Plant miRNA Mediated Defense Response

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 November 2019) | Viewed by 21868

Special Issue Editor

School of Biological Sciences, University of Nebraska, Lincoln 1901 Vine St., Lincoln, NE 68588-0660, USA
Interests: non-coding RNAs; miRNAs and siRNAs; epigenetics; functional genomics; plant molecular biology; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

MicroRNAs (miRNAs) are small non-coding regulatory RNAs that repress gene expression at posttranscriptional levels. They are produced from primary miRNA transcripts and are associated with the effect protein called Argonaut (AGO) to suppress the expression of messenger RNAs containing their complementary sequences.   More than several hundreds of miRNAs, including many conserved ones, have been isolated in plants. Many of them play critical roles in plant defense responses. On one hand, plants often up- or down-regulate the levels or activities of miRNAs in order to prevent infections of bacteria, fungi, oomycetes, parasitic plants, virus and pest infections. On the other hand, pathogens also possess mechanisms to suppress miRNA-mediate defense or to use host miRNAs to facilitate their infection.  Moreover, miRNA-based strategies have also been developed for plants to fight against various pathogens.

In this Special Issue, we are inviting reviews, perspectives, and original research articles to advance our knowledge related to miRNA-mediated plant defense responses. Topics will include, but not limited to, miRNA function and related regulation during plant defense responses, strategies used by pathogens to evade miRNA-mediated defenses and miRNA-based applications to improve plant adaptations.

Dr. Bin Yu
Guest Editor

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Keywords

  • Plants
  • Defense responses
  • miRNAs
  • Virus
  • Bacteria
  • Fungi
  • Pest
  • Parasitic plants

Published Papers (6 papers)

