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. 2020 Sep 29;11(5):e02209-20.
doi: 10.1128/mBio.02209-20.

Endogenous Viral Element-Derived Piwi-Interacting RNAs (piRNAs) Are Not Required for Production of Ping-Pong-Dependent piRNAs from Diaphorina citri Densovirus

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Endogenous Viral Element-Derived Piwi-Interacting RNAs (piRNAs) Are Not Required for Production of Ping-Pong-Dependent piRNAs from Diaphorina citri Densovirus

Jared C Nigg et al. mBio. .

Abstract

Piwi-interacting RNAs (piRNAs) are a class of small RNAs primarily responsible for silencing transposons in the animal germ line. The ping-pong cycle, the posttranscriptional silencing branch of the piRNA pathway, relies on piRNAs produced from endogenous transposon remnants to direct cleavage of transposon RNA via association with Piwi-family Argonaute proteins. In some mosquito species and mosquito-derived cell lines expressing a functionally expanded group of Piwi-family Argonaute proteins, both RNA and DNA viruses are targeted by piRNAs in a manner thought to involve direct processing of exogenous viral RNA into piRNAs. Whether viruses are targeted by piRNAs in nonmosquito species is unknown. Partial integrations of DNA and nonretroviral RNA virus genomes, termed endogenous viral elements (EVEs), are abundant in arthropod genomes and often produce piRNAs that are speculated to target cognate viruses through the ping-pong cycle. Here, we describe a Diaphorina citri densovirus (DcDV)-derived EVE in the genome of Diaphorina citri We found that this EVE gives rise to DcDV-specific primary piRNAs and is unevenly distributed among D. citri populations. Unexpectedly, we found that DcDV is targeted by ping-pong-dependent virus-derived piRNAs (vpiRNAs) in D. citri lacking the DcDV-derived EVE, while four naturally infecting RNA viruses of D. citri are not targeted by vpiRNAs. Furthermore, a recombinant Cricket paralysis virus containing a portion of the DcDV genome corresponding to the DcDV-derived EVE was not targeted by vpiRNAs during infection in D. citri harboring the EVE. These results demonstrate that viruses can be targeted by piRNAs in a nonmosquito species independently of endogenous piRNAs.IMPORTANCE Small RNAs serve as specificity determinants of antiviral responses in insects. Piwi-interacting RNAs (piRNAs) are a class of small RNAs found in animals, and their primary role is to direct antitransposon responses. These responses require endogenous piRNAs complementary to transposon RNA. Additionally, piRNAs have been shown to target RNA and DNA viruses in some mosquito species. In contrast to transposons, targeting of viruses by the piRNA pathway in these mosquito species does not require endogenous piRNAs. Here, we show that piRNAs target a DNA virus, but not RNA viruses, in an agricultural insect pest. We found that targeting of this DNA virus did not require endogenous piRNAs and that endogenous piRNAs did not mediate targeting of an RNA virus with which they shared complementary sequence. Our results highlight differences between mosquitoes and our experimental system and raise the possibility that DNA viruses may be targeted by piRNAs in other species.

Keywords: Diaphorina citri; RNA interference; densovirus; piRNA; small RNA.

