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Rothmann-Meyer W, Naidoo K, de Waal PJ. Spirocerca lupi draft genome, vaccine and anthelmintic targets. Mol Biochem Parasitol 2024; 259:111632. [PMID: 38834134 DOI: 10.1016/j.molbiopara.2024.111632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Spirocerca lupi is a parasitic nematode affecting predominantly domestic dogs. It causes spirocercosis, a disease that is often fatal. The assembled draft genome of S. lupi consists of 13,627 predicted protein-coding genes and is approximately 150 Mb in length. Several known anthelmintic gene targets such as for β-Tubulin, glutamate, and GABA receptors as well as known vaccine gene targets such as cysteine protease inhibitor and cytokines were identified in S. lupi by comparing orthologs of C. elegans anthelmintic gene targets as well as orthologs to known vaccine candidates. New anthelmintic targets were predicted through an inclusion-exclusion strategy and new vaccine targets were predicted through an immunoinformatics approach. New anthelminthic targets include DNA-directed RNA polymerases, chitin synthase, polymerases, and other enzymes. New vaccine targets include cuticle collagens. These gene targets provide a starting platform for new drug identification and vaccine design.
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Affiliation(s)
- Wiekolize Rothmann-Meyer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa; Thermo Fisher Scientific, Hybrid Field Application Scientist & Field Service Engineer, South Africa
| | - Pamela J de Waal
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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2
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Martins YC, Rosa-Gonçalves P, Daniel-Ribeiro CT. Theories of immune recognition: Is anybody right? Immunology 2024. [PMID: 39034280 DOI: 10.1111/imm.13839] [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: 04/15/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024] Open
Abstract
The clonal selection theory (CST) is the centrepiece of the current paradigm used to explain immune recognition and memory. Throughout the past decades, the original CST had been expanded and modified to explain new experimental evidences since its original publication by Burnet. This gave origin to new paradigms that govern experimental immunology nowadays, such as the associative recognition of antigen model and the stranger/danger signal model. However, these new theories also do not fully explain experimental findings such as natural autoimmune immunoglobulins, idiotypic networks, low and high dose tolerance, and dual-receptor T and B cells. To make sense of these empirical data, some authors have been trying to change the paradigm of immune cognition using a systemic approach, analogies with brain processing and concepts from second-order cybernetics. In the present paper, we review the CST and some of the theories/hypotheses derived from it, focusing on immune recognition. We point out their main weaknesses and highlight arguments made by their opponents and believers. We conclude that, until now, none of the proposed theories can fully explain the totality of immune phenomena and that a theory of everything is needed in immunology.
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Affiliation(s)
- Yuri Chaves Martins
- Department of Anesthesiology, Saint Louis University School of Medicine, Saint Louis, Missouri, USA
| | - Pamela Rosa-Gonçalves
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz and Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz and Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Hagadorn KA, Peterson ME, Kole H, Scott B, Skinner J, Diouf A, Takashima E, Ongoiba A, Doumbo S, Doumtabe D, Li S, Sekar P, Yan M, Zhu C, Nagaoka H, Kanoi BN, Li QZ, Long C, Long EO, Kayentao K, Jenks SA, Sanz I, Tsuboi T, Traore B, Bolland S, Miura K, Crompton PD, Hopp CS. Autoantibodies inhibit Plasmodium falciparum growth and are associated with protection from clinical malaria. Immunity 2024:S1074-7613(24)00278-4. [PMID: 38901428 DOI: 10.1016/j.immuni.2024.05.024] [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: 10/24/2023] [Revised: 02/23/2024] [Accepted: 05/30/2024] [Indexed: 06/22/2024]
Abstract
Many infections, including malaria, are associated with an increase in autoantibodies (AAbs). Prior studies have reported an association between genetic markers of susceptibility to autoimmune disease and resistance to malaria, but the underlying mechanisms are unclear. Here, we performed a longitudinal study of children and adults (n = 602) in Mali and found that high levels of plasma AAbs before the malaria season independently predicted a reduced risk of clinical malaria in children during the ensuing malaria season. Baseline AAb seroprevalence increased with age and asymptomatic Plasmodium falciparum infection. We found that AAbs purified from the plasma of protected individuals inhibit the growth of blood-stage parasites and bind P. falciparum proteins that mediate parasite invasion. Protected individuals had higher plasma immunoglobulin G (IgG) reactivity against 33 of the 123 antigens assessed in an autoantigen microarray. This study provides evidence in support of the hypothesis that a propensity toward autoimmunity offers a survival advantage against malaria.
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Affiliation(s)
- Kelly A Hagadorn
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA; Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, USA
| | - Mary E Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Hemanta Kole
- Autoimmunity and Functional Genomics Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Bethany Scott
- Autoimmunity and Functional Genomics Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Padmapriya Sekar
- Molecular and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Mei Yan
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chengsong Zhu
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan; Centre for Malaria Elimination, Institute of Tropical Medicine, Mount Kenya University, Thika, Kenya
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Genecopoeia Inc, Rockville, MD, USA
| | - Carole Long
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Eric O Long
- Molecular and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Scott A Jenks
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology and Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology and Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Takafumi Tsuboi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Silvia Bolland
- Autoimmunity and Functional Genomics Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA.
| | - Christine S Hopp
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA; Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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4
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Penunuri G, Wang P, Corbett-Detig R, Russell SL. A Structural Proteome Screen Identifies Protein Mimicry in Host-Microbe Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588793. [PMID: 38645127 PMCID: PMC11030372 DOI: 10.1101/2024.04.10.588793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Host-microbe systems are evolutionary niches that produce coevolved biological interactions and are a key component of global health. However, these systems have historically been a difficult field of biological research due to their experimental intractability. Impactful advances in global health will be obtained by leveraging in silico screens to identify genes involved in mediating interspecific interactions. These predictions will progress our understanding of these systems and lay the groundwork for future in vitro and in vivo experiments and bioengineering projects. A driver of host-manipulation and intracellular survival utilized by host-associated microbes is molecular mimicry, a critical mechanism that can occur at any level from DNA to protein structures. We applied protein structure prediction and alignment tools to explore host-associated bacterial structural proteomes for examples of protein structure mimicry. By leveraging the Legionella pneumophila proteome and its many known structural mimics, we developed and validated a screen that can be applied to virtually any host-microbe system to uncover signals of protein mimicry. These mimics represent candidate proteins that mediate host interactions in microbial proteomes. We successfully applied this screen to other microbes with demonstrated effects on global health, Helicobacter pylori and Wolbachia , identifying protein mimic candidates in each proteome. We discuss the roles these candidates may play in important Wolbachia -induced phenotypes and show that Wobachia infection can partially rescue the loss of one of these factors. This work demonstrates how a genome-wide screen for candidates of host-manipulation and intracellular survival offers an opportunity to identify functionally important genes in host-microbe systems.
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Palacpac NMQ, Ishii KJ, Arisue N, Tougan T, Horii T. Immune tolerance caused by repeated P. falciparum infection against SE36 malaria vaccine candidate antigen and the resulting limited polymorphism. Parasitol Int 2024; 99:102845. [PMID: 38101534 DOI: 10.1016/j.parint.2023.102845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/27/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
The call for second generation malaria vaccines needs not only the identification of novel candidate antigens or adjuvants but also a better understanding of immune responses and the underlying protective processes. Plasmodium parasites have evolved a range of strategies to manipulate the host immune system to guarantee survival and establish parasitism. These immune evasion strategies hamper efforts to develop effective malaria vaccines. In the case of a malaria vaccine targeting the N-terminal domain of P. falciparum serine repeat antigen 5 (SE36), now in clinical trials, we observed reduced responsiveness (lowered immunogenicity) which may be attributed to immune tolerance/immune suppression. Here, immunogenicity data and insights into the immune responses to SE36 antigen from epidemiological studies and clinical trials are summarized. Documenting these observations is important to help identify gaps for SE36 continued development and engender hope that highly effective blood-stage/multi-stage vaccines can be achieved.
