Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants

Isabel Weinheimer, Yaming Jiu, Minna-Liisa Rajamäki, Olli Matilainen, Jukka Kallijärvi, Wilmer J. Cuellar, Rui Lu, Mart Saarma, Carina I. Holmberg, Jussi Jäntti, Jari P.T. Valkonen

Research output: Contribution to journalArticleScientificpeer-review

16 Citations (Scopus)

Abstract

Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)-mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.
Original languageEnglish
Number of pages25
JournalPLoS Pathogens
Volume11
Issue number3
DOIs
Publication statusPublished - 2015
MoE publication typeA1 Journal article-refereed

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Plant Viruses
RNA Interference
Viruses
Enzymes
Crinivirus
Ipomoea batatas
DNA Viruses
RNA Viruses
Caenorhabditis elegans
Iridovirus
Endoribonucleases
RNA
Replicon
Double-Stranded RNA
Ascoviridae
Small Interfering RNA
Tobacco
Antiviral Agents
Insects
Fishes

Cite this

Weinheimer, I., Jiu, Y., Rajamäki, M-L., Matilainen, O., Kallijärvi, J., Cuellar, W. J., ... Valkonen, J. P. T. (2015). Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. PLoS Pathogens, 11(3). https://doi.org/10.1371/journal.ppat.1004711
Weinheimer, Isabel ; Jiu, Yaming ; Rajamäki, Minna-Liisa ; Matilainen, Olli ; Kallijärvi, Jukka ; Cuellar, Wilmer J. ; Lu, Rui ; Saarma, Mart ; Holmberg, Carina I. ; Jäntti, Jussi ; Valkonen, Jari P.T. / Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. In: PLoS Pathogens. 2015 ; Vol. 11, No. 3.
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title = "Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants",
abstract = "Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)-mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.",
author = "Isabel Weinheimer and Yaming Jiu and Minna-Liisa Rajam{\"a}ki and Olli Matilainen and Jukka Kallij{\"a}rvi and Cuellar, {Wilmer J.} and Rui Lu and Mart Saarma and Holmberg, {Carina I.} and Jussi J{\"a}ntti and Valkonen, {Jari P.T.}",
year = "2015",
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language = "English",
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journal = "PLoS Pathogens",
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Weinheimer, I, Jiu, Y, Rajamäki, M-L, Matilainen, O, Kallijärvi, J, Cuellar, WJ, Lu, R, Saarma, M, Holmberg, CI, Jäntti, J & Valkonen, JPT 2015, 'Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants', PLoS Pathogens, vol. 11, no. 3. https://doi.org/10.1371/journal.ppat.1004711

Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. / Weinheimer, Isabel; Jiu, Yaming; Rajamäki, Minna-Liisa; Matilainen, Olli; Kallijärvi, Jukka; Cuellar, Wilmer J.; Lu, Rui; Saarma, Mart; Holmberg, Carina I.; Jäntti, Jussi; Valkonen, Jari P.T.

In: PLoS Pathogens, Vol. 11, No. 3, 2015.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants

AU - Weinheimer, Isabel

AU - Jiu, Yaming

AU - Rajamäki, Minna-Liisa

AU - Matilainen, Olli

AU - Kallijärvi, Jukka

AU - Cuellar, Wilmer J.

AU - Lu, Rui

AU - Saarma, Mart

AU - Holmberg, Carina I.

AU - Jäntti, Jussi

AU - Valkonen, Jari P.T.

PY - 2015

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N2 - Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)-mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.

AB - Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)-mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.

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DO - 10.1371/journal.ppat.1004711

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VL - 11

JO - PLoS Pathogens

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SN - 1553-7366

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Weinheimer I, Jiu Y, Rajamäki M-L, Matilainen O, Kallijärvi J, Cuellar WJ et al. Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. PLoS Pathogens. 2015;11(3). https://doi.org/10.1371/journal.ppat.1004711