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Kittichotirat W, Rujirawat T, Patumcharoenpol P, Krajaejun T. Comparative Genomic Analysis Reveals Gene Content Diversity, Phylogenomic Contour, Putative Virulence Determinants, and Potential Diagnostic Markers within Pythium insidiosum Traits. J Fungi (Basel) 2023; 9:jof9020169. [PMID: 36836284 PMCID: PMC9962146 DOI: 10.3390/jof9020169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
Pythium insidiosum has successfully evolved into a human/animal filamentous pathogen, causing pythiosis, a life-threatening disease, worldwide. The specific rDNA-based genotype of P. insidiosum (clade I, II, or III) is associated with the different hosts and disease prevalence. Genome evolution of P. insidiosum can be driven by point mutations, pass vertically to the offspring, and diverge into distinct lineages, leading to different virulence, including the ability to be unrecognized by the host. We conducted comprehensive genomic comparisons of 10 P. insidiosum strains and 5 related Pythium species using our online "Gene Table" software to investigate the pathogen's evolutionary history and pathogenicity. In total, 245,378 genes were found in all 15 genomes and grouped into 45,801 homologous gene clusters. Gene contents among P. insidiosum strains varied by as much as 23%. Our results showed a strong agreement between the phylogenetic analysis of 166 core genes (88,017 bp) identified across all genomes and the hierarchical clustering analysis of gene presence/absence profiles, suggesting divergence of P. insidiosum into two groups, clade I/II and clade III strains, and the subsequent segregation of clade I and clade II. A stringent gene content comparison using the Pythium Gene Table provided 3263 core genes exclusively presented in all P. insidiosum strains but no other Pythium species, which could involve host-specific pathogenesis and serve as biomarkers for diagnostic purposes. More studies focusing on characterizing the biological function of the core genes (including the just-identified putative virulence genes encoding hemagglutinin/adhesin and reticulocyte-binding protein) are needed to explore the biology and pathogenicity of this pathogen.
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Affiliation(s)
- Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Bangkok 10400, Thailand
- Correspondence: ; Tel.: +(662)-201-1452
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The molecular dialog between oomycete effectors and their plant and animal hosts. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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3
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Secretome Profiling by Proteogenomic Analysis Shows Species-Specific, Temperature-Dependent, and Putative Virulence Proteins of Pythium insidiosum. J Fungi (Basel) 2022; 8:jof8050527. [PMID: 35628782 PMCID: PMC9144242 DOI: 10.3390/jof8050527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
In contrast to most pathogenic oomycetes, which infect plants, Pythium insidiosum infects both humans and animals, causing a difficult-to-treat condition called pythiosis. Most patients undergo surgical removal of an affected organ, and advanced cases could be fetal. As a successful human/animal pathogen, P. insidiosum must tolerate body temperature and develop some strategies to survive and cause pathology within hosts. One of the general pathogen strategies is virulence factor secretion. Here, we used proteogenomic analysis to profile and validate the secretome of P. insidiosum, in which its genome contains 14,962 predicted proteins. Shotgun LC–MS/MS analysis of P. insidiosum proteins prepared from liquid cultures incubated at 25 and 37 °C mapped 2980 genome-predicted proteins, 9.4% of which had a predicted signal peptide. P. insidiosum might employ an alternative secretory pathway, as 90.6% of the validated secretory/extracellular proteins lacked the signal peptide. A comparison of 20 oomycete genomes showed 69 P. insidiosum–specific secretory/extracellular proteins, and these may be responsible for the host-specific infection. The differential expression analysis revealed 14 markedly upregulated proteins (particularly cyclophilin and elicitin) at body temperature which could contribute to pathogen fitness and thermotolerance. Our search through a microbial virulence database matched 518 secretory/extracellular proteins, such as urease and chaperones (including heat shock proteins), that might play roles in P. insidiosum virulence. In conclusion, the identification of the secretome promoted a better understanding of P. insidiosum biology and pathogenesis. Cyclophilin, elicitin, chaperone, and urease are top-listed secreted/extracellular proteins with putative pathogenicity properties. Such advances could lead to developing measures for the efficient detection and treatment of pythiosis.
