mgr-mir-9 implicates Meloidogyne graminicola infection in rice by targeting the effector MgPDI

doi:10.1016/j.jia.2022.08.127

Journal of Integrative Agriculture

2023, Vol. 22

Issue (5): 1445-1454 DOI: 10.1016/j.jia.2022.08.127

Plant Protection

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mgr-mir-9 implicates Meloidogyne graminicola infection in rice by targeting the effector MgPDI

TIAN Zhong-ling¹, ZHOU Jia-yan¹, ZHENG Jing-wu², HAN Shao-jie^{2, 3#}

¹ Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, P.R.China

² Laboratory of Plant Nematology, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, P.R.China

³ Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, P.R.China

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摘要

MicroRNAs (miRNAs)是一类重要的非编码RNA，在包括植物寄生线虫在内的一系列动物中均是重要的内源性基因调控因子。拟禾本科根结线虫系一种定居性植物内寄生虫，主要侵染危害水稻，严重影响水稻生产。目前关于拟禾本科根结线虫的研究主要集中在效应子在线虫寄生过程中的功能研究方面。而拟禾本科根结线虫miRNA如何对其自身效应子表达进行调控而影响线虫侵染的机制鲜有报道。本研究对拟禾本科根结线虫二龄幼虫（J2）的3个文库进行小RNA测序，共获得49,767,105条clean reads。通过进一步的注释，共鉴定出233个已知miRNAs和21个新miRNAs。在已知的miRNAs中，mgr-lin-4、mgr-mir-1、mgr-mir-100、mgr-mir-86、mgr-mir-279、mgr-mir-87、mgr-mir-71、mgr-mir-9、mgr-mir-50、mgr-mir-72和mgr-mir-34的丰度最高。基于实时荧光定量PCR对随机选取的5个miRNA表达水平进行了测定，定量检测结果与小RNA测序结果相符。由于miRNA是动物体内重要的调控因子，我们推测这些miRNAs可能在拟禾本科根结线虫的J2龄期调控效应子的表达，而促进其侵染。利用双荧光素酶报告基因检测验证mgr-mir-9能够靶向拟禾本科根结线虫侵染相关的重要效应子基因MgPDI；此外，用mgr-mir-9 mimics浸泡后的二龄幼虫体内MgPDI基因表达下调，线虫繁殖能力下降，证实了mgr-mir-9参与调控拟禾本科根结线虫的早期侵染。本研究首次报道了拟禾本科根结线虫miRNA在早期侵染过程中通过调控自身效应子的表达而行使重要功能，为应用相关miRNA及其靶向的效应因子作为拟禾本科根结线虫防治的新靶标提供了理论支持。

Abstract

MicroRNAs (miRNAs), a class of small non-coding RNAs, are crucial endogenous gene regulators in a range of animals, including plant-parasitic nematodes. Meloidogyne graminicola is an obligate sedentary endoparasite of rice and causes significant yield losses. A number of studies focused on the roles of M. graminicola effectors during the parasitic process; however, how nematode miRNAs regulate its effectors needs elucidating. In this research, we analyzed a cluster of M. graminicola miRNAs obtained at the second-stage juveniles (J2s) stage that are closely linked to the regulation of M. graminicola effectors. There are 49 767 105 total clean reads obtained from three libraries. A total of 233 known miRNAs and 21 novel miRNAs were identified. Among the known miRNAs, mgr-lin-4, mgr-mir-1, mgr-mir-100, mgr-mir-86, mgr-mir-279, mgr-mir-87, mgr-mir-71, mgr-mir-9, mgr-mir-50, mgr-mir-72, and mgr-mir-34 are the most abundant 11 miRNAs families. Moreover, the expression levels of selected miRNAs were validated by real-time quantitative PCR. We hypothesized that these miRNAs might regulate the expression of secreted effectors during the J2s stage to facilitate its infection. Consistent with this, we found that mgr-mir-9 targets MgPDI, an important M. graminicola effector mRNA. In addition to that, J2s treated with mgr-mir-9 mimics showed down-regulation of MgPDI expression and reduced reproductive ability, alluding mgr-mir-9 is involved in nematode infection. These results provide novel insight into the regulatory functions of M. graminicola miRNAs during the infection and identify miRNAs and their effector targets as potential key management targets to limit parasite survival during the early stages of infection.

Keywords: microRNA function Meloidogyne graminicola deep sequencing Dual-Luciferase Reporter Assay System protein disulfide isomerase

Received: 23 May 2022 Accepted: 22 June 2022

Fund:

This work was financially supported by the National Natural Science Foundation of China (32001877).

About author: TIAN Zhong-ling, E-mail: zltian@zjsru.edu.cn; #Correspondence HAN Shao-jie, E-mail: hanshaojie@zju.edu.cn

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TIAN Zhong-ling, ZHOU Jia-yan, ZHENG Jing-wu, HAN Shao-jie. 2023.

mgr-mir-9 implicates Meloidogyne graminicola infection in rice by targeting the effector MgPDI . Journal of Integrative Agriculture, 22(5): 1445-1454.