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Affiliation(s)
- Nirianne Marie Q Palacpac
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Ken J Ishii
- Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan; Laboratory of Vaccine Science, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
| | - Nobuko Arisue
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Takahiro Tougan
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Toshihiro Horii
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
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Rich KD, Srivastava S, Muthye VR, Wasmuth JD. Identification of potential molecular mimicry in pathogen-host interactions. PeerJ 2023; 11:e16339. [PMID: 37953771 PMCID: PMC10637249 DOI: 10.7717/peerj.16339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023] Open
Abstract
Pathogens have evolved sophisticated strategies to manipulate host signaling pathways, including the phenomenon of molecular mimicry, where pathogen-derived biomolecules imitate host biomolecules. In this study, we resurrected, updated, and optimized a sequence-based bioinformatics pipeline to identify potential molecular mimicry candidates between humans and 32 pathogenic species whose proteomes' 3D structure predictions were available at the start of this study. We observed considerable variation in the number of mimicry candidates across pathogenic species, with pathogenic bacteria exhibiting fewer candidates compared to fungi and protozoans. Further analysis revealed that the candidate mimicry regions were enriched in solvent-accessible regions, highlighting their potential functional relevance. We identified a total of 1,878 mimicked regions in 1,439 human proteins, and clustering analysis indicated diverse target proteins across pathogen species. The human proteins containing mimicked regions revealed significant associations between these proteins and various biological processes, with an emphasis on host extracellular matrix organization and cytoskeletal processes. However, immune-related proteins were underrepresented as targets of mimicry. Our findings provide insights into the broad range of host-pathogen interactions mediated by molecular mimicry and highlight potential targets for further investigation. This comprehensive analysis contributes to our understanding of the complex mechanisms employed by pathogens to subvert host defenses and we provide a resource to assist researchers in the development of novel therapeutic strategies.
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Affiliation(s)
- Kaylee D. Rich
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - Shruti Srivastava
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - Viraj R. Muthye
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
| | - James D. Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, Alberta, Canada
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7
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Mistry S, Gouripeddi R, Facelli JC. Prioritization of infectious epitopes for translational investigation in type 1 diabetes etiology. J Autoimmun 2023; 140:103115. [PMID: 37774556 PMCID: PMC10965504 DOI: 10.1016/j.jaut.2023.103115] [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] [Received: 06/01/2023] [Revised: 07/28/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023]
Abstract
Molecular mimicry is one mechanism by which infectious agents are thought to trigger islet autoimmunity in type 1 diabetes. With a growing number of reported infectious agents and islet antigens, strategies to prioritize the study of infectious agents are critically needed to expedite translational research into the etiology of type 1 diabetes. In this work, we developed an in-silico pipeline for assessing molecular mimicry in type 1 diabetes etiology based on sequence homology, empirical binding affinity to specific MHC molecules, and empirical potential for T-cell immunogenicity. We then assess whether potential molecular mimics were conserved across other pathogens known to infect humans. Overall, we identified 61 potentially high-impact molecular mimics showing sequence homology, strong empirical binding affinity, and empirical immunogenicity linked with specific MHC molecules. We further found that peptide sequences from 32 of these potential molecular mimics were conserved across several human pathogens. These findings facilitate translational evaluation of molecular mimicry in type 1 diabetes etiology by providing a curated and prioritized list of peptides from infectious agents for etiopathologic investigation. These results may also provide evidence for generation of infectious and HLA-specific preclinical models and inform future screening and preventative efforts in genetically susceptible populations.
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Affiliation(s)
- Sejal Mistry
- Department of Biomedical Informatics, University of Utah, Salt Lake City, USA; Center of Excellence for Exposure Health Informatics, University of Utah, Salt Lake City, USA
| | - Ramkiran Gouripeddi
- Department of Biomedical Informatics, University of Utah, Salt Lake City, USA; Center of Excellence for Exposure Health Informatics, University of Utah, Salt Lake City, USA; Clinical and Translational Science Institute, University of Utah, Salt Lake City, USA
| | - Julio C Facelli
- Department of Biomedical Informatics, University of Utah, Salt Lake City, USA; Center of Excellence for Exposure Health Informatics, University of Utah, Salt Lake City, USA; Clinical and Translational Science Institute, University of Utah, Salt Lake City, USA.
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8
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Alshamrani S, Mashraqi MM, Alzamami A, Alturki NA, Almasoudi HH, Alshahrani MA, Basharat Z. Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates in Clostridioides difficile and Prospects of Mimic-Based Vaccine Design: An In Silico Approach. Microorganisms 2023; 11:2300. [PMID: 37764144 PMCID: PMC10536613 DOI: 10.3390/microorganisms11092300] [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: 07/01/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular mimicry, a phenomenon in which microbial or environmental antigens resemble host antigens, has been proposed as a potential trigger for autoimmune responses. In this study, we employed a bioinformatics approach to investigate the role of molecular mimicry in Clostridioides difficile-caused infections and the induction of autoimmune disorders due to this phenomenon. Comparing proteomes of host and pathogen, we identified 23 proteins that exhibited significant sequence homology and were linked to autoimmune disorders. The disorders included rheumatoid arthritis, psoriasis, Alzheimer's disease, etc., while infections included viral and bacterial infections like HIV, HCV, and tuberculosis. The structure of the homologous proteins was superposed, and RMSD was calculated to find the maximum deviation, while accounting for rigid and flexible regions. Two sequence mimics (antigenic, non-allergenic, and immunogenic) of ≥10 amino acids from these proteins were used to design a vaccine construct to explore the possibility of eliciting an immune response. Docking analysis of the top vaccine construct C2 showed favorable interactions with HLA and TLR-4 receptor, indicating potential efficacy. The B-cell and T-helper cell activity was also simulated, showing promising results for effective immunization against C. difficile infections. This study highlights the potential of C. difficile to trigger autoimmunity through molecular mimicry and vaccine design based on sequence mimics that trigger a defensive response.
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Affiliation(s)
- Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah 11961, Saudi Arabia;
| | - Norah A. Alturki
- Clinical Laboratory Science Department, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia;
| | - Hassan H. Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (S.A.); (H.H.A.); (M.A.A.)
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Martins YC, Jurberg AD, Daniel-Ribeiro CT. Visiting Molecular Mimicry Once More: Pathogenicity, Virulence, and Autoimmunity. Microorganisms 2023; 11:1472. [PMID: 37374974 DOI: 10.3390/microorganisms11061472] [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: 02/20/2023] [Revised: 04/13/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023] Open
Abstract
The concept of molecular mimicry describes situations in which antigen sharing between parasites and hosts could benefit pathogen evasion from host immune responses. However, antigen sharing can generate host responses to parasite-derived self-like peptides, triggering autoimmunity. Since its conception, molecular mimicry and the consequent potential cross-reactivity following infections have been repeatedly described in humans, raising increasing interest among immunologists. Here, we reviewed this concept focusing on the challenge of maintaining host immune tolerance to self-components in parasitic diseases. We focused on the studies that used genomics and bioinformatics to estimate the extent of antigen sharing between proteomes of different organisms. In addition, we comparatively analyzed human and murine proteomes for peptide sharing with proteomes of pathogenic and non-pathogenic organisms. We conclude that, although the amount of antigenic sharing between hosts and both pathogenic and non-pathogenic parasites and bacteria is massive, the degree of this antigen sharing is not related to pathogenicity or virulence. In addition, because the development of autoimmunity in response to infections by microorganisms endowed with cross-reacting antigens is rare, we conclude that molecular mimicry by itself is not a sufficient factor to disrupt intact self-tolerance mechanisms.
