT RNA is mediated by the core proteins of an influenza B virus. This result ruled out the possibility that inhibition of reporter gene expression was due to a general toxic effect induced by NEP. Analysis of the virus-specific RNA species that accumulated in cells expressing the type A recombinant core proteins and NEP showed that there was an important reduction in the levels of minireplicon-derived vRNA, cRNA, and mRNA molecules. Taken together, the results obtained suggest a regulatory role for NEP during virus-specific RNA synthesis, and this finding is discussed regarding the biological implications for the virus life cycle.

To get insights into the role played by each of the influenza A virus polypeptides in morphogenesis and virus particle assembly, the generation of virus-like particles (VLPs) has been examined in COS-1 cell cultures expressing, from recombinant plasmids, different combinations of the viral structural proteins. The presence of VLPs was examined biochemically, following centrifugation of the supernatants collected from transfected cells through sucrose cushions and immunoblotting, and by electron-microscopic analysis. It is demonstrated that the matrix (M1) protein is the only viral component which is essential for VLP formation and that the viral ribonucleoproteins are not required for virus particle formation. It is also shown that the M1 protein, when expressed alone, assembles into virus-like budding particles, which are released in the culture medium, and that the recombinant M1 protein accumulates intracellularly, forming tubular structures. All these results are discussed with regard to the roles played by the virus polypeptides during virus assembly.

FtsZ filaments participate in bacterial cell division, but it is still not clear how their dynamic polymerization and shape exert force on the underlying membrane. We present a theoretical description of individual filaments that incorporates information from molecular dynamic simulations. The structure of the crystallized Methanococcus jannaschii FtsZ dimer was used to model a FtsZ pentamer that showed a curvature and a twist. The estimated bending and torsion angles between monomers and their fluctuations were included in the theoretical description. The MD data also permitted positioning the curvature with respect to the protein coordinates and allowed us to explore the effect of the relative orientation of the preferred curvature with respect to the surface plane. We find that maximum tension is attained when filaments are firmly attached and oriented with their curvature perpendicular to the surface and that the twist serves as a valve to release or to tighten the tension exerted by the curved filaments on the membrane. The theoretical model also shows that the presence of torsion can explain the shape distribution of short filaments observed by Atomic Force Microscopy in previously published experiments. New experiments with FtsZ covalently attached to lipid membranes show that the filament on-plane curvature depends on lipid head charge, confirming the predicted monomer orientation effects. This new model underlines the fact that the combination of the three elements, filament curvature, twist and the strength and orientation of its surface attachment, can modulate the force exerted on the membrane during cell division. © 2014 The Royal Society of Chemistry., Comunidad de Madrid; to MVe), DIVINOCELL FP7 HEALTHF3-2009-223431 (European Commision to MVe and P.G-P.), Plan Nacional BIO2008-04478-C03-00 (Ministerio de Ciencia e Innovación; to MVe), CONSOLIDER INGENIO 2010 CSD2007-00010 (Ministerio de Ciencia e Innovación; to MVe) FIS2010-22047-C05-01 (Ministerio de Ciencia e Innovación,to P.T.)

Surface-enhanced Raman scattering (SERS) spectroscopy has been applied to detect the interaction of the FtsZ protein from Escherichia coli, an essential component of the bacterial division machinery, with either a soluble variant of the ZipA protein (that provides membrane tethering to FtsZ) or the bacterial membrane (containing the full-length ZipA naturally incorporated), on silver-coated polystyrene micrometer-sized beads. The engineered microbeads were used not only to support the bilayers but also to offer a stable support with a high density of SERS hot spots, allowing the detection of ZipA structural changes linked to the binding of FtsZ. These changes were different upon incubating the coated beads with FtsZ polymers (GTP form) as compared to oligomers (GDP form) and more pronounced when the plasmonic sensors were coated with natural bacterial membranes. © 2012 American Chemical Society., European Research Council through Advanced Grant 267867, PLASMAQUO; the Human Frontier Science Program through Grant RGP0050/2010; The European Commission through Contract HEALTH-F3-2009-223431; the Spanish Government through Grants CTQ2011-23167; BIO2011-28941-C03; IPT-2011-0964-900000; SAF2011-13156-E

