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...
Published in: | PLoS Neglected Tropical Diseases |
---|---|
Main Authors: | , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2011
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pntd.0001176 https://doaj.org/article/76d7c68e9ada4a76a3ae2502ae38023c |
id |
ftdoajarticles:oai:doaj.org/article:76d7c68e9ada4a76a3ae2502ae38023c |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:76d7c68e9ada4a76a3ae2502ae38023c 2023-05-15T15:13:21+02:00 RNAi effector diversity in nematodes. 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 2011-06-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0001176 https://doaj.org/article/76d7c68e9ada4a76a3ae2502ae38023c EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC3110158?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0001176 https://doaj.org/article/76d7c68e9ada4a76a3ae2502ae38023c PLoS Neglected Tropical Diseases, Vol 5, Iss 6, p e1176 (2011) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2011 ftdoajarticles https://doi.org/10.1371/journal.pntd.0001176 2022-12-30T21:04:27Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLoS Neglected Tropical Diseases 5 6 e1176 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 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. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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 in Journal/Newspaper |
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 |
title |
RNAi effector diversity in nematodes. |
title_short |
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_sort |
rnai effector diversity in nematodes. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2011 |
url |
https://doi.org/10.1371/journal.pntd.0001176 https://doaj.org/article/76d7c68e9ada4a76a3ae2502ae38023c |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 5, Iss 6, p e1176 (2011) |
op_relation |
http://europepmc.org/articles/PMC3110158?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0001176 https://doaj.org/article/76d7c68e9ada4a76a3ae2502ae38023c |
op_doi |
https://doi.org/10.1371/journal.pntd.0001176 |
container_title |
PLoS Neglected Tropical Diseases |
container_volume |
5 |
container_issue |
6 |
container_start_page |
e1176 |
_version_ |
1766343916664127488 |