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Medhasi S, Chindamporn A, Worasilchai N. A Review: Antimicrobial Therapy for Human Pythiosis. Antibiotics (Basel) 2022; 11:antibiotics11040450. [PMID: 35453202 PMCID: PMC9029071 DOI: 10.3390/antibiotics11040450] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 01/14/2023] Open
Abstract
Human pythiosis is associated with poor prognosis with significant mortality caused by Pythium insidiosum. Antimicrobials’ in vitro and in vivo results against P. insidiosum are inconsistent. Although antimicrobials are clinically useful, they are not likely to achieve therapeutic success alone without surgery and immunotherapy. New therapeutic options are therefore needed. This non-exhaustive review discusses the rationale antimicrobial therapy, minimum inhibitory concentrations, and efficacy of antibacterial and antifungal agents against P. insidiosum. This review further provides insight into the immunomodulating effects of antimicrobials that can enhance the immune response to infections. Current data support using antimicrobial combination therapy for the pharmacotherapeutic management of human pythiosis. Also, the success or failure of antimicrobial treatment in human pythiosis might depend on the immunomodulatory effects of drugs. The repurposing of existing drugs is a safe strategy for anti-P. insidiosum drug discovery. To improve patient outcomes in pythiosis, we suggest further research and a deeper understanding of P. insidiosum virulence factors, host immune response, and host immune system modification by antimicrobials.
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Affiliation(s)
- Sadeep Medhasi
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Navaporn Worasilchai
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Immunomodulation of Natural Products Research Group, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: ; Tel.: +66-2218-1065
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History and Perspective of Immunotherapy for Pythiosis. Vaccines (Basel) 2021; 9:vaccines9101080. [PMID: 34696188 PMCID: PMC8539095 DOI: 10.3390/vaccines9101080] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022] Open
Abstract
The fungus-like microorganism Pythium insidiosum causes pythiosis, a life-threatening infectious disease increasingly reported worldwide. Antimicrobial drugs are ineffective. Radical surgery is an essential treatment. Pythiosis can resume post-surgically. Immunotherapy using P. insidiosum antigens (PIA) has emerged as an alternative treatment. This review aims at providing up-to-date information of the immunotherapeutic PIA, with the focus on its history, preparation, clinical application, outcome, mechanism, and recent advances, in order to promote the proper use and future development of this treatment modality. P. insidiosum crude extract is the primary source of immunotherapeutic antigens. Based on 967 documented human and animal (mainly horses) pythiosis cases, PIA immunotherapy reduced disease morbidity and mortality. Concerning clinical outcomes, 19.4% of PIA-immunized human patients succumbed to vascular pythiosis instead of 41.0% in unimmunized cases. PIA immunotherapy may not provide an advantage in a local P. insidiosum infection of the eye. Both PIA-immunized and unimmunized horses with pythiosis showed a similar survival rate of ~70%; however, demands for surgical intervention were much lesser in the immunized cases (22.8% vs. 75.2%). The proposed PIA action involves switching the non-protective T-helper-2 to protective T-helper-1 mediated immunity. By exploring the available P. insidiosum genome data, synthetic peptides, recombinant proteins, and nucleic acids are potential sources of the immunotherapeutic antigens worth investigating. The PIA therapeutic property needs improvement for a better prognosis of pythiosis patients.
