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Langleib M, Calvelo J, Costábile A, Castillo E, Tort JF, Hoffmann FG, Protasio AV, Koziol U, Iriarte A. Evolutionary analysis of species-specific duplications in flatworm genomes. Mol Phylogenet Evol 2024; 199:108141. [PMID: 38964593 DOI: 10.1016/j.ympev.2024.108141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 06/15/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.
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Affiliation(s)
- Mauricio Langleib
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Estela Castillo
- Laboratorio de Biología Parasitaria, Instituto de Higiene, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, United States of America; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, United States of America
| | - Anna V Protasio
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, United Kingdom
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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2
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Serrat J, Torres-Valle M, López-García M, Becerro-Recio D, Siles-Lucas M, González-Miguel J. Molecular Characterization of the Interplay between Fasciola hepatica Juveniles and Laminin as a Mechanism to Adhere to and Break through the Host Intestinal Wall. Int J Mol Sci 2023; 24:ijms24098165. [PMID: 37175870 PMCID: PMC10179147 DOI: 10.3390/ijms24098165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Fasciola hepatica is the main causative agent of fasciolosis, a zoonotic parasitic disease of growing public health concern. F. hepatica metacercariae are ingested by the host and excyst in the intestine, thereby releasing the newly excysted juveniles (FhNEJ), which traverse the gut wall and migrate towards the biliary ducts. Since blocking F. hepatica development is challenging after crossing of the intestinal wall, targeting this first step of migration might result in increased therapeutic success. The intestinal extracellular matrix (ECM) is constituted by a network of structural proteins, including laminin (LM) and fibronectin (FN), that provide mechanical support while acting as physical barrier against intestinal pathogens. Here, we employed ELISA and immunofluorescent assays to test for the presence of LM- and FN-binding proteins on a tegument-enriched antigenic fraction of FhNEJ, and further determined their identity by two-dimensional electrophoresis coupled to mass spectrometry. Additionally, we performed enzymatic assays that revealed for the first time the capability of the juvenile-specific cathepsin L3 to degrade LM, and that LM degradation by FhNEJ proteins is further potentiated in the presence of host plasminogen. Finally, a proteomic analysis showed that the interaction with LM triggers protein changes in FhNEJ that may be relevant for parasite growth and adaptation inside the mammalian host. Altogether, our study provides valuable insights into the molecular interplay between FhNEJ and the intestinal ECM, which may lead to the identification of targetable candidates for the development of more effective control strategies against fasciolosis.
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Affiliation(s)
- Judit Serrat
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - María Torres-Valle
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Marta López-García
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - David Becerro-Recio
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Mar Siles-Lucas
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Javier González-Miguel
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
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3
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Rohweder PJ, Jiang Z, Hurysz BM, O'Donoghue AJ, Craik CS. Multiplex substrate profiling by mass spectrometry for proteases. Methods Enzymol 2022; 682:375-411. [PMID: 36948708 PMCID: PMC10201391 DOI: 10.1016/bs.mie.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteolysis is a central regulator of many biological pathways and the study of proteases has had a significant impact on our understanding of both native biology and disease. Proteases are key regulators of infectious disease and misregulated proteolysis in humans contributes to a variety of maladies, including cardiovascular disease, neurodegeneration, inflammatory diseases, and cancer. Central to understanding a protease's biological role, is characterizing its substrate specificity. This chapter will facilitate the characterization of individual proteases and complex, heterogeneous proteolytic mixtures and provide examples of the breadth of applications that leverage the characterization of misregulated proteolysis. Here we present the protocol of Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS), a functional assay that quantitatively characterizes proteolysis using a synthetic library of physiochemically diverse, model peptide substrates, and mass spectrometry. We present a detailed protocol as well as examples of the use of MSP-MS for the study of disease states, for the development of diagnostic and prognostic tests, for the generation of tool compounds, and for the development of protease-targeted drugs.
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Affiliation(s)
- Peter J Rohweder
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States
| | - Brianna M Hurysz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States.
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States.
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Exploiting Comparative Omics to Understand the Pathogenic and Virulence-Associated Protease: Anti-Protease Relationships in the Zoonotic Parasites Fasciola hepatica and Fasciola gigantica. Genes (Basel) 2022; 13:genes13101854. [PMID: 36292739 PMCID: PMC9601652 DOI: 10.3390/genes13101854] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
The helminth parasites, Fasciola hepatica and Fasciola gigantica, are the causative agents of fasciolosis, a global and economically important disease of people and their livestock. Proteases are pivotal to an array of biological processes related to parasitism (development, feeding, immune evasion, virulence) and therefore their action requires strict regulation by parasite anti-proteases (protease inhibitors). By interrogating the current publicly available Fasciola spp. large sequencing datasets, including several genome assemblies and life cycle stage-specific transcriptome and proteome datasets, we reveal the complex profile and structure of proteases and anti-proteases families operating at various stages of the parasite's life cycle. Moreover, we have discovered distinct profiles of peptidases and their cognate inhibitors expressed by the parasite stages in the intermediate snail host, reflecting the different environmental niches in which they move, develop and extract nutrients. Comparative genomics revealed a similar cohort of peptidase inhibitors in F. hepatica and F. gigantica but a surprisingly reduced number of cathepsin peptidases genes in the F. gigantica genome assemblies. Chromosomal location of the F. gigantica genes provides new insights into the evolution of these gene families, and critical data for the future analysis and interrogation of Fasciola spp. hybrids spreading throughout the Asian and African continents.