Eukaryotic cells respond to DNA damage by activating damage checkpoint pathways, which arrest cell cycle progression and induce gene expression. We isolated a full-length cDNA encoding a 49-kDa protein from Leishmania major, which exhibited significant deduced amino acid sequence homology with the annotated Leishmania sp. DNA damage-inducible (Ddi1-like) protein, as well as with the Ddi1 protein from Saccharomyces cerevisiae. In contrast to the previously described Ddi1 protein, the protein from L. major displays three domains: (1) an NH2-terminal ubiquitin like; (2) a COOH terminal ubiquitin-associated; (3) a retroviral aspartyl proteinase, containing the typical D[S/T]G signature. The function of the L. major Ddi1-like recombinant protein was investigated after expression in baculovirus/insect cells and biochemical analysis, revealing preferential substrate selectivity for aspartyl proteinase A2 family substrates, with optimal activity in acidic conditions. The proteolytic activity was inhibited by aspartyl proteinase inhibitors. Molecular modeling of the retroviral domain of the Ddi1-like Leishmania protein revealed a dimer structure that contained a double Asp-Ser-Gly-Ala amino acid sequence motif, in an almost identical geometry to the exhibited by the homologous retroviral aspartyl protease domain of yeast Ddi1 protein. Our results indicate that the isolated Ddi1-like protein is a functional aspartyl proteinase in L. major, opening possibility to be considered as a potential target for novel antiparasitic drugs. Electronic supplementary material The online version of this article (doi:10.1007/s12192-012-0368-9) contains supplementary material, which is available to authorized users.

The mitochondrial 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase deficiency (MIM 600234) is an autosomic recessive inborn error of metabolism, hard to characterize and probably underdiagnosed (Thompson et al., 1997). The enzyme failure is caused by mutations in the gene HMGCS2, located in chromosome 1. The illness was first diagnosed in 1997 (Thompson et al., 1997), in a six-year old boy, who presented a semicomatose state after three days with gastroenteritis and diet (Bouchard et al., 2001). Up to date, only eight patients have been reported with an estimated incidence of

FtsZ, the prokaryotic ortholog of tubulin, assembles into polymers in the bacterial division ring. The interfaces between monomers contain a GTP molecule, but the relationship between polymerization and GTPase activity is not unequivocally proven. A set of short FtsZ polymers were modelled and the formation of active GTPase structures was monitored using molecular dynamics. Only the interfaces nearest the polymer ends exhibited an adequate geometry for GTP hydrolysis. Simulated conversion of interfaces from close-to-end to internal position and vice versa resulted in their spontaneous rearrangement between active and inactive conformations. This predicted behavior of FtsZ polymer ends was supported by in vitro experiments. © 2012 Federation of European Biochemical Societies., Ministerio de Ciencia e Innovación (BIO2008-04178, SAF2007-61926, IPT2011-0964-900000, SAF2011-13156-E); Comunidad de Madrid (S-BIO-0260/2006; European Commission (FP7 HEALTH-F3-2009-223431; HEALTH-2011- 278603); Ramón y Cajal ; European Social Fund to Biomol-Informatics; Fundación Ramón Areces