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Kharel A, Islam MT, Rookes J, Cahill D. How to Unravel the Key Functions of Cryptic Oomycete Elicitin Proteins and Their Role in Plant Disease. PLANTS 2021; 10:plants10061201. [PMID: 34204633 PMCID: PMC8231210 DOI: 10.3390/plants10061201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022]
Abstract
Pathogens and plants are in a constant battle with one another, the result of which is either the restriction of pathogen growth via constitutive or induced plant defense responses or the pathogen colonization of plant cells and tissues that cause disease. Elicitins are a group of highly conserved proteins produced by certain oomycete species, and their sterol binding ability is recognized as an important feature in sterol–auxotrophic oomycetes. Elicitins also orchestrate other aspects of the interactions of oomycetes with their plant hosts. The function of elicitins as avirulence or virulence factors is controversial and is dependent on the host species, and despite several decades of research, the function of these proteins remains elusive. We summarize here our current understanding of elicitins as either defense-promoting or defense-suppressing agents and propose that more recent approaches such as the use of ‘omics’ and gene editing can be used to unravel the role of elicitins in host–pathogen interactions. A better understanding of the role of elicitins is required and deciphering their role in host–pathogen interactions will expand the strategies that can be adopted to improve disease resistance and reduce crop losses.
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Chechi JL, Rotchanapreeda T, da Paz GS, Prado AC, Oliveira AL, Vieira JCS, Buzalaf MAR, Rodrigues AM, dos Santos LD, Krajaejun T, Bosco SDMG. Prospecting Biomarkers for Diagnostic and Therapeutic Approaches in Pythiosis. J Fungi (Basel) 2021; 7:jof7060423. [PMID: 34071174 PMCID: PMC8229905 DOI: 10.3390/jof7060423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Pythiosis, whose etiological agent is the oomycete Pythium insidiosum, is a life-threatening disease that occurs mainly in tropical and subtropical countries, affecting several animal species. It is frequently found in horses in Brazil and humans in Thailand. The disease is difficult to diagnose because the pathogen’s hyphae are often misdiagnosed as mucoromycete fungi in histological sections. Additionally, there is no specific antigen to use for rapid diagnosis, the availability of which could improve the prognosis in different animal species. In this scenario, we investigated which P. insidiosum antigens are recognized by circulating antibodies in horses and humans with pythiosis from Brazil and Thailand, respectively, using 2D immunoblotting followed by mass spectrometry for the identification of antigens. We identified 23 protein spots, 14 recognized by pooled serum from horses and humans. Seven antigens were commonly recognized by both species, such as the heat-shock cognate 70 KDa protein, the heat-shock 70 KDa protein, glucan 1,3-beta-glucosidase, fructose-bisphosphate aldolase, serine/threonine-protein phosphatase, aconitate hydratase, and 14-3-3 protein epsilon. These results demonstrate that there are common antigens recognized by the immune responses of horses and humans, and these antigens may be studied as biomarkers for improving diagnosis and treatment.
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Affiliation(s)
- Jéssica Luana Chechi
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.C.P.); (J.C.S.V.)
- Correspondence: (J.L.C.); (S.d.M.G.B.)
| | - Tiwa Rotchanapreeda
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.R.); (T.K.)
| | - Giselle Souza da Paz
- Faculty of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu 18618-681, Brazil; (G.S.d.P.); (A.L.O.)
| | - Ana Carolina Prado
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.C.P.); (J.C.S.V.)
| | - Alana Lucena Oliveira
- Faculty of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu 18618-681, Brazil; (G.S.d.P.); (A.L.O.)
| | - José Cavalcante Souza Vieira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.C.P.); (J.C.S.V.)
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo (USP), Bauru 17012-901, Brazil;
| | - Anderson Messias Rodrigues
- Department of Microbiology, Immunology and Parasitology, Cell Biology Division, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil;
| | - Lucilene Delazari dos Santos
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP), Botucatu 18610-307, Brazil;
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP), Botucatu 18618-687, Brazil
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.R.); (T.K.)
| | - Sandra de Moraes Gimenes Bosco
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.C.P.); (J.C.S.V.)
- Faculty of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu 18618-681, Brazil; (G.S.d.P.); (A.L.O.)
- Correspondence: (J.L.C.); (S.d.M.G.B.)