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Barbour T, Cwiklinski K, Lalor R, Dalton JP, De Marco Verissimo C. The Zoonotic Helminth Parasite Fasciola hepatica: Virulence-Associated Cathepsin B and Cathepsin L Cysteine Peptidases Secreted by Infective Newly Excysted Juveniles (NEJ). Animals (Basel) 2021; 11:ani11123495. [PMID: 34944270 PMCID: PMC8698070 DOI: 10.3390/ani11123495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Fasciolosis, caused by the worm parasite Fasciola hepatica (liver fluke), is a global disease of farm animals and a neglected disease of humans. Infection arises from the ingestion of resistant metacercariae that contaminate vegetation. Within the intestine, the parasite excysts as an active larvae, the newly excysted juvenile (NEJ), that borrows through the intestinal wall to infect the host and migrates to the liver. NEJ release, tissue penetration and migration are facilitated by enzymes secreted by the parasite, namely, cathepsin B1 (FhCB1), cathepsin B2 (FhCB2), cathepsin B3 (FhCB3) and cathepsin L3 (FhCL3). While our knowledge of these enzymes is growing, we have yet to understand why the parasites require all four of them to invade the host. In this study, we produced functional recombinant forms of these enzymes and demonstrated that they vary greatly in terms of activity, optimal pH and substrate specificity, suggesting that, combined, these enzymes provide the parasite with an efficient digestion system for different host tissues and molecules. We also identified several compounds that inhibited the activity of these enzymes, but did not affect the ability of the larvae to excyst or survive. However, this does not exclude these enzymes as targets for development of drugs or vaccines. Abstract Fasciolosis caused by Fasciola hepatica is a major global disease of livestock and an important neglected helminthiasis of humans. Infection arises when encysted metacercariae are ingested by the mammalian host. Within the intestine, the parasite excysts as a newly excysted juvenile (NEJ) that penetrates the intestinal wall and migrates to the liver. NEJ excystment and tissue penetration are facilitated by the secretion of cysteine peptidases, namely, cathepsin B1 (FhCB1), cathepsin B2 (FhCB2), cathepsin B3 (FhCB3) and cathepsin L3 (FhCL3). While our knowledge of these peptidases is growing, we have yet to understand why multiple enzymes are required for parasite invasion. Here, we produced functional recombinant forms of these four peptidases and compared their physio-biochemical characteristics. Our studies show great variation of their pH optima for activity, substrate specificity and inhibitory profile. Carboxy-dipeptidase activity was exhibited exclusively by FhCB1. Our studies suggest that, combined, these peptidases create a powerful hydrolytic cocktail capable of digesting the various host tissues, cells and macromolecules. Although we found several inhibitors of these enzymes, they did not show potent inhibition of metacercarial excystment or NEJ viability in vitro. However, this does not exclude these peptidases as targets for future drug or vaccine development.
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Affiliation(s)
- Tara Barbour
- School of Biological Science, Queen’s University Belfast, Belfast BT9 7BL, UK; (T.B.); (K.C.); (J.P.D.)
| | - Krystyna Cwiklinski
- School of Biological Science, Queen’s University Belfast, Belfast BT9 7BL, UK; (T.B.); (K.C.); (J.P.D.)
- Molecular Parasitology Laboratory, Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, H91 TK33 Galway, Ireland;
| | - Richard Lalor
- Molecular Parasitology Laboratory, Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, H91 TK33 Galway, Ireland;
| | - John Pius Dalton
- School of Biological Science, Queen’s University Belfast, Belfast BT9 7BL, UK; (T.B.); (K.C.); (J.P.D.)
- Molecular Parasitology Laboratory, Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, H91 TK33 Galway, Ireland;
| | - Carolina De Marco Verissimo
- School of Biological Science, Queen’s University Belfast, Belfast BT9 7BL, UK; (T.B.); (K.C.); (J.P.D.)
- Molecular Parasitology Laboratory, Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, H91 TK33 Galway, Ireland;
- Correspondence:
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Design of a Peptide-Carrier Vaccine Based on the Highly Immunogenic Fasciola hepatica Leucine Aminopeptidase. Methods Mol Biol 2021; 2137:191-204. [PMID: 32399930 DOI: 10.1007/978-1-0716-0475-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Many studies have shown that the degree of organization and repetitiveness of an antigen correlates with its efficiency to induce a B-cell response and production of neutralizing antibodies. Here we describe the design of a chimeric protein based on the hexamer form of the highly immunogenic Fasciola hepatica leucine aminopeptidase as a carrier system of small peptides with potential use as a multiepitope vaccine.
