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Chagoya-Fuentes JL, Gaona-López J, Hernández-Carbajal GR, Torres-Guerrero H, Lammoglia-Villagómez MA, Huerta-Peña J, Pérez-Brígido CD, Jácome-Sosa E, Nieto-Rosaliano SO, Rojas-Ronquillo R, Grostieta E, Becker I, Sánchez-Montes S. First confirmed case of equine pythiosis in Northern Veracruz, Mexico. Acta Trop 2024; 254:107195. [PMID: 38548212 DOI: 10.1016/j.actatropica.2024.107195] [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: 01/29/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
A clinical case of an adult horse with invasive, ulcerative, proliferative, pyogranulomatous disease of the skin (tumor) in the shoulder region is presented. The mass had a granulomatous and crater-shaped appearance, with serosanguinous discharge and the presence of fistulas with caseous material. The tumor was removed by surgery and sent to the laboratory for diagnosis. Histopathology was performed using Grocott-Gomori methenamine silver stain. The presence of necrotic material, fibrosis, infiltrated cells, and brown-colored hyphae, characteristic of members of the genus Pythium, were observed. To identify the infecting species, conventional PCRs for the amplification of the ITS-1 was carried out. Histopathological and PCR tests confirmed infection by a Pythium insidiosum strain closely associated with previous records from the US and Central America. Our report represents the first molecularly confirmed case of equine pythiosis in Mexico.
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Affiliation(s)
- Jorge Luis Chagoya-Fuentes
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Jair Gaona-López
- Facultad de Ciencias Biológicas y Agropecuarias región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Gabriela R Hernández-Carbajal
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico.
| | - Haydee Torres-Guerrero
- Laboratorio de Micología Básica, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Miguel A Lammoglia-Villagómez
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Javier Huerta-Peña
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Carlos D Pérez-Brígido
- Facultad de Ciencias Biológicas y Agropecuarias región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Edelmira Jácome-Sosa
- Facultad de Ciencias Biológicas y Agropecuarias región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Sergio Omar Nieto-Rosaliano
- Facultad de Ciencias Biológicas y Agropecuarias región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Rebeca Rojas-Ronquillo
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico
| | - Estefania Grostieta
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ingeborg Becker
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sokani Sánchez-Montes
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias región Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano, Veracruz, Mexico; Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
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Wang G, Burrill HM, Podzikowski LY, Eppinga MB, Zhang F, Zhang J, Schultz PA, Bever JD. Dilution of specialist pathogens drives productivity benefits from diversity in plant mixtures. Nat Commun 2023; 14:8417. [PMID: 38110413 PMCID: PMC10728191 DOI: 10.1038/s41467-023-44253-4] [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: 03/07/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.
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Affiliation(s)
- Guangzhou Wang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China.
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
| | - Haley M Burrill
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- The Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Laura Y Podzikowski
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Maarten B Eppinga
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Junling Zhang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Peggy A Schultz
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Environmental Studies Program, University of Kansas, Lawrence, KS, 66045, USA
| | - James D Bever
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
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3
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Ai G, Si J, Cheng Y, Meng R, Wu Z, Xu R, Wang X, Zhai Y, Peng H, Li Y, Dou D, Jing M. The oomycete-specific BAG subfamily maintains protein homeostasis and promotes pathogenicity in an atypical HSP70-independent manner. Cell Rep 2023; 42:113391. [PMID: 37930886 DOI: 10.1016/j.celrep.2023.113391] [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: 05/04/2023] [Revised: 09/08/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Protein homeostasis is vital for organisms and requires chaperones like the conserved Bcl-2-associated athanogene (BAG) co-chaperones that bind to the heat shock protein 70 (HSP70) through their C-terminal BAG domain (BD). Here, we show an unconventional BAG subfamily exclusively found in oomycetes. Oomycete BAGs feature an atypical N-terminal BD with a short and oomycete-specific α1 helix (α1'), plus a C-terminal small heat shock protein (sHSP) domain. In oomycete pathogen Phytophthora sojae, both BD-α1' and sHSP domains are required for P. sojae BAG (PsBAG) function in cyst germination, pathogenicity, and unfolded protein response assisting in 26S proteasome-mediated degradation of misfolded proteins. PsBAGs form homo- and heterodimers through their unique BD-α1' to function properly, with no recruitment of HSP70s to form the common BAG-HSP70 complex found in other eukaryotes. Our study highlights an oomycete-exclusive protein homeostasis mechanism mediated by atypical BAGs, which provides a potential target for oomycete disease control.
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Affiliation(s)
- Gan Ai
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Jierui Si
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Cheng
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Meng
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Zishan Wu
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Ruofei Xu
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodan Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100091, China
| | - Ying Zhai
- USDA-ARS, Crop Diseases, Pests and Genetics Research Unit, Parlier, CA 93648, USA
| | - Hao Peng
- USDA-ARS, Crop Diseases, Pests and Genetics Research Unit, Parlier, CA 93648, USA
| | - Yurong Li
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Daolong Dou
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China.
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Krajaejun T, Patumcharoenpol P, Rujirawat T, Kittichotirat W, Tangphatsornruang S. MGI short-read genome assemblies of Pythium insidiosum (reclassified as Pythium periculosum) strains Pi057C3 and Pi050C3. BMC Res Notes 2023; 16:316. [PMID: 37932861 PMCID: PMC10629006 DOI: 10.1186/s13104-023-06587-6] [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: 11/28/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVES Pythium insidiosum causes a difficult-to-treat infectious condition called pythiosis, with high morbidity and mortality. So far, genome data of at least 10 strains of P. insidiosum, primarily classified in the phylogenetic clades I and II, have been sequenced using various next-generation sequencing platforms. The MGI short-read platform was employed to obtain genome data of 2 clade-III strains of P. insidiosum (recently reclassified as Pythium periculosum) from patients in Thailand and the United States. This work is a part of our attempt to generate a comprehensive genome database from diverse pathogen strains. DATA DESCRIPTION A 150-bp paired-end library was prepared from a gDNA sample of P. insidiosum (P. periculosum) strains Pi057C3 and Pi050C3 (also known as ATCC90586) to generate draft genome sequences using an MGISEQ-2000RS sequencer. As a result, for the strain Pi057C3, we obtained a 42.5-Mb assembled genome (164x coverage) comprising 14,134 contigs, L50 of 241, N50 of 45,748, 57.6% CG content, and 12,147 ORFs. For the strain Pi050C3, we received a 43.3-Mb draft genome (230x coverage) containing 14,511 contigs, L50 of 245, N50 of 45,208, 57.7% CG content, and 12,249 ORFs. The genome sequences have been deposited in the NCBI/DDBJ databases under the accession numbers JAKCXM000000000.1 (strain Pi057C3) and JAKCXL000000000.1 (strain Pi050C3).