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8
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Chen H, Raffaele S, Dong S. Silent control: microbial plant pathogens evade host immunity without coding sequence changes. FEMS Microbiol Rev 2021; 45:6095737. [PMID: 33440001 DOI: 10.1093/femsre/fuab002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Both animals and plants have evolved a robust immune system to surveil and defeat invading pathogenic microbes. Evasion of host immune surveillance is the key for pathogens to initiate successful infection. To evade the host immunity, plant pathogens evolved a variety of strategies such as masking themselves from host immune recognitions, blocking immune signaling transductions, reprogramming immune responses and adapting to immune microenvironmental changes. Gain of new virulence genes, sequence and structural variations enables plant pathogens to evade host immunity through changes in the genetic code. However, recent discoveries demonstrated that variations at the transcriptional, post-transcriptional, post-translational and glycome level enable pathogens to cope with the host immune system without coding sequence changes. The biochemical modification of pathogen associated molecular patterns and silencing of effector genes emerged as potent ways for pathogens to hide from host recognition. Altered processing in mRNA activities provide pathogens with resilience to microenvironment changes. Importantly, these hiding variants are directly or indirectly modulated by catalytic enzymes or enzymatic complexes and cannot be revealed by classical genomics alone. Unveiling these novel host evasion mechanisms in plant pathogens enables us to better understand the nature of plant disease and pinpoints strategies for rational diseases management in global food protection.
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Affiliation(s)
- Han Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, 24 Chemin de Borde Rouge - Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France
| | - Suomeng Dong
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
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Noman A, Aqeel M, Irshad MK, Qari SH, Hashem M, Alamri S, AbdulMajeed AM, Al-Sadi AM. Elicitins as molecular weapons against pathogens: consolidated biotechnological strategy for enhancing plant growth. Crit Rev Biotechnol 2020; 40:821-832. [PMID: 32546015 DOI: 10.1080/07388551.2020.1779174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To fight against pathogens, defense systems in plants mainly depend upon preformed as well as induced responses. Pathogen detection activates induced responses and signals are transmitted for coordinated cellular events in order to restrict infection and spread. In spite of significant developments in manipulating genes, transcription factors and proteins for their involvement in immunity, absolute tolerance/resistance to pathogens has not been seen in plants/crops. Defense responses, among diverse plant types, to different pathogens involve modifications at the physio-biochemical and molecular levels. Secreted by oomycetes, elicitins are small, highly conserved and sterol-binding extracellular proteins with PAMP (pathogen associated molecular patterns) functions and are capable of eliciting plant defense reactions. Belonging to multigene families in oomycetes, elicitins are different from other plant proteins and show a different affinity for binding sterols and other lipids. These function for sterols binding to catalyze their inter-membrane and intra- as well as inter-micelle transport. Importantly, elicitins protect plants by inducing HR (hypersensitive response) and systemic acquired resistance. Despite immense metabolic significance and the involvement in defense activities, elicitins have not yet been fully studied and many questions regarding their functional activities remain to be explained. In order to address multiple questions associated with the role of elicitins, we have reviewed the understanding and topical advancements in plant defense mechanisms with a particular interest in elicitin-based defense actions and metabolic activities. This article offers potential attributes of elicitins as the biological control of plant diseases and can be considered as a baseline toward a more profound understanding of elicitins.
