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Research article - Peer-reviewed, 2014

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

Åsman, Anna; Vetukuri, Ramesh; Jahan, Sultana; Fogelqvist, Johan; Corcoran, Pádraic; Avrova, Anna; Whisson, Stephen; Dixelius, Christina

Abstract

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.

Keywords

Argonaute; Dicer; Phytophthora infestans; Potato; RNA silencing; Small RNA; tRF; tRNA

Published in

BMC Microbiology
2014, volume: 14, article number: 308
Publisher: BIOMED CENTRAL LTD

Authors' information

Åsman, Anna
Swedish University of Agricultural Sciences, Department of Plant Biology
Vetukuri, Ramesh (Ramesh, Vetukuri)
Swedish University of Agricultural Sciences, Department of Plant Biology
Jahan, Sultana
Swedish University of Agricultural Sciences, Department of Plant Biology
Swedish University of Agricultural Sciences, Department of Plant Biology
Corcoran, Pádraic (Corcoran, Pádraic)
Swedish University of Agricultural Sciences, Department of Plant Biology
Avrova, Anna
The James Hutton Institute
Whisson, Stephen
The James Hutton Institute
Swedish University of Agricultural Sciences, Department of Plant Biology

Associated SLU-program

SLU Network Plant Protection

UKÄ Subject classification

Developmental Biology
Plant Biotechnology
Biochemistry and Molecular Biology

Publication Identifiers

DOI: https://doi.org/10.1186/s12866-014-0308-1

URI (permanent link to this page)

https://res.slu.se/id/publ/66818