The first crystal structure of human RNase6 reveals a novel substrate binding and cleavage site arrangement

Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at a 1.72 Å resolution, being the first report for the protein threedimensional structure and thereby setting the basis for functional studies. The structure shows an overall kidney shaped globular fold shared with the other known family members. Three sulphate anions bound to RNase 6 were found, interacting to residues at the main active site (His15, His122 and Gln14) and cationic surface exposed residues (His36, His39, Arg66 and His67). Kinetic characterization, together with prediction of protein -nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison to the pancreatic RNase type, its structure includes lineage specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5' end can provide an endonuclease type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His36-His39 dyad that facilitates the polynucleotide substrate catalysis

Insights into the Antimicrobial Mechanism of Action of Human RNase6 : Structural Determinants for Bacterial Cell Agglutination and Membrane Permeation

Human Ribonuclease 6 is a secreted protein belonging to the ribonuclease A (RNaseA) superfamily, a vertebrate specific family suggested to arise with an ancestral host defense role. Tissue distribution analysis revealed its expression in innate cell types, showing abundance in monocytes and neutrophils. Recent evidence of induction of the protein expression by bacterial infection suggested an antipathogen function in vivo. In our laboratory, the antimicrobial properties of the protein have been evaluated against Gram-negative and Gram-positive species and its mechanism of action was characterized using a membrane model. Interestingly, our results indicate that RNase6, as previously reported for RNase3, is able to specifically agglutinate Gram-negative bacteria as a main trait of its antimicrobial activity. Moreover, a side by side comparative analysis with the RN6(1-45) derived peptide highlights that the antimicrobial activity is mostly retained at the protein N-terminus. Further work by site directed mutagenesis and structural analysis has identified two residues involved in the protein antimicrobial action (Trp1 and Ile13) that are essential for the cell agglutination properties. This is the first structure-functional characterization of RNase6 antimicrobial properties, supporting its contribution to the infection focus clearance

Exploring the mechanisms of action of human secretory RNase 3 and RNase 7 against Candida albicans

Human antimicrobial RNases, which belong to the vertebrate RNase A superfamily and are secreted upon infection, display a wide spectrum of antipathogen activities. In this work, we examined the antifungal activity of the eosinophil RNase 3 and the skin-derived RNase 7, two proteins expressed by innate cell types that are directly involved in the host defense against fungal infection. Candida albicans has been selected as a suitable working model for testing RNase activities toward a eukaryotic pathogen. We explored the distinct levels of action of both RNases on yeast by combining cell viability and membrane model assays together with protein labeling and confocal microscopy. Site-directed mutagenesis was applied to ablate either the protein active site or the key anchoring region for cell binding. This is the first integrated study that highlights the RNases' dual mechanism of action. Along with an overall membrane-destabilization process, the RNases could internalize and target cellular RNA. The data support the contribution of the enzymatic activity for the antipathogen action of both antimicrobial proteins, which can be envisaged as suitable templates for the development of novel antifungal drugs. We suggest that both human RNases work as multitasking antimicrobial proteins that provide a first line immune barrier

Unveiling the multifaceted antimicrobial mechanism of action of human host defence RNases

