Plant protect themselves with the help of small ribonucleic acids (sRNAs) dependent immune system. RNA silencing is a robust strategy developed by plants to defend against pathogen attack. It also plays a role in genome stability and protects plant against invading nucleic acid such as transgenes and viruses (Ellendorff et al., 2009). During gene expression, deoxyribonucleic acid (DNA) is copied in a molecule of messenger RNA (mRNA) and is then translated into proteins with the help of other RNA molecules like transfer RNA (tRNA) and ribosomal RNA (rRNA). One of the major features of RNA interference machinery (RNAi) is the production of sRNAs of 20 – 30 nucleotide long noncoding RNA molecule that regulate gene expression through RNA silencing (Zamore and Haley 2005; Islam et al., 2018; Bilir et al., 2022).
RNA interference machinery is a conserved regulatory mechanism to combat pathogens and control expression of endogenous genes (Liu et al., 2020;Bilir et al., 2022). The machinery of RNA silencing (also known as RNAi) in plants consists of three core components (Zhu et al., 2019):
- RNA-dependent RNA polymerases (RDRs), which are responsible for catalyzing the biosynthesis of double stranded RNAs (dsRNAs) from a single stranded RNA (ssRNA) template
- DICER-Like (DCL) proteins, which cleaves dsRNA or single-stranded hairpin RNA into sRNA and
- Argonaute (AGO) proteins, which are guided by sRNAs and bind to the target mRNAs in a sequence complementary manner, leading to mRNA cleavage or translation inhibition.
Small RNAs are generated by endoribonucleases DICER or DICER-like and are loaded into argonaute proteins to induce silencing of genes with complementary sequences (Chen 2009; Weiberg and Jin 2015). DICER is a ribonuclease III (RNase III) enzyme that specifically cleave double-stranded RNAs (Bernstein et al., 2001). AGO bind sRNA and use them as a guide to silence target gene at the transcriptional or the post transcriptional level (Fang and Qi 2016). Some sRNAs are mobile signals in plants that transmit gene silencing from cell to cell or systemically over a long distance through vasculature (Brosnan and Voinnet 2011; Sarkies and Miska 2014). Different sRNA can move throughout the plant, transport to plant pathogen via extracellular vesicles (Tang et al., 2022).
Plant small RNAs are divided into two classes: a short interfering RNAs (siRNAs) and microRNAs (miRNAs) which may regulate plant immunity in response to pathogen attack (Huang et al., 2016; Islam et al. 2018). siRNAs and miRNA are 21 – 25 nucleotides and generated from long dsRNA precursor by DICER (Moazed 2009), yielding mature miRNA which may influence gene transcript levels and translation (Huang et al., 2020). siRNAs generated from long dsRNA and may require RNA-dependent RNA polymerase (Huang et al., 2016). Both miRNAs and siRNAs can induce post transcriptional gene silencing (PTGS) by messenger RNA (mRNA) cleavage/degradation or translational inhibition via RNA-induced silencing complex (RISC), whereas transcriptional gene silencing (TGS) results in either DNA methylation, histone modification or chromatin modification, which is usually mediated by siRNAs and some specific miRNA (Vaucheret 2006; Wu et al., 2010).
Small RNA from host plant enters pathogen cell during invasion and silence pathogen genes. This process has been exploited through Host-Induced Gene Silencing (HIGS), where plant transgenes that produce sRNAs are engineered to silence pest and pathogen genes (Bilir et al., 2022). Plant pathogen Phytophthora genome encodes several hundred of cytoplasmic effector which can target plant RNAi machinery disabling plant immune response (Xiong et al., 2014). Small RNA are regulators and act in different tier of plant immunity including pathogen-associated molecular patterns-triggered immunity (PTI) and effector-triggered immunity (ETI). Plant utilize RNA silencing machinery to facilitate PTI and ETI to defend themselves against the pathogen attack or facilitate defense against insect herbivores (Huang et al., 2016). Pathogens on the other hand generate effectors and sRNA to counter. Bacteria, fungi and oomycetes after penetrating the plant cell wall localize in intercellular space for amplification. Fungi oomycetes enter cell in the late infection stages (Huang et al., 2016). Recognition of pathogen activates PTI. PTI requires miRNAs and siRNAs which act as a key fine-tuning regulators of plant hormones including auxin abscisic acid, salicylic acid and jasmonic acid pathways (Zhang et al., 2011).
Many pathogens deliver effector proteins into host cell to suppress host immunity, whereas plants have evolved resistance protein to recognize effector and trigger robust resistance. Transposable elements (TEs) are hot spots of sRNA production which regulates and fine-tune the expression of effector genes and host plant resistance (R) genes. TEs are mobile genomic elements. TE activity is essential for maintaining genome integrity (Weiberg et al., 2014). Transposable elements transposition shapes the repertoires of effector genes in pathogens and R genes in plants. In pathogen, sRNAs regulate expression of TEs and of TE-associated protein effector genes, sRNA effectors are delivered into host cells to manipulate expression of host defense genes (Weiberg et al., 2014). In plants sRNAs epigenetically controls R-gene expression, which activates defense genes upon infection. It is possible that plants may also deliver plant RNA or protein molecules into the pathogen cells. This may affect plant-pathogen interaction and contribute to host plant resistance, pathogen virulence and host adaptation (Weiberg et al., 2014).
