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Regulations by Small RNA in Plant Development and Beyond
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Regulations by Small RNA in Plant Development and Beyond

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 July 2019) | Viewed by 36127

Special Issue Editors

Dr. Giorgio Gambino

E-Mail Website
Guest Editor
Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Torino, Italy
Interests: small RNAs; virus; grapevine; plant-pathogen interaction; genetic transformation; functional genomics; methylation; biotic stress
Special Issues, Collections and Topics in MDPI journals
Dr. Chiara Pagliarani

E-Mail Website
Guest Editor
Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 10125 Torino, Italy
Interests: miRNA signalling; grapevine; transcriptional changes; genotype-environment interaction; molecular mechanisms of stress responses; drought stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants are subjected to several environmental stimuli during their lifetime and a fine transcriptome reprogramming is needed to allow the balance between the plant response to numerous stress factors and processes of plant growth and development. In this context, non-coding RNAs (ncRNAs) are fundamental players in the transcriptional and epigenetic regulatory mechanisms involved in the development and environmental adaptation of plants. Basing on their biogenesis, small RNAs are classified in different categories, such as miRNAs, siRNAs, and long ncRNAs, each exerting specific functions in gene regulation that often overlap with hormonal signalling cascades. Although in the last decade there was a real explosion of studies on plant small RNAs, many elements of RNA signalling pathways are still unsolved.

Papers submitted to this Special Issue should report novel and timely results unveiling key aspects of small RNA functions and the related silencing machinery in plants, including DNA methylation. Particular attention is directed to research studies concerning significant advances in small RNA-mediated signalling pathways crucial for the understanding of plant development, and of physiological and molecular responses to abiotic and biotic stress. Groundbreaking insights shedding new light on MIRNA genes and/or the diversification of miRNA biogenesis and functionality in plants are welcome as well.

Dr. Giorgio Gambino
Dr. Chiara Pagliarani
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

  • small non-coding RNAs
  • plant development
  • stress response
  • small RNA signalling
  • DNA methylation
  • environmental adaptation
  • miRNA targets
  • gene-silencing networks

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Published Papers (7 papers)

