{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T07:56:06Z","timestamp":1790582166225,"version":"4.1.0"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100006502","name":"Defense Sciences Office, DARPA","doi-asserted-by":"publisher","award":["D17AP00034"],"award-info":[{"award-number":["D17AP00034"]}],"id":[{"id":"10.13039\/100006502","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Stress Biology"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>RNA plays a central role in cellular dynamics, mediating the formation of proteins from genetic information. Thus, there is great interest in technologies that can alter RNA content of a cell to achieve desired outcomes. RNA targeting CRISPR\u2012Cas13 enables precise, sequence-guided targeting of RNA to disrupt translation and can therefore be used for cellular engineering. However, guide RNA from CRISPR systems can silence target transcripts independent of the Cas13 protein, complicating the deployment of CRISPR-Cas13 for biotechnology. To prevent Cas13-independent silencing and encourage Cas13-mediated transcript reduction, we explored the use of viral suppressors of RNAi. Here, we report that expression of two viral suppressors of RNAi, HcPro and P19, unexpectedly blocked Cas13-mediated transcript silencing in addition to Cas13-independent RNAi-like silencing. To further understand how HcPro blocks Cas13-mediated silencing, we expressed an RNA silencing-deficient HcPro mutant for RNA-targeting assays. The results demonstrate that mutant HcPro failed to suppress Cas13-dependent silencing, indicating that HcPro RNAi suppression also interferes with Cas13 silencing. These results suggest that plant viruses may be primed to overcome engineered CRISPR-Cas13 antiviral resistance through the activity of previously evolved RNAi silencing suppressors.<\/jats:p>","DOI":"10.1007\/s44154-026-00339-9","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T07:13:32Z","timestamp":1790579612000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plant viral suppressors HcPro and P19 inhibit CRISPR-Cas13-mediated transcript interference"],"prefix":"10.1007","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0231-4551","authenticated-orcid":false,"given":"Veerendra K.","family":"Sharma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5778-7850","authenticated-orcid":false,"given":"Sandeep","family":"Marla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2719-4701","authenticated-orcid":false,"given":"David E.","family":"Cook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"339_CR1","doi-asserted-by":"publisher","unstructured":"Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353:aaf5573. https:\/\/doi.org\/10.1126\/science.aaf5573","DOI":"10.1126\/science.aaf5573"},{"key":"339_CR2","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1038\/nature24049","volume":"550","author":"OO Abudayyeh","year":"2017","unstructured":"Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F\u00a0(2017) RNA targeting with CRISPR\u2013Cas13. Nature 550:280\u2013284. https:\/\/doi.org\/10.1038\/nature24049","journal-title":"Nature"},{"key":"339_CR3","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1126\/science.aax7063","volume":"365","author":"OO Abudayyeh","year":"2019","unstructured":"Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F\u00a0(2019) A cytosine deaminase for programmable single-base RNA editing. Science 365:382\u2013386. https:\/\/doi.org\/10.1126\/science.aax7063","journal-title":"Science"},{"key":"339_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-017-1381-1","volume":"19","author":"R Aman","year":"2018","unstructured":"Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M\u00a0(2018) RNA virus interference via CRISPR\/Cas13a system in plants. Genome Biol 19:1. https:\/\/doi.org\/10.1186\/s13059-017-1381-1","journal-title":"Genome Biol"},{"key":"339_CR5","doi-asserted-by":"publisher","first-page":"13079","DOI":"10.1073\/pnas.95.22.13079","volume":"95","author":"R Anandalakshmi","year":"1998","unstructured":"Anandalakshmi R, Pruss GJ, Ge X, Marathe R, Mallory AC, Smith TH, Vance VB (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci\u00a0U S A 95:13079\u201313084. https:\/\/doi.org\/10.1073\/pnas.95.22.13079","journal-title":"Proc Natl Acad