La presente tesis doctoral se encuentra integrada dentro del estudio a gran escala de la estructura-función de las ribonucleasas antimicrobianas humanas. Estas proteínas catiónicas y de bajo peso molecular son secretadas por la mayoría de los organismos vertebrados agrupándose dentro la superfamilia de la ribonucleasa A, una de las enzimas mejor caracterizadas del siglo XX. De interés remarcable podríamos considerar su amplio abanico de propiedades biológicas, teniendo en cuenta su diverso historial de propiedades biológicas no catalíticas, convirtiéndolas en un buen modelo de proteínas multifunción. Junto a su principal característica como enzima catalizador de ácidos ribonucleicos, es importante destacar también otro tipo de propiedades biológicas no menos esenciales, como su actividad antimicrobiana, que comparten miembros distantes de la familia sugiriendo una función ancestral en el sistema inmune. Además, se ha visto que la expresión de algunas RNasas humanas puede ser inducida en procesos infecciosos. En particular, las RNasas estudiadas en este trabajo, las RNasas humanas 3, 6 y 7, se expresan principalmente en eosinófilos, monocitos y células epiteliales, respectivamente. Estas proteínas muestran una alta cationicidad debido a su alta proporción de residuos básicos y una notable actividad antimicrobiana frente a una amplia gama de patógenos humanos. Nuestro grupo de investigación posee una larga trayectoria en el estudio del mecanismo de acción de las ribonucleasas humanas y el trabajo teórico-experimental que se presenta en esta tesis ha contribuido a consolidar el actual proyecto de investigación. Los principales avances llevados a cabo por la presente tesis doctoral se enumeran a continuación: - La caracterización del mecanismo antimicrobiano de la ribonucleasa 6, evaluando sus propiedades microbicidas frente a patógenos y modelos de membrana. Concretamente se ha revelado su actividad aglutinadora además de demostrarse que su actividad antimicrobiana está localizada básicamente en su extremo Nterminal. - La resolución de la primera estructura tridimensional de la ribonucleasa 6, obtenida a 1.72 Å, que ha permitido asentar las bases estructurales para futuros estudios funcionales. Análisis complementarios sobre su caracterización cinética y predicción de complejos con diferentes ligandos han revelado sitios de unión y de catálisis que posteriormente han sido confirmados mediante mutagénesis dirigida. - El estudio de la efectiva actividad antipatogena a nivel intracelular que presentan las ribonucleasas 3,6 y 7 asi como sus péptidos derivados N-terminales frente a micobacterias en un modelo de macrófagos infectados. - La expansión del conocimiento sobre las bases antipatogenas de diferentes péptidos y proteínas antimicrobianas que participan en la erradicación de las infecciones por micobacterias, asi como las terapias derivadas. - La caracterización del mecanismo antimicrobiano de los 8 peptidos N-terminales derivados de las ribonucleasas frente a Candida albicans, como modelo de patógeno eucariota Como conclusión, los resultados presentados en esta tesis contribuyen a profundizar en la comprensión de las bases moleculares del papel que desempeñan algunas ribonucleasas en el sistema inmune y expandir el proyecto al diseño de agentes terapéuticos basados en péptidos antimicrobianos con el objetivo de erradicar enfermedades infecciosas causadas por patógenos resistentes.The present doctoral thesis is integrated into the large-scale study of the structure and function of human antimicrobial ribonucleases. These cationic and low molecular weight proteins are grouped into the ribonuclease A superfamily, considered one of the best characterized enzymes of the twentieth century. The RNase A superfamily is specific for vertebrates and has attracted remarkable interest due to the diversity of displayed biological properties; and represents an excellent example of a multifunctional protein´s family. Together with the main enzymatic activity we must highlight other biological properties such as the angiogenic, immunomodulatory and antimicrobial activities. The reported antimicrobial activity of distantly related family members in early vertebrates suggests that the family arouse with an ancestral function in host defence. Besides, the expression of several human RNases has been reported to be induced by infection. In particular, the RNases studied in this work, the human RNases 3, 6 and 7, are mainly expressed in eosinophils, monocytes and epithelial cells respectively. These proteins show a high cationicity due to the high proportion of basic residues and a remarkable antimicrobial activity against a wide range of human pathogens. Our research group has a consolidated experience in the study of the mechanism of action of human ribonucleases and the experimental work presented in this thesis is contributing to this overall research project. The main results achieved by the present PhD study are outlined below: - The characterization of the antimicrobial mechanism of RNase 6, both in bacteria cell cultures and using membrane models. Results highlight that the antimicrobial and cell agglutinating activities are mainly located at the N-terminus. - The resolution of the first three-dimensional structure of ribonuclease 6, obtained at 1.72 Å, which has set the structural basis for future functional studies. The kinetic characterization of RNase 6 mutant variants and the prediction of protein- substrate complexes have identified the enzyme nucleotide binding sites. - The study of the intracellular activity of ribonucleases 3, 6 and 7 and their derived Nterminal peptides against intracellular resident mycobacteria using a macrophage infected model. - The analysis of the anti-pathogenic mechanism of action of human antimicrobial proteins and peptides in mycobacterial infections and their applied therapies. - The comparative characterization of the antimicrobial mechanism of action of human RNases and their N-terminal derived peptides towards Candida albicans, as an eukaryote pathogen model. The results presented in this thesis will contribute to the understanding of the role of human RNases in the immune system and provide the structure- function basis to expand the initial project into the design of novel peptide mimetic therapeutics agents towards the eradication of resistant infectious diseases

Unveiling the multifaceted antimicrobial mechanism of action of human host defence RNases