We have modeled a 3D structure for the C-type lectin domain of the African swine fever virus protein EP153R, based on the structure of CD69, CD94 and Ly49A cell receptors, and this model predicts that a dimer of EP153R may establish an asymmetric interaction with one MHC-I molecule. A functional consequence of this interaction could be the modulation of MHC-I expression. By using both transfection and virus infection experiments, we demonstrate here that EP153R inhibits MHC-I membrane expression, most probably by impairing the exocytosis process, without affecting the synthesis or glycosylation of MHC antigens. Interestingly, the EP153-mediated control of MHC requires the intact configuration of the lectin domain of the viral protein, and specifically the R133 residue. Interference of EP153R gene expression during virus infection and studies using virus recombinants with the EP153R gene deleted further support the inhibitory role of the viral lectin on the expression of MHC-I antigens., This work was supported by grants from the Spanish Ministerio de Ciencia y Tecnología (BFU2007-63110/BMC), from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement KBBE- 211691- ASFRISK and from Laboratorios del Dr. Esteve, SA, and also by institutional grants from the Fundación Ramón Areces and Banco Santander Central Hispano. C.H. and A.G.G. also acknowledge financial support from the Centro de Investigación en Sanidad Animal (CISA).

FtsZ, the best-known prokaryotic division protein, assembles at midcell with other proteins forming a ring during septation. Widely conserved in bacteria, FtsZ represents the ancestor of tubulin. In the presence of GTP it forms polymers able to associate into multi-stranded flexible structures. FtsZ research is aimed at determining the role of the Z-ring in division, describing the polymerization and potential force-generating mechanisms and evaluating the roles of nucleotide exchange and hydrolysis. Systems to reconstruct the FtsZ ring in vitro have been described and some of its mechanical properties have been reproduced using in silico modeling. We discuss current research in FtsZ, some of the controversies, and finally propose further research needed to complete a model of FtsZ action that reconciles its in vitro properties with its role in division.

Central nervous system administration of C75 produces hypophagia and weight loss in rodents identifying C75 as a potential drug against obesity and type 2 diabetes. However, the mechanism underlying this effect is unknown. Here we show that C75-CoA is generated chemically, in vitro and in vivo from C75 and that it is a potent inhibitor of carnitine palmitoyltranferase 1 (CPT1), the rate-limiting step of fatty-acid oxidation. Three-D docking and kinetic analysis support the inhibitory effect of C75-CoA on CPT1. Central nervous system administration of C75 in rats led to C75-CoA production, inhibition of CPT1 and lower body weight and food intake. Our results suggest that inhibition of CPT1, and thus increased availability of fatty acids in the hypothalamus, contribute to the pharmacological mechanism of C75 to decrease food intake.

The strains of Thermus thermophilus that contain the nitrate respiration conjugative element (NCE) replace their aerobic respiratory chain by an anaerobic counterpart made of the Nrc-NADH dehydrogenase and the Nar-nitrate reductase in response to nitrate and oxygen depletion. This replacement depends on DnrS and DnrT, two homologues to sensory transcription factors encoded in a bicistronic operon by the NCE. DnrS is an oxygen-sensitive protein required in vivo to activate transcription on its own dnr promoter and on that of the nar operon, but not required for the expression of the nrc operon. In contrast, DnrT is required for the transcription of these three operons and also for the repression of nqo, the operon that encodes the major respiratory NADH dehydrogenase expressed during aerobic growth. Thermophilic in vitro assays revealed that low DnrT concentrations allows the recruitment of the T. thermophilus RNA polymerase sigma(A) holoenzyme to the nrc promoter and its transcription, whereas higher DnrT concentrations are required to repress transcription on the nqo promoter. In conclusion, our data show a complex autoinducible mechanism by which DnrT functions as the transcriptional switch that allows the NCE to take the control of the respiratory metabolism of its host during adaptation to anaerobic growth.