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Affiliation(s)
- Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Science, Lanzhou University, Lanzhou, Gansu, PR China
| | - Muhammad Kashif Irshad
- Department of Environmental Sciences, Government College University, Faisalabad, Pakistan
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed Hashem
- College of Science, Department of Biology, King Khalid University, Abha, Saudi Arabia.,Faculty of Science, Botany and Microbiology Department, Assiut University, Assiut, Egypt
| | - Saad Alamri
- College of Science, Department of Biology, King Khalid University, Abha, Saudi Arabia.,Prince Sultan Ben Abdulaziz Center for Environmental and Tourism Research and Studies, King Khalid University, Abha, Saudi Arabia
| | - Awatif M AbdulMajeed
- Biology Department, Faculty of Science, University of Tabook, Umluj, Saudi Arabia
| | - Abdullah M Al-Sadi
- College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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10
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Chitasombat MN, Jongkhajornpong P, Lekhanont K, Krajaejun T. Recent update in diagnosis and treatment of human pythiosis. PeerJ 2020; 8:e8555. [PMID: 32117626 PMCID: PMC7036273 DOI: 10.7717/peerj.8555] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/13/2020] [Indexed: 12/20/2022] Open
Abstract
Human pythiosis is an infectious condition with high morbidity and mortality. The causative agent is the oomycete microorganism Pythium insidiosum. The pathogen inhabits ubiquitously in a wet environment, and direct exposure to the pathogen initiates the infection. Most patients with pythiosis require surgical removal of the affected organ, and many patients die from the disease. Awareness of pythiosis among healthcare personnel is increasing. In this review, we summarized and updated information on the diagnosis and treatment of human pythiosis. Vascular and ocular pythiosis are common clinical manifestations. Recognition of the typical clinical features of pythiosis is essential for early diagnosis. The definitive diagnosis of the disease requires laboratory testing, such as microbiological, serological, molecular, and proteomic assays. In vascular pythiosis, surgical intervention to achieve the organism-free margin of the affected tissue, in combination with the use of antifungal drugs and P. insidiosum immunotherapy, remains the recommended treatment. Ocular pythiosis is a serious condition and earliest therapeutic penetrating keratoplasty with wide surgical margin is the mainstay treatment. Thorough clinical assessment is essential in all patients to evaluate the treatment response and detect an early sign of the disease recurrence. In conclusion, early diagnosis and proper management are the keys to an optimal outcome of the patients with pythiosis.
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Affiliation(s)
- Maria Nina Chitasombat
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Passara Jongkhajornpong
- Department of Ophthalmology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kaevalin Lekhanont
- Department of Ophthalmology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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11
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Chechi JL, Franckin T, Barbosa LN, Alves FCB, Leite ADL, Buzalaf MAR, Delazari Dos Santos L, Bosco SDMG. Inferring putative virulence factors for Pythium insidiosum by proteomic approach. Med Mycol 2019; 57:92-100. [PMID: 29373751 DOI: 10.1093/mmy/myx166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 01/05/2018] [Indexed: 12/23/2022] Open
Abstract
Pythium insidiosum is the etiologic agent of pythiosis, a life-threatening disease that affects human and animals, has difficult diagnosis, and therapy. Studies on protein characterization of P. insidiosum are scarce, so we aimed to determine the protein profile of P. insidiosum by mass spectrometry and bioinformatics strategies targeting in proteins that may act as putative virulence factors. Therefore, an extraction protocol was standardized to obtain the total proteins of P. insidiosum. By the analysis of Image Master 2D Platinum software, it was found that 186 spots ranging between 12 and 89 KDa and isoelectric point from 4 to 7. By the analysis of 2D-SDS-PAGE it was possible to visualize and excise 103 spots, which were hydrolyzed with trypsin and submitted to mass spectrometry, resulting in the identification of 36 different proteins. Three of them were classified as proteins supposedly related to virulence factors due to its functions, such as glucan 1,3-beta glucosidase, Heat shock protein (Hsp) 70 and enolase. These results may contribute to a better understanding of the virulence factors of this medically important oomycete, as well as to subsidize new studies on diagnosis and therapeutic approaches.