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
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Krajaejun T, Patumcharoenpol P, Rujirawat T, Kittichotirat W, Tangphatsornruang S, Lohnoo T, Yingyong W. PacBio long read-assembled draft genome of Pythium insidiosum strain Pi-S isolated from a Thai patient with pythiosis. BMC Res Notes 2023; 16:271. [PMID: 37833791 PMCID: PMC10576409 DOI: 10.1186/s13104-023-06532-7] [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: 10/01/2022] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
OBJECTIVES Pythium insidiosum is the causative agent of pythiosis, a difficult-to-treat condition, in humans and animals worldwide. Biological information about this filamentous microorganism is sparse. Genomes of several P. insidiosum strains were sequenced using the Illumina short-read NGS platform, producing incomplete genome sequence data. PacBio long-read platform was employed to obtain a better-quality genome of Pythium insidiosum. The obtained genome data could promote basic research on the pathogen's biology and pathogenicity. DATA DESCRIPTION gDNA sample was extracted from the P. insidiosum strain Pi-S for whole-genome sequencing by PacBio long-read NGS platform. Raw reads were assembled using CANU (v2.1), polished using ARROW (SMRT link version 5.0.1), aligned with the original raw PacBio reads using pbmm2 (v1.2.1), consensus sequence checked using ARROW, and gene predicted using Funannotate pipeline (v1.7.4). The genome completion was assessed using BUSCO (v4.0.2). As a result, 840 contigs (maximum length: 1.3 Mb; N50: 229.9 Kb; L50: 70) were obtained. Sequence assembly showed a genome size of 66.7 Mb (178x coverage; 57.2% G-C content) that contained 20,375 ORFs. A BUSCO-based assessment revealed 85.5% genome completion. All assembled contig sequences have been deposited in the NCBI database under the accession numbers BBXB02000001 - BBXB02000840.
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, 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
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Burrill HM, Wang G, Bever JD. Rapid differentiation of soil and root microbiomes in response to plant composition and biodiversity in the field. ISME COMMUNICATIONS 2023; 3:31. [PMID: 37076650 PMCID: PMC10115818 DOI: 10.1038/s43705-023-00237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/15/2023] [Accepted: 03/29/2023] [Indexed: 04/21/2023]
Abstract
Research suggests that microbiomes play a major role in structuring plant communities and influencing ecosystem processes, however, the relative roles and strength of change of microbial components have not been identified. We measured the response of fungal, arbuscular mycorrhizal fungal (AMF), bacteria, and oomycete composition 4 months after planting of field plots that varied in plant composition and diversity. Plots were planted using 18 prairie plant species from three plant families (Poaceae, Fabaceae, and Asteraceae) in monoculture, 2, 3, or 6 species richness mixtures and either species within multiple families or one family. Soil cores were collected and homogenized per plot and DNA were extracted from soil and roots of each plot. We found that all microbial groups responded to the planting design, indicating rapid microbiome response to plant composition. Fungal pathogen communities were strongly affected by plant diversity. We identified OTUs from genera of putatively pathogenic fungi that increased with plant family, indicating likely pathogen specificity. Bacteria were strongly differentiated by plant family in roots but not soil. Fungal pathogen diversity increased with planted species richness, while oomycete diversity, as well as bacterial diversity in roots, decreased. AMF differentiation in roots was detected with individual plant species, but not plant family or richness. Fungal saprotroph composition differentiated between plant family composition in plots, providing evidence for decomposer home-field advantage. The observed patterns are consistent with rapid microbiome differentiation with plant composition, which could generate rapid feedbacks on plant growth in the field, thereby potentially influencing plant community structure, and influence ecosystem processes. These findings highlight the importance of native microbial inoculation in restoration.
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Braga CQ, Milech A, dos Santos Bermann C, Ianiski LB, Stibbe PC, de Lemos AB, Bonel J, de Avila Botton S, Pereira DIB. Exposure of Culex quinquefasciatus to the oomycete Pythium insidiosum: A protocol for in vitro studies. Fungal Biol 2023; 127:969-974. [PMID: 37024156 DOI: 10.1016/j.funbio.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/06/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Pythium insidiosum causes pythiosis, an infection that affects different species of mammals, including humans, and inhabits marshy ecosystems of tropical, subtropical, and temperate regions worldwide. Therefore, this study proposes a protocol to expose Culex quinquefasciatus to P. insidiosum zoospores. Cx. quinquefasciatus immatures (eggs, larvae, and pupae) were exposed to zoospores (8x103 zoospores/mL) of the oomycete for 24 h. The exposure of Cx. quinquefasciatus to the zoospores from L1 to the emergence of adults was evaluated, and P. insidiosum detection was performed by microbiological culture, polymerase chain reaction, and histopathological analysis of stage 4 larvae. The protocol used to produce Cx. quinquefasciatus colonies and adapted for this study proved viable for research on the interaction between P. insidiosum and this Culicidae species. Moreover, P. insidiosum presence was evident in all larval stages of the mosquito, although the presence of the oomycete was not detected in the eggs, pupae, and adults. This study is a pioneer in the development of a protocol to evaluate Cx. quinquefasciatus exposure to P. insidiosum zoospores, and under experimental conditions, P. insidiosum can establish itself in Cx. quinquefasciatus larval stages. The developed protocol is expected to serve as a basis for developing studies to evaluate the interactions of P. insidiosum with these mosquitoes and shed more light on the participation of culicids in expanding the ecological niche of P. insidiosum.
