International Journal of Molecular Sciences

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20 pages, 3471 KiB

Open AccessArticle

The Copper-microRNA Pathway Is Integrated with Developmental and Environmental Stress Responses in Arabidopsis thaliana

by Ana Perea-García, Amparo Andrés-Bordería, Peter Huijser and Lola Peñarrubia

Int. J. Mol. Sci. 2021, 22(17), 9547; https://doi.org/10.3390/ijms22179547 - 2 Sep 2021

Cited by 18 | Viewed by 2789

Abstract

As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such [...] Read more.

As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such as miR398 and miR408 are conserved, as well as the signal transduction pathway to induce them under Cu deficiency. The Arabidopsis thaliana SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family member SPL7 binds to the cis-regulatory motifs present in the promoter regions of genes expressed under Cu deficiency, including Cu-miRNAs. The expression of several other SPL transcription factor family members is regulated by miR156. This regulatory miR156-SPL module plays a crucial role in developmental phase transitions while integrating internal and external cues. Here, we show that Cu deficiency also affects miR156 expression and that SPL3 overexpressing plants, resistant to miR156 regulation, show a severe decrease in SPL7-mediated Cu deficiency responses. These include the expression of Cu-miRNAs and their targets and is probably due to competition between SPL7 and miR156-regulated SPL3 in binding to cis-regulatory elements in Cu-miRNA promoters. Thus, the conserved SPL7-mediated Cu-miRNA pathway could generally be affected by the miR156-SPL module, thereby underscoring the integration of the Cu-miRNA pathway with developmental and environmental stress responses in Arabidopsis thaliana. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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21 pages, 4221 KiB

Open AccessArticle

MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo (Citrus grandis Osbeck)

by Heli Pan, Shiheng Lyu, Yanqiong Chen, Shirong Xu, Jianwen Ye, Guixin Chen, Shaohua Wu, Xiaoting Li, Jianjun Chen and Dongming Pan

Int. J. Mol. Sci. 2021, 22(17), 9348; https://doi.org/10.3390/ijms22179348 - 28 Aug 2021

Cited by 9 | Viewed by 2822

Abstract

‘Liuyuezaoyou’ is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck ‘Guanximiyou’. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key [...] Read more.

‘Liuyuezaoyou’ is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck ‘Guanximiyou’. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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28 pages, 27499 KiB

Open AccessArticle

Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes

by Marina Dermastia, Blaž Škrlj, Rebeka Strah, Barbara Anžič, Špela Tomaž, Maja Križnik, Christina Schönhuber, Monika Riedle-Bauer, Živa Ramšak, Marko Petek, Aleš Kladnik, Nada Lavrač, Kristina Gruden, Thomas Roitsch, Günter Brader and Maruša Pompe-Novak

Int. J. Mol. Sci. 2021, 22(7), 3531; https://doi.org/10.3390/ijms22073531 - 29 Mar 2021

Cited by 12 | Viewed by 4287

Abstract

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput [...] Read more.

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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25 pages, 7200 KiB

Open AccessArticle

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 Are Involved in the Regulation of Male Sterility in PTGMS Rice

by Yujun Sun, Xinguo Xiong, Qian Wang, Lan Zhu, Lei Wang, Ying He and Hanlai Zeng

Int. J. Mol. Sci. 2021, 22(5), 2260; https://doi.org/10.3390/ijms22052260 - 24 Feb 2021

Cited by 26 | Viewed by 3494

Abstract

A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems [...] Read more.

A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified—166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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20 pages, 16160 KiB

Open AccessArticle

Maize microRNA166 Inactivation Confers Plant Development and Abiotic Stress Resistance

by Na Li, Tianxiao Yang, Zhanyong Guo, Qiusheng Wang, Mao Chai, Mingbo Wu, Xiaoqi Li, Weiya Li, Guangxian Li, Jihua Tang, Guiliang Tang and Zhanhui Zhang

Int. J. Mol. Sci. 2020, 21(24), 9506; https://doi.org/10.3390/ijms21249506 - 14 Dec 2020

Cited by 35 | Viewed by 4337

Abstract

MicroRNAs are important regulators in plant developmental processes and stress responses. In this study, we generated a series of maize STTM166 transgenic plants. Knock-down of miR166 resulted in various morphological changes, including rolled leaves, enhanced abiotic stress resistance, inferior yield-related traits, vascular pattern [...] Read more.