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Affiliation(s)
- Jéssica Luana Chechi
- Department of Microbiology and Immunology, Univ. Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil
| | - Tarsila Franckin
- Department of Microbiology and Immunology, Univ. Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil
| | - Lidiane Nunes Barbosa
- Department of Microbiology and Immunology, Univ. Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.,Center for the Studies of Venoms and Venomous Animals (CEVAP), Univ Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil
| | | | - Aline de Lima Leite
- Department of Biological Sciences, Bauru School of Dentistry, University of Sao Paulo (USP), Bauru, Brazil
| | | | - Lucilene Delazari Dos Santos
- Center for the Studies of Venoms and Venomous Animals (CEVAP), Univ Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.,Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), Univ Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil
| | - Sandra de Moraes Gimenes Bosco
- Department of Microbiology and Immunology, Univ. Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil.,Center for the Studies of Venoms and Venomous Animals (CEVAP), Univ Estadual Paulista (UNESP), Botucatu, Sao Paulo, Brazil
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12
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Rujirawat T, Patumcharoenpol P, Lohnoo T, Yingyong W, Kumsang Y, Payattikul P, Tangphatsornruang S, Suriyaphol P, Reamtong O, Garg G, Kittichotirat W, Krajaejun T. Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses. Sci Rep 2018. [PMID: 29515152 PMCID: PMC5841299 DOI: 10.1038/s41598-018-22540-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Pythium insidiosum is a human-pathogenic oomycete. Many patients infected with it lose organs or die. Toward the goal of developing improved treatment options, we want to understand how Py. insidiosum has evolved to become a successful human pathogen. Our approach here involved the use of comparative genomic and other analyses to identify genes with possible functions in the pathogenicity of Py. insidiosum. We generated an Oomycete Gene Table and used it to explore the genome contents and phylogenomic relationships of Py. insidiosum and 19 other oomycetes. Initial sequence analyses showed that Py. insidiosum is closely related to Pythium species that are not pathogenic to humans. Our analyses also indicated that the organism harbours secreted and adhesin-like proteins, which are absent from related species. Putative virulence proteins were identified by comparison to a set of known virulence genes. Among them is the urease Ure1, which is absent from humans and thus a potential diagnostic and therapeutic target. We used mass spectrometric data to successfully validate the expression of 30% of 14,962 predicted proteins and identify 15 body temperature (37 °C)-dependent proteins of Py. insidiosum. This work begins to unravel the determinants of pathogenicity of Py. insidiosum.
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Affiliation(s)
- Thidarat Rujirawat
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Preecha Patumcharoenpol
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.,Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Tassanee Lohnoo
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wanta Yingyong
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yothin Kumsang
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Penpan Payattikul
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sithichoke Tangphatsornruang
- Genomic Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Gagan Garg
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Floreat, WA, Australia
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Patel S, Rauf A, Khan H. The relevance of folkloric usage of plant galls as medicines: Finding the scientific rationale. Biomed Pharmacother 2017; 97:240-247. [PMID: 29091872 DOI: 10.1016/j.biopha.2017.10.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022] Open
Abstract
Galls, the abnormal growths in plants, induced by virus, bacteria, fungi, nematodes, arthropods, or even other plants, are akin to cancers in fauna. The galls which occur in a myriad of forms are phytochemically-distinct from the normal plant tissues, for these are the sites of tug-of-war, just like the granuloma in animals. To counter the stressors, in the form of the effector proteins of the invaders, the host plants elaborate a large repertoire of metabolites, which they normally will not produce. Perturbation of the jasmonic acid pathway, and the overexpression of auxin, and cytokinin, promote the tissue proliferation and the resultant galls. Though the plant family characteristics and the attackers determine the gall biochemistry, most of the galls are rich in bioactive phytochemicals such as phenolic acids, anthocyanins, purpurogallin, flavonoids, tannins, steroids, triterpenes, alkaloids, lipophilic components (tanshinone) etc. Throughout the long trajectory of evolution, humans have learned to use the galls as therapeutics, much like other plant parts. In diverse cultures, the evidence of folkloric usage of galls abound. Among others, galls from the plant genus like Rhus, Pistacia, Quercus, Terminalia etc. are popular as ethnomedicine. This review mines the literature on galling agents, and the medicinal relevance of galls.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, 92182, USA.