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Affiliation(s)
- Yuri Chaves Martins
- Department of Anesthesiology, Saint Louis University School of Medicine, St. Louis, MO 63110, USA
| | - Arnon Dias Jurberg
- Instituto de Educação Médica, Campus Vista Carioca, Universidade Estácio de Sá, Rio de Janeiro 20071-004, RJ, Brazil
- Laboratório de Animais Transgênicos, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, RJ, Brazil
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária and Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21041-250, RJ, Brazil
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10
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Rashidi S, Mansouri R, Ali-Hassanzadeh M, Muro A, Nguewa P, Manzano-Román R. The most prominent modulated annexins during parasitic infections. Acta Trop 2023; 243:106942. [PMID: 37172709 DOI: 10.1016/j.actatropica.2023.106942] [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: 02/27/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Annexins (ANXs) exert different functions in cell biological and pathological processes and are thus known as double or multi-faceted proteins. These sophisticated proteins might express on both parasite structure and secretion and in parasite-infected host cells. In addition to the characterization of these pivotal proteins, describing their mechanism of action can be also fruitful in recognizing their roles in the pathogenesis of parasitic infections. Accordingly, this study presents the most prominent ANXs thus far identified and their relevant functions in parasites and infected host cells during pathogenesis, especially in the most important intracellular protozoan parasitic infections including leishmaniasis, toxoplasmosis, malaria and trypanosomiasis. The data provided in this study demonstrate that the helminth parasites most probably express and secret ANXs to develop pathogenesis while the modulation of the host-ANXs could be employed as a crucial strategy by intracellular protozoan parasites. Moreover, such data highlight that the use of analogs of both parasite and host ANX peptides (which mimic or regulate ANXs physiological functions through various strategies) might suggest novel therapeutic insights into the treatment of parasitic infections. Furthermore, due to the prominent immunoregulatory activities of ANXs during most parasitic infections and the expression levels of these proteins in some parasitic infected tissues, such multifunctional proteins might be also potentially relevant as vaccine and diagnostic biomarkers. We also suggest some prospects and insights that could be useful and applicable to form the basis of future experimental studies.
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Affiliation(s)
- Sajad Rashidi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran; Department of Medical Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Reza Mansouri
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Mohammad Ali-Hassanzadeh
- Department of Immunology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Antonio Muro
- Infectious and Tropical Diseases Group (e-INTRO), Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain
| | - Paul Nguewa
- University of Navarra, ISTUN Institute of Tropical Health, Department of Microbiology and Parasitology. IdiSNA (Navarra Institute for Health Research), c/ Irunlarrea 1, 31008 Pamplona, Spain.
| | - Raúl Manzano-Román
- Infectious and Tropical Diseases Group (e-INTRO), Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain.
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11
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Saleh BH, Lugaajju A, Storry JR, Persson KEM. Autoantibodies against red blood cell antigens are common in a malaria endemic area. Microbes Infect 2023; 25:105060. [PMID: 36270601 DOI: 10.1016/j.micinf.2022.105060] [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: 11/15/2021] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
Plasmodium falciparum malaria can cause severe anemia. Even after treatment, hematocrit can decrease. The role of autoantibodies against erythrocytes is not clearly elucidated and how common they are, or what they are directed against, is still largely unknown. We have investigated antibodies against erythrocytes in healthy adult men living in a highly malaria endemic area in Uganda. We found antibodies in more than half of the individuals, which is significantly more than in a non-endemic area (Sweden). Some of the Ugandan samples had a broad reactivity where it was not possible to determine the exact target of the autoantibodies, but we also found specific antibodies directed against erythrocyte surface antigens known to be of importance for merozoite invasion such as glycophorin A (anti-Ena, anti-M) and glycophorin B (anti-U, anti-S). In addition, several autoantibodies had partial specificities against glycophorin C and the blood group systems Rh, Diego (located on Band 3), Duffy (located on ACKR1), and Cromer (located on CD55), all of which have been described to be important for malaria and therefore of interest for understanding how autoantibodies could potentially stop parasites from entering the erythrocyte. In conclusion, specific autoantibodies against erythrocytes are common in a malaria endemic area.
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Affiliation(s)
- Bandar Hasan Saleh
- Department of Laboratory Medicine, Lund University, Skåne University Hospital Lund, Klinikgatan 19, 22185 Lund, Sweden; Faculty of Medicine, Department of Medical Microbiology and Parasitology, King Abdulaziz University, Building 7, 21589 Jeddah, Saudi Arabia
| | - Allan Lugaajju
- Department of Laboratory Medicine, Lund University, Skåne University Hospital Lund, Klinikgatan 19, 22185 Lund, Sweden; School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Klinikgatan 26, Lund, Sweden; Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office for Medical Services, Region Skåne, Akutgatan 8, Lund, Sweden
| | - Kristina E M Persson
- Department of Laboratory Medicine, Lund University, Skåne University Hospital Lund, Klinikgatan 19, 22185 Lund, Sweden.
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12
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Bhoj P, Togre N, Khatri V, Goswami K. Harnessing Immune Evasion Strategy of Lymphatic Filariae: A Therapeutic Approach against Inflammatory and Infective Pathology. Vaccines (Basel) 2022; 10:vaccines10081235. [PMID: 36016123 PMCID: PMC9415972 DOI: 10.3390/vaccines10081235] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
Human lymphatic filariae have evolved numerous immune evasion strategies to secure their long-term survival in a host. These strategies include regulation of pattern recognition receptors, mimicry with host glycans and immune molecules, manipulation of innate and adaptive immune cells, induction of apoptosis in effector immune cells, and neutralization of free radicals. This creates an anti-inflammatory and immunoregulatory milieu in the host: a modified Th2 immune response. Therefore, targeting filarial immunomodulators and manipulating the filariae-driven immune system against the filariae can be a potential therapeutic and prophylactic strategy. Filariae-derived immunosuppression can also be exploited to treat other inflammatory diseases and immunopathologic states of parasitic diseases, such as cerebral malaria, and to prevent leishmaniasis. This paper reviews immunomodulatory mechanisms acquired by these filariae for their own survival and their potential application in the development of novel therapeutic approaches against parasitic and inflammatory diseases. Insight into the intricate network of host immune-parasite interactions would aid in the development of effective immune-therapeutic options for both infectious and immune-pathological diseases.
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Affiliation(s)
| | - Namdev Togre
- Department of Biological Sciences, University of Texas, El Paso, TX 79968, USA
- Correspondence: (N.T.); (K.G.)
| | | | - Kalyan Goswami
- All India Institute of Medical Sciences, Saguna, Kalyani 741245, India
- Correspondence: (N.T.); (K.G.)
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13
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Shome M, Chung Y, Chavan R, Park JG, Qiu J, LaBaer J. Serum autoantibodyome reveals that healthy individuals share common autoantibodies. Cell Rep 2022; 39:110873. [PMID: 35649350 PMCID: PMC9221390 DOI: 10.1016/j.celrep.2022.110873] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
Autoantibodies are a hallmark of both autoimmune disease and cancer, but
they also occur in healthy individuals. Here, we perform a meta-analysis of nine
datasets and focus on the common autoantibodies shared by healthy individuals.
We report 77 common autoantibodies based on the protein microarray data obtained
from probing 182 healthy individual sera on 7,653 human proteins and an
additional 90 healthy individual sera on 1,666 human proteins. There is no
gender bias; however, the number of autoantibodies increase with age, plateauing
around adolescence. We use a bioinformatics pipeline to determine possible
molecular-mimicry peptides that can contribute to the elicitation of these
common autoantibodies. There is enrichment of intrinsic properties of proteins
like hydrophilicity, basicity, aromaticity, and flexibility for common
autoantigens. Subcellular localization and tissue-expression analysis reveal
that several common autoantigens are sequestered from the circulating
autoantibodies. Shome et al. performed a meta-analysis to discover the common
autoantibodies found in healthy individuals. These common autoantibodies appear
and increase during youth and plateau at adolescence. Bioinformatics techniques
demonstrate the potential role of molecular mimicry in their production as well
as several common intrinsic biochemical properties.