MicroRNAs are important regulators in plant developmental processes and stress responses. In this study, we generated a series of maize STTM166 transgenic plants. Knock-down of miR166 resulted in various morphological changes, including rolled leaves, enhanced abiotic stress resistance, inferior yield-related traits, vascular pattern and epidermis structures, tassel architecture, as well as abscisic acid (ABA) level elevation and indole acetic acid (IAA) level reduction in maize. To profile miR166 regulated genes, we performed RNA-seq and qRT-PCR analysis. A total of 178 differentially expressed genes (DEGs) were identified, including 118 up-regulated and 60 down-regulated genes. These DEGs were strongly enriched in cell and intercellular components, cell membrane system components, oxidoreductase activity, single organism metabolic process, carbohydrate metabolic process, and oxidation reduction process. These results indicated that miR166 plays important roles in auxin and ABA interaction in monocots, yet the specific mechanism may differ from dicots. The enhanced abiotic stress resistance is partly caused via rolling leaves, high ABA content, modulated vascular structure, and the potential changes of cell membrane structure. The inferior yield-related traits and late flowering are partly controlled by the decreased IAA content, the interplay of miR166 with other miRNAs and AGOs. Taken together, the present study uncovered novel functions of miR166 in maize, and provide insights on applying short tandem target mimics (STTM) technology in plant breeding. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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23 pages, 3140 KiB

Open AccessArticle

Molecular Manipulation of MicroRNA397 Abundance Influences the Development and Salt Stress Response of Arabidopsis thaliana

by Duc Quan Nguyen, Christopher W. Brown, Joseph L. Pegler, Andrew L. Eamens and Christopher P. L. Grof

Int. J. Mol. Sci. 2020, 21(21), 7879; https://doi.org/10.3390/ijms21217879 - 23 Oct 2020

Cited by 20 | Viewed by 3155

Abstract

Arabidopsis thaliana (Arabidopsis) has been used extensively as a heterologous system for molecular manipulation to genetically characterize both dicotyledonous and monocotyledonous plant species. Here, we report on Arabidopsis transformant lines molecularly manipulated to over-accumulate the small regulatory RNA microRNA397 (miR397) from [...] Read more.

Arabidopsis thaliana (Arabidopsis) has been used extensively as a heterologous system for molecular manipulation to genetically characterize both dicotyledonous and monocotyledonous plant species. Here, we report on Arabidopsis transformant lines molecularly manipulated to over-accumulate the small regulatory RNA microRNA397 (miR397) from the emerging C₄ monocotyledonous grass model species Setaria viridis (S. viridis). The generated transformant lines, termed SvMIR397 plants, displayed a range of developmental phenotypes that ranged from a mild, wild-type-like phenotype, to a severe, full dwarfism phenotype. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR)-based profiling of the SvMIR397 transformant population revealed a strong correlation between the degree of miR397 over-accumulation, repressed LACCASE (LAC) target gene expression, reduced lignin content, and the severity of the developmental phenotype displayed by SvMIR397 transformants. Further, exposure of SvMIR397 transformants to a 7-day regime of salt stress revealed the SvMIR397 transformant lines to be more sensitive to the imposed stress than were wild-type Arabidopsis plants. Taken together, the findings reported here via the use of Arabidopsis as a heterologous system show that the S. viridis miR397 small regulatory RNA is able to repress the expression of three Arabidopsis LAC genes which led to reduced lignin content and increased salt stress sensitivity. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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28 pages, 6816 KiB

Open AccessArticle

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

by Haipei Liu, Amanda J. Able and Jason A. Able

Int. J. Mol. Sci. 2020, 21(17), 6017; https://doi.org/10.3390/ijms21176017 - 21 Aug 2020

Cited by 30 | Viewed by 4345

Abstract

Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of [...] Read more.

Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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18 pages, 1794 KiB

Open AccessArticle

High-Throughput Sequencing and Expression Analysis Suggest the Involvement of Pseudomonas putida RA-Responsive microRNAs in Growth and Development of Arabidopsis

by Ram Jatan, Puneet Singh Chauhan and Charu Lata

Int. J. Mol. Sci. 2020, 21(15), 5468; https://doi.org/10.3390/ijms21155468 - 30 Jul 2020

Cited by 15 | Viewed by 3192

Abstract

Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores [...] Read more.

Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of Arabidopsis upon P. putida RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in Arabidopsis, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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18 pages, 2711 KiB

Open AccessArticle

BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa

by Bo Zhou, Jingtong Leng, Yanyun Ma, Pengzhen Fan, Yuhua Li, Haifang Yan and Qijiang Xu

Int. J. Mol. Sci. 2020, 21(12), 4326; https://doi.org/10.3390/ijms21124326 - 17 Jun 2020

Cited by 24 | Viewed by 4336

Abstract

Comprehensive research in various plants shows that the metabolic pathway of anthocyanin biosynthesis is affected by environmental factors and regulated by microRNAs through post-transcriptional regulation. In seedlings of Brassica rapa Tsuda, the accumulation of anthocyanin is induced by light. However, the roles of [...] Read more.

