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Genetic manipulations in helminth parasites. J Parasit Dis 2023; 47:203-214. [PMID: 36712591 PMCID: PMC9869838 DOI: 10.1007/s12639-023-01567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Screening of vaccine or drug target in parasitic helminth is hindered by lack of robust tool for functional studies of parasite protein which account for the availability of only a few anti-helminthic vaccines, diagnostic assay and slower pace of development of an anthelmintic drug. With the piling up of parasite transcriptomic and genomic data, in silico screening for possible vaccine/drug target could be validated by functional characterization of proteins by RNA interference or CRISPR/Cas9. These reverse genetic engineering tools have opened up a better avenue and opportunity for screening parasitic proteins in vitro as well as in vivo. RNA interference provides a technique for silencing targeted mRNA transcript for understanding a gene function in helminth as evidence by work in Caenorhabditis elegans. Recent genetic engineering tool, CRISPR/Cas9 allows knock-out/deletion of the desired gene in parasitic helminths and the other provision it provides in terms of gene knock-in/insertion in parasite genome is still to be explored in future. This manuscript discussed the work that has been carried out on RNAi and CRISPR/Cas9 for functional studies of helminth parasitic proteins.
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Wang R, Li Y, Li D, Zhang W, Wang X, Wen X, Liu Z, Feng Y, Zhang X. Identification of the Extracellular Nuclease Influencing Soaking RNA Interference Efficiency in Bursaphelenchus xylophilus. Int J Mol Sci 2022; 23:ijms232012278. [PMID: 36293134 PMCID: PMC9603779 DOI: 10.3390/ijms232012278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022] Open
Abstract
RNA interference (RNAi) efficiency dramatically varies among different nematodes, which impacts research on their gene function and pest control. Bursaphelenchus xylophilus is a pine wood nematode in which RNAi-mediated gene silencing has unstable interference efficiency through soaking in dsRNA solutions, the factors of which remain unknown. Using agarose gel electrophoresis, we found that dsRNA can be degraded by nematode secretions in the soaking system which is responsible for the low RNAi efficiency. Based on the previously published genome and secretome data of B. xylophilus, 154 nucleases were screened including 11 extracellular nucleases which are potential factors reducing RNAi efficacy. To confirm the function of nucleases in RNAi efficiency, eight extracellular nuclease genes (BxyNuc1-8) were cloned in the genome. BxyNuc4, BxyNuc6 and BxyNuc7 can be upregulated in response to dsGFP, considered as the major nuclease performing dsRNA degradation. After soaking with the dsRNA of nucleases BxyNuc4/BxyNuc6/BxyNuc7 and Pat10 gene (ineffective in RNAi) simultaneously for 24 h, the expression of Pat10 gene decreased by 23.25%, 26.05% and 11.29%, respectively. With soaking for 36 h, the expression of Pat10 gene decreased by 43.25% and 33.25% in dsBxyNuc6+dsPat10 and dsBxyNuc7+dsPat10 groups, respectively. However, without dsPat10, dsBxyNuc7 alone could cause downregulation of Pat10 gene expression, while dsBxyNuc6 could not disturb this gene. In conclusion, the nuclease BxyNuc6 might be a major barrier to the RNAi efficiency in B. xylophilus.
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Affiliation(s)
- Ruijiong Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-010-62888578
| | - Dongzhen Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xuan Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaojian Wen
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhenkai Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuqian Feng
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing l00091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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3
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Choudhary S, Kashyap SS, Martin RJ, Robertson AP. Advances in our understanding of nematode ion channels as potential anthelmintic targets. Int J Parasitol Drugs Drug Resist 2022; 18:52-86. [PMID: 35149380 PMCID: PMC8841521 DOI: 10.1016/j.ijpddr.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022]
Abstract
Ion channels are specialized multimeric proteins that underlie cell excitability. These channels integrate with a variety of neuromuscular and biological functions. In nematodes, the physiological behaviors including locomotion, navigation, feeding and reproduction, are regulated by these protein entities. Majority of the antinematodal chemotherapeutics target the ion channels to disrupt essential biological functions. Here, we have summarized current advances in our understanding of nematode ion channel pharmacology. We review cys-loop ligand gated ion channels (LGICs), including nicotinic acetylcholine receptors (nAChRs), acetylcholine-chloride gated ion channels (ACCs), glutamate-gated chloride channels (GluCls), and GABA (γ-aminobutyric acid) receptors, and other ionotropic receptors (transient receptor potential (TRP) channels and potassium ion channels). We have provided an update on the pharmacological properties of these channels from various nematodes. This article catalogs the differences in ion channel composition and resulting pharmacology in the phylum Nematoda. This diversity in ion channel subunit repertoire and pharmacology emphasizes the importance of pursuing species-specific drug target research. In this review, we have provided an overview of recent advances in techniques and functional assays available for screening ion channel properties and their application.
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Affiliation(s)
- Shivani Choudhary
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Sudhanva S Kashyap
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Richard J Martin
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
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4
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Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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5
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Iqbal S, Jones MGK, Fosu-Nyarko J. RNA interference of an orthologue of Dicer of Meloidogyne incognita alludes to the gene's importance in nematode development. Sci Rep 2021; 11:11156. [PMID: 34045504 PMCID: PMC8160347 DOI: 10.1038/s41598-021-90363-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Dicers and dicer-like enzymes play an essential role in small RNA processing in eukaryotes. Nematodes are thought to encode one dicer, DCR-1; only that for Caenorhabditis spp. is well-characterised. Using genomic sequences of eight root-knot nematodes (Meloidogyne spp.), we identified putative coding sequences typical of eukaryotic DICERS. We noted that the primary and secondary structures of DICERS they encode were different for different Meloidogyne species and even for isolates of the same species, suggesting paralogy for the gene. One of the genes for M. incognita (Midcr-1.1) expressed in eggs, juvenile stage 2 and adults, with the highest expression in the adult females. All the Meloidogyne DICERS had seven major domains typical of those for Caenorhabditis spp. and humans with very similar protein folding. RNAi of Midcr-1.1 in J2s using seven dsRNAs, each based on sequences encoding the domains, induced mild paralysis but measurable knockdown was detected in J2s treated with five of the dsRNAs. For four of the dsRNAs, the RNAi effect lasted and reduced the nematode’s infectivity. Also, host plant delivery of dsRNAs complementary to coding sequences of the Dicer Dimerisation domain impaired development, reducing nematode infection by 71%. These results confirm the importance of the gene to nematode health.
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Affiliation(s)
- Sadia Iqbal
- Crop Biotechnology Research Group, College of Science, Health, Engineering and Education, WA State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia.
| | - Michael G K Jones
- Crop Biotechnology Research Group, College of Science, Health, Engineering and Education, WA State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia
| | - John Fosu-Nyarko
- Crop Biotechnology Research Group, College of Science, Health, Engineering and Education, WA State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia.