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Research

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14 pages, 1329 KiB  
Article
Exposure to High-Intensity Light Systemically Induces Micro-Transcriptomic Changes in Arabidopsis thaliana Roots
by Barczak-Brzyżek Anna, Brzyżek Grzegorz, Koter Marek, Gawroński Piotr and Filipecki Marcin
Int. J. Mol. Sci. 2019, 20(20), 5131; https://doi.org/10.3390/ijms20205131 - 16 Oct 2019
Cited by 11 | Viewed by 3595
Abstract
In full sunlight, plants often experience a light intensity exceeding their photosynthetic capacity and causing the activation of a set of photoprotective mechanisms. Numerous reports have explained, on the molecular level, how plants cope with light stress locally in photosynthesizing leaves; however, the [...] Read more.
In full sunlight, plants often experience a light intensity exceeding their photosynthetic capacity and causing the activation of a set of photoprotective mechanisms. Numerous reports have explained, on the molecular level, how plants cope with light stress locally in photosynthesizing leaves; however, the response of below-ground organs to above-ground perceived light stress is still largely unknown. Since small RNAs are potent integrators of multiple processes including stress responses, here, we focus on changes in the expression of root miRNAs upon high-intensity-light (HL) stress. To achieve this, we used Arabidopsis thaliana plants growing in hydroponic conditions. The expression of several genes that are known as markers of redox changes was examined over time, with the results showing that typical HL stress signals spread to the below-ground organs. Additionally, micro-transcriptomic analysis of systemically stressed roots revealed a relatively limited reaction, with only 17 up-regulated and five down-regulated miRNAs. The differential expression of candidates was confirmed by RT-qPCR. Interestingly, the detected differences in miRNA abundance disappeared when the roots were separated from the shoots before HL treatment. Thus, our results show that the light stress signal is induced in rosettes and travels through the plant to affect root miRNA levels. Although the mechanism of this regulation is unknown, the engagement of miRNA may create a regulatory platform orchestrating adaptive responses to various simultaneous stresses. Consequently, further research on systemically HL-regulated miRNAs and their respective targets has the potential to identify attractive sequences for engineering stress tolerance in plants. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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21 pages, 1836 KiB  
Article
Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing
by Weiying Zeng, Zudong Sun, Zhenguang Lai, Shouzhen Yang, Huaizhu Chen, Xinghai Yang, Jiangrong Tao and Xiangmin Tang
Int. J. Mol. Sci. 2019, 20(12), 2966; https://doi.org/10.3390/ijms20122966 - 18 Jun 2019
Cited by 14 | Viewed by 3235
Abstract
Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA [...] Read more.
Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean’s defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on—as well as their negatively regulated differentially expressed target genes—may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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16 pages, 4797 KiB  
Article
Development-Related miRNA Expression and Target Regulation during Staggered In Vitro Plant Regeneration of Tuxpeño VS-535 Maize Cultivar
by Brenda A. López-Ruiz, Vasti T. Juárez-González, Estela Sandoval-Zapotitla and Tzvetanka D. Dinkova
Int. J. Mol. Sci. 2019, 20(9), 2079; https://doi.org/10.3390/ijms20092079 - 27 Apr 2019
Cited by 20 | Viewed by 4517
Abstract
In vitro plant regeneration addresses basic questions of molecular reprogramming in the absence of embryonic positional cues. The process is highly dependent on the genotype and explant characteristics. However, the regulatory mechanisms operating during organ differentiation from in vitro cultures remain largely unknown. [...] Read more.
In vitro plant regeneration addresses basic questions of molecular reprogramming in the absence of embryonic positional cues. The process is highly dependent on the genotype and explant characteristics. However, the regulatory mechanisms operating during organ differentiation from in vitro cultures remain largely unknown. Recently, miRNAs have emerged as key regulators during embryogenic callus induction, plant differentiation, auxin responses and totipotency. Here, we explored how development-related miRNA switches the impact on their target regulation depending on physiological and molecular events taking place during maize Tuxpeño VS-535 in vitro plant regeneration. Three callus types with distinctive regeneration potential were characterized by microscopy and histological preparations. The embryogenic calli (EC) showed higher miRNA levels than non-embryogenic tissues (NEC). An inverse correlation for miR160 and miR166 targets was found during EC callus induction, whereas miR156, miR164 and miR394 displayed similar to their targets RNA accumulation levels. Most miRNA accumulation switches took place early at regenerative spots coincident with shoot apical meristem (SAM) establishment, whereas miR156, miR160 and miR166 increased at further differentiation stages. Our data uncover particular miRNA-mediated regulation operating for maize embryogenic tissues, supporting their regulatory role in early SAM establishment and basipetala growth during the in vitro regeneration process. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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16 pages, 4365 KiB  
Article
MicroRNAome Profile of Euphorbia kansui in Response to Methyl Jasmonate
by Peng Li, Zheni Tian, Qing Zhang, Yue Zhang, Meng Wang, Xiaoai Fang, Wenjing Shi and Xia Cai
Int. J. Mol. Sci. 2019, 20(6), 1267; https://doi.org/10.3390/ijms20061267 - 13 Mar 2019
Cited by 4 | Viewed by 2999
Abstract
miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the [...] Read more.
miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the relevant regulatory mechanisms of Euphorbia kansui in response to methyl jasmonate (MeJA) through Illumina RNA-Seq. As a result, we identified 875 miRNAs corresponding to 11,277 target mRNAs, among them, 168 known miRNA families representing 6019 target mRNAs sequences were obtained. 452 miRNA-mRNA pairs presented an anti-correlationship (Cor < −0.50 and p-value of correlation ≤ 0.05). The miRNA with a fold change ≥ 2 and a p (p-Value) < 0.05 in pairwise comparison were identified as significant differentially expressed miRNAs (DEMs). The DEMs in MeJA treatment of 0, 24, 36 and 48 h were compared by using Short Time Expression Miner (STEM) cluster and 4 significant gene profiles (p-value ≤ 0.02) were identified. Through the kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) enrichment analysis on all miRNA targets, we identified 33 mRNAs in terpenoid biosynthesis, which were regulated by miRNAs under MeJA treatment, so the miRNA maybe involved in the response of E. kansui plant to exogenous MeJA and the results would provide very useful information on illustrating the regulatory mechanism of E. kansui and also provide an overall view of the miRNAs response to MeJA stress of a non-model plant. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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Review