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Affiliation(s)
- Mahasish Shome
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA; College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Ramani Chavan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jin G Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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Tayal S, Bhatia V, Mehrotra T, Bhatnagar S. ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. Amino Acids 2022; 54:923-934. [PMID: 35487995 PMCID: PMC9054641 DOI: 10.1007/s00726-022-03163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/09/2022] [Indexed: 11/26/2022]
Abstract
Molecular mimicry of host proteins by pathogens constitutes a strategy to hijack the host pathways. At present, there is no dedicated resource for mimicked domains and motifs in the host-pathogen interactome. In this work, the experimental host-pathogen (HP) and host-host (HH) protein-protein interactions (PPIs) were collated. The domains and motifs of these proteins were annotated using CD Search and ScanProsite, respectively. Host and pathogen proteins with a shared host interactor and similar domain/motif constitute a mimicry pair exhibiting global structural similarity (domain mimicry pair; DMP) or local sequence motif similarity (motif mimicry pair; MMP). Mimicry pairs are likely to be co-expressed and co-localized. 1,97,607 DMPs and 32,67,568 MMPs were identified in 49,265 experimental HP-PPIs and organized in a web-based resource, ImitateDB ( http://imitatedb.sblab-nsit.net ) that can be easily queried. The results are externally integrated using hyperlinked domain PSSM ID, motif ID, protein ID and PubMed ID. Kinase, UL36, Smc and DEXDc were frequent DMP domains whereas protein kinase C phosphorylation, casein kinase 2 phosphorylation, glycosylation and myristoylation sites were frequent MMP motifs. Novel DMP domains SANT, Tudor, PhoX and MMP motif microbody C-terminal targeting signal, cornichon signature and lipocalin signature were proposed. ImitateDB is a novel resource for identifying mimicry in interacting host and pathogen proteins.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India
| | - Venugopal Bhatia
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Tanya Mehrotra
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India.
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India.
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Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide. Acta Trop 2021; 221:106013. [PMID: 34146538 PMCID: PMC8255030 DOI: 10.1016/j.actatropica.2021.106013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022]
Abstract
AIM This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes. METHODS 1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. Aligned sequences in the respective organisms' proteomes are searched with blastp. 3. Binding predictions of the identified SARS-CoV-2 peptide to HLA supertype representatives are performed. 4. Blastp searches of predicted epitopes that bind strongly to the identified HLA allele are performed by limiting searches to H. sapiens and Plasmodium species, separately. 5. Peptides with minimum 60% identity to the predicted epitopes are found in results. 6. Peptides among those, which bind strongly to the same HLA allele, are predicted. 7. Step-4 is repeated by limiting searches to H. sapiens, followed by the remaining steps until step-7, for peptides sourced by Plasmodium species after step-6. RESULTS SARS-CoV-2 peptide with single letter amino acid code CFLGYFCTCYFGLFC has the highest identity to P. vivax. Its YFCTCYFGLF part is predicted to bind strongly to HLA-A*24:02. Peptides in the human proteome both homologous to YFCTCYFGLF and with a strong binding affinity to HLA-A*24:02 are YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF. Such peptides in the Plasmodium species' proteomes are FFYTFYFELF, YFVACLFILF, and YFPTITFHLF. The first one belonging to P. falciparum has a homologous peptide (YFYLFSLELF) in the human proteome, which also has a strong binding affinity to the same HLA allele. CONCLUSION Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 can be related to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.
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16
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Chulanetra M, Chaicumpa W. Revisiting the Mechanisms of Immune Evasion Employed by Human Parasites. Front Cell Infect Microbiol 2021; 11:702125. [PMID: 34395313 PMCID: PMC8358743 DOI: 10.3389/fcimb.2021.702125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
For the establishment of a successful infection, i.e., long-term parasitism and a complete life cycle, parasites use various diverse mechanisms and factors, which they may be inherently bestowed with, or may acquire from the natural vector biting the host at the infection prelude, or may take over from the infecting host, to outmaneuver, evade, overcome, and/or suppress the host immunity, both innately and adaptively. This narrative review summarizes the up-to-date strategies exploited by a number of representative human parasites (protozoa and helminths) to counteract the target host immune defense. The revisited information should be useful for designing diagnostics and therapeutics as well as vaccines against the respective parasitic infections.
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Affiliation(s)
- Monrat Chulanetra
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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17
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Naturally Acquired Antibodies against Plasmodium falciparum: Friend or Foe? Pathogens 2021; 10:pathogens10070832. [PMID: 34357982 PMCID: PMC8308493 DOI: 10.3390/pathogens10070832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Antibodies are central to acquired immunity against malaria. Plasmodium falciparum elicits antibody responses against many of its protein components, but there is also formation of antibodies against different parts of the red blood cells, in which the parasites spend most of their time. In the absence of a decisive intervention such as a vaccine, people living in malaria endemic regions largely depend on naturally acquired antibodies for protection. However, these antibodies do not confer sterile immunity and the mechanisms of action are still unclear. Most studies have focused on the inhibitory effect of antibodies, but here, we review both the beneficial as well as the potentially harmful roles of naturally acquired antibodies, as well as autoantibodies formed in malaria. We discuss different studies that have sought to understand acquired antibody responses against P. falciparum antigens, and potential problems when different antibodies are combined, such as in naturally acquired immunity.
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Armijos-Jaramillo V, Espinosa N, Vizcaíno K, Santander-Gordón D. A Novel In Silico Method for Molecular Mimicry Detection Finds a Formin with the Potential to Manipulate the Maize Cell Cytoskeleton. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:815-825. [PMID: 33755496 DOI: 10.1094/mpmi-11-20-0332-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Molecular mimicry is one of the evolutionary strategies that parasites use to manipulate the host metabolism and perform an effective infection. This phenomenon has been observed in several animal and plant pathosystems. Despite the relevance of this mechanism in pathogenesis, little is known about it in fungus-plant interactions. For that reason, we performed an in silico method to select plausible mimicry candidates for the Ustilago maydis-maize interaction. Our methodology used a tripartite sequence comparison between the parasite, the host, and nonparasitic organisms' genomes. Furthermore, we used RNA sequencing information to identify gene coexpression, and we determined subcellular localization to detect potential cases of colocalization in the imitator-imitated pairs. With these approximations, we found a putative extracellular formin in U. maydis with the potential to rearrange the host cell cytoskeleton. In parallel, we detected at least two maize genes involved in the cytoskeleton rearrangement differentially expressed under U. maydis infection; thus, this find increases the expectation for the potential mimicry role of the fungal protein. The use of several sources of data led us to develop a strict and replicable in silico methodology to detect molecular mimicry in pathosystems with enough information available. Furthermore, this is the first time that a genomewide search has been performed to detect molecular mimicry in a U. maydis-maize system. Additionally, to allow the reproducibility of this experiment and the use of this pipeline, we created a Web server called Molecular Mimicry Finder.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
| | - Nicole Espinosa
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Karla Vizcaíno
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Daniela Santander-Gordón
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
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Murray D, Petrey D, Honig B. Integrating 3D structural information into systems biology. J Biol Chem 2021; 296:100562. [PMID: 33744294 PMCID: PMC8095114 DOI: 10.1016/j.jbc.2021.100562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
Systems biology is a data-heavy field that focuses on systems-wide depictions of biological phenomena necessarily sacrificing a detailed characterization of individual components. As an example, genome-wide protein interaction networks are widely used in systems biology and continuously extended and refined as new sources of evidence become available. Despite the vast amount of information about individual protein structures and protein complexes that has accumulated in the past 50 years in the Protein Data Bank, the data, computational tools, and language of structural biology are not an integral part of systems biology. However, increasing effort has been devoted to this integration, and the related literature is reviewed here. Relationships between proteins that are detected via structural similarity offer a rich source of information not available from sequence similarity, and homology modeling can be used to leverage Protein Data Bank structures to produce 3D models for a significant fraction of many proteomes. A number of structure-informed genomic and cross-species (i.e., virus–host) interactomes will be described, and the unique information they provide will be illustrated with a number of examples. Tissue- and tumor-specific interactomes have also been developed through computational strategies that exploit patient information and through genetic interactions available from increasingly sensitive screens. Strategies to integrate structural information with these alternate data sources will be described. Finally, efforts to link protein structure space with chemical compound space offer novel sources of information in drug design, off-target identification, and the identification of targets for compounds found to be effective in phenotypic screens.