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7
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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8
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Celias DP, Corvo I, Silvane L, Tort JF, Chiapello LS, Fresno M, Arranz A, Motrán CC, Cervi L. Cathepsin L3 From Fasciola hepatica Induces NLRP3 Inflammasome Alternative Activation in Murine Dendritic Cells. Front Immunol 2019; 10:552. [PMID: 30967874 PMCID: PMC6438957 DOI: 10.3389/fimmu.2019.00552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022] Open
Abstract
The production of IL-1-family cytokines such as IL-1β and IL-18 is finely regulated by inflammasome activation after the recognition of pathogens associated molecular pattern (PAMPs) and danger associated molecular patterns (DAMPs). However, little is known about the helminth-derived molecules capable of activating the inflammasome. In the case of the helminth trematode Fasciola hepatica, the secretion of different cathepsin L cysteine peptidases (FhCL) is crucial for the parasite survival. Among these enzymes, cathepsin L3 (FhCL3) is expressed mainly in the juvenile or invasive stage. The ability of FhCL3 to digest collagen has demonstrated to be critical for intestinal tissue invasion during juvenile larvae migration. However, there is no information about the interaction of FhCL3 with the immune system. It has been shown here that FhCL3 induces a non-canonical inflammasome activation in dendritic cells (DCs), leading to IL-1β and IL-18 production without a previous microbial priming. Interestingly, this activation was depending on the cysteine protease activity of FhCL3 and the NLRP3 receptor, but independent of caspase activation. We also show that FhCL3 is internalized by DCs, promoting pro-IL-1β cleavage to its mature and biologically active form IL-1β, which is released to the extracellular environment. The FhCL3-induced NLRP3 inflammasome activation conditions DCs to promote a singular adaptive immune response, characterized by increased production of IFN-γ and IL-13. These data reveal an unexpected ability of FhCL3, a helminth-derived molecule, to activate the NLRP3 inflammasome, which is independent of the classical mechanism involving caspase activation.
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Affiliation(s)
- Daiana Pamela Celias
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Córdoba, Argentina
| | - Ileana Corvo
- Laboratorio de Investigación y Desarrollo de Moléculas Bioactivas, CENUR Litoral Norte - Sede Paysandú, Universidad de la República, Paysandú, Uruguay
| | - Leonardo Silvane
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Córdoba, Argentina
| | - José Francisco Tort
- Departmento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura Silvina Chiapello
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Córdoba, Argentina
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa (CSIC), Madrid, Spain
| | - Alicia Arranz
- Centro de Biología Molecular Severo Ochoa (CSIC), Madrid, Spain
| | - Claudia Cristina Motrán
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Córdoba, Argentina
| | - Laura Cervi
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), CONICET, Córdoba, Argentina
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9
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Cwiklinski K, Donnelly S, Drysdale O, Jewhurst H, Smith D, De Marco Verissimo C, Pritsch IC, O'Neill S, Dalton JP, Robinson MW. The cathepsin-like cysteine peptidases of trematodes of the genus Fasciola. ADVANCES IN PARASITOLOGY 2019; 104:113-164. [PMID: 31030768 DOI: 10.1016/bs.apar.2019.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fasciolosis caused by trematode parasites of the genus Fasciola is a global disease of livestock, particularly cattle, sheep, water buffalo and goats. It is also a major human zoonosis with reports suggesting that 2.4-17 million people are infected worldwide, and 91.1 million people currently living at risk of infection. A unique feature of these worms is their reliance on a family of developmentally-regulated papain-like cysteine peptidases, termed cathepsins. These proteolytic enzymes play central roles in virulence, infection, tissue migration and modulation of host innate and adaptive immune responses. The availability of a Fasciola hepatica genome, and the exploitation of transcriptomic and proteomic technologies to probe parasite growth and development, has enlightened our understanding of the cathepsin-like cysteine peptidases. Here, we clarify the structure of the cathepsin-like cysteine peptidase families and, in this context, review the phylogenetics, structure, biochemistry and function of these enzymes in the host-parasite relationship.
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Affiliation(s)
- Krystyna Cwiklinski
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Sheila Donnelly
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom; The School of Life Sciences, University of Technology Sydney (UTS), Ultimo, Sydney, NSW, Australia
| | - Orla Drysdale
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Heather Jewhurst
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - David Smith
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | | | - Izanara C Pritsch
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom; Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | - Sandra O'Neill
- School of Biotechnology, Dublin City University, Dublin, Republic of Ireland
| | - John P Dalton
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Mark W Robinson
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom.
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10
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Grote A, Caffrey CR, Rebello KM, Smith D, Dalton JP, Lustigman S. Cysteine proteases during larval migration and development of helminths in their final host. PLoS Negl Trop Dis 2018; 12:e0005919. [PMID: 30138448 PMCID: PMC6107106 DOI: 10.1371/journal.pntd.0005919] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neglected tropical diseases caused by metazoan parasites are major public health concerns, and therefore, new methods for their control and elimination are needed. Research over the last 25 years has revealed the vital contribution of cysteine proteases to invasion of and migration by (larval) helminth parasites through host tissues, in addition to their roles in embryogenesis, molting, egg hatching, and yolk degradation. Their central function to maintaining parasite survival in the host has made them prime intervention targets for novel drugs and vaccines. This review focuses on those helminth cysteine proteases that have been functionally characterized during the varied early stages of development in the human host and embryogenesis.
