RNAi effector diversity in nematodes.
While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-06-01
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| Series: | PLoS Neglected Tropical Diseases |
| Online Access: | https://doi.org/10.1371/journal.pntd.0001176 |
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| _version_ | 1850128714234331136 |
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| author | Johnathan J Dalzell Paul McVeigh Neil D Warnock Makedonka Mitreva David McK Bird Pierre Abad Colin C Fleming Tim A Day Angela Mousley Nikki J Marks Aaron G Maule |
| author_facet | Johnathan J Dalzell Paul McVeigh Neil D Warnock Makedonka Mitreva David McK Bird Pierre Abad Colin C Fleming Tim A Day Angela Mousley Nikki J Marks Aaron G Maule |
| author_sort | Johnathan J Dalzell |
| collection | DOAJ |
| description | While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes. |
| format | Article |
| id | doaj-art-76d7c68e9ada4a76a3ae2502ae38023c |
| institution | OA Journals |
| issn | 1935-2727 1935-2735 |
| language | English |
| publishDate | 2011-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Neglected Tropical Diseases |
| spelling | doaj-art-76d7c68e9ada4a76a3ae2502ae38023c2025-08-20T02:33:12ZengPublic Library of Science (PLoS)PLoS Neglected Tropical Diseases1935-27271935-27352011-06-0156e117610.1371/journal.pntd.0001176RNAi effector diversity in nematodes.Johnathan J DalzellPaul McVeighNeil D WarnockMakedonka MitrevaDavid McK BirdPierre AbadColin C FlemingTim A DayAngela MousleyNikki J MarksAaron G MauleWhile RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes.https://doi.org/10.1371/journal.pntd.0001176 |
| spellingShingle | Johnathan J Dalzell Paul McVeigh Neil D Warnock Makedonka Mitreva David McK Bird Pierre Abad Colin C Fleming Tim A Day Angela Mousley Nikki J Marks Aaron G Maule RNAi effector diversity in nematodes. PLoS Neglected Tropical Diseases |
| title | RNAi effector diversity in nematodes. |
| title_full | RNAi effector diversity in nematodes. |
| title_fullStr | RNAi effector diversity in nematodes. |
| title_full_unstemmed | RNAi effector diversity in nematodes. |
| title_short | RNAi effector diversity in nematodes. |
| title_sort | rnai effector diversity in nematodes |
| url | https://doi.org/10.1371/journal.pntd.0001176 |
| work_keys_str_mv | AT johnathanjdalzell rnaieffectordiversityinnematodes AT paulmcveigh rnaieffectordiversityinnematodes AT neildwarnock rnaieffectordiversityinnematodes AT makedonkamitreva rnaieffectordiversityinnematodes AT davidmckbird rnaieffectordiversityinnematodes AT pierreabad rnaieffectordiversityinnematodes AT colincfleming rnaieffectordiversityinnematodes AT timaday rnaieffectordiversityinnematodes AT angelamousley rnaieffectordiversityinnematodes AT nikkijmarks rnaieffectordiversityinnematodes AT aarongmaule rnaieffectordiversityinnematodes |