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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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Zhu Y, Shan X, Zhou J, Zhen Q, Song J, Yuan Z, Zhao H, Wang Z. Complete Genome Sequence of Pythium oligandrum, Isolated from Rhizosphere Soils of Chinese Angelica sinensis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1127-1130. [PMID: 36384030 DOI: 10.1094/mpmi-04-22-0091-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Most of the Pythium species are pathogenic to a wide range of economically important crops and, sometimes, can even cause diseases in animals and humans. An exception is that the soil-inhabiting P. oligandrum is an effective biocontrol agent against a diverse suite of pathogens and promotes plant growth. In this work, we sequenced the whole genome of P. oligandrum PO-1, isolated from rhizosphere soils of Chinese Angelica sinensis, using a combination of long-read single-molecule real-time sequencing technology (Pacific Biosciences [PacBio]) and Illumina sequencing. The 2.5-Gb and 5.2-Gb bases were generated respectively. The sequencing depths were 93× with PacBio and 145× with Illumina sequencing. With the PacBio sequencing results further corrected by Illumina sequencing, the genome was assembled into 71 scaffolds with a total size of 39.10 Mb (N50 = 1.45 Mb; L50 = 9)and the longest scaffold is 3.49 Mb. Genome annotation identifies 15,632 protein-coding genes and 0.47 Mb of transposable elements. Our genomic assembly and annotation have been greatly improved compared with the already released three genomes of P. oligandrum. This genomic data will provide valuable information to understand the mechanism underlying its biocontrol potentials and will also facilitate the dissection of genome evolution and environmental adaptation within the genus Pythium. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Ying Zhu
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Xiaoliang Shan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 31140, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianping Zhou
- Natural Energy Research Institute, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Qun Zhen
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Jie Song
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Zhilin Yuan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongwei Zhao
- Natural Energy Research Institute, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China
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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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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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Mohammadi M, Smith EA, Stanghellini ME, Kaundal R. Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire. Int J Mol Sci 2021; 22:ijms22169002. [PMID: 34445718 PMCID: PMC8396444 DOI: 10.3390/ijms22169002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.
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Affiliation(s)
- Mojtaba Mohammadi
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Eric A. Smith
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Michael E. Stanghellini
- Department of Microbiology and Plant Pathology, University of California, 900 University Ave., Riverside, CA 92521, USA; (M.M.); (E.A.S.); (M.E.S.)
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, 4820 Old Main Hill, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, 4700 Old Main Hill, Logan, UT 84322, USA
- Correspondence: ; Tel.: +1-(435)-797-4117; Fax: +1-(435)-797-2766
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Yang K, Dong X, Li J, Wang Y, Cheng Y, Zhai Y, Li X, Wei L, Jing M, Dou D. Type 2 Nep1-Like Proteins from the Biocontrol Oomycete Pythium oligandrum Suppress Phytophthora capsici Infection in Solanaceous Plants. J Fungi (Basel) 2021; 7:496. [PMID: 34206578 PMCID: PMC8303654 DOI: 10.3390/jof7070496] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
As a non-pathogenic oomycete, the biocontrol agent Pythium oligandrum is able to control plant diseases through direct mycoparasite activity and boosting plant immune responses. Several P. oligandrum elicitors have been found to activate plant immunity as microbe-associated molecular patterns (MAMPs). Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are a group of MAMPs widely distributed in eukaryotic and prokaryotic plant pathogens. However, little is known about their distribution and functions in P. oligandrum and its sister species Pythium periplocum. Here, we identified a total of 25 NLPs from P. oligandrum (PyolNLPs) and P. periplocum (PypeNLPs). Meanwhile, we found that PyolNLPs/PypeNLPs genes cluster in two chromosomal segments, and our analysis suggests that they expand by duplication and share a common origin totally different from that of pathogenic oomycetes. Nine PyolNLPs/PypeNLPs induced necrosis in Nicotiana benthamiana by agroinfiltration. Eight partially purified PyolNLPs/PypeNLPs were tested for their potential biocontrol activity. PyolNLP5 and PyolNLP7 showed necrosis-inducing activity in N. benthamiana via direct protein infiltration. At sufficient concentrations, they both significantly reduced disease severity and suppressed the in planta growth of Phytophthora capsici in solanaceous plants including N. benthamiana (tobacco), Solanum lycopersicum (tomato) and Capsicum annuum (pepper). Our assays suggest that the Phytophthora suppression effect of PyolNLP5 and PyolNLP7 is irrelevant to reactive oxygen species (ROS) accumulation. Instead, they induce the expression of antimicrobial plant defensin genes, and the induction depends on their conserved nlp24-like peptide pattern. This work demonstrates the biocontrol role of two P. oligandrum NLPs for solanaceous plants, which uncovers a novel approach of utilizing NLPs to develop bioactive formulae for oomycete pathogen control with no ROS-caused injury to plants.
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Affiliation(s)
- Kun Yang
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Xiaohua Dong
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Jialu Li
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Yi Wang
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Yang Cheng
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Xiaobo Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou 510640, China;
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Maofeng Jing
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
| | - Daolong Dou
- The Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (X.D.); (J.L.); (Y.W.); (Y.C.)
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Immunological Cross-Reactivity of Proteins Extracted from the Oomycete Pythium insidiosum and the Fungus Basidiobolus ranarum Compromises the Detection Specificity of Immunodiagnostic Assays for Pythiosis. J Fungi (Basel) 2021; 7:jof7060474. [PMID: 34208304 PMCID: PMC8231275 DOI: 10.3390/jof7060474] [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: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/10/2023] Open
Abstract
Pythiosis, a life-threatening disease caused by Pythium insidiosum, has been increasingly diagnosed worldwide. A recently developed immunochromatographic test (ICT) enables the rapid diagnosis of pythiosis. During the 3-year clinical implementation of ICT in Thailand, we collected the laboratory reports of 38 animals with suspected pythiosis and detected ICT false-positive results in three horses and a dog with basidiobolomycosis. P. insidiosum and Basidiobolus ranarum cause infections with indistinguishable clinical and microscopic features. This study investigated cross-reactive antibodies by probing P. insidiosum and B. ranarum crude extracts and cell-free synthesized I06 protein (encoded in P. insidiosum genome, not other fungi) against a panel of pythiosis, basidiobolomycosis, rabbit anti-I06 peptide, and control sera by Western blot analyses. ICT false-positive results occurred from the cross-reactivity of anti-B. ranarum antibodies to the 15, 50, 60, and 120 kDa proteins of P. insidiosum, not double infections caused by both pathogens. Notably, ICT could help to screen pythiosis, and the positive test requires confirmation by culture or molecular method. The detection specificity of ICT requires improvement. The crude extract containing multispecies antigens needs replacement with a refined P. insidiosum-specific protein. We proposed that the 55 kDa I06 protein is an excellent candidate for developing a more specific serodiagnostic test for pythiosis.