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Ochola J, Coyne D, Cortada L, Haukeland S, Ng'ang'a M, Hassanali A, Opperman C, Torto B. Cyst nematode bio-communication with plants: implications for novel management approaches. PEST MANAGEMENT SCIENCE 2021; 77:1150-1159. [PMID: 32985781 PMCID: PMC7894489 DOI: 10.1002/ps.6105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 05/03/2023]
Abstract
Bio-communication occurs when living organisms interact with each other, facilitated by the exchange of signals including visual, auditory, tactile and chemical. The most common form of bio-communication between organisms is mediated by chemical signals, commonly referred to as 'semiochemicals', and it involves an emitter releasing the chemical signal that is detected by a receiver leading to a phenotypic response in the latter organism. The quality and quantity of the chemical signal released may be influenced by abiotic and biotic factors. Bio-communication has been reported to occur in both above- and below-ground interactions and it can be exploited for the management of pests, such as cyst nematodes, which are pervasive soil-borne pests that cause significant crop production losses worldwide. Cyst nematode hatching and successful infection of hosts are biological processes that are largely influenced by semiochemicals including hatching stimulators, hatching inhibitors, attractants and repellents. These semiochemicals can be used to disrupt interactions between host plants and cyst nematodes. Advances in RNAi techniques such as host-induced gene silencing to interfere with cyst nematode hatching and host location can also be exploited for development of synthetic resistant host cultivars. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Juliet Ochola
- International Centre of Insect Physiology and EcologyNairobiKenya
- Chemistry DepartmentKenyatta UniversityNairobiKenya
| | - Danny Coyne
- East Africa, International Institute of Tropical AgricultureNairobiKenya
- Department of Biology, Section NematologyGhent UniversityGhentBelgium
| | - Laura Cortada
- East Africa, International Institute of Tropical AgricultureNairobiKenya
- Department of Biology, Section NematologyGhent UniversityGhentBelgium
| | - Solveig Haukeland
- International Centre of Insect Physiology and EcologyNairobiKenya
- Norwegian Institute of Bioeconomy ResearchÅsNorway
| | | | | | - Charles Opperman
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Baldwyn Torto
- International Centre of Insect Physiology and EcologyNairobiKenya
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Hagen J, Sarkies P, Selkirk ME. Lentiviral transduction facilitates RNA interference in the nematode parasite Nippostrongylus brasiliensis. PLoS Pathog 2021; 17:e1009286. [PMID: 33497411 PMCID: PMC7864396 DOI: 10.1371/journal.ppat.1009286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/05/2021] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
Animal-parasitic nematodes have thus far been largely refractory to genetic manipulation, and methods employed to effect RNA interference (RNAi) have been ineffective or inconsistent in most cases. We describe here a new approach for genetic manipulation of Nippostrongylus brasiliensis, a widely used laboratory model of gastrointestinal nematode infection. N. brasiliensis was successfully transduced with Vesicular Stomatitis Virus glycoprotein G (VSV-G)-pseudotyped lentivirus. The virus was taken up via the nematode intestine, RNA reverse transcribed into proviral DNA, and transgene transcripts produced stably in infective larvae, which resulted in expression of the reporter protein mCherry. Improved transgene expression was achieved by incorporating the C. elegans hlh11 promoter and the tbb2 3´-UTR into viral constructs. MicroRNA-adapted short hairpin RNAs delivered in this manner were processed correctly and resulted in partial knockdown of β-tubulin isotype-1 (tbb-iso-1) and secreted acetylcholinesterase B (ache-B). The system was further refined by lentiviral delivery of double stranded RNAs, which acted as a trigger for RNAi following processing and generation of 22G-RNAs. Virus-encoded sequences were detectable in F1 eggs and third stage larvae, demonstrating that proviral DNA entered the germline and was heritable. Lentiviral transduction thus provides a new means for genetic manipulation of parasitic nematodes, including gene silencing and expression of exogenous genes. The complex life cycle of parasitic nematodes makes them very difficult to manipulate genetically, and methods to delete or silence genes which are routinely used in other organisms are ineffective in most species of nematodes which infect animals. This has hindered attempts to understand the function of defined genes and proteins, and their roles in development and interaction of nematode parasites with their host. We show here that foreign genetic material can be introduced into a widely used laboratory model of intestinal nematode infection by using a viral vector. The vector was modified to improve transgene expression, and a reporter protein expressed by transduced nematode larvae in vitro. We subsequently utilised the viral vector to deliver double stranded RNA molecules to the larvae. These molecules were processed along known pathways, resulting in partial knockdown of two test genes. This system represents a new means of genetically manipulating nematode parasites, and will aid in understanding their complex biology, in addition to defining new targets for control of infection.
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Affiliation(s)
- Jana Hagen
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Murray E. Selkirk
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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8
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Nganso BT, Sela N, Soroker V. A genome-wide screening for RNAi pathway proteins in Acari. BMC Genomics 2020; 21:791. [PMID: 33183236 PMCID: PMC7659050 DOI: 10.1186/s12864-020-07162-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari. RESULTS Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. CONCLUSIONS Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.
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Affiliation(s)
- Beatrice T Nganso
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Noa Sela
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel
| | - Victoria Soroker
- Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel.
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Hahnel SR, Dilks CM, Heisler I, Andersen EC, Kulke D. Caenorhabditis elegans in anthelmintic research - Old model, new perspectives. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:237-248. [PMID: 33249235 PMCID: PMC7704361 DOI: 10.1016/j.ijpddr.2020.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022]
Abstract
For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
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Affiliation(s)
| | - Clayton M Dilks
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | | - Erik C Andersen
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
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10
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Ma G, Gasser RB, Wang T, Korhonen PK, Young ND. Toward integrative 'omics of the barber's pole worm and related parasitic nematodes. INFECTION GENETICS AND EVOLUTION 2020; 85:104500. [PMID: 32795511 DOI: 10.1016/j.meegid.2020.104500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid sequencing, mass spectrometry and computational biology have facilitated the identification, annotation and analysis of genes, transcripts, proteins and metabolites in model nematodes (Caenorhabditis elegans and Pristionchus pacificus) and socioeconomically important parasitic nematodes (Clades I, III, IV and V). Significant progress has been made in genomics and transcriptomics as well as in the proteomics and lipidomics of Haemonchus contortus (the barber's pole worm) - one of the most pathogenic representatives of the order Strongylida. Here, we review salient aspects of genomics, transcriptomics, proteomics, lipidomics, glycomics and functional genomics, and discuss the rise of integrative 'omics of this economically important parasite. Although our knowledge of the molecular biology, genetics and biochemistry of H. contortus and related species has progressed significantly, much remains to be explored, particularly in areas such as drug resistance, unique/unknown genes, host-parasite interactions, parasitism and the pathogenesis of disease, by integrating the use of multiple 'omics methods. This approach should lead to a better understanding of H. contortus and its relatives at a 'systems biology' level, and should assist in developing new interventions against these parasites.
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Affiliation(s)
- Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China; Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
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11
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D’Amelio S, Lombardo F, Pizzarelli A, Bellini I, Cavallero S. Advances in Omic Studies Drive Discoveries in the Biology of Anisakid Nematodes. Genes (Basel) 2020; 11:E801. [PMID: 32679891 PMCID: PMC7397233 DOI: 10.3390/genes11070801] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/28/2023] Open
Abstract
Advancements in technologies employed in high-throughput next-generation sequencing (NGS) methods are supporting the spread of studies that, combined with advances in computational biology and bioinformatics, have greatly accelerated discoveries within basic and biomedical research for many parasitic diseases. Here, we review the most updated "omic" studies performed on anisakid nematodes, a family of marine parasites that are causative agents of the fish-borne zoonosis known as anisakiasis or anisakidosis. Few deposited data on Anisakis genomes are so far available, and this still hinders the deep and highly accurate characterization of biological aspects of interest, even as several transcriptomic and proteomic studies are becoming available. These have been aimed at discovering and characterizing molecules specific to peculiar developmental parasitic stages or tissues, as well as transcripts with pathogenic potential as toxins and allergens, with a broad relevance for a better understanding of host-pathogen relationships and for the development of reliable diagnostic tools.
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Affiliation(s)
| | | | | | | | - Serena Cavallero
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (S.D.); (F.L.); (A.P.); (I.B.)
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12
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Iqbal S, Fosu-Nyarko J, Jones MGK. Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode, Meloidogyne incognita Results in Diverse Responses Including Increase and No Change in Expression of Some Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:328. [PMID: 32265973 PMCID: PMC7105803 DOI: 10.3389/fpls.2020.00328] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/05/2020] [Indexed: 05/07/2023]
Abstract
Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative.
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Affiliation(s)
| | - John Fosu-Nyarko
- Plant Biotechnology Research Group, College of Science, Health, Engineering and Education, WA State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
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13
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Castelletto ML, Gang SS, Hallem EA. Recent advances in functional genomics for parasitic nematodes of mammals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb206482. [PMID: 32034038 DOI: 10.1242/jeb.206482] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human-parasitic nematodes infect over a quarter of the world's population and are a major cause of morbidity in low-resource settings. Currently available treatments have not been sufficient to eliminate infections in endemic areas, and drug resistance is an increasing concern, making new treatment options a priority. The development of new treatments requires an improved understanding of the basic biology of these nematodes. Specifically, a better understanding of parasitic nematode development, reproduction and behavior may yield novel drug targets or new opportunities for intervention such as repellents or traps. Until recently, our ability to study parasitic nematode biology was limited because few tools were available for their genetic manipulation. This is now changing as a result of recent advances in the large-scale sequencing of nematode genomes and the development of new techniques for their genetic manipulation. Notably, skin-penetrating gastrointestinal nematodes in the genus Strongyloides are now amenable to transgenesis, RNAi and CRISPR/Cas9-mediated targeted mutagenesis, positioning the Strongyloides species as model parasitic nematode systems. A number of other mammalian-parasitic nematodes, including the giant roundworm Ascaris suum and the tissue-dwelling filarial nematode Brugia malayi, are also now amenable to transgenesis and/or RNAi in some contexts. Using these tools, recent studies of Strongyloides species have already provided insight into the molecular pathways that control the developmental decision to form infective larvae and that drive the host-seeking behaviors of infective larvae. Ultimately, a mechanistic understanding of these processes could lead to the development of new avenues for nematode control.