Sci"},{"key":"339_CR6","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1016\/j.virol.2009.11.010","volume":"397","author":"D Barajas","year":"2010","unstructured":"Barajas D, Nagy PD (2010) Ubiquitination of tombusvirus p33 replication protein plays a role in virus replication and binding to the host Vps23p ESCRT protein. Virology 397:358. https:\/\/doi.org\/10.1016\/j.virol.2009.11.010","journal-title":"Virology"},{"key":"339_CR7","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1007\/978-81-322-1620-9_18","volume-title":"Approaches to plant stress and their management","author":"S Basu","year":"2014","unstructured":"Basu S, Sharma VK, Bhattacharyya D, Chakraborty S (2014) An overview of antiviral RNA silencing in plant: biogenesis, host\u2013virus interaction and potential applications. In: Gaur RK, Sharma P (eds) Approaches to plant stress and their management. Springer, New Delhi.\u00a0https:\/\/doi.org\/10.1007\/978-81-322-1620-9_18"},{"key":"339_CR8","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1038\/s41587-021-00822-w","volume":"39","author":"EL Blanchard","year":"2021","unstructured":"Blanchard EL, Vanover D, Bawage SS, Tiwari PM, Rotolo L, Beyersdorf J, Peck HE, Bruno NC, Hincapie R, Michel F, Murray J, Sadhwani H, Vanderheyden B, Finn MG, Brinton MA, Lafontaine ER, Hogan RJ, Zurla C, Santangelo PJ\u00a0(2021) Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents. Nat Biotechnol 39:717\u2013726. https:\/\/doi.org\/10.1038\/s41587-021-00822-w","journal-title":"Nat Biotechnol"},{"key":"339_CR9","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1038\/nature11723","volume":"493","author":"J Bondy-Denomy","year":"2013","unstructured":"Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR\/Cas bacterial immune system. Nature 493:429\u2013432. https:\/\/doi.org\/10.1038\/nature11723","journal-title":"Nature"},{"key":"339_CR10","doi-asserted-by":"publisher","first-page":"1996","DOI":"10.1111\/pbi.13386","volume":"18","author":"Y Cai","year":"2020","unstructured":"Cai Y, Chen L, Zhang Y, Yuan S, Su Q, Sun S, Wu C, Yao W, Han T, Hou W\u00a0(2020) Target base editing in soybean using a modified CRISPR\/Cas9 system. Plant Biotechnol J 18:1996\u20131998. https:\/\/doi.org\/10.1111\/pbi.13386","journal-title":"Plant Biotechnol J"},{"key":"339_CR11","doi-asserted-by":"publisher","first-page":"2755","DOI":"10.1073\/pnas.1814380116","volume":"116","author":"A Canto-Pastor","year":"2019","unstructured":"Canto-Pastor A, Santos BA, Valli AA, Summers W, Schornack S, Baulcombe DC (2019) Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato. Proc Natl Acad Sci USA 116:2755\u20132760. https:\/\/doi.org\/10.1073\/pnas.1814380116","journal-title":"Proc Natl Acad Sci USA"},{"key":"339_CR12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr218","volume":"39","author":"T Cermak","year":"2011","unstructured":"Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF\u00a0(2011a) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39:e82. https:\/\/doi.org\/10.1093\/nar\/gkr218","journal-title":"Nucleic Acids Res"},{"key":"339_CR13","doi-asserted-by":"publisher","first-page":"e82","DOI":"10.1093\/nar\/gkr218","volume":"39","author":"T Cermak","year":"2011","unstructured":"Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF\u00a0(2011b) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39:e82. https:\/\/doi.org\/10.1093\/nar\/gkr218","journal-title":"Nucleic Acids Res"},{"key":"339_CR14","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1111\/j.1365-313X.2010.04163.x","volume":"62","author":"T Csorba","year":"2010","unstructured":"Csorba T, L\u00f3zsa R, Hutv\u00e1gner G, Burgy\u00e1n J (2010) Polerovirus protein P0 prevents the assembly of small RNA-containing RISC complexes and leads to degradation of ARGONAUTE1. Plant J Cell Mol Biol 62:463\u2013472. https:\/\/doi.org\/10.1111\/j.1365-313X.2010.04163.x","journal-title":"Plant J Cell Mol Biol"},{"key":"339_CR15","doi-asserted-by":"publisher","unstructured":"Del Toro FJ, Donaire L, Aguilar E, Chung BN, Tenllado F, Canto T (2017) Potato virus Y HCPro Suppression of antiviral silencing in Nicotiana benthamiana plants correlates with its ability to bind in vivo to 21- and 22-nucleotide small RNAs of viral sequence. J Virol 