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Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. Genome data of four Pythium insidiosum strains from the phylogenetically-distinct clades I, II, and III. BMC Res Notes 2021; 14:197. [PMID: 34020710 PMCID: PMC8139067 DOI: 10.1186/s13104-021-05610-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 01/10/2023] Open
Abstract
Objectives We employed the Illumina NGS platform to sequence genomes of 4 different strains of the pathogenic oomycete Pythium insidiosum, the causative agent of pythiosis. These strains were isolated from humans in Thailand (n=3) and the United States (n=1), and phylogenetically classified into clade-I, -II, and -III. Our study augmented the completeness of the P. insidiosum genome database for exploration of the biology, evolution, and pathogenesis of the pathogen. Data description One paired-end library (180-bp insert) was prepared from a gDNA sample of P. insidiosum strains ATCC200269 (clade-I), Pi19 (clade-II), MCC18 (clade-II), and SIMI4763 (clade-III) for whole-genome sequencing by Illumina HiSeq2000/HiSeq2500 NGS platform. A range of 28.459.4 million raw reads, accounted for 3.07.3Gb, were obtained and assembled into the genome sizes of 47.1Mb (15,153 contigs; 85% completeness; 19,329 open reading frames [ORFs]) for strain ATCC200269, 35.4Mb (14,576 contigs; 83% completeness; 13,895 ORFs) for strain Pi19, 34.5Mb (11,084 contigs; 84% completeness; 13,249 ORFs) for strain MCC18, and 47.1Mb (15,162 contigs; 85% completeness; 19,340 ORFs) for strain SIMI4763. The genome data can be downloaded from the NCBI/DDBJ databases under the accessions BCFN00000000.1 (ATCC200269), BCFS00000000.1 (Pi19), BCFT00000000.1 (MCC18), and BCFU00000000.1 (SIMI4763).
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand.
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 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
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16
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Mar Htun Z, Laikul A, Pathomsakulwong W, Yurayart C, Lohnoo T, Yingyong W, Kumsang Y, Payattikul P, Sae-Chew P, Rujirawat T, Jittorntam P, Jaturapaktrarak C, Chongtrakool P, Krajaejun T. Identification and Biotyping of Pythium insidiosum Isolated from Urban and Rural Areas of Thailand by Multiplex PCR, DNA Barcode, and Proteomic Analyses. J Fungi (Basel) 2021; 7:242. [PMID: 33804838 PMCID: PMC8063814 DOI: 10.3390/jof7040242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/20/2022] Open
Abstract
Pythium insidiosum causes pythiosis, a fatal infectious disease of humans and animals worldwide. Prompt diagnosis and treatment are essential to improve the clinical outcome of pythiosis. Diagnosis of P. insidiosum relies on immunological, molecular, and proteomic assays. The main treatment of pythiosis aims to surgically remove all affected tissue to prevent recurrent infection. Due to the marked increase in case reports, pythiosis has become a public health concern. Thailand is an endemic area of human pythiosis. To obtain a complete picture of how the pathogen circulates in the environment, we surveyed the presence of P. insidiosum in urban (Bangkok) and rural areas of Thailand. We employed the hair-baiting technique to screen for P. insidiosum in 500 water samples. Twenty-seven culture-positive samples were identified as P. insidiosum by multiplex PCR, multi-DNA barcode (rDNA, cox1, cox2), and mass spectrometric analyses. These environmental strains of P. insidiosum fell into Clade-II and -III genotypes and exhibited a close phylogenetic/proteomic relationship with Thai clinical strains. Biodiversity of the environmental strains also existed in a local habitat. In conclusion, P. insidiosum is widespread in Thailand. A better understanding of the ecological niche of P. insidiosum could lead to the effective prevention and control of this pathogen.
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Affiliation(s)
- Zin Mar Htun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
- Department of Microbiology, University of Medicine, Mandalay 05024, Myanmar
| | - Aree Laikul
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | | | - Chompoonek Yurayart
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Tassanee Lohnoo
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Wanta Yingyong
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Yothin Kumsang
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Penpan Payattikul
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Pattarana Sae-Chew
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Paisan Jittorntam
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Chalisa Jaturapaktrarak
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (W.Y.); (Y.K.); (P.P.); (P.S.-C.); (T.R.); (P.J.); (C.J.)
| | - Piriyaporn Chongtrakool
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
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Grover M, Barkoulas M. C. elegans as a new tractable host to study infections by animal pathogenic oomycetes. PLoS Pathog 2021; 17:e1009316. [PMID: 33662043 PMCID: PMC7932123 DOI: 10.1371/journal.ppat.1009316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Manish Grover
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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18
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Loop-mediated Isothermal Amplification (LAMP) for Identification of Pythium insidiosum. Int J Infect Dis 2020; 101:149-159. [PMID: 32987181 DOI: 10.1016/j.ijid.2020.09.1430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Pythium insidiosum causes a life-threatening condition called pythiosis. High morbidity and mortality of pythiosis are consequences of delayed diagnosis. We aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of P. insidiosum for use in remote areas, where pythiosis is prevalent. METHODS We designed four LAMP primers to amplify the rDNA sequence. A side-by-side comparison evaluated performances of LAMP and the previously-established multiplex PCR (M-PCR), using gDNA samples extracted from colonies of P. insidiosum (n = 28) and other fungi (n = 54), and tissues of animals with (n = 16) or without (n = 13) pythiosis. RESULTS LAMP demonstrated a 50% shorter assay duration (1.5 h) and a 10-fold lower limit of detection (10-4 ng) than did M-PCR. Based on colony-extracted gDNAs, LAMP and M-PCR correctly reported P. insidiosum in all 28 samples, providing 100% sensitivity. While M-PCR did not amplify all fungal controls (100% specificity), LAMP falsely detected one organism (98% specificity). Based on the clinical samples, LAMP and M-PCR provided an equivalently-high specificity (100%). However, LAMP showed a markedly-higher sensitivity than that of M-PCR (88% vs. 56%). CONCLUSIONS LAMP is a simple, useful, efficient assay for the detection of P. insidiosum in clinical specimens and pure cultures in resource-limited laboratories.