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16 pages, 1764 KiB  
Review
A Regulatory Network for miR156-SPL Module in Arabidopsis thaliana
by Chenfei Zheng, Meixia Ye, Mengmeng Sang and Rongling Wu
Int. J. Mol. Sci. 2019, 20(24), 6166; https://doi.org/10.3390/ijms20246166 - 6 Dec 2019
Cited by 96 | Viewed by 8395
Abstract
Vegetative phase changes in plants describes the transition between juvenile and adult phases of vegetative growth before flowering. It is one of the most fundamental mechanisms for plants to sense developmental signals, presenting a complex process involving many still-unknown determinants. Several studies in [...] Read more.
Vegetative phase changes in plants describes the transition between juvenile and adult phases of vegetative growth before flowering. It is one of the most fundamental mechanisms for plants to sense developmental signals, presenting a complex process involving many still-unknown determinants. Several studies in annual and perennial plants have identified the conservative roles of miR156 and its targets, SBP/SPL genes, in guiding the switch of plant growth from juvenile to adult phases. Here, we review recent progress in understanding the regulation of miR156 expression and how miR156-SPLs mediated plant age affect other processes in Arabidopsis. Powerful high-throughput sequencing techniques have provided rich data to systematically study the regulatory mechanisms of miR156 regulation network. From this data, we draw an expanded miR156-regulated network that links plant developmental transition and other fundamental biological processes, gaining novel and broad insight into the molecular mechanisms of plant-age-related processes in Arabidopsis. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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19 pages, 617 KiB  
Review
Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants
by Chiara Pagliarani and Giorgio Gambino
Int. J. Mol. Sci. 2019, 20(17), 4306; https://doi.org/10.3390/ijms20174306 - 3 Sep 2019
Cited by 22 | Viewed by 5113
Abstract
Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic [...] Read more.
Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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17 pages, 847 KiB  
Review
Small RNA Functions as a Trafficking Effector in Plant Immunity
by Chen Zhu, Ting Liu, Ya-Nan Chang and Cheng-Guo Duan
Int. J. Mol. Sci. 2019, 20(11), 2816; https://doi.org/10.3390/ijms20112816 - 9 Jun 2019
Cited by 22 | Viewed by 7531
Abstract
Small RNAs represent a class of small but powerful agents that regulate development and abiotic and biotic stress responses during plant adaptation to a constantly challenging environment. Previous findings have revealed the important roles of small RNAs in diverse cellular processes. The recent [...] Read more.
Small RNAs represent a class of small but powerful agents that regulate development and abiotic and biotic stress responses during plant adaptation to a constantly challenging environment. Previous findings have revealed the important roles of small RNAs in diverse cellular processes. The recent discovery of bidirectional trafficking of small RNAs between different kingdoms has raised many interesting questions. The subsequent demonstration of exosome-mediated small RNA export provided a possible tool for further investigating how plants use small RNAs as a weapon during the arms race between plant hosts and pathogens. This review will focus on discussing the roles of small RNAs in plant immunity in terms of three aspects: the biogenesis of extracellular small RNAs and the transportation and trafficking small RNA-mediated gene silencing in pathogens. Full article
(This article belongs to the Special Issue Regulations by Small RNA in Plant Development and Beyond)
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