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Gene silencing mechanisms in Phytophthora infestans

Vetukuri, Ramesh Raju (2012). Gene silencing mechanisms in Phytophthora infestans. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2012:26
ISBN 978-91-576-7662-7
[Doctoral thesis]

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Abstract

The hemibiotrophic oomycete, Phytophthora infestans, causes late blight on potato and tomato. This destructive pathogen is well known for the rapidity with which it overcomes host resistance. This thesis focuses on the molecular basis of gene (RNA) silencing in P. infestans and the role it may have in its genome biology and pathogenesis. A comparative genomic approach identified 51 genes from nine gene families, encoding Dicer-like (PiDcl1), Argonaute (PiAgo), RNA-dependent RNA polymerase (PiRdr1), Histone eacetylases, histone methyltransferases, DEAD helicases, chromodomain proteins,and a class 1 RNaseIII with a possible role in gene silencing. It was shown by knockdown of PiDcl1,
PiAgo1, and PiHda1 (Histone deacetylase) expression, that these components were involved in maintaining transcriptional (heterochromatic) silencing in P. infestans.

The large genome of P. infestans (~ 240 Mb) is composed of approximately 75% transposons and repeats. The genome has a bimodal architecture, consisting of a highly conserved and tightly packed core genome that is interrupted by transposons and repeats. The genes encoding the RxLR and Crinkler (CRN) effector classes that are critical to plant infection are predominantly located in the repeat and
transposon rich regions. Small RNAs (sRNA) of 40 nt, homologous to a non-autonomous short interspersed retrotransposable element infSINEm were found. A sense orientation transcriptional fusion of infSINEm to the PiAvr3a (RxLR) effector gene led to silencing of both the introduced fusion and endogenous homologous sequences. Hence, it was concluded that P. infestans likely uses RNA
silencing to minimize the activity of transposons and might influence expression of effector encoding
genes in close proximity.

Deep sequencing of sRNA from different life cycle stages of two P. infestans isolates, that differ in their disease causing abilities, revealed 21, 25/26, and 32 nt size classes of sRNAs that were predominantly derived from transposons. Effector gene-derived sRNAs were also present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Knockdown of
Dicer and Argonaute gene expression provided evidence that biogenesis of 21 nt sRNAs is Dicerdependent,while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, six miRNA candidates, and sRNAs that mapped to mitochondrial, tRNA and genomic
hotspots were identified. sRNAs and RNA silencing in P. infestans have features characteristic of both plants and animals.

Authors/Creators:Vetukuri, Ramesh Raju
Title:Gene silencing mechanisms in Phytophthora infestans
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :30 May 2012
Volume:2012:26
Number of Pages:68
Papers/manuscripts:
NumberReferences
I.Vetukuri, R.R., Avrova, A.O., Grenville-Briggs, L.J., van West, P., Söderbom, F., Savenkov, E.I., Whisson, S.C. and Dixelius, C. (2011) Evidence for involvement of Dicer-like, Argonaute, and Histone Deacetylase proteins in gene silencing in Phytophthora infestans. Mol. Plant Pathol. 12:772-785.
II.Vetukuri, R.R., Zhendong, T., Avrova, A.O., Savenkov, E.I., Dixelius, C. and Whisson, S.C. (2011) Silencing of the PiAvr3a effector-encoding gene from Phytophthora infestans by transcriptional fusion to a short interspersed element. Fungal Biol. 115:1225-1233.
III.Vetukuri, R.R., Åsman, A.K.M., Tellgren-Roth, C., Jahan, S.N., Reimegård, J., Fogelqvist, J., Savenkov, E., Söderbom, F., Avrova, A.O., Whisson, S.C. and Dixelius, C. (2012). Biogenesis of small RNAs homologous to effector-encoding genes and transposable elements in the oomycete, Phytophthora infestans. (Manuscript)
IV.Vetukuri, R.R., Åsman, A.K.M., Jahan, S.N., Fogelqvist, J., Reimegård, J., Avrova, A.O., Whisson, S.C. and Dixelius, C. (2012) Deep sequencing reveals diverse classes of small RNAs derived from genomic hotspots, tRNA and the mitochondrial genome in Phytophthora infestans. (Manuscript)
Place of Publication:Uppsala
Publisher:Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-7662-7
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:F Plant production > F30 Plant genetics and breeding
H Protection of plants and stored products > H20 Plant diseases
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:phytophthora infestans, pathogens, genes, rna, effectors, gene expression, solanum tuberosum, disease resistance
Keywords:Small RNAs, Gene silencing, Oomycetes, Dicer, Effectors, RxLRs, Phytophthora Infestans, AVR3a, SINE, RNA silencing, Argonaute, Histone deacetylase, Potato
URN:NBN:urn:nbn:se:slu:epsilon-e-550
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-550
ID Code:8917
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
External funders:FORMAS
Deposited By: MR Ramesh.R Vetukuri
Deposited On:31 May 2012 10:41
Metadata Last Modified:02 Dec 2014 10:51

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