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Delavaux CS, Schemanski JL, House GL, Tipton AG, Sikes B, Bever JD. Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands. ISME JOURNAL 2020; 15:304-317. [PMID: 32958849 PMCID: PMC7852655 DOI: 10.1038/s41396-020-00783-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
Soil-borne pathogens structure plant communities, shaping their diversity, and through these effects may mediate plant responses to climate change and disturbance. Little is known, however, about the environmental determinants of plant pathogen communities. Therefore, we explored the impact of climate gradients and anthropogenic disturbance on root-associated pathogens in grasslands. We examined the community structure of two pathogenic groups-fungal pathogens and oomycetes-in undisturbed and anthropogenically disturbed grasslands across a natural precipitation and temperature gradient in the Midwestern USA. In undisturbed grasslands, precipitation and temperature gradients were important predictors of pathogen community richness and composition. Oomycete richness increased with precipitation, while fungal pathogen richness depended on an interaction of precipitation and temperature, with precipitation increasing richness most with higher temperatures. Disturbance altered plant pathogen composition and precipitation and temperature had a reduced effect on pathogen richness and composition in disturbed grasslands. Because pathogens can mediate plant community diversity and structure, the sensitivity of pathogens to disturbance and climate suggests that degradation of the pathogen community may mediate loss, or limit restoration of, native plant diversity in disturbed grasslands, and may modify plant community response to climate change.
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Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA. .,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA.
| | - Josh L Schemanski
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Geoffrey L House
- National Ecological Observatory Network, Boulder, CO, 80301, USA
| | - Alice G Tipton
- Department of Science, Technology, and Mathematics, Lincoln University, 821 Taylor Drive, 205 Daniel Hall, Jefferson City, MO, 65101, USA
| | - Benjamin Sikes
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
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20
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Ai G, Yang K, Ye W, Tian Y, Du Y, Zhu H, Li T, Xia Q, Shen D, Peng H, Jing M, Xia A, Dou D. Prediction and Characterization of RXLR Effectors in Pythium Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1046-1058. [PMID: 32330072 DOI: 10.1094/mpmi-01-20-0010-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuee Tian
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Protection, Henan University of Science and Technology, Luoyang 471000, China
| | - Yaxin Du
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingyue Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, U.S.A
| | - Maofeng Jing
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. Draft genome sequence of the oomycete Pythium destruens strain ATCC 64221 from a horse with pythiosis in Australia. BMC Res Notes 2020; 13:329. [PMID: 32646477 PMCID: PMC7346664 DOI: 10.1186/s13104-020-05168-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/30/2020] [Indexed: 02/08/2023] Open
Abstract
Objectives Genome sequences are a vital resource for accelerating the biological exploration of an organism of interest. Pythium destruens (a synonym of Pythium insidiosum) causes a difficult-to-treat infectious disease called pythiosis worldwide. Detection and management of pythiosis are challenging. Basic knowledge of the disease is lacking. Genomes of this organism isolated from different continents (i.e., Asia and the Americas) have been sequenced and publicly available. Here, we sequenced the genome of an Australian isolate of P. destruens. Genome data will facilitate the comparative analysis of this and related species at the molecular level. Data description Genomic DNA of the P. destruens strain ATCC 64221, isolated from a horse with pythiosis in Australia, was used to prepare one paired-end library (with 180-bp insert) for next-generation sequencing, using the Illumina HiSeq 2500 short-read platform. Raw reads were cleaned and assembled by several bioinformatics tools. A total of 20,860,454 processed reads, accounted for 2,614,890,553 total bases, can be assembled into a 37.8-Mb genome, consisting 13,060 contigs (average length: 2896 bases; range: 300–142,967), N50 of 11,370 bases, and 2.9% ‘N’ composition. The genome was determined 85.9% completeness, contained 14,424 predicted genes, and can be retrieved online at the NCBI/DDBJ databases under the accession number BCFQ01000000.1.
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand.
| | - Preecha Patumcharoenpol
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 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
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22
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Rotchanapreeda T, Kumsang Y, Sae-Chew P, Rujirawat T, Lohnoo T, Yingyong W, Payattikul P, Reamtong O, Krajaejun T. Expression, purification, and characterization of the recombinant exo-1,3-β-glucanase (Exo1) of the pathogenic oomycete Pythium insidiosum. Heliyon 2020; 6:e04237. [PMID: 32596527 PMCID: PMC7306600 DOI: 10.1016/j.heliyon.2020.e04237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/21/2020] [Accepted: 06/15/2020] [Indexed: 11/28/2022] Open
Abstract
Pythiosis is a deadly infectious disease of humans and animals living in tropical and subtropical countries. The causative agent is the oomycete Pythium insidiosum. Treatment of pythiosis is challenging. The use of antimicrobial agents usually fails in the treatment of pythiosis. Many patients undergo surgical removal of an infected organ (i.e., eye, arm, and leg). The immunotherapeutic vaccine, prepared from the crude extract of P. insidiosum, shows limited efficacy against pythiosis. The fatal outcome occurs in patients with advanced disease. There are urgent needs for an effective therapeutic modality for pythiosis. Recently, the exo-1,3-β-glucanase (Exo1) has been identified as a conserve immunoreactive protein of P. insidiosum. Exo1 was predicted to reside at the cell membrane and hydrolyze cell wall β-glucan during cell growth. An Exo1 ortholog is absent in the human genome, making it an appealing target for drug or vaccine development. We attempted to clone and express the codon-optimized exo1 gene of P. insidiosum in E. coli. To solve the inclusion body formation, expression and purification of Exo1 were achievable in the denaturing condition using SDS- and urea-based buffers. Exo1 lacked hydrolytic activity due to the absence of proper protein folding and post-translational modifications. ELISA and Western blot analyses demonstrated the immunoreactivity of Exo1 against pythiosis sera. In conclusion, we successfully expressed and purified the immunoreactive Exo1 protein of P. insidiosum. The recombinant Exo1 can be produced at an unlimited amount and could serve as an extra protein to enhance the effectiveness of the current form of the vaccine against pythiosis.