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Affiliation(s)
- Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Karina M. Rebello
- Laboratório de Toxinologia and Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - David Smith
- School of Biological Sciences, Medical Biology Centre, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
- Department of Microbiology and Immunology, School of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John P. Dalton
- School of Biological Sciences, Medical Biology Centre, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Sara Lustigman
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
- * E-mail:
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11
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Corvo I, Ferraro F, Merlino A, Zuberbühler K, O'Donoghue AJ, Pastro L, Pi-Denis N, Basika T, Roche L, McKerrow JH, Craik CS, Caffrey CR, Tort JF. Substrate Specificity of Cysteine Proteases Beyond the S 2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L. Front Mol Biosci 2018; 5:40. [PMID: 29725596 PMCID: PMC5917446 DOI: 10.3389/fmolb.2018.00040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
Cysteine proteases are widespread in all life kingdoms, being central to diverse physiological processes based on a broad range of substrate specificity. Paralogous Fasciola hepatica cathepsin L proteases are essential to parasite invasion, tissue migration and reproduction. In spite of similarities in their overall sequence and structure, these enzymes often exhibit different substrate specificity. These preferences are principally determined by the amino acid composition of the active site's S2 subsite (pocket) of the enzyme that interacts with the substrate P2 residue (Schetcher and Berger nomenclature). Although secreted FhCL1 accommodates aliphatic residues in the S2 pocket, FhCL2 is also efficient in cleaving proline in that position. To understand these differences, we engineered the FhCL1 S2 subsite at three amino acid positions to render it identical to that present in FhCL2. The substitutions did not produce the expected increment in proline accommodation in P2. Rather, they decreased the enzyme's catalytic efficiency toward synthetic peptides. Nonetheless, a change in the P3 specificity was associated with the mutation of Leu67 to Tyr, a hinge residue between the S2 and S3 subsites that contributes to the accommodation of Gly in S3. Molecular dynamic simulations highlighted changes in the spatial distribution and secondary structure of the S2 and S3 pockets of the mutant FhCL1 enzymes. The reduced affinity and catalytic efficiency of the mutant enzymes may be due to a narrowing of the active site cleft that hinders the accommodation of substrates. Because the variations in the enzymatic activity measured could not be exclusively allocated to those residues lining the active site, other more external positions might modulate enzyme conformation, and, therefore, catalytic activity.
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Affiliation(s)
- Ileana Corvo
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Florencia Ferraro
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Kathrin Zuberbühler
- Department of Pharmaceutical Chemistry, Pharmacology, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Lucía Pastro
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Natalia Pi-Denis
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Tatiana Basika
- Departamento de Biología Celular y Molecular, Unidad de Biología Parasitaria, Facultad de Ciencias, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Leda Roche
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - James H McKerrow
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, Pharmacology, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Conor R Caffrey
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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12
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Cwiklinski K, Jewhurst H, McVeigh P, Barbour T, Maule AG, Tort J, O'Neill SM, Robinson MW, Donnelly S, Dalton JP. Infection by the Helminth Parasite Fasciola hepatica Requires Rapid Regulation of Metabolic, Virulence, and Invasive Factors to Adjust to Its Mammalian Host. Mol Cell Proteomics 2018; 17:792-809. [PMID: 29321187 PMCID: PMC5880117 DOI: 10.1074/mcp.ra117.000445] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
The parasite Fasciola hepatica infects a broad range of mammals with
impunity. Following ingestion of parasites (metacercariae) by the host, newly
excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall
and migrate to the liver. Successful infection takes just a few hours and involves
negotiating hurdles presented by host macromolecules, tissues and micro-environments,
as well as the immune system. Here, transcriptome and proteome analysis of ex
vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude
of metabolic and developmental alterations that take place in order for the parasite
to establish infection. We found that metacercariae despite being encased in a cyst
are metabolically active, and primed for infection. Following excystment, NEJ expend
vital energy stores and rapidly adjust their metabolic pathways to cope with their
new and increasingly anaerobic environment. Temperature increases induce neoblast
proliferation and the remarkable up-regulation of genes associated with growth and
development. Cysteine proteases synthesized by gastrodermal cells are secreted to
facilitate invasion and tissue degradation, and tegumental transporters, such as
aquaporins, are varied to deal with osmotic/salinity changes. Major proteins of the
total NEJ secretome include proteases, protease inhibitors and anti-oxidants, and an
array of immunomodulators that likely disarm host innate immune effector cells. Thus,
the challenges of infection by F. hepatica parasites are met by
rapid metabolic and physiological adjustments that expedite tissue invasion and
immune evasion; these changes facilitate parasite growth, development and maturation.
Our molecular analysis of the critical processes involved in host invasion has
identified key targets for future drug and vaccine strategies directed at preventing
parasite infection.
