Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism

© 2017 Soldano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins

A disordered region retains the full protease inhibitor activity and the capacity to induce CD8+ T cells in vivo of the oral vaccine adjuvant U-Omp19

U-Omp19 is a bacterial protease inhibitor from Brucella abortus that inhibits gastrointestinal and lysosomal proteases, enhancing the half-life and immunogenicity of co-delivered antigens. U-Omp19 is a novel adjuvant that is in preclinical development with various vaccine candidates. However, the molecular mechanisms by which it exerts these functions and the structural elements responsible for these activities remain unknown. In this work, a structural, biochemical, and functional characterization of U-Omp19 is presented. Dynamic features of U-Omp19 in solution by NMR and the crystal structure of its C-terminal domain are described. The protein consists of a compact C-terminal beta-barrel domain and a flexible N-terminal domain. The latter domain behaves as an intrinsically disordered protein and retains the full protease inhibitor activity against pancreatic elastase, papain and pepsin. This domain also retains the capacity to induce CD8+ T cells in vivo of U-Omp19. This information may lead to future rationale vaccine designs using U-Omp19 as an adjuvant to deliver other proteins or peptides in oral formulations against infectious diseases, as well as to design strategies to incorporate modifications in its structure that may improve its adjuvanticity.Fil: Darriba, María Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Pueblas Castro, Celeste. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Coria, Lorena M. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Bruno, Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Cerutti, María Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Chemes, Lucía B. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Cassataro, Juliana. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Pasquevich, Karina A. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Darriba, María Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Pueblas Castro, Celeste. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Coria, Lorena M. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Bruno, Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Cerutti, María Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Chemes, Lucía B. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Cassataro, Juliana. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Pasquevich, Karina A. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Otero, Lisandro H. Fundación Instituto Leloir. Plataforma Argentina de Biología Estructural y Metabolómica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Klinke, Sebastián. Fundación Instituto Leloir. Plataforma Argentina de Biología Estructural y Metabolómica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Rasia, Rodolfo M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario. Plataforma Argentina de Biología Estructural y Metabolómica; Argentina

Structural basis for the broad specificity of a new family of amino-acid racemases

Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical d-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family membersResearch in the Cava laboratory is supported by the MINECO, Spain (RYC-2010-06241), Universidad Autonoma de Madrid (UAM-38) and by the Knut and Alice Wallenberg Foundation (KAW). Additionally, this work was supported by the BFU2011-25326 MEC grant (JAH), by the S2010/BMD-2457 grant from CAM (JAH) and by HHMI (MKW

Exaptation of two ancient immune proteins into a new dimeric pore-forming toxin in snails

The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles, however MACPFs with pore-forming toxic function in venoms and poisons are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that can affect the digestive and nervous systems of potential predators. We report the three-dimensional structure of PmPV2, at 17.2 A resolution determined by negative-stain electron microscopy and its solution structure by small angle X-ray scattering (SAXS). We found that PV2s differ from nearly all MACPFs in two respects: it is a dimer in solution and protomers combine two immune proteins into an AB toxin. The MACPF chain is linked by a single disulfide bond to a tachylectin chain, and two heterodimers are arranged head-to-tail by non-covalent forces in the native protein. MACPF domain is fused with a putative new Ct-accessory domain exclusive to invertebrates. The tachylectin is a six-bladed β-propeller, similar to animal tectonins. We experimentally validated the predicted functions of both subunits and demonstrated for the first time that PV2s are true pore-forming toxins. The tachylectin “B” delivery subunit would bind to target membranes, and then the MACPF “A” toxic subunit would disrupt lipid bilayers forming large pores altering the plasma membrane conductance. These results indicate that PV2s toxicity evolved by linking two immune proteins where their combined preexisting functions gave rise to a new toxic entity with a novel role in defense against predation. This structure is an unparalleled example of protein exaptation.Instituto de Investigaciones Bioquímicas de La PlataInstituto de Estudios Inmunológicos y Fisiopatológico

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.DFG, 221545957, SFB 1078: Proteinfunktion durch ProtonierungsdynamikEC/H2020/664726/EU/EMBL Interdisciplinary, International and Intersectorial Postdocs/EI3PO

Desarrollo de un suero equino hiperinmune para el tratamiento de COVID-19 en Argentina