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Affiliation(s)
- Tiwa Rotchanapreeda
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yothin Kumsang
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pattarana Sae-Chew
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 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
| | - Penpan Payattikul
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Automated Cell-Free Multiprotein Synthesis Facilitates the Identification of a Secretory, Oligopeptide Elicitor-Like, Immunoreactive Protein of the Oomycete Pythium insidiosum. mSystems 2020; 5:5/3/e00196-20. [PMID: 32398276 PMCID: PMC7219551 DOI: 10.1128/msystems.00196-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Technical limitations of conventional biotechnological methods (i.e., genetic engineering and protein synthesis) prevent extensive functional studies of the massive amounts of genetic information available today. We employed a cell-free protein synthesis system to rapidly and simultaneously generate multiple proteins from genetic codes of the oomycete Pythium insidiosum, which causes the life-threatening disease called pythiosis, in humans and animals worldwide. We aimed to screen for potential diagnostic and therapeutic protein targets of this pathogen. Eighteen proteins were synthesized. Of the 18 proteins, one was a secreted immunoreactive protein, called I06, that triggered host immunity and was recognized explicitly by all tested sera from pythiosis patients. It is one of the OPEL proteins; these proteins are present only in the unique group of microorganisms called oomycetes. Here, we demonstrated that cell-free protein synthesis was useful for the production of multiple proteins to facilitate functional studies and identify a potential target for diagnosis and treatment of pythiosis. Protein production relies on time-consuming genetic engineering and in vivo expression, which is a bottleneck for functional studies in the postgenomic era. Cell-free protein synthesis (CFPS) overcomes the limitation of in vivo protein biosynthesis by processing in vitro transcription and translation of multiple genes to proteins within hours. We employed an automated CFPS to simultaneously synthesize proteins from 24 genes of the oomycete Pythium insidiosum (which causes the life-threatening disease pythiosis) and screen for a diagnostic and therapeutic target. CFPS successfully synthesized 18 proteins (∼75% success rate). One protein, namely, I06, was explicitly recognized by all pythiosis sera, but not control sera, tested. Py. insidiosum secreted a significant amount of I06. The protein architecture of I06 is compatible with the oligopeptide elicitor (OPEL) of the phylogenetically related plant-pathogenic oomycete Phytophthora parasitica. The OPEL-like I06 protein of Py. insidiosum can stimulate host antibody responses, similar to the P. parasitica OPEL that triggers plant defense mechanisms. OPEL-like I06 homologs are present only in the oomycetes. Py. insidiosum contains two OPEL-like I06 homologs, but only one of the two homologs was expressed during hyphal growth. Twenty-nine homologs derived from 15 oomycetes can be phylogenetically divided into two groups. The OPEL-like genes might occur in the common ancestor, before independently undergoing gene gain and loss during the oomycete speciation. In conclusion, CFPS offers a fast in vitro protein synthesis. CFPS simultaneously generated multiple proteins of Py. insidiosum and facilitated the identification of the secretory OPEL-like I06 protein, a potential target for the development of a control measure against the pathogen. IMPORTANCE Technical limitations of conventional biotechnological methods (i.e., genetic engineering and protein synthesis) prevent extensive functional studies of the massive amounts of genetic information available today. We employed a cell-free protein synthesis system to rapidly and simultaneously generate multiple proteins from genetic codes of the oomycete Pythium insidiosum, which causes the life-threatening disease called pythiosis, in humans and animals worldwide. We aimed to screen for potential diagnostic and therapeutic protein targets of this pathogen. Eighteen proteins were synthesized. Of the 18 proteins, one was a secreted immunoreactive protein, called I06, that triggered host immunity and was recognized explicitly by all tested sera from pythiosis patients. It is one of the OPEL proteins; these proteins are present only in the unique group of microorganisms called oomycetes. Here, we demonstrated that cell-free protein synthesis was useful for the production of multiple proteins to facilitate functional studies and identify a potential target for diagnosis and treatment of pythiosis.
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24
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Abstract
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland.
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25
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Jaturapaktrarak C, Payattikul P, Lohnoo T, Kumsang Y, Laikul A, Pathomsakulwong W, Yurayart C, Tonpitak W, Krajaejun T. Protein A/G-based enzyme-linked immunosorbent assay for detection of anti-Pythium insidiosum antibodies in human and animal subjects. BMC Res Notes 2020; 13:135. [PMID: 32143691 PMCID: PMC7059324 DOI: 10.1186/s13104-020-04981-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/26/2020] [Indexed: 12/03/2022] Open
Abstract
Objectives Pythiosis is a deadly infectious disease caused by Pythium insidiosum. Reports of both human and animal pythiosis are on the rise worldwide. Prognosis of the pythiosis patients relies on early diagnosis and prompt treatment. There are needs for an immunodiagnostic test that can detect the disease in both humans and animals. This study aims at reporting an optimized protocol for the development of a protein A/G-based enzyme-linked immunosorbent assay (ELISA) for the detection of anti-P. insidiosum antibody in multiple host species. Results A total of 25 pythiosis and 50 control sera, obtained from humans, horses, dogs, cats, and cows, were recruited for the assay development. With a proper ELISA cutoff point, all pythiosis sera can ultimately be distinguished from the control sera. The successfully-developed protein A/G-based ELISA can detect the anti-P. insidiosum antibodies in serum samples of both humans and animals. It is a versatile, feasible-to-develop, and functional immunodiagnostic assay for pythiosis.
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Affiliation(s)
- Chalisa Jaturapaktrarak
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Penpan Payattikul
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tassanee Lohnoo
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yothin Kumsang
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Aree Laikul
- Department of Large Animal and Wildlife Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | | | - Chompoonek Yurayart
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Walaiporn Tonpitak
- Department of Microbiology, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Bangkok, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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26
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Rujirawat T, Patumcharoenpol P, Kittichotirat W, Krajaejun T. Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5525202. [PMID: 31260041 PMCID: PMC6601393 DOI: 10.1093/database/baz082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/01/2019] [Accepted: 05/29/2019] [Indexed: 11/14/2022]
Abstract
Oomycetes form a unique group of the fungal-like, aquatic, eukaryotic microorganisms. Lifestyle and pathogenicity of the oomycetes are diverse. Many pathogenic oomycetes affect a broad range of plants and cause enormous economic loss annually. Some pathogenic oomycetes cause destructive and deadly diseases in a variety of animals, including humans. No effective antimicrobial agent against the oomycetes is available. Genomic data of many oomycetes are currently available. Comparative analyses of the oomycete genomes must be performed to better understand the oomycete biology and virulence, as well as to identify conserved and biologically important proteins that are potential diagnostic and therapeutic targets of these organisms. However, a tool that facilitates comparative genomic studies of the oomycetes is lacking. Here, we described in detail the Oomycete Gene Table, which is an online user-friendly bioinformatic tool, designed to search, analyze, compare and visualize gene contents of 20 oomycetes in a customizable table. Genomic contents of other oomycete species, when available, can be added to the existing database. Some of the applications of the Oomycete Gene Table include investigations of phylogenomic relationships, as well as identifications of biologically important and pathogenesis-related genes of oomycetes. In summary, the Oomycete Gene Table is a simple and useful tool for comparative genomic analyses of oomycetes.