91(12):e00367\u2013e00317. https:\/\/doi.org\/10.1128\/JVI.00367-17","DOI":"10.1128\/JVI.00367-17"},{"key":"339_CR16","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/nature19802","volume":"538","author":"A East-Seletsky","year":"2016","unstructured":"East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA\u00a0(2016) Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:270\u2013273. https:\/\/doi.org\/10.1038\/nature19802","journal-title":"Nature"},{"key":"339_CR17","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/j.cj.2024.07.007","volume":"12","author":"L Gao","year":"2024","unstructured":"Gao L, Xie L, Xiao Y, Cheng XG, Pu RS, Zhang ZH, Liu Y, Gao SP, Zhang ZL, Qu HR, Zhi HJ, Li K (2024) CRISPR\/CasRx-mediated resistance to Soybean mosaic virus in soybean. Crop J 12:1093\u20131101. https:\/\/doi.org\/10.1016\/j.cj.2024.07.007","journal-title":"Crop J"},{"issue":"2","key":"339_CR18","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1105\/tpc.109.073056","volume":"22","author":"H Garcia-Ruiz","year":"2010","unstructured":"Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC\u00a0(2010) Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during turnip mosaic virus infection. Plant Cell 22(2):481\u2013496. https:\/\/doi.org\/10.1105\/tpc.109.073056","journal-title":"Plant Cell"},{"key":"339_CR19","doi-asserted-by":"publisher","unstructured":"Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC (2015) Roles and programming of Arabidopsis ARGONAUTE proteins during turnip mosaic virus Infection. PLoS Pathog 11(3):e1004755. https:\/\/doi.org\/10.1371\/journal.ppat.1004755","DOI":"10.1371\/journal.ppat.1004755"},{"key":"339_CR20","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1126\/science.aam9321","volume":"356","author":"JS Gootenberg","year":"2017","unstructured":"Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F\u00a0(2017) Nucleic acid detection with CRISPR-Cas13a\/C2c2. Science 356:438\u2013442. https:\/\/doi.org\/10.1126\/science.aam9321","journal-title":"Science"},{"issue":"11","key":"339_CR21","doi-asserted-by":"publisher","first-page":"1143157","DOI":"10.3389\/fbioe.2023.1143157","volume":"9","author":"C Guo","year":"2023","unstructured":"Guo C, Ma X, Gao F, Guo Y (2023) Off-target effects in CRISPR\/Cas9 gene editing. Front Bioeng Biotechnol 9(11):1143157. https:\/\/doi.org\/10.3389\/fbioe.2023.1143157","journal-title":"Front Bioeng Biotechnol"},{"key":"339_CR22","doi-asserted-by":"publisher","first-page":"1224","DOI":"10.1016\/j.cell.2017.07.037","volume":"170","author":"LB Harrington","year":"2017","unstructured":"Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA\u00a0(2017) A broad-spectrum inhibitor of CRISPR-Cas9. Cell 170:1224\u20131233.e15. https:\/\/doi.org\/10.1016\/j.cell.2017.07.037","journal-title":"Cell"},{"key":"339_CR23","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1126\/science.adr3656","volume":"388","author":"VM Hayes","year":"2025","unstructured":"Hayes VM, Zhang JT, Katz MA, Li Y, Kocsis B, Brinkley DM, Jia N (2025) Meeske AJ (2025) RNA-mediated CRISPR-Cas13 inhibition through crRNA structural mimicry. Science 388:387\u2013391. https:\/\/doi.org\/10.1126\/science.adr3656","journal-title":"Science"},{"key":"339_CR24","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/S0076-6879(04)92002-2","volume":"392","author":"C Helliwell","year":"2003","unstructured":"Helliwell C, Waterhouse P (2003) Constructs and methods for hairpin RNA-mediated gene silencing in plants. Methods Enzymol 392:24\u201335. https:\/\/doi.org\/10.1016\/S0076-6879(04)92002-2","journal-title":"Methods Enzymol"},{"key":"339_CR25","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/nbt831","volume":"6","author":"AL Jackson","year":"2003","unstructured":"Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 6:635\u2013637. https:\/\/doi.org\/10.1038\/nbt831","journal-title":"Nat Biotechnol"},{"key":"339_CR26","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1094\/MPMI-4-247","volume":"4","author":"L Kawchuk","year":"1991","unstructured":"Kawchuk L (1991) Sense and antisense RNA-mediated resistance to potato leafroll virus in Russet Burbank potato plants. Mol Plant Microbe Interact 4:247. https:\/\/doi.org\/10.1094\/MPMI-4-247","journal-title":"Mol Plant Microbe