C75 is a potential drug for the treatment of obesity. It was first identified as a competitive, irreversible inhibitor of fatty acid synthase (FAS). It has also been described as a malonyl-CoA analogue that antagonizes the allosteric inhibitory effect of malonyl-CoA on carnitine palmitoyltransferase I (CPT I), the main regulatory enzyme involved in fatty acid oxidation. On the basis of MALDI-TOF analysis, we now provide evidence that C75 can be transformed to its C75-CoA derivative. Unlike the activation produced by C75, the CoA derivative is a potent competitive inhibitor that binds tightly but reversibly to CPT I. IC50 values for yeast-overexpressed L- or M-CPT I isoforms, as well as for purified mitochondria from rat liver and muscle, were within the same range as those observed for etomoxiryl-CoA, a potent inhibitor of CPT I. When a pancreatic INS(823/13), muscle L6E9, or kidney HEK293 cell line was incubated directly with C75, fatty acid oxidation was inhibited. This suggests that C75 could be transformed in the cell to its C75-CoA derivative, inhibiting CPT I activity and consequently fatty acid oxidation. In vivo, a single intraperitoneal injection of C75 in mice produced short-term inhibition of CPT I activity in mitochondria from the liver, soleus, and pancreas, indicating that C75 could be transformed to its C75-CoA derivative in these tissues. Finally, in silico molecular docking studies showed that C75-CoA occupies the same pocket in CPT I as palmitoyl-CoA, suggesting an inhibiting mechanism based on mutual exclusion. Overall, our results describe a novel role for C75 in CPT I activity, highlighting the inhibitory effect of its C75-CoA derivative.

The double-stranded RNA (dsRNA)-dependent protein kinase PKR activates NF-κB via the IκB kinase (IKK) complex, but little is known about additional molecules that may be involved in this pathway. Analysis of the PKR sequence enabled us to identify two putative TRAF-interacting motifs. The viability of such an interaction was further suggested by computer modeling. Here, we present evidence of the colocalization and physical interaction between PKR and TRAF family proteins in vivo, as shown by immunoprecipitation and confocal microscopy experiments. This interaction is induced upon PKR dimerization. Most importantly, we show that the binding between PKR and TRAFs is functionally relevant, as observed by the absence of NF-κB activity upon PKR expression in cells genetically deficient in TRAF2 and TRAF5 or after expression of TRAF dominant negative molecules. On the basis of sequence information and mutational and computer docking analyses, we favored a TRAF-PKR interaction model in which the C-terminal domain of TRAF binds to a predicted TRAF interaction motif present in the PKR kinase domain. Altogether, our data suggest that TRAF family proteins are key components located downstream of PKR that have an important role in mediating activation of NF-κB by the dsRNA-dependent protein kinase., This investigation was supported by research grants BMC2002- 03246 and BIO2000-0340-P4 from Spain and QLK2-CT2002-00954 from the European Union to M.E., by grants SAF2000-0028 and FIPSE to J.A., and by the Fundación Ramón Areces (P.G.-P.). H.N. is supported by a grant from the Human Frontier Science Program. M.A.G. and J.G. were supported by fellowships from the Ministerio de Ciencia y Tecnología, Madrid, Spain.

The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Here we show by electron microscopy that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT. Three-dimensional reconstruction of the CCT:PFD complex based on cryoelectron microscopy reveals that PFD binds to each of the CCT rings in a unique conformation through two specific CCT subunits that are placed in a 1,4 arrangement. This defines the phasing of the CCT rings and suggests a handoff mechanism for PFD.

A chimera of the two immunodominant African swine fever (ASF) virus proteins p54 and p30 was constructed by insertion of the gene CP204L into a Not I restriction site of E183L gene. The resulting chimeric protein p54/30, expressed by a recombinant baculovirus in insect cells and in Trichoplusia ni larvae, retained antigenic determinants present in both proteins and reacted in Western blot with a collection of sera from inapparent ASF virus carrier pigs. Remarkably, pigs immunized with the chimeric protein developed neutralizing antibodies and survived the challenge with a virulent African swine fever virus, presenting a reduction of about two logs in maximum viremia titers with respect to control pigs. In conclusion, this study revealed that the constructed chimeric protein may have utility as a serological diagnostic reagent and for further immunological studies that may provide new insights on mechanisms of protective immunity to ASFV.