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Affiliation(s)
- Thidarat Rujirawat
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand.,Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand.,Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Ngamwongwan Road, Jatujak District, Bangkok 10900, Thailand
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian Chai Thale Road, Bang Khun Thian District, Bangkok 10150, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian Chai Thale Road, Bang Khun Thian District Bangkok 10150, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand
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The glycoside hydrolase 18 family chitinases are associated with development and virulence in the mosquito pathogen Pythium guiyangense. Fungal Genet Biol 2019; 135:103290. [PMID: 31707113 DOI: 10.1016/j.fgb.2019.103290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/24/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022]
Abstract
Chitinases, the enzymes responsible for the biological degradation of chitin, participate in numerous physiological processes such as nutrition, parasitism, morphogenesis and immunity in various organisms. However, the genome-wide distribution, evolution and biological functions of chitinases are rarely reported in oomycetes. This study systematically investigated the glycoside hydrolase 18 (GH18) family of chitinases from the mosquito pathogenic oomycete, Pythium guiyangense using bioinformatics and experimental assays. A total of 3 pairs of GH18 chitinase genes distributed in three distinct phylogenic clusters were identified from P. guiyangense genome, which is consistent with the ones in plant pathogenic oomycetes. Further transcriptional analysis revealed that Pgchi1/2 was highly expressed at the development stages, while Pgchi3/4 and Pgchi5/6 were up-regulated at the infection stages. The biological function analysis of chitinase genes using genetic transformation silencing method showed that silencing of Pgchi1/2 resulted in reduced zoospore production, without affecting the virulence. However, attenuation of Pgchi3/4 and Pgchi5/6 genes regulated not only oxidative stress responses, but also led to decreased infection rates to mosquito larvae. Taken together, this study provides a comprehensive overview of P. guiyangense chitinase family and reveals their diverse roles in the development, stress response, and virulence, which would elucidate insightful information on the molecular mechanism of chitinase in entomopathogenic pathogens.
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28
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Leoro-Garzon P, Gonedes AJ, Olivera IE, Tartar A. Oomycete metabarcoding reveals the presence of Lagenidium spp. in phytotelmata. PeerJ 2019; 7:e7903. [PMID: 31632856 PMCID: PMC6796956 DOI: 10.7717/peerj.7903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/16/2019] [Indexed: 11/20/2022] Open
Abstract
The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome. In this study, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5% of these reads taxonomically associated to oomycetes, and Lagenidium spp., respectively. Newly designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. sequences, with a majority of variants clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.
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Affiliation(s)
- Paula Leoro-Garzon
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States of America
| | - Andrew J Gonedes
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States of America
| | - Isabel E Olivera
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States of America
| | - Aurélien Tartar
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States of America
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Krajaejun T, Reamtong O, Lohnoo T, Yingyong W, Thammasudjarit R. Assessment of temperature-dependent proteomes of Pythium insidiosum by using the SWISS-PROT database. Med Mycol 2019; 57:918-921. [PMID: 30649412 DOI: 10.1093/mmy/myy164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/19/2018] [Accepted: 12/26/2018] [Indexed: 02/02/2023] Open
Abstract
Pythium insidiosum causes the life-threatening disease, called pythiosis. Information on microbial pathogenesis could lead to an effective method of infection control. This study aims at assessing temperature-dependent proteomes, and identifying putative virulence factors of P. insidiosum. Protein extracts from growths at 25°C and 37°C were analyzed by mass spectrometry and SWISS-PROT database. A total of 1052 proteins were identified. Upon exposure to increased temperature, 219 proteins were markedly expressed, eight of which were putative virulence factors of P. insidiosum. These temperature-dependent proteins should be further investigated for their roles in pathogenesis, and some of which could be potential therapeutic targets.
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 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
| | - Ratchainant Thammasudjarit
- Section of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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30
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Shen D, Dong Y, Wei Y, Zhang M, Wang J, Tang Z, Xia Q, Nyawira KT, Jing M, Dou D, Xia A. Genome-wide and functional analyses of tyrosine kinase-like family genes reveal potential roles in development and virulence in mosquito pathogen Pythium guiyangense. Fungal Genet Biol 2019; 130:11-18. [DOI: 10.1016/j.fgb.2019.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/04/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022]
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The Repurposed Drug Disulfiram Inhibits Urease and Aldehyde Dehydrogenase and Prevents In Vitro Growth of the Oomycete Pythium insidiosum. Antimicrob Agents Chemother 2019; 63:AAC.00609-19. [PMID: 31138572 DOI: 10.1128/aac.00609-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/18/2019] [Indexed: 11/20/2022] Open
Abstract
Pythium insidiosum is an oomycete microorganism that causes a life-threatening infectious disease, called pythiosis, in humans and animals. The disease has been increasingly reported worldwide. Conventional antifungal drugs are ineffective against P. insidiosum Treatment of pythiosis requires the extensive removal of infected tissue (i.e., eye and leg), but inadequate surgery and recurrent infection often occur. A more effective treatment is needed for pythiosis patients. Drug repurposing is a promising strategy for the identification of a U.S. Food and Drug Administration-approved drug for the control of P. insidiosum Disulfiram has been approved to treat alcoholism, but it exhibits antimicrobial activity against various pathogens. In this study, we explored whether disulfiram possesses an anti-P. insidiosum activity. A total of 27 P. insidiosum strains, isolated from various hosts and geographic areas, were susceptible to disulfiram in a dose-dependent manner. The MIC range of disulfiram against P. insidiosum (8 to 32 mg/liter) was in line with that of other pathogens. Proteogenomic analysis indicated that several potential targets of disulfiram (i.e., aldehyde dehydrogenase and urease) were present in P. insidiosum By homology modeling and molecular docking, disulfiram can bind the putative aldehyde dehydrogenase and urease of P. insidiosum at low energies (i.e., -6.1 and -4.0 Kcal/mol, respectively). Disulfiram diminished the biochemical activities of these enzymes. In conclusion, disulfiram can inhibit the growth of many pathogenic microorganisms, including P. insidiosum The drug can bind and inactivate multiple proteins of P. insidiosum, which may contribute to its broad antimicrobial property. Drug repurposing of disulfiram could be a new treatment option for pythiosis.