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Affiliation(s)
- Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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14
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Karunanithi S, Oruganti V, de Wijn R, Drews F, Cheaib M, Nordström K, Simon M, Schulz MH. Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium. DNA Res 2020; 27:5825730. [PMID: 32339224 PMCID: PMC7315353 DOI: 10.1093/dnares/dsaa005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/21/2020] [Indexed: 11/29/2022] Open
Abstract
Supply of exogenous dsRNA (exo-dsRNA), either by injection or by feeding, is a fast and powerful alternative to classical knockout studies. The biotechnical potential of feeding techniques is evident from the numerous studies focusing on oral administration of dsRNA to control pests and viral infection in crops/animal farming. We aimed to dissect the direct and indirect effects of exo-dsRNA feeding on the endogenous short interfering RNA (endo-siRNA) populations of the free-living ciliate Paramecium. We introduced dsRNA fragments against Dicer1 (DCR1), involved in RNA interference (RNAi) against exo- and few endo-siRNAs, and an RNAi unrelated gene, ND169. Any feeding, even the control dsRNA, diminishes genome wide the accumulation of endo-siRNAs and mRNAs. This cannot be explained by direct off-target effects and suggests mechanistic overlaps of the exo- and endo-RNAi mechanisms. Nevertheless, we observe a stronger down-regulation of mRNAs in DCR1 feeding compared with ND169 knockdown. This is likely due to the direct involvement of DCR1 in endo-siRNA accumulation. We further observed a cis-regulatory effect on mRNAs that overlap with phased endo-siRNAs. This interference of exo-dsRNA with endo-siRNAs warrants further investigations into secondary effects in target species/consumers, risk assessment of dsRNA feeding applications, and environmental pollution with dsRNA.
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Affiliation(s)
- Sivarajan Karunanithi
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany
| | - Vidya Oruganti
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Raphael de Wijn
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Franziska Drews
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Miriam Cheaib
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Karl Nordström
- Genetics/Epigenetics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany
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15
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Abstract
Purpose of Review This paper constitutes an update of recent studies on the general biology, molecular genetics, and cellular biology of Strongyloides spp. and related parasitic nematodes. Recent Findings Increasingly, human strongyloidiasis is considered the most neglected of neglected tropical diseases. Despite this, the last 5 years has seen remarkable advances in the molecular biology of Strongyloides spp. Genome sequences for S. stercoralis, S. ratti, S. venezuelensis, S. papillosus, and the related parasite Parastrongyloides trichosuri were created, annotated, and analyzed. These genomic resources, along with a practical transgenesis platform for Strongyloides spp., aided a major achievement, the advent of targeted mutagenesis via CRISPR/Cas9 in S. stercoralis and S. ratti. The genome sequences have also enabled significant molecular epidemiologic and phylogenetic findings on human strongyloidiasis, including the first genetic evidence of zoonotic transmission of S. stercoralis between dogs and humans. Studies of molecular signaling pathways identified the nuclear receptor Ss-DAF-12 as one that can be manipulated in the parasite by exogenous application of its steroid ligands. The chemotherapeutic implications of this were unscored by a study in which a Ss-DAF-12 ligand suppressed autoinfection by S. stercoralis in a new murine model of human strongyloidiasis. Summary Seminal advances in genomics of Strongyloides spp. have transformed research into strongyloidiasis, facilitating fundamental phylogenetic and epidemiologic studies and aiding the deployment of CRISPR/Cas9 gene disruption and editing as functional genomic tools in Strongyloides spp. Studies of Ss-DAF-12 signaling in S. stercoralis demonstrated the potential of this pathway as a novel chemotherapeutic target in parasitic nematodes.
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Affiliation(s)
- Tegegn G. Jaleta
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James B. Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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16
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Tian ZL, Wang ZH, Maria M, Qu N, Zheng JW. Meloidogyne graminicola protein disulfide isomerase may be a nematode effector and is involved in protection against oxidative damage. Sci Rep 2019; 9:11949. [PMID: 31420562 PMCID: PMC6697734 DOI: 10.1038/s41598-019-48474-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 08/06/2019] [Indexed: 11/08/2022] Open
Abstract
The rice root-knot nematode, Meloidogyne graminicola, is a serious pest in most rice-growing countries. Usually, nematodes employ antioxidants to counteract the harm of reactive oxygen species (ROS) and facilitate their infection. Here the gene encoding M. graminicola protein disulphide isomerase (MgPDI) was identified. The deduced protein is highly conserved in the putative active-site Cys-Gly-His-Cys. In situ hybridization showed that MgPDI was specifically localized within esophageal glands of pre-parasitic second stage juveniles (J2s). MgPDI was significantly up-regulated in the late parasitic J2s. Characterization of the recombinant protein showed that the purified MgPDI exhibited similar activities to other oxidases/isomerases such as the refolding of the scrambled RNase and insulin disulfide reductase and the protection of plasmid DNA and living cells from ROS damage. In addition, silencing of MgPDI by RNA interference in the pre-parasitic J2s lowered their multiplication factor. MgPDI expression was up-regulated in the presence of exogenous H2O2, whereas MgPDI silencing resulted in an increase in mortality under H2O2 stress. MgPDI is localized in the apoplast when transient expression in Nicotiana benthamiana leaves. The results indicated that MgPDI plays important roles in the reproduction and pathogenicity of M. graminicola and it also contributes to protecting nematodes from exogenous H2O2 stress.
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Affiliation(s)
- Zhong-Ling Tian
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China
| | - Ze-Hua Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China
| | - Munawar Maria
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China
| | - Nan Qu
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China
| | - Jing-Wu Zheng
- Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, P.R. China.
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Hangzhou, 310058, P.R. China.
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17
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Blyuss KB, Fatehi F, Tsygankova VA, Biliavska LO, Iutynska GO, Yemets AI, Blume YB. RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants. FRONTIERS IN PLANT SCIENCE 2019; 10:483. [PMID: 31057585 PMCID: PMC6479188 DOI: 10.3389/fpls.2019.00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.
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Affiliation(s)
| | - Farzad Fatehi
- Department of Mathematics, University of Sussex, Brighton, United Kingdom
| | - Victoria A. Tsygankova
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Compounds, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla O. Biliavska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Galyna O. Iutynska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla I. Yemets
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yaroslav B. Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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18
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Marr EJ, Wright HW, Sargison ND, Nisbet AJ, Burgess STG. Gene silencing by RNA interference in the ectoparasitic mite, Psoroptes ovis. Vet Res 2018; 49:112. [PMID: 30382906 PMCID: PMC6211577 DOI: 10.1186/s13567-018-0608-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/24/2018] [Indexed: 11/10/2022] Open
Abstract
The presence of components of the RNA interference (RNAi) pathway in Psoroptes ovis, an ectoparasitic mite responsible for psoroptic mange, was investigated through interrogation of the P. ovis genome. Homologues of transcripts representing critical elements for achieving effective RNAi in the mite, Tetranychus urticae and the model organisms Caenorhabditis elegans and Drosophila melanogaster were identified and, following the development of a non-invasive immersion method of double stranded RNA delivery, gene silencing by RNAi was successfully demonstrated in P. ovis. Significant reductions in transcript levels were achieved for three target genes which encode the Group 2 allergen (Pso o 2), mu-class glutathione S-transferase (PoGST-mu1) and beta-tubulin (Poβtub). This is the first demonstration of RNAi in P. ovis and provides a mechanism for mining transcriptomic and genomic datasets for novel control targets against this economically important ectoparasite.
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Affiliation(s)
- Edward J Marr
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK.,Institute of Immunology and Infection Research, The King's Buildings, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland, UK
| | - Harry W Wright
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian, EH25 9RG, Scotland, UK
| | - Alasdair J Nisbet
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK
| | - Stewart T G Burgess
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, EH26 0PZ, Scotland, UK.