Interact"},{"key":"339_CR27","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1016\/j.cell.2018.02.033","volume":"173","author":"S Konermann","year":"2018","unstructured":"Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD\u00a0(2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173:665\u2013676.e14. https:\/\/doi.org\/10.1016\/j.cell.2018.02.033","journal-title":"Cell"},{"key":"339_CR28","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1038\/sj.emboj.7600096","volume":"23","author":"L Lakatos","year":"2004","unstructured":"Lakatos L, Szittya G, Silhavy D, Burgy\u00e1n J (2004) Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. EMBO J 23:876\u2013884. https:\/\/doi.org\/10.1038\/sj.emboj.7600096","journal-title":"EMBO J"},{"key":"339_CR29","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/S0958-1669(00)00190-7","volume":"12","author":"WX Li","year":"2001","unstructured":"Li WX, Ding SW (2001) Viral suppressors of RNA silencing. Curr Opin Biotechnol 12:150\u2013154. https:\/\/doi.org\/10.1016\/S0958-1669(00)00190-7","journal-title":"Curr Opin Biotechnol"},{"key":"339_CR30","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1038\/nbt.2199","volume":"30","author":"T Li","year":"2012","unstructured":"Li T, Liu B, Spalding MH, Weeks DP, Yang B\u00a0(2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390\u2013392. https:\/\/doi.org\/10.1038\/nbt.2199","journal-title":"Nat Biotechnol"},{"key":"339_CR31","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1038\/nbt.2654","volume":"31","author":"J-F Li","year":"2013","unstructured":"Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J\u00a0(2013) Multiplex and homologous recombination-mediated plant genome editing via guide RNA\/Cas9. Nat Biotechnol 31:688\u2013691. https:\/\/doi.org\/10.1038\/nbt.2654","journal-title":"Nat Biotechnol"},{"key":"339_CR32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0046451","volume":"7","author":"D Liu","year":"2012","unstructured":"Liu D, Shi L, Han C, Yu J, Li D, Zhang Y\u00a0(2012) Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR. PLoS ONE 7:e46451. https:\/\/doi.org\/10.1371\/journal.pone.0046451","journal-title":"PLoS ONE"},{"key":"339_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1881-2","volume":"20","author":"A Mahas","year":"2019","unstructured":"Mahas A, Aman R, Mahfouz M (2019) CRISPR-Cas13d mediates robust RNA virus interference in plants. Genome Biol 20:263. https:\/\/doi.org\/10.1186\/s13059-019-1881-2","journal-title":"Genome Biol"},{"key":"339_CR34","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1104\/pp.110.164806","volume":"154","author":"I Marton","year":"2010","unstructured":"Marton I, Zuker A, Shklarman E, Zeevi V, Tovkach A, Roffe S, Ovadis M, Tzfira T, Vainstein A\u00a0(2010) Nontransgenic genome modification in plant cells. Plant Physiol 154:1079\u20131087. https:\/\/doi.org\/10.1104\/pp.110.164806","journal-title":"Plant Physiol"},{"key":"339_CR35","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1126\/science.abb6151","volume":"369","author":"AJ Meeske","year":"2020","unstructured":"Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA\u00a0(2020) A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Science 369:54\u201359. https:\/\/doi.org\/10.1126\/science.abb6151","journal-title":"Science"},{"key":"339_CR36","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1111\/tpj.12704","volume":"80","author":"S Schiml","year":"2014","unstructured":"Schiml S, Fauser F, Puchta H (2014) The CRISPR\/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J 80:1139\u20131150. https:\/\/doi.org\/10.1111\/tpj.12704","journal-title":"Plant J"},{"key":"339_CR37","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1105\/tpc.105.039834","volume":"18","author":"R Schwab","year":"2006","unstructured":"Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D\u00a0(2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121\u20131133. https:\/\/doi.org\/10.1105\/tpc.105.039834","journal-title":"Plant Cell"},{"key":"339_CR38","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/nbt.2650","volume":"31","author":"Q Shan","year":"2013","unstructured":"Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C\u00a0(2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686\u2013688. https:\/\/doi.org\/10.1038\/nbt.2650","journal-title":"Nat