La presente tesis doctoral se encuentra integrada dentro del estudio a gran escala de la estructura-función de las ribonucleasas antimicrobianas humanas. Estas proteínas catiónicas y de bajo peso molecular son secretadas por la mayoría de los organismos vertebrados agrupándose dentro la superfamilia de la ribonucleasa A, una de las enzimas mejor caracterizadas del siglo XX. De interés remarcable podríamos considerar su amplio abanico de propiedades biológicas, teniendo en cuenta su diverso historial de propiedades biológicas no catalíticas, convirtiéndolas en un buen modelo de proteínas multifunción. Junto a su principal característica como enzima catalizador de ácidos ribonucleicos, es importante destacar también otro tipo de propiedades biológicas no menos esenciales, como su actividad antimicrobiana, que comparten miembros distantes de la familia sugiriendo una función ancestral en el sistema inmune. Además, se ha visto que la expresión de algunas RNasas humanas puede ser inducida en procesos infecciosos. En particular, las RNasas estudiadas en este trabajo, las RNasas humanas 3, 6 y 7, se expresan principalmente en eosinófilos, monocitos y células epiteliales, respectivamente. Estas proteínas muestran una alta cationicidad debido a su alta proporción de residuos básicos y una notable actividad antimicrobiana frente a una amplia gama de patógenos humanos. Nuestro grupo de investigación posee una larga trayectoria en el estudio del mecanismo de acción de las ribonucleasas humanas y el trabajo teórico-experimental que se presenta en esta tesis ha contribuido a consolidar el actual proyecto de investigación. Los principales avances llevados a cabo por la presente tesis doctoral se enumeran a continuación: La caracterización del mecanismo antimicrobiano de la ribonucleasa 6, evaluando sus propiedades microbicidas frente a patógenos y modelos de membrana. Concretamente se ha revelado su actividad aglutinadora además de demostrarse que su actividad antimicrobiana está localizada básicamente en su extremo Nterminal. La resolución de la primera estructura tridimensional de la ribonucleasa 6, obtenida a 1.72 Å, que ha permitido asentar las bases estructurales para futuros estudios funcionales. Análisis complementarios sobre su caracterización cinética y predicción de complejos con diferentes ligandos han revelado sitios de unión y de catálisis que posteriormente han sido confirmados mediante mutagénesis dirigida. - El estudio de la efectiva actividad antipatogena a nivel intracelular que presentan las ribonucleasas 3,6 y 7 asi como sus péptidos derivados N-terminales frente a micobacterias en un modelo de macrófagos infectados. La expansión del conocimiento sobre las bases antipatogenas de diferentes péptidos y proteínas antimicrobianas que participan en la erradicación de las infecciones por micobacterias, asi como las terapias derivadas. La caracterización del mecanismo antimicrobiano de los 8 peptidos N-terminales derivados de las ribonucleasas frente a Candida albicans, como modelo de patógeno eucariota Como conclusión, los resultados presentados en esta tesis contribuyen a profundizar en la comprensión de las bases moleculares del papel que desempeñan algunas ribonucleasas en el sistema inmune y expandir el proyecto al diseño de agentes terapéuticos basados en péptidos antimicrobianos con el objetivo de erradicar enfermedades infecciosas causadas por patógenos resistentes.The present doctoral thesis is integrated into the large-scale study of the structure and function of human antimicrobial ribonucleases. These cationic and low molecular weight proteins are grouped into the ribonuclease A superfamily, considered one of the best characterized enzymes of the twentieth century. The RNase A superfamily is specific for vertebrates and has attracted remarkable interest due to the diversity of displayed biological properties; and represents an excellent example of a multifunctional protein's family. Together with the main enzymatic activity we must highlight other biological properties such as the angiogenic, immunomodulatory and antimicrobial activities. The reported antimicrobial activity of distantly related family members in early vertebrates suggests that the family arouse with an ancestral function in host defence. Besides, the expression of several human RNases has been reported to be induced by infection. In particular, the RNases studied in this work, the human RNases 3, 6 and 7, are mainly expressed in eosinophils, monocytes and epithelial cells respectively. These proteins show a high cationicity due to the high proportion of basic residues and a remarkable antimicrobial activity against a wide range of human pathogens. Our research group has a consolidated experience in the study of the mechanism of action of human ribonucleases and the experimental work presented in this thesis is contributing to this overall research project. The main results achieved by the present PhD study are outlined below: - The characterization of the antimicrobial mechanism of RNase 6, both in bacteria cell cultures and using membrane models. Results highlight that the antimicrobial and cell agglutinating activities are mainly located at the N-terminus. - The resolution of the first three-dimensional structure of ribonuclease 6, obtained at 1.72 Å, which has set the structural basis for future functional studies. The kinetic characterization of RNase 6 mutant variants and the prediction of protein- substrate complexes have identified the enzyme nucleotide binding sites. - The study of the intracellular activity of ribonucleases 3, 6 and 7 and their derived Nterminal peptides against intracellular resident mycobacteria using a macrophage infected model. - The analysis of the anti-pathogenic mechanism of action of human antimicrobial proteins and peptides in mycobacterial infections and their applied therapies. - The comparative characterization of the antimicrobial mechanism of action of human RNases and their N-terminal derived peptides towards Candida albicans, as an eukaryote pathogen model. The results presented in this thesis will contribute to the understanding of the role of human RNases in the immune system and provide the structure- function basis to expand the initial project into the design of novel peptide mimetic therapeutics agents towards the eradication of resistant infectious diseases