La enfermedad denominada COVID-19 es causada por el coronavirus SARS-CoV-2 y es actualmente considerada una pandemia a nivel global. El desarrollo de vacunas es sin duda la mejor estrategia a largo plazo, pero debido a la emergencia sanitaria, existe una necesidad urgente de encontrar soluciones rápidas y efectivas para el tratamiento de la enfermedad. Hasta la fecha, el uso de plasma de convalecientes es la única inmunoterapia disponible para pacientes hospitalizados con COVID-19. El uso de anticuerpos policlonales equinos (EpAbs) es otra alternativa terapéutica interesante. La nueva generación de EpAbs incluyen el procesamiento y purificación de los mismos y la obtención de fragmentos F(ab’)2 con alta pureza y un excelente perfil de seguridad en humanos. Los EpAbs son fáciles de producir, lo cual permite el desarrollo rápido y la elaboración a gran escala de un producto terapéutico. En este trabajo mostramos el desarrollo de un suero terapéutico obtenido luego de la inmunización de caballos utilizando el receptor-binding domain de la glicoproteína Spike del virus. Nuestro producto mostró ser alrededor de 50 veces más potente en ensayos de seroneutralización in vitro que el promedio de los plasmas de convalecientes. Estos resultados nos permitirían testear la seguridad y eficacia de nuestro producto en ensayos clínicos de fase 2/3 a realizarse a partir de julio de 2020 en la zona metropolitana de Buenos Aires, Argentina.The disease named COVID-19, caused by the SARS-CoV-2 coronavirus, is currently generating a global pandemic. Vaccine development is no doubt the best long-term immunological approach, but in the current epidemiologic and health emergency there is a need for rapid and effective solutions. Convalescent plasma is the only antibody-based therapy available for COVID-19 patients to date. Equine polyclonal antibodies (EpAbs) put forward a sound alternative. The new generation of processed and purified EpAbs containing highly purified F(ab’)2 fragments demonstrated to be safe and well tolerated. EpAbs are easy to manufacture allowing a fast development and scaling up for a treatment. Based on these ideas, we present a new therapeutic product obtained after immunization of horses with the receptor-binding domain of the viral Spike glycoprotein. Our product shows around 50 times more potency in in vitro seroneutralization assays than the average of convalescent plasma. This result may allow us to test the safety and efficacy of this product in a phase 2/3 clinical trial to be conducted in July 2020 in the metropolitan area of Buenos Aires, Argentina.Fil: Zylberman, Vanesa. Inmunova; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sanguineti, Santiago. Inmunova; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pontoriero, Andrea. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Higa, Sandra V.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Cerutti, Maria Laura. Universidad Nacional de San Martín. Centro de Rediseño e Ingeniería de Proteínas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Morrone Seijo, Susana María. Inmunova; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pardo, Romina Paola. Inmunova; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Muñoz, Luciana. Inmunova; ArgentinaFil: Acuña Intieri, María Eugenia. Universidad Nacional de San Martín. Centro de Rediseño e Ingeniería de Proteínas; ArgentinaFil: Alzogaray, Vanina Andrea. 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: Avaro, Martín M.. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Benedetti, Estefanía. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Berguer, Paula Mercedes. 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: Bocanera, Laura. mAbxience; ArgentinaFil: Bukata, Lucas. Inmunova; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bustelo, Marina S.. Inmunova; ArgentinaFil: Campos, Ana M.. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Colonna, Mariana. Inmunova; ArgentinaFil: Correa, Elisa. mAbxience; ArgentinaFil: Cragnaz, Lucí­a. mAbxience; ArgentinaFil: Dattero, María E.. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Dellafiore, María Andrea. mAbxience; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Foscaldi, Sabrina Andrea. 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: González, Joaquí­n V.. Inmunova; ArgentinaFil: Guerra, Luciano Lucas. mAbxience; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Klinke, Sebastian. 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: Labanda, María Soledad. 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: Lauché, Constanza Elena. Inmunova; ArgentinaFil: López, Juan C.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Martínez, Anabela M.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Otero, Lisandro Horacio. 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: Peyric, Elías H.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Ponziani, Pablo F.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Ramondino, Romina. Inmunova; ArgentinaFil: Rinaldi, Jimena Julieta. 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: Rodrí­guez, Santiago. mAbxience; ArgentinaFil: Russo, Javier E.. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Russo, Mara Laura. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Saavedra, Soledad Lorena. Instituto Biológico Argentino S.A.I.C.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Seigelchifer, Mauricio. mAbxience; ArgentinaFil: Sosa, Santiago. 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: Vilariño, Claudio. Universidad Nacional de San Martín. Centro de Rediseño e Ingeniería de Proteínas; ArgentinaFil: López Biscayart, Patricia. Instituto Biológico Argentino S.A.I.C.; ArgentinaFil: Corley, Esteban. mAbxience; ArgentinaFil: Spatz, Linus. Inmunova; ArgentinaFil: Baumeister, Elsa. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; ArgentinaFil: Goldbaum, Fernando Alberto. Universidad Nacional de San Martín. Centro de Rediseño e Ingeniería de Proteínas; Argentina. Inmunova; Argentina. 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