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Affiliation(s)
- Diana Murray
- Department of Systems Biology, Columbia University, New York, New York, USA
| | - Donald Petrey
- Department of Systems Biology, Columbia University, New York, New York, USA
| | - Barry Honig
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Department of Medicine, Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York, USA.
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20
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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21
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Mourão LC, Cardoso-Oliveira GP, Braga ÉM. Autoantibodies and Malaria: Where We Stand? Insights Into Pathogenesis and Protection. Front Cell Infect Microbiol 2020; 10:262. [PMID: 32596165 PMCID: PMC7300196 DOI: 10.3389/fcimb.2020.00262] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/04/2020] [Indexed: 12/16/2022] Open
Abstract
Autoantibodies are frequently reported in patients with malaria, but whether they contribute to protection or to pathology is an issue of debate. A large body of evidence indicates that antibodies against host-self components are associated to malaria clinical outcomes such as cerebral malaria, renal dysfunction and anemia. Nonetheless, self-reactive immunoglobulins induced during an infection can also mediate protection. In light of these controversies, we summarize here the latest findings in our understanding of autoimmune responses in malaria, focusing on Plasmodium falciparum and Plasmodium vivax. We review the main targets of self-antibody responses in malaria as well as the current, but still limited, knowledge of their role in disease pathogenesis or protection.
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Affiliation(s)
- Luiza Carvalho Mourão
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Érika Martins Braga
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Leow CY, Willis C, Leow CH, Hofmann A, Jones M. Molecular characterization of Schistosoma mansoni tegument annexins and comparative analysis of antibody responses following parasite infection. Mol Biochem Parasitol 2019; 234:111231. [PMID: 31628972 DOI: 10.1016/j.molbiopara.2019.111231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/16/2019] [Accepted: 10/08/2019] [Indexed: 01/05/2023]
Abstract
Schistosomes are parasitic blood flukes that infect approximately 250 million people worldwide. The disease known as schistosomiasis, is the second most significant tropical parasitic disease after malaria. Praziquantel is the only effective drug currently licensed for schistosomiasis and there are concerns about resistance to the drug. There has been much effort to develop vaccines against schistosomiasis to produce long-term protection in endemic regions. Surface-associated proteins, and in particular, those expressed in the body wall, or tegument, have been proposed as potential vaccine targets. Of these, annexins are thought to be of integral importance for the stability of this apical membrane system. Here, we present the structural and immunobiochemical characterization of four homologous annexins namely annexin B30, annexin B5a, annexin B7a and annexin B5b from S. mansoni. Bioinformatics analysis showed that there was no signal peptide predicted for any annexin in this study. Further analysis showed that each of all four annexin protein possesses a primary structure consisting of a short but variable N-terminal region and a long C-terminal core containing four homologous annexin repeats (I-IV), which contain five alpha-helices. The life cycle expression profile of each annexin was assessed using quantitative PCR. The results showed that the overall transcript levels of the each of four homologous annexins were relatively low in the egg stage, but increased gradually after the transition of cercariae (the invasive schistosome larvae) to schistosomula (the post-invasive larvae). Circular dichroism (CD) demonstrated that rAnnexin B30, rAnnexin B5a and rAnnexin 7a were folded, showing a secondary structure content rich in alpha-helices. The membrane binding affinity was enhanced when rAnnexin B30, rAnnexin B5a and rAnnexin 7a was incubated in the presence of Ca2+. All annexin members evaluated in this study were immunolocalized to the tegument, with immunoreactivity also occurring in cells and in muscle of adult parasites. All four recombinant annexins were immunoreactive and they were recognized by the sera of mice infected with S. mansoni. In conclusion, the overall results present the molecular characterization of annexin B30, annexin B5a, annexin B7a and annexin B5b from S. mansoni in host-parasite interactions and strongly suggest that the molecules could be useful candidates for vaccine or diagnostic development.
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Affiliation(s)
- Chiuan Yee Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Charlene Willis
- School of Environment and Science, Griffith University, Brisbane, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Andreas Hofmann
- Structural Chemistry Program, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Australia
| | - Malcolm Jones
- School of Veterinary Science, University of Queensland, Gatton, Australia
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23
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Mourão LC, Baptista RDP, de Almeida ZB, Grynberg P, Pucci MM, Castro-Gomes T, Fontes CJF, Rathore S, Sharma YD, da Silva-Pereira RA, Bemquerer MP, Braga ÉM. Anti-band 3 and anti-spectrin antibodies are increased in Plasmodium vivax infection and are associated with anemia. Sci Rep 2018; 8:8762. [PMID: 29884876 PMCID: PMC5993813 DOI: 10.1038/s41598-018-27109-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022] Open
Abstract
Clearance of non-infected red blood cells (nRBCs) is one of the main components of anemia associated with Plasmodium vivax malaria. Recently, we have shown that anemic patients with P. vivax infection had elevated levels of anti-RBCs antibodies, which could enhance in vitro phagocytosis of nRBCs and decrease their deformability. Using immunoproteomics, here we characterized erythrocytic antigens that are differentially recognized by autoantibodies from anemic and non-anemic patients with acute vivax malaria. Protein spots exclusively recognized by anemic P. vivax-infected patients were identified by mass spectrometry revealing band 3 and spectrin as the main targets. To confirm this finding, antibody responses against these specific proteins were assessed by ELISA. In addition, an inverse association between hemoglobin and anti-band 3 or anti-spectrin antibodies levels was found. Anemic patients had higher levels of IgG against both band 3 and spectrin than the non-anemic ones. To determine if these autoantibodies were elicited because of molecular mimicry, we used in silico analysis and identified P. vivax proteins that share homology with human RBC proteins such as spectrin, suggesting that infection drives autoimmune responses. These findings suggest that band 3 and spectrin are potential targets of autoantibodies that may be relevant for P. vivax malaria-associated anemia.
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Affiliation(s)
- Luiza Carvalho Mourão
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | - Maíra Mazzoni Pucci
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Thiago Castro-Gomes
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Sumit Rathore
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Yagya D Sharma
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | | | | | - Érika Martins Braga
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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24
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Garg A, Kumari B, Kumar R, Kumar M. miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry. Front Microbiol 2017; 8:2053. [PMID: 29109711 PMCID: PMC5660332 DOI: 10.3389/fmicb.2017.02053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/06/2017] [Indexed: 11/13/2022] Open
Abstract
Autoimmune diseases emerge due to several reasons, of which molecular mimicry i.e., similarity between the host's and pathogen's interacting peptides is an important reason. In the present study we have reported a database of only experimentally verified peptide sequences, which exhibit molecular mimicry. The database is named as miPepBase (Mimicry Peptide Database) and contains comprehensive information about mimicry proteins and peptides of both host (and model organism) and pathogen. It also provides information about physicochemical properties of protein and mimicry peptides, which might be helpful in predicting the nature of protein and optimization of protein expression. The miPepBase can be searched using a keyword or, by autoimmune disease(s) or by a combination of host and pathogen taxonomic group or their name. To facilitate the search of proteins and/or epitope in miPepBase, which is similar to the user's interest, BLAST search tool is also incorporated. miPepBase is an open access database and available at http://proteininformatics.org/mkumar/mipepbase.