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19
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Caffrey CR, Goupil L, Rebello KM, Dalton JP, Smith D. Cysteine proteases as digestive enzymes in parasitic helminths. PLoS Negl Trop Dis 2018; 12:e0005840. [PMID: 30138310 PMCID: PMC6107103 DOI: 10.1371/journal.pntd.0005840] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We briefly review cysteine proteases (orthologs of mammalian cathepsins B, L, F, and C) that are expressed in flatworm and nematode parasites. Emphasis is placed on enzyme activities that have been functionally characterized, are associated with the parasite gut, and putatively contribute to degrading host proteins to absorbable nutrients [1–4]. Often, gut proteases are expressed as multigene families, as is the case with Fasciola [5] and Haemonchus [6], presumably expanding the range of substrates that can be degraded, not least during parasite migration through host tissues [5]. The application of the free-living planarian and Caenorhabditis elegans as investigative models for parasite cysteine proteases is discussed. Finally, because of their central nutritive contribution, targeting the component gut proteases with small-molecule chemical inhibitors and understanding their utility as vaccine candidates are active areas of research [7].
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Affiliation(s)
- Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Louise Goupil
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- Department of Biology, University of San Francisco, San Francisco, California, United States of America
| | - Karina M. Rebello
- Laboratório de Toxinologia and Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - John P. Dalton
- School of Biological Sciences, Medical Biology Centre, Queen´s University Belfast, Belfast, United Kingdom
| | - David Smith
- School of Biological Sciences, Medical Biology Centre, Queen´s University Belfast, Belfast, United Kingdom
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20
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Gosal SS, Wani SH. RNAi for Resistance Against Biotic Stresses in Crop Plants. BIOTECHNOLOGIES OF CROP IMPROVEMENT, VOLUME 2 2018. [PMCID: PMC7123769 DOI: 10.1007/978-3-319-90650-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA interference (RNAi)-based gene silencing has become one of the most successful strategies in not only identifying gene function but also in improving agronomical traits of crops by silencing genes of different pathogens/pests and also plant genes for improvement of desired trait. The conserved nature of RNAi pathway across different organisms increases its applicability in various basic and applied fields. Here we attempt to summarize the knowledge generated on the fundamental mechanisms of RNAi over the years, with emphasis on insects and plant-parasitic nematodes (PPNs). This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests. But, there are some limitations too which restrict wider applications of this technology to its full potential. Further refinement of this technology in terms of resolving these shortcomings constitutes one of the thrust areas in present RNAi research. Nevertheless, its application especially in breeding agricultural crops resistant against biotic stresses will certainly offer the possible solutions for some of the breeding objectives which are otherwise unattainable.
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Affiliation(s)
- Satbir Singh Gosal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir India
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21
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Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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22
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Tool-Driven Advances in Neuropeptide Research from a Nematode Parasite Perspective. Trends Parasitol 2017; 33:986-1002. [DOI: 10.1016/j.pt.2017.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 01/21/2023]
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23
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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24
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Yuan W, Zhou H, Lok JB, Lei W, He S, Gasser RB, Zhou R, Fang R, Zhou Y, Zhao J, Hu M. Functional genomic exploration reveals that Ss-RIOK-1 is essential for the development and survival of Strongyloides stercoralis larvae. Int J Parasitol 2017; 47:933-940. [PMID: 28780152 DOI: 10.1016/j.ijpara.2017.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/15/2017] [Accepted: 06/13/2017] [Indexed: 11/25/2022]
Abstract
Protein kinase RIOK-1 is a non-ribosomal factor essential for rRNA cleavage and ribosome small subunit maturation. It is encoded in all eukaryotic organisms. The RIOK-1 encoding gene of Caenorhabditis elegans (Ce-riok-1) is expressed in the neuronal and reproductive systems in larvae and adults of this free-living nematode, and it supports larval growth and development of the adult gonad. In spite of its recognised roles in model organisms such as C. elegans, little is known about the function of this molecule in parasitic nematodes. In a previous study, we characterised the structure, transcriptional profiles and in vivo transcriptional expression patterns of the Ss-riok-1 of human and canine parasitic nematode Strongyloides stercoralis. Here, we extend previous work to undertake functional studies, using transgenesis to assess the roles of Ss-RIOK-1 in the development of S. stercoralis. The results revealed that recombinant Ss-RIOK-1 with D282A mutation at its catalytic site lost its kinase phosphorylation activity in vitro. Both wild-type and mutant Ss-RIOK-1s were expressed in the cytoplasm of neurons and some hypodermal cells in the wild-type strain (UPD) of S. stercoralis. Larvae expressing the dominant negative mutant Ss-RIOK-1 that lost the catalytic activity had a decreased mobility and a severe defect in development to the infective L3 stage. Our findings demonstrated that Ss-RIOK-1 is essential for the development and survival of free-living larvae of S. stercoralis, and that catalytic activity is essential for its function in the parasitic nematode.
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Affiliation(s)
- Wang Yuan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huan Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - James B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Weiqiang Lei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Siyuan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Robin B Gasser
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yanqin Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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Ali MA, Azeem F, Abbas A, Joyia FA, Li H, Dababat AA. Transgenic Strategies for Enhancement of Nematode Resistance in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:750. [PMID: 28536595 PMCID: PMC5422515 DOI: 10.3389/fpls.2017.00750] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
Plant parasitic nematodes (PPNs) are obligate biotrophic parasites causing serious damage and reduction in crop yields. Several economically important genera parasitize various crop plants. The root-knot, root lesion, and cyst nematodes are the three most economically damaging genera of PPNs on crops within the family Heteroderidae. It is very important to devise various management strategies against PPNs in economically important crop plants. Genetic engineering has proven a promising tool for the development of biotic and abiotic stress tolerance in crop plants. Additionally, the genetic engineering leading to transgenic plants harboring nematode resistance genes has demonstrated its significance in the field of plant nematology. Here, we have discussed the use of genetic engineering for the development of nematode resistance in plants. This review article also provides a detailed account of transgenic strategies for the resistance against PPNs. The strategies include natural resistance genes, cloning of proteinase inhibitor coding genes, anti-nematodal proteins and use of RNA interference to suppress nematode effectors. Furthermore, the manipulation of expression levels of genes induced and suppressed by nematodes has also been suggested as an innovative approach for inducing nematode resistance in plants. The information in this article will provide an array of possibilities to engineer resistance against PPNs in different crop plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Amjad Abbas
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
| | - Faiz A. Joyia
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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Morris R, Wilson L, Sturrock M, Warnock ND, Carrizo D, Cox D, Maule AG, Dalzell JJ. A neuropeptide modulates sensory perception in the entomopathogenic nematode Steinernema carpocapsae. PLoS Pathog 2017; 13:e1006185. [PMID: 28253355 PMCID: PMC5333901 DOI: 10.1371/journal.ppat.1006185] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/15/2017] [Indexed: 11/19/2022] Open
Abstract
Entomopathogenic nematodes (EPNs) employ a sophisticated chemosensory apparatus to detect potential hosts. Understanding the molecular basis of relevant host-finding behaviours could facilitate improved EPN biocontrol approaches, and could lend insight to similar behaviours in economically important mammalian parasites. FMRFamide-like peptides are enriched and conserved across the Phylum Nematoda, and have been linked with motor and sensory function, including dispersal and aggregating behaviours in the free living nematode Caenorhabditis elegans. The RNA interference (RNAi) pathway of Steinernema carpocapsae was characterised in silico, and employed to knockdown the expression of the FMRFamide-like peptide 21 (GLGPRPLRFamide) gene (flp-21) in S. carpocapsae infective juveniles; a first instance of RNAi in this genus, and a first in an infective juvenile of any EPN species. Our data show that 5 mg/ml dsRNA and 50 mM serotonin triggers statistically significant flp-21 knockdown (-84%***) over a 48 h timecourse, which inhibits host-finding (chemosensory), dispersal, hyperactive nictation and jumping behaviours. However, whilst 1 mg/ml dsRNA and 50 mM serotonin also triggers statistically significant flp-21 knockdown (-51%**) over a 48 h timecourse, it does not trigger the null sensory phenotypes; statistically significant target knockdown can still lead to false negative results, necessitating appropriate experimental design. SPME GC-MS volatile profiles of two EPN hosts, Galleria mellonella and Tenebrio molitor reveal an array of shared and unique compounds; these differences had no impact on null flp-21 RNAi phenotypes for the behaviours assayed. Localisation of flp-21 / FLP-21 to paired anterior neurons by whole mount in situ hybridisation and immunocytochemistry corroborates the RNAi data, further suggesting a role in sensory modulation. These data can underpin efforts to study these behaviours in other economically important parasites, and could facilitate molecular approaches to EPN strain improvement for biocontrol.
