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BMC Microbiol. 2014 Dec 10;14:308. doi: 10.1186/s12866-014-0308-1.

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.

Author information

1
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Anna.Asman@slu.se.
2
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Ramesh.Vetukuri@slu.se.
3
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Sultana.Jahan@slu.se.
4
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Johan.Fogelqvist@slu.se.
5
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. padraiccorcoran1@gmail.com.
6
Current affiliation: Department of Evolutionary Biology, Uppsala University, SE-75236, Uppsala, Sweden. padraiccorcoran1@gmail.com.
7
Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Anna.Avrova@hutton.ac.uk.
8
Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Steve.Whisson@hutton.ac.uk.
9
Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Christina.Dixelius@slu.se.

Abstract

BACKGROUND:

The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host.

RESULTS:

To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line.

CONCLUSIONS:

Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans.

PMID:
25492044
PMCID:
PMC4272539
DOI:
10.1186/s12866-014-0308-1
[Indexed for MEDLINE]
Free PMC Article

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