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Affiliation(s)
- Krystyna Cwiklinski
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK;
| | - Heather Jewhurst
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Paul McVeigh
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK.,§Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Tara Barbour
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Aaron G Maule
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK.,§Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jose Tort
- ¶Departamento de Genética, Facultad de Medicina, Universidad de la República, Uruguay
| | | | - Mark W Robinson
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK.,§Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Sheila Donnelly
- **The i3 Institute and School of Medical and Molecular Biosciences, University of Technology, Sydney, Australia
| | - John P Dalton
- From the ‡School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, UK.,§Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, Northern Ireland, UK
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13
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Ferraro F, Merlino A, dell´Oca N, Gil J, Tort JF, Gonzalez M, Cerecetto H, Cabrera M, Corvo I. Identification of Chalcones as Fasciola hepatica Cathepsin L Inhibitors Using a Comprehensive Experimental and Computational Approach. PLoS Negl Trop Dis 2016; 10:e0004834. [PMID: 27463369 PMCID: PMC4962987 DOI: 10.1371/journal.pntd.0004834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Increased reports of human infections have led fasciolosis, a widespread disease of cattle and sheep caused by the liver flukes Fasciola hepatica and Fasciola gigantica, to be considered an emerging zoonotic disease. Chemotherapy is the main control measure available, and triclabendazole is the preferred drug since is effective against both juvenile and mature parasites. However, resistance to triclabendazole has been reported in several countries urging the search of new chemical entities and target molecules to control fluke infections. METHODOLOGY/PRINCIPLE FINDINGS We searched a library of forty flavonoid derivatives for inhibitors of key stage specific Fasciola hepatica cysteine proteases (FhCL3 and FhCL1). Chalcones substituted with phenyl and naphtyl groups emerged as good cathepsin L inhibitors, interacting more frequently with two putative binding sites within the active site cleft of the enzymes. One of the compounds, C34, tightly bounds to juvenile specific FhCL3 with an IC50 of 5.6 μM. We demonstrated that C34 is a slow-reversible inhibitor that interacts with the Cys-His catalytic dyad and key S2 and S3 pocket residues, determinants of the substrate specificity of this family of cysteine proteases. Interestingly, C34 induces a reduction in NEJ ability to migrate through the gut wall and a loss of motility phenotype that leads to NEJ death within a week in vitro, while it is not cytotoxic to bovine cells. CONCLUSIONS/SIGNIFICANCE Up to date there are no reports of in vitro screening for non-peptidic inhibitors of Fasciola hepatica cathepsins, while in general these are considered as the best strategy for in vivo inhibition. We have identified chalcones as novel inhibitors of the two main Cathepsins secreted by juvenile and adult liver flukes. Interestingly, one compound (C34) is highly active towards the juvenile enzyme reducing larval ability to penetrate the gut wall and decreasing NEJ´s viability in vitro. These findings open new avenues for the development of novel agents to control fluke infection and possibly other helminthic diseases.
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Affiliation(s)
- Florencia Ferraro
- Laboratorio de Investigación y Desarrollo de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Nicolás dell´Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jorge Gil
- Laboratorio de Reproducción Animal, Producción y Reproducción de Rumiantes, Departamento de Ciencias Biológicas, CENUR Litoral Norte-Facultad de Veterinaria, Universidad de la República, Paysandú, Uruguay
| | - José F. Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mercedes Gonzalez
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Hugo Cerecetto
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Cabrera
- Laboratorio de Investigación y Desarrollo de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ileana Corvo
- Laboratorio de Investigación y Desarrollo de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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14
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Bibo-Verdugo B, O'Donoghue AJ, Rojo-Arreola L, Craik CS, García-Carreño F. Complementary Proteomic and Biochemical Analysis of Peptidases in Lobster Gastric Juice Uncovers the Functional Role of Individual Enzymes in Food Digestion. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:201-214. [PMID: 26613762 DOI: 10.1007/s10126-015-9681-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
Crustaceans are a diverse group, distributed in widely variable environmental conditions for which they show an equally extensive range of biochemical adaptations. Some digestive enzymes have been studied by purification/characterization approaches. However, global analysis is crucial to understand how digestive enzymes interplay. Here, we present the first proteomic analysis of the digestive fluid from a crustacean (Homarus americanus) and identify glycosidases and peptidases as the most abundant classes of hydrolytic enzymes. The digestion pathway of complex carbohydrates was predicted by comparing the lobster enzymes to similar enzymes from other crustaceans. A novel and unbiased substrate profiling approach was used to uncover the global proteolytic specificity of gastric juice and determine the contribution of cysteine and aspartic acid peptidases. These enzymes were separated by gel electrophoresis and their individual substrate specificities uncovered from the resulting gel bands. This new technique is called zymoMSP. Each cysteine peptidase cleaves a set of unique peptide bonds and the S2 pocket determines their substrate specificity. Finally, affinity chromatography was used to enrich for a digestive cathepsin D1 to compare its substrate specificity and cold-adapted enzymatic properties to mammalian enzymes. We conclude that the H. americanus digestive peptidases may have useful therapeutic applications, due to their cold-adaptation properties and ability to hydrolyze collagen.
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Affiliation(s)
- Betsaida Bibo-Verdugo
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle IPN 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S., 23096, Mexico
| | - Anthony J O'Donoghue
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Liliana Rojo-Arreola
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle IPN 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S., 23096, Mexico
- Center for Discovery and Innovation in Parasitic Diseases, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Fernando García-Carreño
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle IPN 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S., 23096, Mexico.