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Affiliation(s)
- Robert Morris
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Leonie Wilson
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Matthew Sturrock
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Neil D. Warnock
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Daniel Carrizo
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Deborah Cox
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Aaron G. Maule
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Johnathan J. Dalzell
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
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Ratnappan R, Vadnal J, Keaney M, Eleftherianos I, O'Halloran D, Hawdon JM. RNAi-mediated gene knockdown by microinjection in the model entomopathogenic nematode Heterorhabditis bacteriophora. Parasit Vectors 2016; 9:160. [PMID: 26993791 PMCID: PMC4797128 DOI: 10.1186/s13071-016-1442-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/21/2022] Open
Abstract
Background Parasitic nematodes threaten the health of humans and livestock and cause a major financial and socioeconomic burden to modern society. Given the widespread distribution of diseases caused by parasitic nematodes there is an urgent need to develop tools that will elucidate the genetic complexity of host-parasite interactions. Heterorhabditis bacteriophora is a parasitic nematode that allows simultaneous monitoring of nematode infection processes and host immune function, and offers potential as a tractable model for parasitic nematode infections. However, molecular tools to investigate these processes are required prior to its widespread acceptance as a robust model organism. In this paper we describe microinjection in adult H. bacteriophora as a suitable means of dsRNA delivery to knockdown gene transcripts. Methods RNA interference was used to knockdown four genes by injecting dsRNA directly into the gonad of adult hermaphrodite nematodes. RNAi phenotypes were scored in the F1 progeny on the fifth day post-injection, and knockdown of gene-specific transcripts was quantified with real-time quantitative RT-PCR (qRT-PCR). Results RNAi injection in adult hermaphrodites significantly decreased the level of target transcripts to varying degrees when compared with controls. The genes targeted by RNAi via injection included cct-2, nol-5, dpy-7, and dpy-13. In each case, RNAi knockdown was confirmed phenotypically by examining the progeny of injected animals, and also confirmed at the transcriptional level by real-time qRT-PCR. Conclusions Here we describe for the first time the successful use of microinjection to knockdown gene transcripts in H. bacteriophora. This technique can be used widely to study the molecular basis of parasitism.
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Affiliation(s)
- Ramesh Ratnappan
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Jonathan Vadnal
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Melissa Keaney
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Ioannis Eleftherianos
- Department of Biological Sciences, George Washington University, Science and Engineering Hall, suite 6000, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Damien O'Halloran
- Department of Biological Sciences, George Washington University, Science and Engineering Hall, suite 6000, 800 22nd Street NW, Washington, DC, 20052, USA.,Institute for Neuroscience, George Washington University, 636 Ross Hall, 2300 I Street NW, Washington, DC, 20052, USA
| | - John M Hawdon
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA.
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Wang M, Wang D, Zhang X, Wang X, Liu W, Hou X, Huang X, Xie B, Cheng X. Double-stranded RNA-mediated interference of dumpy genes in Bursaphelenchus xylophilus by feeding on filamentous fungal transformants. Int J Parasitol 2016; 46:351-60. [PMID: 26953254 DOI: 10.1016/j.ijpara.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/05/2023]
Abstract
RNA interference (RNAi) is a valuable tool for studying gene function in vivo and provides a functional genomics platform in a wide variety of organisms. The pinewood nematode, Bursaphelenchus xylophilus, is a prominent invasive plant-parasitic nematode and has become a serious worldwide threat to forest ecosystems. Presently, the complete genome sequence of B. xylophilus has been published, and research involving genome-wide functional analyses is likely to increase. In this study, we describe the construction of an effective silencing vector, pDH-RH, which contains a transcriptional unit for a hairpin loop structure. Utilising this vector, double-stranded (ds)RNAs with sequences homologous to the target genes can be expressed in a transformed filamentous fungus via Agrobacterium tumefaciens-mediated transformation technology, and can subsequently induce the knockdown of target gene mRNA expression in B. xylophilus by allowing the nematode to feed on the fungal transformants. Four dumpy genes (Bx-dpy-2, 4, 10 and 11) were used as targets to detect RNAi efficiency. By allowing the nematode to feed on target gene-transformed Fusarium oxysporum strains, target transcripts were knocked down 34-87% compared with those feeding on the wild-type strain as determined by real-time quantitative PCR (RT-qPCR). Morphological RNAi phenotypes were observed, displaying obviously reduced body length; weak dumpy or small (short and thin) body size; or general abnormalities. Moreover, compensatory regulation and non-specific silencing of dpy genes were found in B. xylophilus. Our results indicate that RNAi delivery by feeding in B. xylophilus is a successful technique. This platform may provide a new opportunity for undertaking RNAi-based, genome-wide gene functional studies in vitro in B. xylophilus. Moreover, as B. xylophilus feeds on endophytic fungi when a host has died, RNAi feeding technology will offer the prospect for developing a novel control strategy for the nematode. Furthermore, this platform may also be applicable to other parasitic nematodes that have a facultative, fungivorous habit.
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Affiliation(s)
- Meng Wang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Diandong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Yangtze Normal University, Chongqing 408100, China
| | - Xi Zhang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xu Wang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Wencui Liu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaomeng Hou
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaoyin Huang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xinyue Cheng
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing 100875, China.
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Mohandas N, Hu M, Stroehlein AJ, Young ND, Sternberg PW, Lok JB, Gasser RB. Reconstruction of the insulin-like signalling pathway of Haemonchus contortus. Parasit Vectors 2016; 9:64. [PMID: 26842675 PMCID: PMC4741068 DOI: 10.1186/s13071-016-1341-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Background In the present study, we reconstructed the insulin/insulin-like growth factor 1 signalling (IIS) pathway for Haemonchus contortus, which is one of the most important eukaryotic pathogens of livestock worldwide and is related to the free-living nematode Caenorhabditis elegans. Methods We curated full-length open-reading frames from assembled transcripts, defined the complement of genes that encode proteins involved in this pathway and then investigated the transcription profiles of these genes for all key developmental stages of H. contortus. Results The core components of the IIS pathway are similar to their respective homologs in C. elegans. However, there is considerable variation in the numbers of isoforms between H. contortus and C. elegans and an absence of AKT-2 and DDL-2 homologs from H. contortus. Interestingly, DAF-16 has a single isoform in H. contortus compared with 12 in C. elegans, suggesting novel functional roles in the parasitic nematode. Some IIS proteins, such as DAF-18 and SGK-1, vary in their functional domains, indicating distinct roles from their homologs in C. elegans. Conclusions This study paves the way for the further characterization of key signalling pathways in other socioeconomically important parasites and should help understand the complex mechanisms involved in developmental processes. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1341-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Namitha Mohandas
- The University of Melbourne, Faculty of Veterinary and Agricultural Sciences, Parkville, VIC, Australia.
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Andreas J Stroehlein
- The University of Melbourne, Faculty of Veterinary and Agricultural Sciences, Parkville, VIC, Australia.
| | - Neil D Young
- The University of Melbourne, Faculty of Veterinary and Agricultural Sciences, Parkville, VIC, Australia.
| | - Paul W Sternberg
- HHMI, Division of Biology, California Institute of Technology, Pasadena, CA, USA.
| | - James B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA, 19104, USA.
| | - Robin B Gasser
- The University of Melbourne, Faculty of Veterinary and Agricultural Sciences, Parkville, VIC, Australia.
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Long Y, Cao B, Yu L, Tukayo M, Feng C, Wang Y, Luo D. Angiostrongylus cantonensis cathepsin B-like protease (Ac-cathB-1) is involved in host gut penetration. ACTA ACUST UNITED AC 2015; 22:37. [PMID: 26682577 PMCID: PMC4684300 DOI: 10.1051/parasite/2015037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/27/2015] [Indexed: 12/17/2022]
Abstract
Although the global spread of the emerging zoonosis, human angiostrongyliasis, has attracted increasing attention, understanding of specific gene function has been impeded by the inaccessibility of genetic manipulation of the pathogen nematode causing this disease, Angiostrongylus cantonensis. Many parasitic proteases play key roles in host-parasite interactions, but those of A. cantonensis are always expressed as the inactive form in prokaryotic expression systems, thereby impeding functional studies. Hence, a lentiviral system that drives secreted expression of target genes fused to a Myc-His tag was used to obtain recombinant Ac-cathB-1 with biological activity. Although this class of proteases was always reported to function in nutrition and immune evasion in parasitic nematodes, recombinant Ac-cathB-1 was capable of hydrolysis of fibronectin and laminin as well as the extracellular matrix of IEC-6 monolayer, so that the intercellular space of the IEC-6 monolayer increased 5.15 times as compared to the control, while the shape of the adherent cells partly rounded up. This suggests a probable role for this protease in intestinal epithelial penetration. The inhibition of Ac-cathB-1 enzymatic activity with antiserum partly suppressed larval penetration ability in the isolated intestine. Thus, an effective system for heterologous expression of parasite proteases is presented for studying gene function in A. cantonensis; and Ac-cathB-1 was related to larval penetration ability in the host small intestine.