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Affiliation(s)
- Anjali Garg
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Bandana Kumari
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Ravindra Kumar
- Department of Biophysics, University of Delhi, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, New Delhi, India
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Zanzoni A, Spinelli L, Braham S, Brun C. Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. MICROBIOME 2017; 5:89. [PMID: 28793925 PMCID: PMC5551000 DOI: 10.1186/s40168-017-0307-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 07/13/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS We devised a computational strategy to identify putative secreted F. nucleatum proteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements. FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138 FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, six of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer. CONCLUSIONS Overall, our computational analysis identified candidate virulence proteins potentially involved in the F. nucleatum-human cross-talk in the context of gastrointestinal diseases.
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Affiliation(s)
- Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France.
| | - Lionel Spinelli
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Shérazade Braham
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Christine Brun
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
- CNRS, Marseille, France
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Li BW, McNulty SN, Rosa BA, Tyagi R, Zeng QR, Gu KZ, Weil GJ, Mitreva M. Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini. Parasit Vectors 2016; 9:497. [PMID: 27619014 PMCID: PMC5020434 DOI: 10.1186/s13071-016-1785-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
Background Paragonimiasis is an important and widespread neglected tropical disease. Fifteen Paragonimus species are human pathogens, but two of these, Paragonimus westermani and P. skrjabini, are responsible for the bulk of human disease. Despite their medical and economic significance, there is limited information on the gene content and expression of Paragonimus lung flukes. Results The transcriptomes of adult P. westermani and P. skrjabini were studied with deep sequencing technology. Approximately 30 million reads per species were assembled into 21,586 and 25,825 unigenes for P. westermani and P. skrjabini, respectively. Many unigenes showed homology with sequences from other food-borne trematodes, but 1,217 high-confidence Paragonimus-specific unigenes were identified. Analyses indicated that both species have the potential for aerobic and anaerobic metabolism but not de novo fatty acid biosynthesis and that they may interact with host signaling pathways. Some 12,432 P. westermani and P. skrjabini unigenes showed a clear correspondence in bi-directional sequence similarity matches. The expression of shared unigenes was mostly well correlated, but differentially expressed unigenes were identified and shown to be enriched for functions related to proteolysis for P. westermani and microtubule based motility for P. skrjabini. Conclusions The assembled transcriptomes of P. westermani and P. skrjabini, inferred proteins, and extensive functional annotations generated for this project (including identified primary sequence similarities to various species, protein domains, biological pathways, predicted proteases, molecular mimics and secreted proteins, etc.) represent a valuable resource for hypothesis driven research on these medically and economically important species. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1785-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ben-Wen Li
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha N McNulty
- The McDonnell Genome Institute at Washington University, St. Louis, MO, USA
| | - Bruce A Rosa
- The McDonnell Genome Institute at Washington University, St. Louis, MO, USA
| | - Rahul Tyagi
- The McDonnell Genome Institute at Washington University, St. Louis, MO, USA
| | - Qing Ren Zeng
- Department of Parasitology, Xiang-Ya School of Medicine, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Kong-Zhen Gu
- Department of Parasitology, Xiang-Ya School of Medicine, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Gary J Weil
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA. .,The McDonnell Genome Institute at Washington University, St. Louis, MO, USA.
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Masachis S, Segorbe D, Turrà D, Leon-Ruiz M, Fürst U, El Ghalid M, Leonard G, López-Berges MS, Richards TA, Felix G, Di Pietro A. A fungal pathogen secretes plant alkalinizing peptides to increase infection. Nat Microbiol 2016; 1:16043. [PMID: 27572834 DOI: 10.1038/nmicrobiol.2016.43] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/02/2016] [Indexed: 11/09/2022]
Abstract
Plant infections caused by fungi are often associated with an increase in the pH of the surrounding host tissue(1). Extracellular alkalinization is thought to contribute to fungal pathogenesis, but the underlying mechanisms are poorly understood. Here, we show that the root-infecting fungus Fusarium oxysporum uses a functional homologue of the plant regulatory peptide RALF (rapid alkalinization factor)(2,3) to induce alkalinization and cause disease in plants. An upshift in extracellular pH promotes infectious growth of Fusarium by stimulating phosphorylation of a conserved mitogen-activated protein kinase essential for pathogenicity(4,5). Fungal mutants lacking a functional Fusarium (F)-RALF peptide failed to induce host alkalinization and showed markedly reduced virulence in tomato plants, while eliciting a strong host immune response. Arabidopsis plants lacking the receptor-like kinase FERONIA, which mediates the RALF-triggered alkalinization response(6), displayed enhanced resistance against Fusarium. RALF homologues are found across a number of phylogenetically distant groups of fungi, many of which infect plants. We propose that fungal pathogens use functional homologues of alkalinizing peptides found in their host plants to increase their infectious potential and suppress host immunity.
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Affiliation(s)
- Sara Masachis
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - David Segorbe
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - David Turrà
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Mercedes Leon-Ruiz
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Ursula Fürst
- Zentrum für Molekularbiologie der Pflanzen, University Tübingen, 72076 Tübingen, Germany
| | - Mennat El Ghalid
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Guy Leonard
- Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Manuel S López-Berges
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | | | - Georg Felix
- Zentrum für Molekularbiologie der Pflanzen, University Tübingen, 72076 Tübingen, Germany
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
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Cai P, Gobert GN, You H, McManus DP. The Tao survivorship of schistosomes: implications for schistosomiasis control. Int J Parasitol 2016; 46:453-63. [PMID: 26873753 DOI: 10.1016/j.ijpara.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/06/2023]
Abstract
Schistosomiasis, caused by blood flukes of the genus Schistosoma, is a major public health problem which contributes substantially to the economic and financial burdens of many nations in the developing world. An array of survival strategies, such as the unique structure of the tegument which acts as a major host-parasite interface, immune modulation mechanisms, gene regulation, and apoptosis and self-renewal have been adopted by schistosome parasites over the course of long-term evolution with their mammalian definitive hosts. Recent generation of complete schistosome genomes together with numerous biological, immunological, high-throughput "-omics" and gene function studies have revealed the Tao or strategies that schistosomes employ not only to promote long-term survival, but also to ensure effective life cycle transmission. New scenarios for the future control of this important neglected tropical disease will present themselves as our understanding of these Tao increases.
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Affiliation(s)
- Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia.
| | - Geoffrey N Gobert
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Hong You
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Queensland, Australia.
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Abstract
Cancer is a general name for more than 100 malignant diseases. It is postulated that all cancers start from a single abnormal cell that grows out of control. Untreated cancers can cause serious consequences and deaths. Great progress has been made in cancer research that has significantly improved our knowledge and understanding of the nature and mechanisms of the disease, but the origins of cancer are far from being well understood due to the limitations of suitable model systems and to the complexities of the disease. In view of the fact that cancers are found in various species of vertebrates and other metazoa, here, we suggest that cancer also occurs in parasitic protozoans such as Trypanosoma brucei, a blood parasite, and Toxoplasma gondii, an obligate intracellular pathogen. Without treatment, these protozoan cancers may cause severe disease and death in mammals, including humans. The simpler genomes of these single-cell organisms, in combination with their complex life cycles and fascinating life cycle differentiation processes, may help us to better understand the origins of cancers and, in particular, leukemias.
