Functions of miRNA during Host-Pathogen Interactions - An Overview
Authors: A. Kandan, J. Akhtar, Pardeep Kumar and Z. Khan
Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources (NBPGR), Pusa Campus, New Delhi " 110012

MicroRNAs (miRNAs) defined as a class of short endogenous non-coding small RNA molecules that mediate gene regulation through RNA silencing at the post-transcriptional level. These miRNAs primary transcripts form are precursor RNAs, which have a partially double-stranded stem-loop structure and later which are processed by DCL proteins to release mature miRNAs. All plants are widely subjected to attack by various fungal pathogens and their interactions are quite interesting. Multiple interaction effects between plant and fungus reflects the nutrient acquisition strategies of the pathogen as well as the defense strategies of plants under different environmental conditions. Basic innate effectors and resistance gene mediated resistance are the two well known defense mechanisms of the plant under fungal pathogen infection. With the primary innate immune system, plants effectively recognize microbe associated molecular patterns (MAMPs) of potential fungal pathogens through pattern recognition receptors (PRRs) that mediate basic innate defense responses. Resistance gene mediated defense reaction is called as second layer of defense against the fungus. Resistance proteins are mainly intracellular in nature and have the capability to directly or indirectly detect isolate specific fungal pathogen effectors encoded by avirulence genes (Avr) resulting in activation of defense reaction. Few scientists reported miRNAs have emerged as a potential means to study the complex regulatory networks operated during plant-fungus interactions.

Response of host miRNAs during fungus attack

In rice (Oryza sativa), miRNAs profiling of the rice blast fungus Magnaporthe oryzae"challenged resistant and susceptible cultivars revealed induction of miR160 and miR164 in resistant cultivar whereas miR396 is downregulated upon infection in the same resistance cultivar which not observed in the susceptible cultivar shows the positive and negative roles in pathogen effector recognition by plant resistance proteins that induces defense response generally termed as effector triggered immunity (ETI). Transgenic overexpression of miR160 or miR398 in a susceptible rice cultivar leads to appreciable enhanced disease resistance toward M. oryzae, confirming that these two miRNAs (miR160 and miR398) are good positive regulators of defense response against M. oryzae. In wheat challenge inoculation with powdery mildew fungus (Blumeria graminis) in resistant and susceptible cultivar shows induction of miR2008 and miR2012 in resistant wheat cultivar, whereas induction of miR393, miR444, miR827, miR2005, and miR2013 and suppression of miR2001, miR2006, and miR2011 was observed in susceptible wheat cultivar. These host miRNAs in wheat are likely to actively participate in early defense responses of host through regulating hormone signaling pathways, protein and lignin biosynthesis.

In cotton, challenge inoculation with Verticillium dahliae fungus in two cultivars mainly Hai-7124 and Yi-11 showed more than 65 miRNAs exhibited altered expression after infection with V. dahliae fungus. Specifically three miRNAs like Ptc-miR482, PtcmiR1444 and Ptc-miR1448 in cotton target the cleavage of poly phenol oxidase (PPO) gene and disease resistance protein genes which regulate biotic and abiotic stress resistance in plants. Subsequent down-regulation of two miRNAs namely miR482 and miR1448 in V. dahliae infected cotton roots, suggest that increased PPO and disease resistance proteins which play important role in regulating disease signaling network during cotton- V. dahliae fungus interaction. Similarly, miR2118 have been predicted to target TIR-NBS-LRR in cotton infected with V. dahliae fungus. Therefore, downregulation of this miR2118 in V. dahliae infected cotton roots indicates higher accumulation of resistance protein which eventually might be linked to increased defense response in the cotton roots (Yin et al., 2012).

In Solanum melongena challenge inoculation with V. dahliae revealed 33 responsive miRNAs and noted miR393 and miR399 are both highly downregulated after infection, allowing for the accumulation of their target gene auxin receptor, TIR1, and an E2 conjugating enzyme gene, PHO2. Three cultivars of soybean challenge inoculated with Phytophthora sojae revealed miR403 which targets AGO protein genes was downregulated suggesting a positive role of RNAi machinery in host defense against this fungus. In other experiment challenge inoculation of wheat with Puccinia graminis f.sp. tritici showed accumulation of miR1138 which effectively controls eIF-4b (eukaryotic initiation factor-4b) that regulates protein biosynthesis which indicated that Puccinia graminis f.sp. tritici perturbs the host cell function homeostasis by modulating host protein biosynthetic machinery.

Xin and his co-workers (2010) identified 24 miRNAs in wheat in response to inoculation of Erysiphe graminis f.sp. tritici. After inoculation, down-regulation of miR156, miR159, miR164 and miR168 proposed up-regulation of consequent target genes which are involved in stress response, signal transduction, root development and various oxidative stress responses. Few other reports indicated that conserved miRNA are more involved in host defense response against fungi compared to inducible miRNA. For example, conserved miRNAs, miR156, miR164, miR159, miR168, miR169, miR172, miR393, miR398, miR396 and miR1447 indicated upregulation in Populas beijingensis when challenge inoculated with Dothiorella gregaria. Pbe-miR482b, pbe-SR3, pbe-SR23, and pbe-SR25 were observed to be well up-regulated under Dothiorella gregaria infection of P. beijingensis which putatively target proteins involved in disease resistance of the host.

Fungal pathogen has well developed the capability to influence the regulatory defense network of plants by producing various phytohormones. For example, salicyclic acid is involved in host resistance to biotrophic pathogens whereas jasmonic acid and ethylene in contrast mediate host resistance mostly to necrotrophic pathogens. miRNAs also play major role in regulating these phytohormones as miR393 was observed to be induced in wheat infected with Blumeria graminis f.sp. tritici which eventually regulate auxin signaling and defense response by targeting TIR1 in wheat. Likewise, expression of 9 out of 11 miRNAs families was well down-regulated in loblolly pine stem above gall (SAG) infected with fusiform rust disease which showed the regulation of plant defense response by targeting the transcription factors that eventually regulate disease signaling, hormonal signaling and plant development. Thus understanding the role of miRNAs in host-pathogen interactions will give the basic of regulation of disease pathogenesis.


1. Yin Z, Li Y, Han X, Shen F. 2012. Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots. PLoS One 7(4):e35765.

2. Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z, et al. 2010. Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123.

About Author / Additional Info:
Senior Scientist (Plant Pathology), Division of Plant Quarantine, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources (NBPGR), Pusa Campus, New Delhi-110012.