Ambros V. 2004. The functions of animal microRNAs. Nature, 431, 350–355.

Bartel D P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.

Bridge J, Page S L J. 1982. The rice root-knot nematode, Meloidogyne graminicola, on deep water rice (Oryza sativa) subsp. indica). Revue de Nematologie, 5, 225–232.

Bybd D W, Kirkpatrick T, Barker K R. 1983. An improved technique for clearing and staining plant-tissues for detection of nematodes. Journal of Nematology, 15, 142–43.

Cabrera J, Barcala M, Garcia A, Rio-Machin A, Medina C, Jaubert-Possamai S, Favery B, Maizel A, Ruiz-Ferrer V, Fenoll C, Escobar C. 2016. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: A functional role for miR390 and its TAS3-derived tasiRNAs. New Phytologist, 209, 1625–1640.

Carrington J C, Ambros V. 2003. Role of microRNAs in plant and animal development. Science, 301, 336–338.

Castagnone-Sereno P, Danchin E G J, Perfus-Barbeoch L, Abad P. 2013. Diversity and evolution of root-knot nematodes, genus Meloidogyne: New insights from the genomic era. Annual Review of Phytopathology, 51, 203–220.

Chen J, Hu L, Sun L, Lin B, Huang K, Zhuo K, Liao J. 2018. A novel Meloidogyne graminicola effector, MgMO237, interacts with multiple host defence-related proteins to manipulate plant basal immunity and promote parasitism. Molecular Plant Pathology, 19, 1942–1955.

Chen J, Lin B, Huang Q, Hu L, Zhuo K, Liao J. 2017. A novel Meloidogyne graminicola effector, MgGPP, is secreted into host cells and undergoes glycosylation in concert with proteolysis to suppress plant defenses and promote parasitism. PLoS Pathogens, 13, e1006301.

Chen X M. 2005. MicroRNA biogenesis and function in plants. FEBS Letters, 579, 5923–5931.

Coolen M, Katz S, Bally-Cuif L. 2013. miR-9: A versatile regulator of neurogenesis. Frontiers in Cellular Neuroscience, 7, 220.

Ding X, Ye J, Wu X, Huang L, Zhu L, Lin S. 2015. Deep sequencing analyses of pine wood nematode Bursaphelenchus xylophilus microRNAs reveal distinct miRNA expression patterns during the pathological process of pine wilt disease. Gene, 555, 346–356.

Dutta T K, Powers S J, Kerry B R, Gaur H S, Curtis R H C. 2011. Comparison of host recognition, invasion, development and reproduction of Meloidogyne graminicola and M. incognita on rice and tomato. Nematology, 13, 509–520.

Ferris H, Griffiths B S, Porazinska D L, Powers T O, Wang K H, Tenuta M. 2012. Reflections on plant and soil nematode ecology: Past, present and future. Journal of Nematology, 44, 115–126.

Filipowicz W, Bhattacharyya S N, Sonenberg N. 2008. Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? Nature Reviews Genetics, 9, 102–114.

Gebert L F R, MacRae I J. 2019. Regulation of microRNA function in animals. Nature Reviews Molecular Cell Biology, 20, 21–37.

Goverse A, Smant G. 2014. The activation and suppression of plant innate immunity by parasitic nematodes. Annual Review of Phytopathology, 52, 243–265.

Haegeman A, Bauters L, Kyndt T, Rahman M M, Gheysen G. 2013. Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola. Molecular Plant Pathology, 14, 379–390.

Hewezi T, Baum T J. 2013. Manipulation of plant cells by cyst and root-knot nematode effectors. Molecular Plant–Microbe Interactions, 26, 9–16.

Huang G, Allen R, Davis E L, Baum T J, Hussey R S. 2006. Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proceedings of the National Academy of Sciences of the United States of America, 103, 14302–1406.

Huang W K, Ji H L, Gheysen G, Kyndt T. 2016. Thiamine-induced priming against root-knot nematode infection in rice involves lignification and hydrogen peroxide generation. Molecular Plant Pathology, 17, 614–624.

Jones J D G, Dangl J L. 2006. The plant immune system. Nature, 444, 323–329.

Kaur P, Shukla N, Joshi G, VijayaKumar C, Jagannath A, Agarwal M, Goel S, Kumar A. 2017. Genome-wide identification and characterization of miRNAome from tomato (Solanum lycopersicum) roots and root-knot nematode (Meloidogyne incognita) during susceptible interaction. PLoS ONE, 12, e0175178.

Kozomara A, Birgaoanu M, Griffiths-Jones S. 2019. miRBase: from microRNA sequences to function. Nucleic Acids Research, 47, D155–D162.

Krueger J, Rehmsmeier M. 2006. RNAhybrid: MicroRNA target prediction easy, fast and flexible. Nucleic Acids Research, 34, W451–W454.

Kyndt T, Fernandez D, Gheysen G. 2014. Plant-parasitic nematode infections in rice: Molecular and cellular insights. Annual Review of Phytopathology, 52, 1–19.

Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858.

Lee R C, Feinbaum R L, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843–854.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–ΔΔCt method. Methods, 25, 402–408.

Mani V, Assefa A D, Hahn B S. 2021. Transcriptome analysis and miRNA target profiling at various stages of root-knot nematode Meloidogyne incognita development for identification of potential regulatory networks. International Journal of Molecular Sciences, 22, 7442.

Mantelin S, Bellafiore S, Kyndt T. 2017. Meloidogyne graminicola: A major threat to rice agriculture. Molecular Plant Pathology, 18, 3–15.

Pan X, Nichols R L, Li C, Zhang B. 2019. MicroRNA-target gene responses to root knot nematode (Meloidogyne incognita) infection in cotton (Gossypium hirsutum L.). Genomics, 111, 383–390.

Pokharel R R, Abawi G S, Duxbury J M, Smat C D, Wang X, Brito J A. 2010. Variability and the recognition of two races in Meloidogyne graminicola. Australasian Plant Pathology, 39, 326–333.

Quentin M, Abad P, Favery B. 2013. Plant parasitic nematode effectors target host defense and nuclear functions to establish feeding cells. Frontiers in Plant Science, 4, 53.

Rosso M N, Dubrana M P, Cimbolini N, Jaubert S, Abad P. 2005. Application of RNA interference to root-knot nematode genes encoding esophageal gland proteins. Molecular Plant–Microbe Interactions, 18, 615–620.

Schnall-Levin M, Zhao Y, Perrimon N, Berger B. 2010. Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3´ UTRs. Proceedings of the National Academy of Sciences of the United States of America, 107, 15751–15756.

Sevier C S, Kaiser C A. 2002. Formation and transfer of disulphide bonds in living cells. Nature Reviews Molecular Cell Biology, 3, 836–847.

Simon D J, Madison J M, Conery A L, Thompson-Peer K L, Soskis M, Ruvkun G B, Kaplan J M, Kim J K. 2008. The MicroRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell, 133, 903–915.

Stolf B S, Ioannis S, Lopes L R, Vendramin A, Goto H, Laurindo F R M, Shah A M, Santos C X C. 2011. Protein disulfide isomerase and host–pathogen interaction. Thescientific World Journal, 11, 1749–1761.

Subramanian P, Choi I C, Mani V, Park J, Subramaniyam S, Choi K H, Sim J S, Lee C M, Koo J C, Hahn B S. 2016. Stage-wise identification and analysis of mirna from root-knot nematode Meloidogyne incognita. International Journal of Molecular Sciences, 17, 1758.

Tian B, Wang S, Todd T C, Johnson C D, Tang G, Trick H N. 2017. Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics, 18, 572.

Tian Z, Wang Z, Munawar M, Zheng J. 2020. Identification and characterization of a novel protein disulfide isomerase gene (MgPDI2) from Meloidogyne graminicola. International Journal of Molecular Sciences, 21, 9586.

Tian Z L, Barsalote E M, Li X L, Cai R H, Zheng J W. 2017. First report of root-knot nematode, Meloidogyne graminicola, on rice in Zhejiang, Eastern China. Plant Disease, 101, 2152–2153.

Tian Z L, Wang Z H, Maria M, Qu N, Zheng J W. 2019. Meloidogyne graminicola protein disulfide isomerase may be a nematode effector and is involved in protection against oxidative damage, Scientific Reports, 9, 11949.

Trudgill D L, Blok V C. 2001. Apomictic, polyphagous root-knot nematodes: Exceptionally successful and damaging biotrophic root pathogens. Annual Review of Phytopathology, 39, 53–77.

Verstraeten B, Atighi M R, Ruiz-Ferrer V, Escobar C, De Meyer T, Kyndt T. 2021. Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC Genomics, 22, 560.

Wang C, Lower S, Williamson V M. 2009. Application of pluronic gel to the study of root-knot nematode behaviour. Nematology, 11, 453–464.

Wang Y, Mao Z, Yan J, Cheng X, Liu F, Xiao L, Dai L, Luo F, Xie B. 2015. Identification of microRNAs in Meloidogyne incognita using deep sequencing. PLoS ONE, 10, e0133491.

Wightman B, Ha I, Ruvkun G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern-formation in C. elegans. Cell, 75, 855–862.

Zhang B, Wang Q. 2015. MicroRNA-based biotechnology for plant improvement. Journal of Cellular Physiology, 230, 1–15.

Zhang B, Wang Q, Pan X. 2007. MicroRNAs and their regulatory roles in animals and plants. Journal of Cellular Physiology, 210, 279–289.

Zhang Y, Wang Y, Xie F, Li C, Zhang B, Nichols R L, Pan X. 2016. Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing. Functional & Integrative Genomics, 16, 127–142.

Zisoulis D G, Lovci M T, Wilbert M L, Hutt K R, Liang T Y, Pasquinelli A E, Yeo G W. 2010. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nature Structural & Molecular Biology, 17, 173–179.

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