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, 23561, K.P.K, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan
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Marano AV, Gleason FH, Rocha SCO, Pires-Zottarelli CLA, Souza JID. Chapter 17 Crown Oomycetes Have Evolved as Effective Plant and Animal Parasites. Mycology 2017. [DOI: 10.1201/9781315119496-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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15
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Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
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Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
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16
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Evolution of the Sterol Biosynthetic Pathway of Pythium insidiosum and Related Oomycetes Contributes to Antifungal Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02352-16. [PMID: 28115356 DOI: 10.1128/aac.02352-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Pythiosis is a life-threatening infectious disease caused by the oomycete Pythium insidiosum Direct exposure to Py. insidiosum zoospores can initiate infections of the eye, limb, gastrointestinal tract, or skin/subcutaneous tissue. Treatments for pythiosis have mostly relied on surgery. Antifungal drugs are generally ineffective against Py. insidiosum However, one patient with an invasive Py. insidiosum infection recovered completely following treatment with terbinafine and itraconazole. Additionally, the drug target sterol biosynthetic enzymes have been identified in the oomycete Aphanomyces euteiches It remains an open question whether Py. insidiosum is susceptible to the antifungal drugs and harbors any of the known drug target enzymes. Here, we determined the in vitro susceptibilities of terbinafine and itraconazole against 30 isolates of Py. insidiosum We also analyzed endogenous sterols and searched for genes encoding the sterol biosynthetic enzymes in the genomes of Py. insidiosum and related oomycetes. The susceptibility assay showed that the growth of each of the Py. insidiosum isolates was inhibited by the antifungal agents, but only at difficult-to-achieve concentrations, which explains the clinical resistance of the drugs in the treatment of pythiosis patients. Genome searches of Py. insidiosum and related oomycetes demonstrated that these organisms contained an incomplete set of sterol biosynthetic enzymes. Gas chromatographic mass spectrometry did not detect any sterol end products in Py. insidiosum In conclusion, Py. insidiosum possesses an incomplete sterol biosynthetic pathway. Resistance to antifungal drugs targeting enzymes in the ergosterol biosynthetic pathway in Py. insidiosum was due to modifications or losses of some of the genes encoding the drug target enzymes.
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Patel S. In silico analysis of Hepatitis C virus (HCV) polyprotein domains and their comparison with other pathogens and allergens to gain insight on pathogenicity mechanisms. Comput Biol Chem 2016; 65:91-102. [DOI: 10.1016/j.compbiolchem.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/12/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022]
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Development of an Anti-Elicitin Antibody-Based Immunohistochemical Assay for Diagnosis of Pythiosis. J Clin Microbiol 2016; 54:43-8. [PMID: 26719582 DOI: 10.1128/jcm.02113-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pythiosis is an emerging and life-threatening infectious disease of humans and animals living in tropical and subtropical countries and is caused by the fungus-like organism Pythium insidiosum. Antifungals are ineffective against this pathogen. Most patients undergo surgical removal of the infected organ, and many die from advanced infections. Early and accurate diagnosis leads to prompt management and promotes better prognosis for affected patients. Immunohistochemical assays (IHCs) have been developed using rabbit antibodies raised against P. insidiosum crude extract, i.e., culture filtrate antigen (CFA), for the histodiagnosis of pythiosis, but cross-reactivity with pathogenic fungi compromises the diagnostic performance of the IHC. Therefore, there is a need to improve detection specificity. Recently, the elicitin protein, ELI025, was identified in P. insidiosum, but it was not identified in other human pathogens, including true fungi. The ELI025-encoding gene was successfully cloned and expressed as a recombinant protein in Escherichia coli. This study aims to develop a new IHC using the rabbit anti-ELI025 antibody (anti-ELI) and to compare its performance with the previously reported anti-CFA-based IHC. Thirty-eight P. insidiosum histological sections stained positive by anti-ELI-based and anti-CFA-based IHCs indicating 100% detection sensitivity for the two assays. The anti-ELI antibody stained negative for all 49 negative-control sections indicating 100% detection specificity. In contrast, the anti-CFA antibody stained positive for one of the 49 negative controls (a slide prepared from Fusarium-infected tissue) indicating 98% detection specificity. In conclusion, the anti-ELI based IHC is sensitive and specific for the histodiagnosis of pythiosis and is an improvement over the anti-CFA-based assay.
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Lerksuthirat T, Lohnoo T, Rujirawat T, Yingyong W, Jongruja N, Krajaejun T. Geographic variation in the elicitin-like glycoprotein, ELI025, of Pythium insidiosum isolated from human and animal subjects. INFECTION GENETICS AND EVOLUTION 2015; 35:127-33. [DOI: 10.1016/j.meegid.2015.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/09/2015] [Accepted: 08/03/2015] [Indexed: 11/29/2022]
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