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Hebert FO, Phelps L, Samonte I, Panchal M, Grambauer S, Barber I, Kalbe M, Landry CR, Aubin-Horth N. Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes. Parasit Vectors 2015; 8:225. [PMID: 25888917 PMCID: PMC4407394 DOI: 10.1186/s13071-015-0834-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endoparasites with complex life cycles are faced with several biological challenges, as they need to occupy various ecological niches throughout their development. Host phenotypes that increase the parasite's transmission rate to the next host have been extensively described, but few mechanistic explanations have been proposed to describe their proximate causes. In this study we explore the possibility that host phenotypic changes are triggered by the production of mimicry proteins from the parasite by using an ecological model system consisting of the infection of the threespine stickleback (Gasterosteus aculeatus) by the cestode Schistocephalus solidus. METHOD Using RNA-seq data, we assembled 9,093 protein-coding genes from which ORFs were predicted to generate a reference proteome. Based on a previously published method, we built two complementary analysis pipelines to i) establish a general classification of protein similarity among various species (pipeline A) and ii) identify candidate mimicry proteins showing specific host-parasite similarities (pipeline B), a key feature underlying the possibility of molecular mimicry. RESULTS Ninety-four tapeworm proteins showed high local sequence homology with stickleback proteins. Four of these candidates correspond to secreted or membrane proteins that could be produced by the parasite and eventually be released in or be in contact with the host to modulate physiological pathways involved in various phenotypes (e.g. behaviors). One of these candidates belongs to the Wnt family, a large group of signaling molecules involved in cell-to-cell interactions and various developmental pathways. The three other candidates are involved in ion transport and post-translational protein modifications. We further confirmed that these four candidates are expressed in three different developmental stages of the cestode by RT-PCR, including the stages found in the host. CONCLUSION In this study, we identified mimicry candidate peptides from a behavior-altering cestode showing specific sequence similarity with host proteins. Despite their potential role in modulating host pathways that could lead to parasite-induced phenotypic changes and despite our confirmation that they are expressed in the developmental stage corresponding to the altered host behavior, further investigations will be needed to confirm their mechanistic role in the molecular cross-talk taking place between S. solidus and the threespine stickleback.
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Affiliation(s)
- Francois Olivier Hebert
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugènes-Marchand, Québec, G1V 0A6, Canada.
| | - Luke Phelps
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str 2, 24306, Ploen, Germany.
| | - Irene Samonte
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str 2, 24306, Ploen, Germany.
| | - Mahesh Panchal
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str 2, 24306, Ploen, Germany.
| | - Stephan Grambauer
- Department of Biology, Adrian Building, Leicester University, University Road, Leicester, LE1 7RH, UK.
| | - Iain Barber
- Department of Biology, Adrian Building, Leicester University, University Road, Leicester, LE1 7RH, UK.
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str 2, 24306, Ploen, Germany.
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugènes-Marchand, Québec, G1V 0A6, Canada.
| | - Nadia Aubin-Horth
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugènes-Marchand, Québec, G1V 0A6, Canada.
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31
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Via A, Uyar B, Brun C, Zanzoni A. How pathogens use linear motifs to perturb host cell networks. Trends Biochem Sci 2014; 40:36-48. [PMID: 25475989 DOI: 10.1016/j.tibs.2014.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/03/2014] [Accepted: 11/03/2014] [Indexed: 12/31/2022]
Abstract
Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.
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Affiliation(s)
- Allegra Via
- Department of Physics, Sapienza University, 00185 Rome, Italy
| | - Bora Uyar
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christine Brun
- Inserm, UMR1090 TAGC, Marseille F-13288, France; Aix-Marseille Université, UMR1090 TAGC, Marseille F-13288, France; CNRS, Marseille F-13402, France
| | - Andreas Zanzoni
- Inserm, UMR1090 TAGC, Marseille F-13288, France; Aix-Marseille Université, UMR1090 TAGC, Marseille F-13288, France.
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Petrenko P, Doxey AC. mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. Bioinformatics 2014; 31:590-2. [DOI: 10.1093/bioinformatics/btu681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Potential immune mechanisms associated with anemia in Plasmodium vivax malaria: a puzzling question. Infect Immun 2014; 82:3990-4000. [PMID: 25092911 DOI: 10.1128/iai.01972-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The pathogenesis of malaria is complex, generating a broad spectrum of clinical manifestations. One of the major complications and concerns in malaria is anemia, which is responsible for considerable morbidity in the developing world, especially in children and pregnant women. Despite its enormous health importance, the immunological mechanisms involved in malaria-induced anemia remain incompletely understood. Plasmodium vivax, one of the causative agents of human malaria, is known to induce a strong inflammatory response with a robust production of immune effectors, including cytokines and antibodies. Therefore, it is possible that the extent of the immune response not only may facilitate the parasite killing but also may provoke severe illness, including anemia. In this review, we consider potential immune effectors and their possible involvement in generating this clinical outcome during P. vivax infections.
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McElroy EJ, de Buron I. Host Performance as a Target of Manipulation by Parasites: A Meta-Analysis. J Parasitol 2014; 100:399-410. [DOI: 10.1645/13-488.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Barteneva NS, Maltsev N, Vorobjev IA. Microvesicles and intercellular communication in the context of parasitism. Front Cell Infect Microbiol 2013; 3:49. [PMID: 24032108 PMCID: PMC3764926 DOI: 10.3389/fcimb.2013.00049] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/20/2013] [Indexed: 01/18/2023] Open
Abstract
There is a rapidly growing body of evidence that production of microvesicles (MVs) is a universal feature of cellular life. MVs can incorporate microRNA (miRNA), mRNA, mtDNA, DNA and retrotransposons, camouflage viruses/viral components from immune surveillance, and transfer cargo between cells. These properties make MVs an essential player in intercellular communication. Increasing evidence supports the notion that MVs can also act as long-distance vehicles for RNA molecules and participate in metabolic synchronization and reprogramming eukaryotic cells including stem and germinal cells. MV ability to carry on DNA and their general distribution makes them attractive candidates for horizontal gene transfer, particularly between multi-cellular organisms and their parasites; this suggests important implications for the co-evolution of parasites and their hosts. In this review, we provide current understanding of the roles played by MVs in intracellular pathogens and parasitic infections. We also discuss the possible role of MVs in co-infection and host shifting.
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Affiliation(s)
- Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Children's Hospital Boston and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Natasha.Barteneva@ childrens.harvard.edu
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Gowthaman U, Eswarakumar VP. Molecular mimicry: good artists copy, great artists steal. Virulence 2013; 4:433-4. [PMID: 23863600 PMCID: PMC5359722 DOI: 10.4161/viru.25780] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria.
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Affiliation(s)
- Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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A shift to Th2 immune response caused by constitutive expression of IPSE/alpha-1 in transfected pig fibroblasts in mice. Vet Immunol Immunopathol 2013; 152:269-76. [PMID: 23340445 DOI: 10.1016/j.vetimm.2012.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 12/14/2012] [Accepted: 12/28/2012] [Indexed: 01/23/2023]
Abstract
The IPSE/alpha-1 gene (IL-4-inducing principle of Schistosoma mansoni eggs) is a major secreted glycoprotein of S. mansoni eggs that has a potent IL-4-inducing effect. To test the hypothesis that the immune evasion mechanism can be used to overcome the xenograft immune response, the IPSE/alpha-1 gene was transferred into pig fibroblasts, and the transgenic cells were transplanted into KM mice by subcutaneously injecting 10(5)cells per mouse. Cytokine levels were measured to examine the immune response polarization by real-time PCR and ELISA. Mice injected with pig fibroblasts containing a pIRES2-EGFP expression vector were used as a control group. In this group, both cellular and humoral immune responses were activated to reject the grafts alongside increases in all measured cytokine levels. In contrast, the experimental group injected with cells constitutively expressing the IPSE/alpha-1 gene demonstrated a significant decrease in Th1 response cytokines and a significant increase in Th2 response cytokines compared with the control group. These results imply that constitutive IPSE/alpha-1 expression can shift the Th1/Th2 balance of xenograft rejections toward the Th2 response while suppressing the Th1 response. In conclusion, IPSE/alpha-1 could influence the polarization of immune responses during xenograft rejection and suppress the Th1 response. Therefore, this parasitic immune evasion mechanism could be helpful in overcoming xenograft rejection.