Insight into the antifungal mechanism of action of human RNase N-terminus derived peptides

Candida albicans is a polymorphic fungus responsible for mucosal and skin infections. Candida cells establish themselves into biofilm communities resistant to most currently available antifungal agents. An increase of severe infections ensuing in fungal septic shock in elderly or immunosuppressed patients, along with the emergence of drug-resistant strains, urge the need for the development of alternative antifungal agents. In the search for novel antifungal drugs our laboratory demonstrated that two human ribonucleases from the vertebrate-specific RNaseA superfamily, hRNase3 and hRNase7, display a high anticandidal activity. In a previous work, we proved that the N-terminal region of the RNases was sufficient to reproduce most of the parental protein bactericidal activity. Next, we explored their potency against a fungal pathogen. Here, we have tested the N-terminal derived peptides that correspond to the eight human canonical RNases (RN1-8) against planktonic cells and biofilms of C. albicans. RN3 and RN7 peptides displayed the most potent inhibitory effect with a mechanism of action characterized by cell-wall binding, membrane permeabilization and biofilm eradication activities. Both peptides are able to eradicate planktonic and sessile cells, and to alter their gene expression, reinforcing its role as a lead candidate to develop novel antifungal and antibiofilm therapies.This research was funded by the Ministerio de Economía y Competitividad (SAF2017-82158-R and SAF2015-66007P, Fundació La Marató de TV3 (20180310) and Generalitat de Catalunya (2016-PROD-00060). M.T. would like to acknowledge support from the Programa Ramon y Cajal (RYC-2012-09999) and the European Society of Clinical Microbiology and Infectious Diseases though ans ESCMID-2016 grant

The first crystal structure of human RNase6 reveals a novel substrate binding and cleavage site arrangement

Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at a 1.72 Å resolution, being the first report for the protein threedimensional structure and thereby setting the basis for functional studies. The structure shows an overall kidney shaped globular fold shared with the other known family members. Three sulphate anions bound to RNase 6 were found, interacting to residues at the main active site (His15, His122 and Gln14) and cationic surface exposed residues (His36, His39, Arg66 and His67). Kinetic characterization, together with prediction of protein -nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison to the pancreatic RNase type, its structure includes lineage specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5' end can provide an endonuclease type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His36-His39 dyad that facilitates the polynucleotide substrate catalysis

Insights into the Antimicrobial Mechanism of Action of Human RNase6 : Structural Determinants for Bacterial Cell Agglutination and Membrane Permeation

Human Ribonuclease 6 is a secreted protein belonging to the ribonuclease A (RNaseA) superfamily, a vertebrate specific family suggested to arise with an ancestral host defense role. Tissue distribution analysis revealed its expression in innate cell types, showing abundance in monocytes and neutrophils. Recent evidence of induction of the protein expression by bacterial infection suggested an antipathogen function in vivo. In our laboratory, the antimicrobial properties of the protein have been evaluated against Gram-negative and Gram-positive species and its mechanism of action was characterized using a membrane model. Interestingly, our results indicate that RNase6, as previously reported for RNase3, is able to specifically agglutinate Gram-negative bacteria as a main trait of its antimicrobial activity. Moreover, a side by side comparative analysis with the RN6(1-45) derived peptide highlights that the antimicrobial activity is mostly retained at the protein N-terminus. Further work by site directed mutagenesis and structural analysis has identified two residues involved in the protein antimicrobial action (Trp1 and Ile13) that are essential for the cell agglutination properties. This is the first structure-functional characterization of RNase6 antimicrobial properties, supporting its contribution to the infection focus clearance

Exploring the mechanisms of action of human secretory RNase 3 and RNase 7 against Candida albicans

Human antimicrobial RNases, which belong to the vertebrate RNase A superfamily and are secreted upon infection, display a wide spectrum of antipathogen activities. In this work, we examined the antifungal activity of the eosinophil RNase 3 and the skin-derived RNase 7, two proteins expressed by innate cell types that are directly involved in the host defense against fungal infection. Candida albicans has been selected as a suitable working model for testing RNase activities toward a eukaryotic pathogen. We explored the distinct levels of action of both RNases on yeast by combining cell viability and membrane model assays together with protein labeling and confocal microscopy. Site-directed mutagenesis was applied to ablate either the protein active site or the key anchoring region for cell binding. This is the first integrated study that highlights the RNases' dual mechanism of action. Along with an overall membrane-destabilization process, the RNases could internalize and target cellular RNA. The data support the contribution of the enzymatic activity for the antipathogen action of both antimicrobial proteins, which can be envisaged as suitable templates for the development of novel antifungal drugs. We suggest that both human RNases work as multitasking antimicrobial proteins that provide a first line immune barrier