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15
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Dvořák J, Fajtová P, Ulrychová L, Leontovyč A, Rojo-Arreola L, Suzuki BM, Horn M, Mareš M, Craik CS, Caffrey CR, O'Donoghue AJ. Excretion/secretion products from Schistosoma mansoni adults, eggs and schistosomula have unique peptidase specificity profiles. Biochimie 2015; 122:99-109. [PMID: 26409899 DOI: 10.1016/j.biochi.2015.09.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 09/22/2015] [Indexed: 02/03/2023]
Abstract
Schistosomiasis is one of a number of chronic helminth diseases of poverty that severely impact personal and societal well-being and productivity. Peptidases (proteases) are vital to successful parasitism, and can modulate host physiology and immunology. Interference of peptidase action by specific drugs or vaccines can be therapeutically beneficial. To date, research on peptidases in the schistosome parasite has focused on either the functional characterization of individual peptidases or their annotation as part of global genome or transcriptome studies. We were interested in functionally characterizing the complexity of peptidase activity operating at the host-parasite interface, therefore the excretory-secretory products of key developmental stages of Schistosoma mansoni that parasitize the human were examined. Using class specific peptidase inhibitors in combination with a multiplex substrate profiling assay, a number of unique activities derived from endo- and exo-peptidases were revealed in the excretory-secretory products of schistosomula (larval migratory worms), adults and eggs. The data highlight the complexity of the functional degradome for each developmental stage of this parasite and facilitate further enquiry to establish peptidase identity, physiological and immunological function, and utility as drug or vaccine candidates.
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Affiliation(s)
- Jan Dvořák
- Institute of Molecular Genetics, The Czech Academy of Sciences, Prague CZ - 142 20, Czech Republic; Institute of Parasitology, Biology Center, The Czech Academy of Sciences, České Budějovice CZ - 370 05, Czech Republic; Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ - 166 10, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ - 166 10, Czech Republic; First Faculty of Medicine, Charles University in Prague, Prague CZ - 121 08, Czech Republic
| | - Lenka Ulrychová
- Institute of Molecular Genetics, The Czech Academy of Sciences, Prague CZ - 142 20, Czech Republic; Dept. of Parasitology, Faculty of Science, Charles University in Prague, Prague CZ - 128 44, Czech Republic
| | - Adrian Leontovyč
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ - 166 10, Czech Republic; First Faculty of Medicine, Charles University in Prague, Prague CZ - 121 08, Czech Republic
| | - Liliana Rojo-Arreola
- Center for Discovery and Innovation in Parasitic Diseases and the Department of Pathology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Brian M Suzuki
- Center for Discovery and Innovation in Parasitic Diseases and the Department of Pathology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ - 166 10, Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ - 166 10, Czech Republic
| | - Charles S Craik
- Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases and the Department of Pathology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Anthony J O'Donoghue
- Dept. of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
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16
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Korenč M, Lenarčič B, Novinec M. Human cathepsin L, a papain-like collagenase without proline specificity. FEBS J 2015; 282:4328-40. [PMID: 26306868 DOI: 10.1111/febs.13499] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/13/2015] [Accepted: 08/21/2015] [Indexed: 12/01/2022]
Abstract
Several members of the papain-like peptidase family have the ability to degrade collagen molecules by cleaving within the triple helix region of this difficult substrate. A common denominator of these peptidases is their ability to cleave substrates with Pro in the P2 position. In humans, cathepsin K is the best-known papain-like collagenase. Here, we investigate the collagenolytic activity of human cathepsin L, which is closely related to cathepsin K. We show that, despite lacking proline specificity, cathepsin L efficiently cleaves type I collagen within the triple helix region and produces a cleavage pattern similar to that of cathepsin K. We demonstrate that both enzymes have similar affinities for type I collagen and are able to release proteolytic fragments from insoluble collagen. Moreover, cathepsin K is only approximately fourfold more potent than cathepsin L in releasing fragments from reconstituted fibrils of FITC-labeled collagen. Replacing active site residues of cathepsin L with those from cathepsin K introduces cathepsin K-like specificity towards synthetic substrates and increases the collagenolytic activity of cathepsin L. Replacing three residues in the S2 subsite is sufficient to produce a mutant with collagenolytic activity on par with human cathepsin K. These results provide a basis for engineering collagenolytic activity into non-collagenolytic papain-like scaffolds.
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Affiliation(s)
- Matevž Korenč
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Brigita Lenarčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia.,Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Marko Novinec
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
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17
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Hernández Alvarez L, Naranjo Feliciano D, Hernández González JE, de Oliveira Soares R, Barreto Gomes DE, Pascutti PG. Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches. PLoS Negl Trop Dis 2015; 9:e0003759. [PMID: 25978322 PMCID: PMC4433193 DOI: 10.1371/journal.pntd.0003759] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
Background Fasciola hepatica is the causative agent of fascioliasis, a disease affecting grazing animals, causing economic losses in global agriculture and currently being an important human zoonosis. Overuse of chemotherapeutics against fascioliasis has increased the populations of drug resistant parasites. F. hepatica cathepsin L3 is a protease that plays important roles during the life cycle of fluke. Due to its particular collagenolytic activity it is considered an attractive target against the infective phase of F. hepatica. Methodology/Principal Findings Starting with a three dimensional model of FhCL3 we performed a structure-based design of novel inhibitors through a computational study that combined virtual screening, molecular dynamics simulations, and binding free energy (ΔGbind) calculations. Virtual screening was carried out by docking inhibitors obtained from the MYBRIDGE-HitFinder database inside FhCL3 and human cathepsin L substrate-binding sites. On the basis of dock-scores, five compounds were predicted as selective inhibitors of FhCL3. Molecular dynamic simulations were performed and, subsequently, an end-point method was employed to predict ΔGbind values. Two compounds with the best ΔGbind values (-10.68 kcal/mol and -7.16 kcal/mol), comparable to that of the positive control (-10.55 kcal/mol), were identified. A similar approach was followed to structurally and energetically characterize the interface of FhCL3 in complex