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Diagnostic peptide discovery: prioritization of pathogen diagnostic markers using multiple features. PLoS One 2012; 7:e50748. [PMID: 23272069 PMCID: PMC3522711 DOI: 10.1371/journal.pone.0050748] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/23/2012] [Indexed: 11/27/2022] Open
Abstract
The availability of complete pathogen genomes has renewed interest in the development of diagnostics for infectious diseases. Synthetic peptide microarrays provide a rapid, high-throughput platform for immunological testing of potential B-cell epitopes. However, their current capacity prevent the experimental screening of complete “peptidomes”. Therefore, computational approaches for prediction and/or prioritization of diagnostically relevant peptides are required. In this work we describe a computational method to assess a defined set of molecular properties for each potential diagnostic target in a reference genome. Properties such as sub-cellular localization or expression level were evaluated for the whole protein. At a higher resolution (short peptides), we assessed a set of local properties, such as repetitive motifs, disorder (structured vs natively unstructured regions), trans-membrane spans, genetic polymorphisms (conserved vs. divergent regions), predicted B-cell epitopes, and sequence similarity against human proteins and other potential cross-reacting species (e.g. other pathogens endemic in overlapping geographical locations). A scoring function based on these different features was developed, and used to rank all peptides from a large eukaryotic pathogen proteome. We applied this method to the identification of candidate diagnostic peptides in the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We measured the performance of the method by analyzing the enrichment of validated antigens in the high-scoring top of the ranking. Based on this measure, our integrative method outperformed alternative prioritizations based on individual properties (such as B-cell epitope predictors alone). Using this method we ranked 10 million 12-mer overlapping peptides derived from the complete T. cruzi proteome. Experimental screening of 190 high-scoring peptides allowed the identification of 37 novel epitopes with diagnostic potential, while none of the low scoring peptides showed significant reactivity. Many of the metrics employed are dependent on standard bioinformatic tools and data, so the method can be easily extended to other pathogen genomes.
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Godel C, Kumar S, Koutsovoulos G, Ludin P, Nilsson D, Comandatore F, Wrobel N, Thompson M, Schmid CD, Goto S, Bringaud F, Wolstenholme A, Bandi C, Epe C, Kaminsky R, Blaxter M, Mäser P. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEB J 2012; 26:4650-61. [PMID: 22889830 PMCID: PMC3475251 DOI: 10.1096/fj.12-205096] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The heartworm Dirofilaria immitis is an important parasite of dogs. Transmitted by mosquitoes in warmer climatic zones, it is spreading across southern Europe and the Americas at an alarming pace. There is no vaccine, and chemotherapy is prone to complications. To learn more about this parasite, we have sequenced the genomes of D. immitis and its endosymbiont Wolbachia. We predict 10,179 protein coding genes in the 84.2 Mb of the nuclear genome, and 823 genes in the 0.9-Mb Wolbachia genome. The D. immitis genome harbors neither DNA transposons nor active retrotransposons, and there is very little genetic variation between two sequenced isolates from Europe and the United States. The differential presence of anabolic pathways such as heme and nucleotide biosynthesis hints at the intricate metabolic interrelationship between the heartworm and Wolbachia. Comparing the proteome of D. immitis with other nematodes and with mammalian hosts, we identify families of potential drug targets, immune modulators, and vaccine candidates. This genome sequence will support the development of new tools against dirofilariasis and aid efforts to combat related human pathogens, the causative agents of lymphatic filariasis and river blindness.—Godel, C., Kumar, S., Koutsovoulos, G., Ludin, P., Nilsson, D., Comandatore, F., Wrobel, N., Thompson, M., Schmid, C. D., Goto, S., Bringaud, F., Wolstenholme, A., Bandi, C., Epe, C., Kaminsky, R., Blaxter, M., Mäser, P. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets.
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Collins AJ, Schleicher TR, Rader BA, Nyholm SV. Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics. Front Immunol 2012; 3:91. [PMID: 22590467 PMCID: PMC3349304 DOI: 10.3389/fimmu.2012.00091] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/08/2012] [Indexed: 11/13/2022] Open
Abstract
The symbiosis between the squid, Euprymna scolopes, and the bacterium, Vibrio fischeri, serves as a model for understanding interactions between beneficial bacteria and animal hosts. The establishment and maintenance of the association is highly specific and depends on the selection of V. fischeri and exclusion of non-symbiotic bacteria from the environment. Current evidence suggests that the host's cellular innate immune system, in the form of macrophage-like hemocytes, helps to mediate host tolerance of V. fischeri. To begin to understand the role of hemocytes in this association, we analyzed these cells by high-throughput 454 transcriptomic and liquid chromatography/tandem mass spectrometry (LC-MS/MS) proteomic analyses. 454 high-throughput sequencing produced 650, 686 reads totaling 279.9 Mb while LC-MS/MS analyses of circulating hemocytes putatively identified 702 unique proteins. Several receptors involved with the recognition of microbial-associated molecular patterns were identified. Among these was a complete open reading frame to a putative peptidoglycan recognition protein (EsPGRP5) with conserved residues for amidase activity. Assembly of the hemocyte transcriptome showed EsPGRP5 had high coverage, suggesting it is among the 5% most abundant transcripts in circulating hemocytes. Other transcripts and proteins identified included members of the conserved NF-κB signaling pathway, putative members of the complement pathway, the carbohydrate binding protein galectin, and cephalotoxin. Quantitative Real-Time PCR of complement-like genes, cephalotoxin, EsPGRP5, and a nitric oxide synthase showed differential expression in circulating hemocytes from adult squid with colonized light organs compared to those isolated from hosts where the symbionts were removed. These data suggest that the presence of the symbiont influences gene expression of the cellular innate immune system of E. scolopes.
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Affiliation(s)
- Andrew J Collins
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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Sundaramurthi JC, Brindha S, Shobitha SR, Swathi A, Ramanandan P, Hanna LE. In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2012; 12:1312-8. [PMID: 22484107 DOI: 10.1016/j.meegid.2012.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 01/11/2023]
Abstract
Cell-mediated immunity is critical for the control of Mycobacterium tuberculosis infection. We hypothesized that those proteins of M. tuberculosis (MTB) that do not have homologs in humans as well as human gut flora, would mount a good antigenic response in man, and employed a bioinformatics approach to identify MTB antigens capable of inducing a robust cell-mediated immune response in humans. In the first step we identified 624 MTB proteins that had no homologs in humans. Comparison of this set of proteins with the proteome of 77 different microbes that comprise the human gut flora narrowed down the list to 180 proteins unique to MTB. Twenty nine of the 180 proteins are known to be associated with dormancy. Since dormancy associated proteins are known to harbor CTL epitopes, we selected four representative unique proteins and subjected them to epitope analysis using ProPred1. Nineteen novel promiscuous epitopes were identified in the four proteins. Population coverage for 7 of the 19 shortlisted epitopes including Rv3852 (58-KPAEAPVSL, 112-VPLIVAVTL, 118-VTLSLLALL and 123-LALLLIRQL), Rv2706c (66-RPLSGVSFL) Rv3466 (8- RIVEVFDAL and 38-RSLERLECL) was >74%. These novel promiscuous epitopes are conserved in other virulent MTB strains, and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.
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Affiliation(s)
- Jagadish Chandrabose Sundaramurthi
- ICMR-Biomedical Informatics Centre, Department of Clinical Research, National Institute for Research in Tuberculosis (Formerly Tuberculosis Research Centre), Indian Council of Medical Research, Chennai 600 031, Tamil Nadu, India
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