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Figures

FIG 1
FIG 1
A DcDV-like EVE is present in the D. citri genome. (A) Organization of a DcDV-derived EVE identified in D. citri genomic scaffold ScVcwli_3651 by BLASTn followed by manual sequence alignment. The DcDV genome organization is shown on top with the corresponding region of scaffold ScVcwli_365 on the bottom. Numbers above and below the sequence depictions represent nucleotide positions. Blue and red shaded boxes with arrows represent open reading frames (ORFs), and the offset between boxes represents different reading frames. Green shaded boxes without arrows represent the ITRs. Vertical lines inside shaded boxes represent stop codons. The percentage of nucleotide identity between D. citri genomic and corresponding viral genomic regions is given. Annealing positions of PCR primers used in the experiments represented in panels B to D are shown with arrows. NS = nonstructural protein-encoding ORFs, VP = coat protein-encoding ORFs. (B) Confirmation of EVE presence by PCR using primers shown in panel A. The primer 5/6 PCR product was produced by nested PCR using as the template a 1:1,000 dilution of a PCR product produced with primers 3/4. (C) (Upper panel) PCR products produced using primers flanking ENS (primers 2 and 8). (Lower) PCR products produced using primers specific to D. citri actin (primers 9 and 10). (D) Primer 3 or primer 7 was used to generate cDNA from antisense or sense transcripts, respectively. cDNAs were used as the templates for PCR using primers 3 and 7. “+” and “-” indicate PCRs performed using cDNA prepared with (+) or without (-) reverse transcriptase (RT), respectively.
FIG 2
FIG 2
DcDV-specific piRNAs are produced from ENS in D. citri from CRF-CA. (A) Positions of all sRNAs from CRF-CA D. citri mapped to the DcDV genome. Dashed lines indicate the region of the DcDV genome corresponding to ENS. sRNAs are shown as mapped to the genomic strand containing the coding sequence for the NS proteins. Red = antisense sRNAs, blue = sense sRNAs. Read counts represent averages of results from three independent libraries. (B) Length distribution of sRNAs represented in panel A. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (C) Sequence logo of sRNAs represented in panel A. Data represent results from three pooled libraries. (D) Abundance of 27-to-32-nt sRNAs from CRF-CA D. citri mapping to ENS in the indicated tissue types. Read counts for each library were normalized using the read counts per million mapped reads (RPM) method (59). Normalized read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. Average RPM values for each tissue were compared by one-way analysis of variance (ANOVA) and Turkey’s honestly significant difference post hoc test. Significance is indicated by lowercase letters, and tissues sharing a letter do not have significantly different RPM values (P < 0.05).
FIG 3
FIG 3
DcDV is targeted by ping-pong-dependent vpiRNAs in DcDV-infected D. citri insects from CRF-TW. (A) Length distribution of sRNAs mapping to transcribed regions of the DcDV genome in DcDV-infected D. citri insects from CRF-TW. To account for the bidirectional transcription strategy of DcDV, sRNA mapping polarity was assigned from mapping location based on the start and stop positions of the canonical DcDV transcripts. Red = antisense sRNAs, blue = sense sRNAs. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (B) Positions of 27-to-32-nt sRNAs represented in panel A. Red = antisense sRNAs, blue = sense sRNAs. Read counts represent averages of results from three independent libraries. (C) Z-scores for the indicated overlap distances between the 5′ ends of complementary 27-to-32-nt sRNAs represented in panel A. Z-scores represent averages of results from three independent libraries. Error bars indicate standard deviations. (D and E) Sequence logos for the 27-to-32-nt sRNAs represented in panel A. Sequence logos for antisense sRNAs (D) or sense sRNAs (E) are shown. Data represent results from three pooled libraries.
FIG 4
FIG 4
Construction of CrPV-DcDV, a recombinant CrPV mutant containing 57 nt of sequence from the DcDV genome. (A) Genome organization of CrPV-DcDV. Blue rectangles represent the CrPV nonstructural proteins. RdRp = RNA-dependent RNA polymerase. VPg = viral protein genome-linked. Green boxes represent the CrPV structural proteins. The orange rectangle represents the recombinant DcDV sequence, which corresponds to nucleotides 803 to 859 from the DcDV genome. Pink rectangles represent the cleavage site at which the 1A protein is released from the polyprotein. (B and C) Electron micrographs of wild-type CrPV (B) or CrPV-DcDV (C) virions purified from S2 cells transfected with viral RNA (×50,000 magnification). Scale bar is 50 nm. (D) RT-PCR products produced using primers flanking the site into which recombinant DcDV sequence was inserted in CrPV-DcDV (primers 11 and 12). RNA extracted from purified virions (VR) or in vitro-transcribed viral RNA (TR) was used as a template. (E to G) Bright-field microscopy images of S2 cells infected with wild-type CrPV virions (E) or CrPV-DcDV virions (F) or mock infected (G). Images were acquired 72 h post-infection.