References:
Bernstein, E., Caudy, A. A., Hammond, S. M. and Hannon, G. J. 2001 Role for a Bidentate Ribonuclease in the Initiation Step of RNA Interference. Nature 409(6818): 363 – 366
doi: 10.1038/35053110
Bilir, O., Goi, D., Hong, Y., McDowell, J. M. and Tor, M. 2022 Small RNA-based Plant Protection against Diseases. Front. Plant Sci. 13: 951097
doi: 10.3389/fpls.2022.951097
Brosnan, C. A. and Voinnet, O. 2011 Cell-to Cell and Long-Distance siRNA Movement in Plants: Mechanisms and Biological Implications. Curr. Opin. Plant Biol. 14(5): 580 – 587
doi: 10.1016/j.pbi.2011.07.011
Chen, X. 2009 Small RNAs and their Roles in Plant Development. Annu. Rev. Cell Dev. Biol. 25: 21 – 44
doi: 10.1146/annurev.cellbio.042308.113417
Ellendorff, U., Fradin, E. F., de Jonge, R. and Thomma, B. P. H. J. 2009 RNA Silencing is Required for Arabidopsis Defence against Verticillium Wilt Disease. J. Exp. Bot. 60(2): 591 – 602
doi: 10.1093/jxb/ern306
Fang, X. and Qi, Y. 2016 RNAi in Plants: An Argonaute-Centered View. The Plant Cell 28(2): 272 – 285
doi.org/10.1105/tpc.15.00920
Huang, K., Demirci, F., Batish, M., Treible, W., Meyers, B. C. and Caplan, J. L. 2020 Quantitative Super-Resolution Localization of Small RNAs with sRNA-PAINT. Nucleic Acids Research 48(16): e96
doi.org/10.1093/nar/gkaa623
Huang, J., Yang, M. and Zhang, X. 2016 The Function of Small RNAs in Plant Biotic Stress Response. Journal of Integrative Plant Biology 58(4): 312 – 327
doi.org/10.1111/jipb.12463
Islam, W., Norman, A., Qasim, M. and Wang, L. 2018 Plant Responses to Pathogen Attack: Small RNAs in Focus. Int. J. Mol. Sci. 19(2): 515
doi: 10.3390/ijms19020515
Liu, S., Jaouannet, M., Dempsey, D. A., Imani, J., Coustau, C. and Kogel, K-H. 2020 RNA-Based Technologies for Insect Control in Plant Production. Biotech. Adv. 39: 107463
doi.org/10.1016/j.biotechadv.2019.107463
Moazed, D. 2009 Small RNAs in Transcriptional Gene Silencing and Genome Defence. Nature 457(7228): 413 – 420
doi: 10.1038/nature07756
Sarkies, P. and Miska, E. A. 2014 Small RNAs Break Out: The Molecular Cell Biology of Mobile Small RNAs. Nat. Rev. Mol. Cell Biol. 15(8): 525 – 535
doi: 10.1038/nrm3840
Tang, Y., Yan, X., Gu, C. and Yuan, X. 2022 Biogenesis, Trafficking and Function of Small RNAs in Plants. Front. Plant Sci. 13: 825477
doi: 10.3389/fpls.2022.825477
Vaucheret, H. 2006 Post-transcriptional Small RNA Pathways in Plants: Mechanisms and Regulations. Genes Dev. 20(7): 759 – 771
doi: 10.1101/gad.1410506
Weiberg, A. and Jin, H. 2015 Small RNAs-The Secret Agents in the Plant-Pathogen Interactions. Curr. Opin. Plant Biol. 26: 87 – 94
doi: 10.1016/j.pbi.2015.05.033
Weiberg, A., Wang, M., Bellinger, M. and Jin, H. 2014 Small RNAs: A New Paradigm in Plant-Microbe Interactions. Annu. Rev. Phytopathol. 52: 495 – 516
doi: 10.1146/annurev-phyto-102313-045933
Wu, L., Zhou, H., Zhang, Q., Zhang, J., Ni, F., Liu, C. and Qi, Y. 2010 DNA Methylation Mediated by a microRNA Pathway. Mol. Cell 38(3): 465 – 475
doi: 10.1016/j.molcel.2010.03.008
Xiong, Q., Ye, W., Choi, D., Wong, J., Qiao, Y., Tao, K., Wang, Y. and Ma, W. 2014 Phytophthora Suppressor of RNA Silencing 2 is a Conserved RxLR Effector that Promotes Infection in Soybean and Arabidopsis thaliana. Mol. Plant Microbe Interact. 27(12): 1379 – 1389
doi: 10.1094/MPMI-06-14-0190-R
Zamore, P. D. and Haley, B. 2005 Ribo-gnome: The Big World of small RNA. Science 309(5740): 1519-1524
doi: 10.1126/science.1111444
Zhang, W., Gao, S., Zhou, X., Chellappan, P., Chen, Z., Zhou, X., Zhang, X., Fromuth, N., Coutino, G., Coffey, M. and Jin, H. 2011 Bacteria-Responsive microRNAs Regulate Plant Innate Immunity by Modulating Plant Hormone Networks. Plant Mol. Biol. 75(1-2): 93 – 105
doi: 10.1007/s11103-010-9710-8
Zhu, C., Liu, T., Chang, Y-N. and Duan, C-G. 2019 Small RNA Functions as a Trafficking Effector in Plant Immunity. Int. J. Mol. Sci. 20(11): 2816
doi.org/10.3390/ijms20112816
BIOLOGICAL PROCESSES- A NATURE'S GIFT 