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Research

22 pages, 3236 KiB  
Article
Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri
by Shiheng Lyu, Ying Yu, Shirong Xu, Weiwei Cai, Guixin Chen, Jianjun Chen, Dongming Pan and Wenqin She
Genes 2020, 11(1), 17; https://doi.org/10.3390/genes11010017 - 23 Dec 2019
Cited by 8 | Viewed by 3202
Abstract
MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference [...] Read more.
MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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19 pages, 1070 KiB  
Article
MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species
by Ales Eichmeier, Tomas Kiss, Eliska Penazova, Jakub Pecenka, Akila Berraf-Tebbal, Miroslav Baranek, Robert Pokluda, Jana Cechova, David Gramaje and Dariusz Grzebelus
Genes 2019, 10(11), 905; https://doi.org/10.3390/genes10110905 - 07 Nov 2019
Cited by 6 | Viewed by 3488
Abstract
Diaporthe species are important pathogens, saprobes, and endophytes on grapevines. Several species are known, either as agents of pre- or post-harvest infections, as causal agents of many relevant diseases, including swelling arm, trunk cankers, leaf spots, root and fruit rots, wilts, and cane [...] Read more.
Diaporthe species are important pathogens, saprobes, and endophytes on grapevines. Several species are known, either as agents of pre- or post-harvest infections, as causal agents of many relevant diseases, including swelling arm, trunk cankers, leaf spots, root and fruit rots, wilts, and cane bleaching. A growing body of evidence exists that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation, during plant development and responses to biotic and abiotic stresses. In this study, we explored differentially expressed miRNAs in response to Diaporthe eres and Diaporthe bohemiae infection in Vitis vinifera cv. Chardonnay under in vitro conditions. We used computational methods to predict putative miRNA targets in order to explore the involvement of possible pathogen response pathways. We identified 136 known and 41 new miRNA sequence variants, likely generated through post-transcriptional modifications. In the Diaporthe eres treatment, 61 known and 17 new miRNAs were identified while in the Diaporthe bohemiae treatment, 101 known and 21 new miRNAs were revealed. Our results contribute to further understanding the role miRNAs play during plant pathogenesis, which is possibly crucial in understanding disease symptom development in grapevines infected by D. eres and D. bohemiae. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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16 pages, 1990 KiB  
Article
miR403a and SA Are Involved in NbAGO2 Mediated Antiviral Defenses Against TMV Infection in Nicotiana benthamiana
by Pengfei Diao, Qimeng Zhang, Hongyu Sun, Wenjie Ma, Aiping Cao, Ruonan Yu, Jiaojiao Wang, Yiding Niu and Hada Wuriyanghan
Genes 2019, 10(7), 526; https://doi.org/10.3390/genes10070526 - 12 Jul 2019
Cited by 24 | Viewed by 3936
Abstract
RNAi (RNA interference) is an important defense response against virus infection in plants. The core machinery of the RNAi pathway in plants include DCL (Dicer Like), AGO (Argonaute) and RdRp (RNA dependent RNA polymerase). Although involvement of these RNAi components in virus infection [...] Read more.
RNAi (RNA interference) is an important defense response against virus infection in plants. The core machinery of the RNAi pathway in plants include DCL (Dicer Like), AGO (Argonaute) and RdRp (RNA dependent RNA polymerase). Although involvement of these RNAi components in virus infection responses was demonstrated in Arabidopsis thaliana, their contribution to antiviral immunity in Nicotiana benthamiana, a model plant for plant-pathogen interaction studies, is not well understood. In this study, we investigated the role of N. benthamiana NbAGO2 gene against TMV (Tomato mosaic virus) infection. Silencing of NbAGO2 by transient expression of an hpRNA construct recovered GFP (Green fluorescent protein) expression in GFP-silenced plant, demonstrating that NbAGO2 participated in RNAi process in N. benthamiana. Expression of NbAGO2 was transcriptionally induced by both MeSA (Methylsalicylate acid) treatment and TMV infection. Down-regulation of NbAGO2 gene by amiR-NbAGO2 transient expression compromised plant resistance against TMV infection. Inhibition of endogenous miR403a, a predicted regulatory microRNA of NbAGO2, reduced TMV infection. Our study provides evidence for the antiviral role of NbAGO2 against a Tobamovirus family virus TMV in N. benthamiana, and SA (Salicylic acid) mediates this by induction of NbAGO2 expression upon TMV infection. Our data also highlighted that miR403a was involved in TMV defense by regulation of target NbAGO2 gene in N. Benthamiana. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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24 pages, 3393 KiB  
Article
Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing
by María José López-Galiano, Vicente Sentandreu, Amparo C. Martínez-Ramírez, Carolina Rausell, M. Dolores Real, Gemma Camañes, Omar Ruiz-Rivero, Oscar Crespo-Salvador and Inmaculada García-Robles
Genes 2019, 10(6), 475; https://doi.org/10.3390/genes10060475 - 21 Jun 2019
Cited by 16 | Viewed by 4384
Abstract
Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic [...] Read more.
Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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17 pages, 3034 KiB  
Article
Genome-Wide Analysis of the miRNA–mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra
by Bo Zhou, Yutong Kang, Jingtong Leng and Qijiang Xu
Genes 2019, 10(6), 430; https://doi.org/10.3390/genes10060430 - 05 Jun 2019
Cited by 19 | Viewed by 2942
Abstract
Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in [...] Read more.
Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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20 pages, 2384 KiB  
Article
Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing
by Saud M. Alzahrani, Ibrahim A. Alaraidh, Muhammad A. Khan, Hussein M. Migdadi, Salem S. Alghamdi and Abdluaziz A. Alsahli
Genes 2019, 10(4), 303; https://doi.org/10.3390/genes10040303 - 17 Apr 2019
Cited by 23 | Viewed by 3229
Abstract
Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive [...] Read more.
Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive Hassawi-3 and the salt-tolerant ILB4347 genotypes of faba bean, growing under salt stress. A total of 527 miRNAs in Hassawi-3 plants, and 693 miRNAs in ILB4347 plants, were found to be differentially expressed. Additionally, 284 upregulated and 243 downregulated miRNAs in Hassawi-3, and 298 upregulated and 395 downregulated miRNAs in ILB4347 plants growing in control and stress conditions were recorded. Target prediction and annotation revealed that these miRNAs regulate specific salt-responsive genes, which primarily included genes encoding transcription factors and laccases, superoxide dismutase, plantacyanin, and F-box proteins. The salt-responsive miRNAs and their targets were functionally enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, which showed that the miRNAs were involved in salt stress-related biological pathways, including the ABC transporter pathway, MAPK signaling pathway, plant hormone signal transduction, and the phosphatidylinositol signaling system, among others, suggesting that the miRNAs play an important role in the salt stress tolerance of the ILB4347 genotype. These results offer a novel understanding of the regulatory role of miRNAs in the salt response of the salt-tolerant ILB4347 and the salt-sensitive Hassawi-3 faba bean genotypes. Full article
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
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