The ribonucleoprotein (RNP) complexes of Thogoto virus (THOV), a tick-borne orthomyxovirus, have been purified from detergent-lysed virions. The purified RNPs were then disrupted by centrifugation through a CsCl-glycerol gradient to obtain fractions highly enriched in nucleoprotein (NP) and virtually devoid of viral genomic RNA. When these NP-enriched fractions were incubated with a synthetic THOV-like RNA, and the mixtures were transfected into THOV-infected cells, the synthetic RNA was expressed and packaged into THOV particles. Similarly, hybrid mixtures containing purified THOV NP and influenza A virus synthetic RNAs (either a model CAT RNA or a gene encoding the viral neuraminidase), were prepared and transfected into influenza A virus-infected cells. The synthetic CAT RNA, was shown to be expressed and packaged into virus particles, and the neuraminidase gene was rescued into influenza virions. These data are discussed in terms of the similarities observed between THOV and influenza A virus and the potential application of the THOV purified proteins for rescuing synthetic genes into infectious viruses.

In this study we have investigated the generation of African swine fever (ASF) virus variants resistant to neutralizing antibodies after cell culture propagation. All highly passaged ASF viruses analyzed were resistant to neutralization by antisera from convalescent pigs or antibodies generated against individual viral proteins which neutralized low-passage viruses. A molecular analysis of neutralizable and nonneutralizable virus isolates by sequencing of the genes encoding for neutralizing proteins revealed that the absence of neutralization of high-passage viruses is not due to antigenic variability of critical epitopes. A comparative analysis of phospholipid composition of viral membranes between low- and high-passage viruses revealed differences in the relative amount of phosphatidylinositol in these two groups of viruses, independent of the cells in which the viruses were grown. Further purification of low- and high-passage viruses by Percoll sedimentation showed differences in the phospholipid composition identical to those found with the partially purified viruses and confirmed the susceptibility of these viruses to neutralization. The incorporation of phosphatidylinositol into membranes of high-passage viruses rendered a similar neutralization susceptibility to low-passage viruses, in which this is a major phospholipid. In contrast, other phospholipids did not interfere with high-passage virus neutralization, suggesting that phosphatidylinositol is essential for a correct epitope presentation to neutralizing antibodies. Additionally, the removal of phosphatidylinositol from a low-passage virus by a specific lipase transformed this virus from neutralizable to nonneutralizable. These data constitute clear evidence of the importance of the lipid composition of the viral membranes for the protein recognition by antibodies and may account in part for the past difficulties in reproducibly demonstrating ASF virus-neutralizing antibodies by using high-passage viruses.

A persistent non-neutralized African swine fever virus (ASFV) fraction is found with most convalescent swine sera in in vitro neutralization assays. To study this phenomenon, antisera from convalescent pigs infected with different virus isolates and showing complete or incomplete virus neutralization were used. Different experiments determined that incomplete neutralization of ASFV is caused neither by virus aggregation, nor low affinity or stability of virus-antibody complexes. Additionally, attempts to purify antigenic escape mutant viruses from the persistent fraction was also unsuccessful. Nevertheless, competition experiments between sera demonstrated that antibodies present in sera showing persistent fraction inhibited the complete neutralization mediated by antibodies present in sera which neutralize 100% of virus infectivity. These results suggest that induction of blocking antibodies during ASFV infection could represent the main cause for the persistent surviving virus fraction observed in neutralization assays and could also explain the persistent infections observed in some convalescent pigs.

At present, the eradication of African swine fever (ASF) in affected countries is based only on an efficient diagnosis program because of the absence of an available vaccine. The highly antigenic ASF virus proteins p54 and p30, encoded by genes E183L and CP204L respectively, were expressed in baculovirus for diagnostic purposes. A sequence comparison analysis of these genes from different field virus strains which are geographically diverse and isolated in different years, revealed that both genes are completely conserved among the isolates. Partially purified baculovirus-expressed proteins were used in ELISA and Western blot for ASF antibody detection in sera from experimentally inoculated pigs and field sera from ASF innaparent carriers. These comparative analyses showed that p54 presents better reactivity than p30 in Western blot. However, recombinant p30 was more efficient for antibody detection by ELISA, improving the discrimination between positive and negative sera by this technique. These data suggest the convenience of using p30 as ELISA antigen, while p54 should be the selected antigen for ASF virus antibody detection by Western blot. The combined use of both antigens for serodiagnosis of ASF disease will improve the sensitivity of innaparent carriers detection, facilitating also the interpretation of the tests, and eliminating the use of ASF virus in antigen production.