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Abstract
Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.
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Shen D, Tang Z, Wang C, Wang J, Dong Y, Chen Y, Wei Y, Cheng B, Zhang M, Grenville-Briggs LJ, Tyler BM, Dou D, Xia A. Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis. PLoS Genet 2019; 15:e1008116. [PMID: 31017897 PMCID: PMC6502433 DOI: 10.1371/journal.pgen.1008116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 05/06/2019] [Accepted: 04/01/2019] [Indexed: 11/18/2022] Open
Abstract
Pythium guiyangense, an oomycete from a genus of mostly plant pathogens, is an effective biological control agent that has wide potential to manage diverse mosquitoes. However, its mosquito-killing mechanisms are almost unknown. In this study, we observed that P. guiyangense could utilize cuticle penetration and ingestion of mycelia into the digestive system to infect mosquito larvae. To explore pathogenic mechanisms, a high-quality genome sequence with 239 contigs and an N50 contig length of 1,009 kb was generated. The genome assembly is approximately 110 Mb, which is almost twice the size of other sequenced Pythium genomes. Further genome analysis suggests that P. guiyangense may arise from a hybridization of two related but distinct parental species. Phylogenetic analysis demonstrated that P. guiyangense likely evolved from common ancestors shared with plant pathogens. Comparative genome analysis coupled with transcriptome sequencing data suggested that P. guiyangense may employ multiple virulence mechanisms to infect mosquitoes, including secreted proteases and kazal-type protease inhibitors. It also shares intracellular Crinkler (CRN) effectors used by plant pathogenic oomycetes to facilitate the colonization of plant hosts. Our experimental evidence demonstrates that CRN effectors of P. guiyangense can be toxic to insect cells. The infection mechanisms and putative virulence effectors of P. guiyangense uncovered by this study provide the basis to develop improved mosquito control strategies. These data also provide useful knowledge on host adaptation and evolution of the entomopathogenic lifestyle within the oomycete lineage. A deeper understanding of the biology of P. guiyangense effectors might also be useful for management of other important agricultural pests. Utilization of biocontrol agents has emerged as a promising mosquito control strategy, and Pythium guiyangense has wide potential to manage diverse mosquitoes with high efficiency. However, the molecular mechanisms underlying pathological processes remain almost unknown. We observed that P. guiyangense invades mosquito larvae through cuticle penetration and through ingestion of mycelia via the digestive system, jointly accelerating mosquito larvae mortality. We also present a high-quality genome assembly of P. guiyangense that contains two distinct genome complements, which likely resulted from a hybridization of two parental species. Our analyses revealed expansions of kinases, proteases, kazal-type protease inhibitors, and elicitins that may be important for adaptation of P. guiyangense to a mosquito-pathogenic lifestyle. Moreover, our experimental evidence demonstrated that some Crinkler effectors of P. guiyangense can be toxic to insect cells. Our findings suggest new insights into oomycete evolution and host adaptation by animal pathogenic oomycetes. Our new genome resource will enable better understanding of infection mechanisms, with the potential to improve the biological control of mosquitoes and other agriculturally important pests.
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Affiliation(s)
- Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhaoyang Tang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Cong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yumei Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yang Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yun Wei
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Biao Cheng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Meiqian Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | | | - Brett M. Tyler
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Krajaejun T, Kittichotirat W, Patumcharoenpol P, Rujirawat T, Lohnoo T, Yingyong W. Data on whole genome sequencing of the oomycete Pythium insidiosum strain CBS 101555 from a horse with pythiosis in Brazil. BMC Res Notes 2018; 11:880. [PMID: 30537981 PMCID: PMC6290497 DOI: 10.1186/s13104-018-3968-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022] Open
Abstract
Objectives The oomycete Pythium insidiosum infects humans and animals worldwide, and causes the life-threatening condition, called pythosis. Most patients lose infected organs or die from the disease. Comparative genomic analyses of different P. insidiosum strains could provide new insights into its pathobiology, and can lead to discovery of an effective treatment method. Several draft genomes of P. insidiosum are publicly available: three from Asia (Thailand), and one each from North (the United States) and Central (Costa Rica) Americas. We report another draft genome of P. insidiosum isolated from South America (Brazil), to serve as a resource for comprehensive genomic studies. Data description In this study, we report genome sequence of the P. insidiosum strain CBS 101555, isolated from a horse with pythiosis in Brazil. One paired-end (180-bp insert) library of processed genomic DNA was prepared for Illumina HiSeq 2500-based sequencing. Assembly of raw reads provided genome size of 48.9 Mb, comprising 60,602 contigs. A total of 23,254 genes were predicted and classified into 18,305 homologous gene clusters. Compared with the reference genome (the P. insidiosum strain Pi-S), 1,475,337 sequence variants (SNPs and INDELs) were identified in the organism. The genome sequence data has been deposited in DDBJ under the accession numbers BCFP01000001–BCFP01060602.
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand.
| | - Preecha Patumcharoenpol
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, 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
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Krajaejun T, Rujirawat T, Kanpanleuk T, Santanirand P, Lohnoo T, Yingyong W, Kumsang Y, Sae-Chew P, Kittichotirat W, Patumcharoenpol P. Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits. PeerJ 2018; 6:e4821. [PMID: 29888122 PMCID: PMC5993020 DOI: 10.7717/peerj.4821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum.
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Affiliation(s)
- Theerapong Krajaejun
- Department of Pathology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thidarat Rujirawat
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Teerat Kanpanleuk
- Department of Pathology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Ramathibodi Hospital, Mahidol University, 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
| | - Pattarana Sae-Chew
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Preecha Patumcharoenpol
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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