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Affiliation(s)
- Ying Long
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
| | - Binbin Cao
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
| | - Liang Yu
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
| | - Meks Tukayo
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
| | - Chonglv Feng
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
| | - Yinan Wang
- Medical College, Xiamen University, Fujian 361102, P.R. China
| | - Damin Luo
- School of Life Sciences, Xiamen University, Fujian 361102, P.R. China - State Key Laboratory of Cellular Stress Biology, Xiamen University, Fujian 361102, P.R. China
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Ward JD. Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes. Genetics 2015; 201:1279-94. [PMID: 26644478 PMCID: PMC4676526 DOI: 10.1534/genetics.115.182717] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/20/2015] [Indexed: 12/14/2022] Open
Abstract
Recent and rapid advances in genetic and molecular tools have brought spectacular tractability to Caenorhabditis elegans, a model that was initially prized because of its simple design and ease of imaging. C. elegans has long been a powerful model in biomedical research, and tools such as RNAi and the CRISPR/Cas9 system allow facile knockdown of genes and genome editing, respectively. These developments have created an additional opportunity to tackle one of the most debilitating burdens on global health and food security: parasitic nematodes. I review how development of nonparasitic nematodes as genetic models informs efforts to import tools into parasitic nematodes. Current tools in three commonly studied parasites (Strongyloides spp., Brugia malayi, and Ascaris suum) are described, as are tools from C. elegans that are ripe for adaptation and the benefits and barriers to doing so. These tools will enable dissection of a huge array of questions that have been all but completely impenetrable to date, allowing investigation into host-parasite and parasite-vector interactions, and the genetic basis of parasitism.
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Affiliation(s)
- Jordan D Ward
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
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McCoy CJ, Warnock ND, Atkinson LE, Atcheson E, Martin RJ, Robertson AP, Maule AG, Marks NJ, Mousley A. RNA interference in adult Ascaris suum--an opportunity for the development of a functional genomics platform that supports organism-, tissue- and cell-based biology in a nematode parasite. Int J Parasitol 2015; 45:673-8. [PMID: 26149642 PMCID: PMC4563943 DOI: 10.1016/j.ijpara.2015.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 11/03/2022]
Abstract
The sustainable control of animal parasitic nematodes requires the development of efficient functional genomics platforms to facilitate target validation and enhance anthelmintic discovery. Unfortunately, the utility of RNA interference (RNAi) for the validation of novel drug targets in nematode parasites remains problematic. Ascaris suum is an important veterinary parasite and a zoonotic pathogen. Here we show that adult A. suum is RNAi competent, and highlight the induction, spread and consistency of RNAi across multiple tissue types. This platform provides a new opportunity to undertake whole organism-, tissue- and cell-level gene function studies to enhance target validation processes for nematode parasites of veterinary/medical significance.
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Affiliation(s)
- Ciaran J McCoy
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Neil D Warnock
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Louise E Atkinson
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Erwan Atcheson
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Aaron G Maule
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Nikki J Marks
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Angela Mousley
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
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Ma GX, Zhou RQ, Song ZH, Zhu HH, Zhou ZY, Zeng YQ. Molecular mechanism of serine/threonine protein phosphatase 1 (PP1cα-PP1r7) in spermatogenesis of Toxocara canis. Acta Trop 2015; 149:148-54. [PMID: 26026715 DOI: 10.1016/j.actatropica.2015.05.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 01/21/2023]
Abstract
Toxocariasis is one of the most important, but neglected, zoonoses, which is mainly caused by Toxocara canis. To better understand the role of serine/threonine protein phosphatase 1 (PP1) in reproductive processes of male adult T. canis, differential expression analysis was used to reveal the profiles of PP1 catalytic subunit α (PP1cα) gene Tc-stp-1 and PP1 regulatory subunit 7 (PP1r7) gene TcM-1309. Indirect fluorescence immunocytochemistry was carried out to determine the subcellular distribution of PP1cα. Double-stranded RNA interference (RNAi) assays were employed to illustrate the function and mechanism of PP1cα in male adult reproduction. Real-time quantitative PCR (qPCR) showed transcriptional consistency of Tc-stp-1 and TcM-1309 in sperm-producing germline tissues and localization research showed cytoplasmic distribution of PP1cα in sf9 cells, which indicated relevant involvements of PP1cα and PP1r7 in spermatogenesis. Moreover, spatiotemporal transcriptional differences of Tc-stp-1 were determined by gene knockdown analysis, which revealed abnormal morphologies and blocked meiotic divisions of spermatocytes by phenotypic aberration scanning, thereby highlighting the crucial involvement of PP1cα in spermatogenesis. These results revealed a PP1cα-PP1r7 mechanism by which PP1 regulates kinetochore-microtubule interactions in spermatogenesis and provided important clues to identify novel drug or vaccine targets for toxocariasis control.
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Affiliation(s)
- Guang Xu Ma
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Rong Qiong Zhou
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China.
| | - Zhen Hui Song
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Hong Hong Zhu
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Zuo Yong Zhou
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Yuan Qin Zeng
- College of Life Sciences, Southwest University, Chongqing 402460, People's Republic of China
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Hu D, Song X, Xie Y, Zhong X, Wang N, Zheng Y, Gu X, Wang T, Peng X, Yang G. Molecular insights into a tetraspanin in the hydatid tapeworm Echinococcus granulosus. Parasit Vectors 2015; 8:311. [PMID: 26055542 PMCID: PMC4464875 DOI: 10.1186/s13071-015-0926-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 06/02/2015] [Indexed: 02/03/2023] Open
Abstract
Background Cystic echinococcosis (hydatid disease), caused by the tapeworm Echinococcus granulosus (class Cestoda; family Taeniidae), is a neglected tropical disease that results in morbidity and mortality in millions of humans, as well as in huge economic losses in the livestock industry globally. Proteins from the tetraspanin family in parasites have recently become regarded as crucial molecules in interaction with hosts in parasitism and are therefore suitable for the development of vaccines and diagnostic agents. However, no information is available to date on E. granulosus tetraspanin. Methods In this study, a uroplakin-I-like tetraspanin (Eg-TSP1) of E. granulosus was cloned and expressed in E. coli. The immunolocalization of Eg-TSP1 in different life stages of E. granulosus was determined using specific polyclonal antibody. The antibody and cytokine profiles of mice that immunized with recombinant Eg-TSP1 (rEg-TSP1) were measured for the immunogenicity analysis of this protein. Additionally, we use RNA interference method to explore the biological function of Eg-TSP1 in larva of E. granulosus. Results Immunofluorescence analysis showed that endogenous Eg-TSP1 mainly localized in the tegument of larvae and adults. Significantly elevated levels of antibodies IgG1 and IgG2a and of cytokines IFN-γ and IL-12 were observed in the sera of mice after immunization with rEg-TSP1, suggesting a typical T helper (Th)1-mediated immune response elicited by rEg-TSP1. On further probing the role of Eg-TSP1 in E. granulosus by RNA interference, we found that a thinner tegmental distal cytoplasm was induced in protoscoleces treated with siRNA-132 compared to controls. Conclusions This is the first report characterizing a tetraspanin from the tapeworm E. granulosus. Our results suggest that Eg-TSP1 is associated with biogenesis of the tegument and maintenance of structural integrity of E. granulosus and could therefore be a candidate intervention target for control of hydatid disease. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0926-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dandan Hu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Xingju Song
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Xiuqin Zhong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Ning Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Yu Zheng
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Tao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Ya'an, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
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Lourenço-Tessutti IT, Souza Junior JDA, Martins-de-Sa D, Viana AAB, Carneiro RMDG, Togawa RC, de Almeida-Engler J, Batista JAN, Silva MCM, Fragoso RR, Grossi-de-Sa MF. Knock-down of heat-shock protein 90 and isocitrate lyase gene expression reduced root-knot nematode reproduction. PHYTOPATHOLOGY 2015; 105:628-37. [PMID: 26020830 DOI: 10.1094/phyto-09-14-0237-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Crop losses caused by nematode infections are estimated to be valued at USD 157 billion per year. Meloidogyne incognita, a root-knot nematode (RKN), is considered to be one of the most important plant pathogens due to its worldwide distribution and the austere damage it can cause to a large variety of agronomically important crops. RNA interference (RNAi), a gene silencing process, has proven to be a valuable biotechnology alternative method for RKN control. In this study, the RNAi approach was applied, using fragments of M. incognita genes that encode for two essential molecules, heat-shock protein 90 (HSP90) and isocitrate lyase (ICL). Plant-mediated RNAi of these genes led to a significant level of resistance against M. incognita in the transgenic Nicotiana tabacum plants. Bioassays of plants expressing HSP90 dsRNA demonstrated a delay in gall formation and up to 46% reduction in eggs compared with wild-type plants. A reduction in the level of HSP90 transcripts was observed in recovered eggs from plants expressing dsRNA, indicating that gene silencing persisted and was passed along to first progeny. The ICL knock-down had no clear effect on gall formation but resulted in up to 77% reduction in egg oviposition compared with wild-type plants. Our data suggest that both genes may be involved in RKN development and reproduction. Thus, in this paper, we describe essential candidate genes that could be applied to generate genetically modified crops, using the RNAi strategy to control RKN parasitism.