with a peptidic substrate. Finally, through pair-wise and per-residue free energy decomposition we identified residues that are critical for the substrate/ligand binding and for the enzyme specificity. Conclusions/Significance The present study is the first computer-aided drug design approach against F. hepatica cathepsins. Here we predict the principal determinants of binding of FhCL3 in complex with a natural substrate by detailed energetic characterization of protease interaction surface. We also propose novel compounds as FhCL3 inhibitors. Overall, these results will foster the future rational design of new inhibitors against FhCL3, as well as other F. hepatica cathepsins. Fascioliosis is considered an emerging disease in humans, causing important losses in global agriculture through the infection of livestock animals. The outcome of resistant parasites has increased the search for new drugs which may contribute to disease control. In recent decades, Fasciola cathepsins (FhCs) have been defined as the principal virulence factors of this parasite. Despite being in the same protein family, they have different specificities and, thus, distinct roles throughout the fluke life cycle. Differences in specificity have been attributed to a few variations in the sequence of key FhCs subsites. Currently, the structure-based drug design of inhibitors against Fasciola cathepsin Ls (FhCLs) with unknown structures is possible due to the availability of the three-dimensional structure of FhCL1. Our detailed structural analysis of the major infective juvenile enzyme (FhCL3) identifies the molecular determinants for protein binding. Also, novel potential inhibitors against FhCL3 are proposed, which might reduce host invasion and penetration processes. These compounds are predicted to interact with the binding site of the enzyme, therefore they could prevent substrate processing by competitive inhibition. The structure-based drug design strategy described here will be useful for the development of new potent and selective inhibitors against other FhCs.
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Affiliation(s)
- Lilian Hernández Alvarez
- Departamento de Biología Molecular, Centro Nacional de Sanidad Agropecuaria de Cuba (CENSA), San José de las Lajas, Mayabeque, Cuba
| | - Dany Naranjo Feliciano
- Departamento de Biología Molecular, Centro Nacional de Sanidad Agropecuaria de Cuba (CENSA), San José de las Lajas, Mayabeque, Cuba
| | | | - Rosemberg de Oliveira Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Rio de Janeiro, Brazil
| | - Diego Enry Barreto Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Diretoria de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Rio de Janeiro, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- * E-mail:
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18
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Cwiklinski K, Dalton JP, Dufresne PJ, La Course J, Williams DJ, Hodgkinson J, Paterson S. The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution. Genome Biol 2015; 16:71. [PMID: 25887684 PMCID: PMC4404566 DOI: 10.1186/s13059-015-0632-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/13/2015] [Indexed: 12/30/2022] Open
Abstract
Background The liver fluke Fasciola hepatica is a major pathogen of livestock worldwide, causing huge economic losses to agriculture, as well as 2.4 million human infections annually. Results Here we provide a draft genome for F. hepatica, which we find to be among the largest known pathogen genomes at 1.3 Gb. This size cannot be explained by genome duplication or expansion of a single repeat element, and remains a paradox given the burden it may impose on egg production necessary to transmit infection. Despite the potential for inbreeding by facultative self-fertilisation, substantial levels of polymorphism were found, which highlights the evolutionary potential for rapid adaptation to changes in host availability, climate change or to drug or vaccine interventions. Non-synonymous polymorphisms were elevated in genes shared with parasitic taxa, which may be particularly relevant for the ability of the parasite to adapt to a broad range of definitive mammalian and intermediate molluscan hosts. Large-scale transcriptional changes, particularly within expanded protease and tubulin families, were found as the parasite migrated from the gut, across the peritoneum and through the liver to mature in the bile ducts. We identify novel members of anti-oxidant and detoxification pathways and defined their differential expression through infection, which may explain the stage-specific efficacy of different anthelmintic drugs. Conclusions The genome analysis described here provides new insights into the evolution of this important pathogen, its adaptation to the host environment and external selection pressures. This analysis also provides a platform for research into novel drugs and vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0632-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krystyna Cwiklinski
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK.
| | - John Pius Dalton
- School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK. .,Institute of Parasitology, McGill University, Montreal, Quebec, Canada.
| | - Philippe J Dufresne
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada. .,Institut National de Santé Publique du Québec, Montreal, Quebec, Canada.
| | | | - Diana Jl Williams
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Jane Hodgkinson
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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19
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Alvarez Rojas CA, Ansell BRE, Hall RS, Gasser RB, Young ND, Jex AR, Scheerlinck JPY. Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver. Parasit Vectors 2015; 8:124. [PMID: 25885344 PMCID: PMC4382932 DOI: 10.1186/s13071-015-0715-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/04/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Although fascioliasis has been relatively well studied, little is known about the molecular basis of this disease. This is particularly relevant, considering the very different response that sheep have to Fasciola hepatica relative to cattle. The acute phase of this disease is severe in sheep, whereas chronic fascioliasis is more common in cattle. METHODS To begin to explore the host-response to Fasciola in sheep and improve the understanding of the host-pathogen interactions during the parasite's migration through liver parenchyma to the bile duct, we used RNA sequencing (RNA-seq) to investigate livers from sheep infected for eight weeks compared with those from uninfected controls. RESULTS This study identified 572 and 42 genes that were up- and down-regulated, respectively, in infected livers relative to uninfected controls. Our molecular findings provide significant new insights into the mechanisms linked to metabolism, fibrosis and tissue-repair in sheep, and highlight the relative importance of specific components of immune response pathways, which appear to be driven toward a suppression of inflammation. CONCLUSIONS This study is, to our knowledge, the first detailed investigation of the transcriptomic responses in the liver tissue of any host to F. hepatica infection. It defines the involvement of specific genes associated with the host's metabolism, immune response and tissue repair/regeneration, and highlights an apparent overlapping function of many genes involved in these processes.