Biotechnol"},{"key":"339_CR39","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1007\/s00299-015-1795-8","volume":"34","author":"VK Sharma","year":"2015","unstructured":"Sharma VK, Basu S, Chakraborty S (2015) RNAi mediated broad-spectrum transgenic resistance in Nicotiana benthamiana to chilli-infecting begomoviruses. Plant Cell Rep 34:1389\u20131399. https:\/\/doi.org\/10.1007\/s00299-015-1795-8","journal-title":"Plant Cell Rep"},{"key":"339_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-0716-0743-5_1","volume-title":"RNA abundance analysis\u202f: methods and protocols","author":"V Sharma","year":"2021","unstructured":"Sharma V, Zheng W, Huang J, Cook DE (2021) CRISPR-Cas RNA targeting using transient Cas13a expression in Nicotiana benthamiana. In: Jin H, Kaloshian I (eds) RNA abundance analysis\u202f: Methods in Molecular Biology.\u00a0Humana, New York. https:\/\/doi.org\/10.1007\/978-1-0716-0743-5_1"},{"key":"339_CR41","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s13059-021-02586-7","volume":"23","author":"VK Sharma","year":"2022","unstructured":"Sharma VK, Marla S, Zheng W, Mishra D, Huang J, Zhang W, Morris GP, Cook DE\u00a0(2022) CRISPR guides induce gene silencing in plants in the absence of Cas. Genome Biol 23:6. https:\/\/doi.org\/10.1186\/s13059-021-02586-7","journal-title":"Genome Biol"},{"key":"339_CR42","doi-asserted-by":"publisher","unstructured":"Shen J, Zhou X, Shan Y, Yue H, Huang R, Hu J, Xing D (2020) Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun 11:267. https:\/\/doi.org\/10.1038\/s41467-019-14135-9","DOI":"10.1038\/s41467-019-14135-9"},{"key":"339_CR43","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1038\/nature07992","volume":"459","author":"VK Shukla","year":"2009","unstructured":"Shukla VK, Doyon Y, Miller JC,\u00a0DeKelver RC , Moehle EA , Worden SE et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437\u2013441. https:\/\/doi.org\/10.1038\/nature07992","journal-title":"Nature"},{"key":"339_CR44","doi-asserted-by":"publisher","first-page":"3070","DOI":"10.1093\/emboj\/cdf312","volume":"21","author":"D Silhavy","year":"2002","unstructured":"Silhavy D, Moln\u00e1r A, Lucioli A, Szittya G, Hornyik C, Tavazza M, Burgy\u00e1n J\u00a0(2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO J 21:3070\u20133080. https:\/\/doi.org\/10.1093\/emboj\/cdf312","journal-title":"EMBO J"},{"key":"339_CR45","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/35030305","volume":"407","author":"NA Smith","year":"2000","unstructured":"Smith NA, Singh SP, Wang MB, Stoutjesdijk PA, Green AG, Waterhouse PM\u00a0(2000) Total silencing by intron-spliced hairpin RNAs. Nature 407:319\u2013320. https:\/\/doi.org\/10.1038\/35030305","journal-title":"Nature"},{"key":"339_CR46","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1038\/s42003-020-01142-6","volume":"3","author":"PYL Tng","year":"2020","unstructured":"Tng PYL, Carabajal Paladino L, Verkuijl SAN, Purcell J, Merits A, Leftwich PT, Fragkoudis R, Noad R, Alphey L\u00a0(2020) Cas13b-dependent and Cas13b-independent RNA knockdown of viral sequences in mosquito cells following guide RNA expression. Commun Biol 3:413. https:\/\/doi.org\/10.1038\/s42003-020-01142-6","journal-title":"Commun Biol"},{"key":"339_CR47","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/nature07845","volume":"459","author":"JA Townsend","year":"2009","unstructured":"Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF\u00a0(2009) High frequency modification of plant genes using engineered zinc finger nucleases. Nature 459:442\u2013445. https:\/\/doi.org\/10.1038\/nature07845","journal-title":"Nature"},{"key":"339_CR48","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1006\/viro.1999.0156","volume":"268","author":"S Urcuqui-Inchima","year":"2000","unstructured":"Urcuqui-Inchima S, Maia IG, Arruda P, Haenni AL, Bernardi F\u00a0(2000) Deletion mapping of the potyviral helper component-proteinase reveals two regions involved in RNA binding. Virology 268:104\u2013111. https:\/\/doi.org\/10.1006\/viro.1999.0156","journal-title":"Virology"},{"key":"339_CR49","doi-asserted-by":"publisher","unstructured":"Weigel D, Glazebrook J (2008) Genetic analysis of Arabidopsis mutants. Cold Spring Harbor Protoc 