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Affiliation(s)
- Isabela Tristan Lourenço-Tessutti
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - José Dijair Antonino Souza Junior
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Diogo Martins-de-Sa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Antônio Américo Barbosa Viana
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Regina Maria Dechechi Gomes Carneiro
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Roberto Coiti Togawa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Janice de Almeida-Engler
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - João Aguiar Nogueira Batista
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Maria Cristina Mattar Silva
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Rodrigo Rocha Fragoso
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Maria Fatima Grossi-de-Sa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
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Exploring the role of two interacting phosphoinositide 3-kinases of Haemonchus contortus. Parasit Vectors 2014; 7:498. [PMID: 25388625 PMCID: PMC4233088 DOI: 10.1186/s13071-014-0498-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/21/2014] [Indexed: 12/04/2022] Open
Abstract
Background Phosphoinositide 3-kinases (PI3Ks) are relatively conserved and important intracellular lipid kinases involved in signalling and other biological pathways. In the free-living nematode Caenorhabditis elegans, the heterodimeric form of PI3K consists of catalytic (AGE-1) and regulatory (AAP-1) subunits. These subunits are key components of the insulin-like signalling pathway and play roles in the regulation of the entry into and exit from dauer. Although, in parasitic nematodes, similar components are proposed to regulate the transition from free-living or arrested stages to parasitic larvae, nothing is known about PI3Ks in relation to the transition of third-stage larvae (L3s) to parasitism in Haemonchus contortus. Methods An integrated molecular approach was used to investigate age-1 and aap-1 of H. contortus (Hc-age-1 and Hc-aap-1) in C. elegans. Results The two genes Hc-age-1 and Hc-aap-1 were transcribed in all life stages, with the highest levels in the egg, infective L3 and adult female of H. contortus. The expression of these genes was localized to the intestine, contrasting the pattern of their orthologues in C. elegans (where they are expressed in both head neurons and the intestine). The yeast two-hybrid analysis demonstrated that the adaptor-binding domain of Hc-AGE-1 interacted strongly with the Hc-AAP-1; however, this complex did not rescue the function of its orthologue in age-1-deficient C. elegans. Conclusions This is the first time that the PI3K-encoding genes have been characterized from a strongylid parasitic nematode. The findings provide insights into the role of the PI3K heterodimer represented by Hc-age-1 and Hc-aap-1 in the developmental biology of H. contortus. Electronic supplementary material The online version of this article (doi:10.1186/s13071-014-0498-2) contains supplementary material, which is available to authorized users.
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Sarkies P, Miska EA. Small RNAs break out: the molecular cell biology of mobile small RNAs. Nat Rev Mol Cell Biol 2014; 15:525-35. [DOI: 10.1038/nrm3840] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Breugelmans B, Jex AR, Korhonen PK, Mangiola S, Young ND, Sternberg PW, Boag PR, Hofmann A, Gasser RB. Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes. Int J Parasitol 2014; 44:827-36. [PMID: 25038443 DOI: 10.1016/j.ijpara.2014.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 01/07/2023]
Abstract
Despite right open reading frame kinases (RIOKs) being essential for life, their functions, substrates and cellular pathways remain enigmatic. In the present study, gene structures were characterised for 26 RIOKs from draft genomes of parasitic and free-living nematodes. RNA-seq transcription profiles of riok genes were investigated for selected parasitic nematodes and showed that these kinases are transcribed in developmental stages that infect their mammalian host. Three-dimensional structural models of Caenorhabditis elegans RIOKs were predicted, and elucidated functional domains and conserved regions in nematode homologs. These findings provide prospects for functional studies of riok genes in C. elegans, and an opportunity for the design and validation of nematode-specific inhibitors of these enzymes in socioeconomic parasitic worms.
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Affiliation(s)
- Bert Breugelmans
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R Jex
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Stefano Mangiola
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W Sternberg
- Howard Hughes Medical Institute (HHMI), Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Peter R Boag
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Andreas Hofmann
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia; Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Australia
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia.
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Li F, Lok JB, Gasser RB, Korhonen PK, Sandeman MR, Shi D, Zhou R, Li X, Zhou Y, Zhao J, Hu M. Hc-daf-2 encodes an insulin-like receptor kinase in the barber's pole worm, Haemonchus contortus, and restores partial dauer regulation. Int J Parasitol 2014; 44:485-96. [PMID: 24727120 PMCID: PMC4516220 DOI: 10.1016/j.ijpara.2014.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 01/25/2023]
Abstract
Infective L3s (iL3s) of parasitic nematodes share common behavioural, morphological and developmental characteristics with the developmentally arrested (dauer) larvae of the free-living nematode Caenorhabditis elegans. It is proposed that similar molecular mechanisms regulate entry into or exit from the dauer stage in C. elegans, and the transition from free-living to parasitic forms of parasitic nematodes. In C. elegans, one of the key factors regulating the dauer transition is the insulin-like receptor (designated Ce-DAF-2) encoded by the gene Ce-daf-2. However, nothing is known about DAF-2 homologues in most parasitic nematodes. Here, using a PCR-based approach, we identified and characterised a gene (Hc-daf-2) and its inferred product (Hc-DAF-2) in Haemonchus contortus (a socioeconomically important parasitic nematode of ruminants). The sequence of Hc-DAF-2 displays significant sequence homology to insulin receptors (IR) in both vertebrates and invertebrates, and contains conserved structural domains. A sequence encoding an important proteolytic motif (RKRR) identified in the predicted peptide sequence of Hc-DAF-2 is consistent with that of the human IR, suggesting that it is involved in the formation of the IR complex. The Hc-daf-2 gene was transcribed in all life stages of H. contortus, with a significant up-regulation in the iL3 compared with other stages. To compare patterns of expression between Hc-daf-2 and Ce-daf-2, reporter constructs fusing the Ce-daf-2 or Hc-daf-2 promoter to sequence encoding GFP were microinjected into the N2 strain of C. elegans, and transgenic lines were established and examined. Both genes showed similar patterns of expression in amphidial (head) neurons, which relate to sensation and signal transduction. Further study by heterologous genetic complementation in a daf-2-deficient strain of C. elegans (CB1370) showed partial rescue of function by Hc-daf-2. Taken together, these findings provide a first insight into the roles of Hc-daf-2/Hc-DAF-2 in the biology and development of H. contortus, particularly in the transition to parasitism.
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Affiliation(s)
- Facai Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China
| | - James B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Corner of Flemington Road and Park Drive, Parkville, Victoria 3010, Australia; Institute of Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 16-18 Kaiserswerther Street, Berlin 14195, Germany
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Corner of Flemington Road and Park Drive, Parkville, Victoria 3010, Australia
| | - Mark R Sandeman
- School of Applied Sciences and Engineering, Monash University, Northways Road, Churchill, Victoria 3842, Australia
| | - Deshi Shi
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Xiangrui Li
- College of Veterinary Medicine, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, Jiangsu, China
| | - Yanqin Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan 430070, Hubei, China.