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Affiliation(s)
- Cristian A Alvarez Rojas
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Brendan R E Ansell
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Ross S Hall
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Jean-Pierre Y Scheerlinck
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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20
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Molina-Hernández V, Mulcahy G, Pérez J, Martínez-Moreno Á, Donnelly S, O'Neill SM, Dalton JP, Cwiklinski K. Fasciola hepatica vaccine: we may not be there yet but we're on the right road. Vet Parasitol 2015; 208:101-11. [PMID: 25657086 PMCID: PMC4366043 DOI: 10.1016/j.vetpar.2015.01.004] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Major advances have been made in identifying potential vaccine molecules for the control of fasciolosis in livestock but we have yet to reach the level of efficacy required for commercialisation. The pathogenesis of fasciolosis is associated with liver damage that is inflicted by migrating and feeding immature flukes as well as host inflammatory immune responses to parasite-secreted molecules and tissue damage alarm signals. Immune suppression/modulation by the parasites prevents the development of protective immune responses as evidenced by the lack of immunity observed in naturally and experimentally infected animals. In our opinion, future efforts need to focus on understanding how parasites invade and penetrate the tissues of their hosts and how they potentiate and control the ensuing immune responses, particularly in the first days of infection. Emerging 'omics' data employed in an unbiased approach are helping us understand liver fluke biology and, in parallel with new immunological data, to identify molecules that are essential to parasite development and accessible to vaccine-induced immune responses.
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Affiliation(s)
| | - Grace Mulcahy
- Veterinary Science Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Jose Pérez
- School of Veterinary Medicine, University of Cordoba, Córdoba, Spain
| | | | - Sheila Donnelly
- The i3 Institute & School of Medical and Molecular Biosciences, University of Technology, Sydney, Australia
| | | | - John P Dalton
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
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21
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Tóth A, Németh T, Csonka K, Horváth P, Vágvölgyi C, Vizler C, Nosanchuk JD, Gácser A. Secreted Candida parapsilosis lipase modulates the immune response of primary human macrophages. Virulence 2014; 5:555-62. [PMID: 24626151 DOI: 10.4161/viru.28509] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Candida parapsilosis is an important opportunistic pathogen with increasing prevalence. Extracellular lipases have been shown to play an important role in the virulence of pathogenic Candida species. However, studying the role of secreted lipase in C. albicans is challenging due to the lack of a mutant strain deficient in all 10 lipase genes. In contrast, we have previously constructed a lipase mutant C. parapsilosis strain lacking both CpLIP1 and CpLIP2, and shown that it has significantly decreased virulence in various infection models, and is killed more efficiently by mouse macrophages. In the present study, we compared the response of human peripheral blood monocyte-derived macrophages to a wild type (wt) as well as a lipase-deficient (lip(-/-)) C. parapsilosis strain that has been previously established in our lab. Although macrophages phagocytosed both strains with similar efficiency, lipase mutants were killed more efficiently according to fluorescent microscopic analysis. The more efficient killing of lip(-/-) cells was confirmed by CFU-determinations. Phagocytosis of wt and lip(-/-)C. parapsilosis was also examined by flow cytometry, revealing that both strains were internelized to the similar extent by macrophages. Additionally, quantitative imaging analysis revealed that the rate of phagolysosome fusion was higher in case of lip(-/-)C. parapsilosis. Interestingly, macrophages stimulated with lip(-/-)C. parapsilosis showed at least 1.5-fold higher expression of TNFα, IL-1β, IL-6, IL-8, and PTGS-2 after 12 h compared with those infected with wt C. parapsilosis, as determined by qRT-PCR. Furthermore, the lip(-/-)C. parapsilosis strain induced significantly higher TNFα, IL-1β, IL-6, and IL-10 protein production in macrophages after 24 h compared with the wt strain. These findings confirm the role of fungal lipases as important virulence factors during C. parapsilosis infection.
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Affiliation(s)
- Adél Tóth
- Department of Microbiology; University of Szeged; Szeged, Hungary
| | - Tibor Németh
- Department of Microbiology; University of Szeged; Szeged, Hungary
| | - Katalin Csonka
- Department of Microbiology; University of Szeged; Szeged, Hungary
| | - Péter Horváth
- Department of Microbiology; University of Szeged; Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology; University of Szeged; Szeged, Hungary
| | - Csaba Vizler
- Biological Research Center of Hungarian Academy of Sciences; Institute of Biochemistry; Szeged, Hungary
| | - Joshua D Nosanchuk
- Department of Microbiology and Immunology; Albert Einstein College of Medicine; New York, NY USA
| | - Attila Gácser
- Department of Microbiology; University of Szeged; Szeged, Hungary
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