2008:pdb.top35. https:\/\/doi.org\/10.1101\/pdb.top35","DOI":"10.1101\/pdb.top35"},{"key":"339_CR50","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1385\/1-59259-413-1:273","volume":"236","author":"SV Wesley","year":"2003","unstructured":"Wesley SV, Liu Q, Wielopolska A, Ellacott G, Smith N, Singh S, Helliwell C (2003) Custom knock-outs with hairpin RNA-mediated gene silencing. Methods Mol Biol 236:273\u2013286. https:\/\/doi.org\/10.1385\/1-59259-413-1:273","journal-title":"Methods Mol Biol"},{"key":"339_CR51","doi-asserted-by":"publisher","unstructured":"Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock R, Nie B, Zhang J (2019) Generation of virus-resistant potato plants by RNA genome targeting. Plant Biotechnol J 2019;17(9):1814\u20131822. https:\/\/doi.org\/10.1111\/pbi.13102","DOI":"10.1111\/pbi.13102"},{"key":"339_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-023-05205-2","volume":"6","author":"X Zhan","year":"2023","unstructured":"Zhan X, Liu W, Nie B, Zhang F, Zhang J\u00a0(2023) Cas13d-mediated multiplex RNA targeting confers a broad-spectrum resistance against RNA viruses in potato. Commun Biol 6:1\u20139. https:\/\/doi.org\/10.1038\/s42003-023-05205-2","journal-title":"Commun Biol"},{"key":"339_CR53","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1104\/pp.112.205179","volume":"161","author":"Y Zhang","year":"2013","unstructured":"Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF\u00a0(2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol 161:20\u201327. https:\/\/doi.org\/10.1104\/pp.112.205179","journal-title":"Plant Physiol"},{"key":"339_CR54","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1111\/pbi.13095","volume":"17","author":"T Zhang","year":"2019","unstructured":"Zhang T, Zhao Y, Ye J, Cao X, Xu C, Chen B, An H, Jiao Y, Zhang F, Yang X, Zhou G\u00a0(2019) Establishing CRISPR\/Cas13a immune system conferring RNA virus resistance in both dicot and monocot plants. Plant Biotechnol J 17:1185\u20131187. https:\/\/doi.org\/10.1111\/pbi.13095","journal-title":"Plant Biotechnol J"},{"key":"339_CR55","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1111\/jipb.12900","volume":"62","author":"SX Zhou","year":"2020","unstructured":"Zhou SX, Zhu Y, Wang LF, Zheng YP, Chen JF, Li TT, Yang XM, Wang H, Li XP, Ma XC, Zhao JQ, Pu M, Feng H, Li Y, Fan J, Zhang JW, Huang YY, Wang WM\u00a0(2020) Osa-miR1873 fine-tunes rice immunity against Magnaporthe oryzae and yield traits. J Integr Plant Biol 62:1213\u20131226. https:\/\/doi.org\/10.1111\/jipb.12900","journal-title":"J Integr Plant Biol"},{"key":"339_CR56","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.molcel.2019.01.038","volume":"74","author":"Y Zhu","year":"2019","unstructured":"Zhu Y, Gao A, Zhan Q, Wang Y, Feng H, Liu S, Gao G, Serganov A, Gao P\u00a0(2019) Diverse mechanisms of CRISPR-Cas9 inhibition by type IIC anti-CRISPR proteins. Mol Cell 74:296\u2013309.e7. https:\/\/doi.org\/10.1016\/j.molcel.2019.01.038","journal-title":"Mol Cell"}],"container-title":["Stress Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44154-026-00339-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s44154-026-00339-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44154-026-00339-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T07:13:33Z","timestamp":1790579613000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s44154-026-00339-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":56,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["339"],"URL":"https:\/\/doi.org\/10.1007\/s44154-026-00339-9","relation":{},"ISSN":["2097-4418","2731-0450"],"issn-type":[{"value":"2097-4418","type":"print"},{"value":"2731-0450","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,28]]},"assertion":[{"value":"30 April 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 June 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 August 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 September 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All authors agree to publish.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Kansas State University Research Foundation has applied for a patent relating to use of Cas13-independent RNA reduction. This does not impact academic research or the ability to reproduce the described results.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"69"}}