FIG 5
FIG 5
CrPV-DcDV is not targeted by piRNAs during infection initiated by intrathoracic injection of purified virions. (A) Relative viral RNA levels during infection with wild-type CrPV or CrPV-DcDV. Infection was initiated by intrathoracic injection of CRF-CA D. citri with 1,000 TCID50 units of purified virions per insect. Viral RNA levels were assessed by RT-qPCR and normalized based on the expression of actin. The amount of viral RNA present on day 0 was set as 1, and log10 + 1 levels of viral RNA are shown relative to this value. Bars represent the average viral RNA level in five pools of three insects. Error bars indicate standard errors of the means. ** = P < 0.01, two-tailed T-test. (B to F) Analysis of sRNA sequencing data of sRNAs purified from CRF-CA D. citri infected with wild-type CrPV or CrPV-DcDV by intrathoracic injection as described for panel A. sRNA was purified from pools of 25 D. citri collected 5 days postinjection. (B) Length distribution of sRNAs from wild-type CrPV-infected D. citri mapped to the wild-type CrPV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (C) Length distribution of sRNAs from CrPV-DcDV-infected D. citri mapped to the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (D) Length distribution of sRNAs from CrPV-DcDV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (E) Length distribution of sRNAs from wild-type CrPV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (F and G) Sequence logos for 27-to-32-nt sRNAs from CrPV-DcDV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Sequence logos for antisense sRNAs (F) or sense sRNAs (G) are shown. Data represent results from three pooled libraries. (H) Probability of overlap of the 5′ ends of complementary 27-to-32-nt sRNAs mapping to opposite strands of the recombinant DcDV sequence present within the CrPV-DcDV genome during infection with CrPV-DcDV. Probabilities are shown for the indicated overlap distances and represent averages of results from three independent libraries. Error bars indicate standard deviations. The average Z-score and the standard deviation of the Z-score for an overlap length of 10 nt are shown.
FIG 6
FIG 6
CrPV-DcDV is not targeted by piRNAs during infection initiated by oral acquisition of purified virions. (A) Relative viral RNA levels during infection with wild-type CrPV or CrPV-DcDV. Infection was initiated in CRF-CA D. citri by oral acquisition. Insects were allowed to feed for 96 h on a sucrose solution containing 109 TCID50 units/ml of wild-type CrPV or CrPV-DcDV. Following the feeding period, insects were moved to C. macrophylla plants (day 0 post feeding). Viral RNA levels were assessed by RT-qPCR and normalized based on the expression of actin. The amount of viral RNA present on day 0 was set as 1, and viral RNA levels are shown relative to this value. Bars represent the average viral RNA level in seven pools of three insects. Error bars indicate standard errors of the means. (B to F) Analysis of sRNA sequencing data of sRNAs purified from CRF-CA D. citri infected with wild-type CrPV or CrPV-DcDV by oral acquisition as described for panel A. sRNA was purified from pools of 25 D. citri collected 9 days post feeding. (B) Length distribution of sRNAs from wild-type CrPV-infected D. citri mapped to the wild-type CrPV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (C) Length distribution of sRNAs from CrPV-DcDV-infected D. citri mapped to the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (D) Length distribution of sRNAs from CrPV-DcDV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (E) Length distribution of sRNAs from wild-type CrPV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Red = antisense, blue = sense. Read counts represent averages of results from three independent libraries. Error bars indicate standard deviations. (F and G) Sequence logos for 27-to-32-nt sRNAs from CrPV-DcDV-infected D. citri mapped to the recombinant DcDV sequence present within the CrPV-DcDV genome. Sequence logos for antisense sRNAs (F) or sense sRNAs (G) are shown. Data represent results from three pooled libraries. (H) Probability of overlap of the 5′ ends of complementary 27-to-32-nt sRNAs mapping to opposite strands of the recombinant DcDV sequence present within the CrPV-DcDV genome during infection with CrPV-DcDV. Probabilities are shown for the indicated overlap distances and represent averages of results from three independent libraries. Error bars indicate standard deviations. The average Z-score and the standard deviation of the Z-score for an overlap length of 10 nt are shown.

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