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Hoogstrate SW, Volkers RJ, Sterken MG, Kammenga JE, Snoek LB. Nematode endogenous small RNA pathways. WORM 2014; 3:e28234. [PMID: 25340013 PMCID: PMC4205135 DOI: 10.4161/worm.28234] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/05/2014] [Accepted: 02/14/2014] [Indexed: 01/25/2023]
Abstract
The discovery of small RNA silencing pathways has greatly extended our knowledge of gene regulation. Small RNAs have been presumed to play a role in every field of biology because they affect many biological processes via regulation of gene expression and chromatin remodeling. Most well-known examples of affected processes are development, fertility, and maintenance of genome stability. Here we review the role of the three main endogenous small RNA silencing pathways in Caenorhabditis elegans: microRNAs, endogenous small interfering RNAs, and PIWI-interacting RNAs. After providing an entry-level overview on how these pathways function, we discuss research on other nematode species providing insight into the evolution of these small RNA pathways. In understanding the differences between the endogenous small RNA pathways and their evolution, a more comprehensive picture is formed of the functions and effects of small RNAs.
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Affiliation(s)
| | - Rita Jm Volkers
- Laboratory of Nematology; Wageningen University; Wageningen, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology; Wageningen University; Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology; Wageningen University; Wageningen, The Netherlands
| | - L Basten Snoek
- Laboratory of Nematology; Wageningen University; Wageningen, The Netherlands
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Mason L, Amani P, Cross M, Baker J, Bailey UM, Jones MK, Gasser RB, Hofmann A. The Relevance of Structural Biology in Studying Molecules Involved in Parasite–Host Interactions: Potential for Designing New Interventions. Aust J Chem 2014. [DOI: 10.1071/ch14304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
New interventions against infectious diseases require a detailed knowledge and understanding of pathogen–host interactions and pathogeneses at the molecular level. The combination of the considerable advances in systems biology research with methods to explore the structural biology of molecules is poised to provide new insights into these areas. Importantly, exploring three-dimensional structures of proteins is central to understanding disease processes, and establishing structure–function relationships assists in identification and assessment of new drug and vaccine targets. Frequently, the molecular arsenal deployed by invading pathogens, and in particular parasites, reveals a common theme whereby families of proteins with conserved three-dimensional folds play crucial roles in infectious processes, but individual members of such families show high levels of specialisation, which is often achieved through grafting particular structural features onto the shared overall fold. Accordingly, the applicability of predictive methodologies based on the primary structure of proteins or genome annotations is limited, particularly when thorough knowledge of molecular-level mechanisms is required. Such instances exemplify the need for experimental three-dimensional structures provided by protein crystallography, which remain an essential component of this area of research. In the present article, we review two examples of key protein families recently investigated in our laboratories, which could represent intervention targets in the metabolome or secretome of parasites.
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Marker genes for activation of the RNA interference (RNAi) pathway in the free-living nematode Caenorhabditis elegans and RNAi development in the ovine nematode Teladorsagia circumcincta. J Helminthol 2013; 89:208-16. [PMID: 24345514 DOI: 10.1017/s0022149x13000801] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nematode Teladorsagia circumcincta is a major cause of parasitic gastroenteritis in sheep in temperate regions. The development of resistance to the major anthelmintic classes used for its control is a threat to small ruminant farming sustainability. Vaccination is a potential alternative control method for this nematode. Gene datasets can be exploited to identify potential vaccine candidates and these validated further by methods such as RNA interference (RNAi) prior to vaccine trials. Previous reports indicate that RNAi in parasitic nematodes is inconsistent and, to date, there are no internal controls that indicate activation of the RNAi pathway in response to double-stranded RNA (dsRNA). The present aims were to determine whether or not the transcription levels of potential marker genes in the RNAi pathway could indicate activation of the pathway in Caenorhabditis elegans and to develop an RNAi platform in T. circumcincta. In C. elegans, transcript levels of three candidate marker genes, Ce-dcr-1 (Dicer), Ce-ego-1 (Enhancer of Glp-One family member) and Ce-rsd-3 (RNAi Spreading Defective), were analysed and results indicated that activation of the pathway had no effect on transcript levels of these genes. In T. circumcincta, two vaccine candidate genes from the Activation-associated Secreted Protein (ASP) family were targets for knockdown. RNAi experiments showed successful silencing of both targets, although inconsistencies in efficacy were observed. After testing a number of parameters that might affect variability, it was found that the length of the storage period of the larvae plays an important role in the consistency of the RNAi results.
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Chu C, Xin A, Zhou Y, Zhang Y. A simple protocol for producing high-titer lentivirus. Acta Biochim Biophys Sin (Shanghai) 2013; 45:1079-82. [PMID: 24113089 DOI: 10.1093/abbs/gmt112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chen Chu
- Shanghai Key Laboratory for Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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45
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Affiliation(s)
- Peter Sarkies
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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Winter AD, McCormack G, Myllyharju J, Page AP. Prolyl 4-hydroxlase activity is essential for development and cuticle formation in the human infective parasitic nematode Brugia malayi. J Biol Chem 2012; 288:1750-61. [PMID: 23223450 PMCID: PMC3548485 DOI: 10.1074/jbc.m112.397604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4H) are required for formation of extracellular matrices in higher eukaryotes. These enzymes convert proline residues within the repeat regions of collagen polypeptides to 4-hydroxyproline, a modification essential for the stability of the final triple helix. C-P4H are most often oligomeric complexes, with enzymatic activity contributed by the α subunits, and the β subunits formed by protein disulfide isomerase (PDI). Here, we characterize this enzyme class in the important human parasitic nematode Brugia malayi. All potential C-P4H subunits were identified by detailed bioinformatic analysis of sequence databases, function was investigated both by RNAi in the parasite and heterologous expression in Caenorhabditis elegans, whereas biochemical activity and complex formation were examined via co-expression in insect cells. Simultaneous RNAi of two B. malayi C-P4H α subunit-like genes resulted in a striking, highly penetrant body morphology phenotype in parasite larvae. This was replicated by single RNAi of a B. malayi C-P4H β subunit-like PDI. Surprisingly, however, the B. malayi proteins were not capable of rescuing a C. elegans α subunit mutant, whereas the human enzymes could. In contrast, the B. malayi PDI did functionally complement the lethal phenotype of a C. elegans β subunit mutant. Comparison of recombinant and parasite derived material indicates that enzymatic activity may be dependent on a non-reducible covalent link, present only in the parasite. We therefore demonstrate that C-P4H activity is essential for development of B. malayi and uncover a novel parasite-specific feature of these collagen biosynthetic enzymes that may be exploited in future parasite control.
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Affiliation(s)
- Alan D Winter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow G61 1QH, Scotland, United Kingdom.
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Lustigman S, Geldhof P, Grant WN, Osei-Atweneboana MY, Sripa B, Basáñez MG. A research agenda for helminth diseases of humans: basic research and enabling technologies to support control and elimination of helminthiases. PLoS Negl Trop Dis 2012; 6:e1445. [PMID: 22545160 PMCID: PMC3335859 DOI: 10.1371/journal.pntd.0001445] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Successful and sustainable intervention against human helminthiases depends on optimal utilisation of available control measures and development of new tools and strategies, as well as an understanding of the evolutionary implications of prolonged intervention on parasite populations and those of their hosts and vectors. This will depend largely on updated knowledge of relevant and fundamental parasite biology. There is a need, therefore, to exploit and apply new knowledge and techniques in order to make significant and novel gains in combating helminthiases and supporting the sustainability of current and successful mass drug administration (MDA) programmes. Among the fields of basic research that are likely to yield improved control tools, the Disease Reference Group on Helminth Infections (DRG4) has identified four broad areas that stand out as central to the development of the next generation of helminth control measures: 1) parasite genetics, genomics, and functional genomics; 2) parasite immunology; 3) (vertebrate) host–parasite interactions and immunopathology; and 4) (invertebrate) host–parasite interactions and transmission biology. The DRG4 was established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR). The Group was given the mandate to undertake a comprehensive review of recent advances in helminthiases research in order to identify notable gaps and highlight priority areas. This paper summarises recent advances and discusses challenges in the investigation of the fundamental biology of those helminth parasites under the DRG4 Group's remit according to the identified priorities, and presents a research and development agenda for basic parasite research and enabling technologies that will help support control and elimination efforts against human helminthiases.
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Affiliation(s)
- Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, USA.
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