Critical active-site residues identified by site-directed mutagenesis in Pseudomonas aeruginosa phosphorylcholine phosphatase, a new member of the haloacid dehalogenases hydrolase superfamily

Pseudomonas aeruginosa phosphorylcholine phosphatase (PChP), the product of the PA5292 gene, is synthesized when the bacteria are grown with choline, betaine, dimethylglycine, or carnitine. In the presence of Mg(2+), PChP catalyzes the hydrolysis of both phosphorylcholine (PCh) and p-nitrophenylphosphate (p-NPP). PCh saturation curve analysis of the enzyme with or without the signal peptide indicated that the peptide was the fundamental factor responsible for decreasing the affinity of the second site of PChP for PCh, either at pH 5.0 or pH 7.4. PChP contained three conserved motifs characteristic of the haloacid dehalogenases superfamily. In the PChP without the signal peptide, motifs I, II, and III correspond to the residues (31)DMDNT(35), (166)SAA(168), and K(242)/(261)GDTPDSD(267), respectively. To determine the catalytic importance of the D31, D33, T35, S166, K242, D262, D265, and D267 on the enzyme activity, site-directed mutagenesis was performed. D31, D33, D262, and D267 were identified as the more important residues for catalysis. D265 and D267 may be involved in the stabilization of motif III, or might contribute to substrate specificity. The substitution of T35 by S35 resulted in an enzyme with a low PChP activity, but conserves the catalytic sites involved in the hydrolysis of PCh (K(m1) 0.03 mM: , K(m2) 0.5 mM: ) or p-NPP (K(m) 2.1 mM: ). Mutating either S166 or K242 revealed that these residues are also important to catalyze the hydrolysis of both substrates. The substitution of lysine by arginine or by glutamine revealed the importance of the positive charged group, either from the amino or guanidinium groups, because K242Q was inactive, whereas K242R was a functional enzyme

Reduction of the ferric LepHO-heme complex in anaerobic conditions and spontaneous reoxidation.

<p>Time dependent formation (A) and autoxidation (B) of the ferrous heme complex of wild type LepHO (●) and F157I mutant (○) as monitored by variations in absorbance at 426 and 403 nm, respectively. Data extracted from the spectra shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182535#pone.0182535.g005" target="_blank">Fig 5</a>.</p

Absorption spectral changes of the LepHO-heme complex during the NADPH/LepFNR-supported heme degradation.

<p>Time dependent absorption spectra of wild type LepHO (A), F157I (B) and F157A (C), before (---) and after (―) the addition of LepFNR and NADPH: Experimental conditions are as indicated in Materials and methods. The inset shows an enlargement of the spectral region between 500 and 800 nm. The time-dependent decay of the intensity at 403 nm (D) and the increase at 680 nm (E) were obtained from the spectra shown in panels (A) to (C). Wild type LepHO (●); F157I (▼) and F157A (○).</p

Conversion of ferric LepHO-heme complex to verdoheme by addition of H₂O₂.

<p>Time dependent heme hydroxylation of wild type LepHO (●) and F157I mutant (○) by H₂O₂ in aerobic conditions as monitored by increase in absorbance at 671 nm (A) or under anaerobiosis as monitored by decrease in absorbance at 403 nm.</p