The nature of the initial interactions of African swine fever (ASF) virus with target cells is only partially known, and to date only the ASF virus protein p12 has been identified as a viral attachment protein. More recently, antibodies to viral proteins p54 and p30 have been shown to neutralize the virus, inhibiting virus binding and internalization, respectively. Therefore, we investigated the role of these proteins in the receptor-mediated ASF virus endocytosis in swine macrophages, the natural host cells. Proteins p54 and p30, released from ASF virus particles after treatment of virions with a nonionic detergent, bound to virus-sensitive alveolar pig macrophages. Binding of these proteins was found to be specifically inhibited by neutralizing antibodies obtained from a convalescent pig or from pigs immunized with recombinant p54 or p30 proteins. The baculovirus-expressed proteins p54 and p30 retained the same biological properties as the viral proteins, since they also bound specifically to these cells, and their binding was equally inhibited by neutralizing antibodies. Binding of35S-labeled recombinant p54 and p30 proteins to macrophages was specifically competed by an excess of unlabeled p54 and p30, respectively. However, cross-binding inhibition was not observed, suggesting the existence of two different saturable binding sites for these proteins in the susceptible cells. In addition, protein p54 blocked the specific binding of virus particles to the macrophage, while protein p30 blocked virus internalization. Both proteins independently prevented virus infection and in a dose-dependent manner, suggesting that binding interactions mediated by both proteins are necessary to give rise to a productive infection. The relevance of blockade of virus–cell interactions mediated by p54 and p30 in the protective immune response against ASF virus was then investigated. Immunization of pigs with either recombinant p54 or p30 proteins induced neutralizing antibodies which, as expected, inhibited virus attachment or internalization, respectively. However, immunized pigs were not protected against lethal infection and the disease course was not modified in these animals. In contrast, immunization with a combination of p54 and p30 proteins simultaneously stimulated both virus neutralizing mechanisms and modified drastically the disease course, rendering a variable degree of protection ranging from a delay in the onset of the disease to complete protection against virus infection. In conclusion, the above results strongly suggest that proteins p54 and p30 mediate specific interactions between ASF virus and cellular receptors and that simultaneous interference with these two interactions has a complementary effect in antibody-mediated protection.

African swine fever virus induces in convalescent pigs antibodies that neutralized the virus before and after binding to susceptible cells, inhibiting both virus attachment and internalization. A further analysis of the neutralization mechanisms mediated by the different viral proteins showed that antibodies to proteins p72 and p54 are involved in the inhibition of a first step of the replication cycle related to virus attachment, while antibodies to protein p30 are implicated in the inhibition of virus internalization.

This study describes three novel homozygous missense mutations (S75R, S201Y, and D204N) in the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase gene, which caused 3-hydroxy-3-methylglutaric aciduria in patients from Germany, England, and Argentina. Expression studies in Escherichia coli show that S75R and S201Y substitutions completely abolished the HMG-CoA lyase activity, whereas D204N reduced catalytic efficiency to 6.6% of the wild type. We also propose a three-dimensional model for human HMG-CoA lyase containing a (βα)8 (TIM) barrel structure. The model is supported by the similarity with analogous TIM barrel structures of functionally related proteins, by the localization of catalytic amino acids at the active site, and by the coincidence between the shape of the substrate (HMG-CoA) and the predicted inner cavity. The three novel mutations explain the lack of HMG-CoA lyase activity on the basis of the proposed structure: in S75R and S201Y because the new amino acid residues occlude the substrate cavity, and in D204N because the mutation alters the electrochemical environment of the active site. We also report the localization of all missense mutations reported to date and show that these mutations are located in the β-sheets around the substrate cavity. info:eu-repo/semantics/acceptedVersion