Comprehensive research in various plants shows that the metabolic pathway of anthocyanin biosynthesis is affected by environmental factors and regulated by microRNAs through post-transcriptional regulation. In seedlings of Brassica rapa Tsuda, the accumulation of anthocyanin is induced by light. However, the roles of BrmiR828 in the light-induced synthesis of anthocyanin in Brassica rapa remain to be explored. Here, a primary transcript of BrmiR828 was identified to be located on the chromosomes of the A03 sub-genome. Five candidate MYB family genes were predicted as targets of BrmiR828 in the database of Brassica rapa (BRAD, V1.1) by using psRNATarget. The transcript abundance of mature BrmiR828 was reduced in seedlings of Brassica rapa Tsuda under blue light irradiation comparing with dark treatment. However, Real-time PCR showed the transcript level of the five candidate targets, Bra004162, Bra022602, Bra001917, Bra029113, and Bra039763 was up-regulated when the seedlings exposed to blue or UV-A light. Trans-acting siRNA gene 4 (BrTAS4) was also identified to have a higher transcript level under blue and UV-A light irradiation than that in dark treatment. RNA ligase mediated 5′amplification of cDNA ends (RLM-5′ RACE) showed that BrmiR828 can splice the mRNA of Bra039763, Bra022602, and BrTAS4 on binding sites. Phylogenetic analysis of candidate BrMYBs targets along with MYBs from Arabidopsis thaliana showed that Bra039763, Bra004162, Bra001917, Bra029113, and Bra022602 are classified to the same group with AtMYB75, AtMYB114, AtMYB90, AtMYB113, and AtMYB82 which are involved in the anthocyanin biosynthetic pathway. As a result, light-induced down-regulation of BrmiR828 can target BrTAS4, BrPAP1 (Bra039763), MYB82 (Bra022602) to negatively regulate their transcript levels leading to the accumulation of MYB transcription factors that positively regulate anthocyanin biosynthesis in light-exposed seedlings of Brassica rapa. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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19 pages, 3019 KiB

Open AccessArticle

Small RNA and Transcriptome Sequencing Reveals miRNA Regulation of Floral Thermogenesis in Nelumbo nucifera

by Yu Zou, Guanglong Chen, Jing Jin, Ying Wang, Meiling Xu, Jing Peng and Yi Ding

Int. J. Mol. Sci. 2020, 21(9), 3324; https://doi.org/10.3390/ijms21093324 - 8 May 2020

Cited by 9 | Viewed by 4034

Abstract

The sacred lotus (Nelumbo nucifera Gaertn.) can produce heat autonomously and maintain a relatively stable floral chamber temperature for several days when blooming. Floral thermogenesis is critical for flower organ development and reproductive success. However, the regulatory role of microRNA (miRNA) underlying [...] Read more.

The sacred lotus (Nelumbo nucifera Gaertn.) can produce heat autonomously and maintain a relatively stable floral chamber temperature for several days when blooming. Floral thermogenesis is critical for flower organ development and reproductive success. However, the regulatory role of microRNA (miRNA) underlying floral thermogenesis in N. nucifera remains unclear. To comprehensively understand the miRNA regulatory mechanism of thermogenesis, we performed small RNA sequencing and transcriptome sequencing on receptacles from five different developmental stages. In the present study, a total of 172 known miRNAs belonging to 39 miRNA families and 126 novel miRNAs were identified. Twenty-nine thermogenesis-related miRNAs and 3024 thermogenesis-related mRNAs were screened based on their expression patterns. Of those, seventeen differentially expressed miRNAs (DEMs) and 1765 differentially expressed genes (DEGs) had higher expression during thermogenic stages. The upregulated genes in the thermogenic stages were mainly associated with mitochondrial function, oxidoreductase activity, and the energy metabolism process. Further analysis showed that miR156_2, miR395a_5, miR481d, and miR319p may play an important role in heat-producing activity by regulating cellular respiration-related genes. This study provides comprehensive miRNA and mRNA expression profile of receptacle during thermogenesis in N. nucifera, which advances our understanding on the regulation of floral thermogenesis mediated by miRNA. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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Review

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13 pages, 726 KiB

Open AccessReview

miRNA Mediated Regulation and Interaction between Plants and Pathogens

by Xiaoqian Yang, Lichun Zhang, Yuzhang Yang, Markus Schmid and Yanwei Wang

Int. J. Mol. Sci. 2021, 22(6), 2913; https://doi.org/10.3390/ijms22062913 - 13 Mar 2021

Cited by 55 | Viewed by 6277

Abstract

Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial [...] Read more.

Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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16 pages, 607 KiB

Open AccessReview

RNAi Mediated Hypoxia Stress Tolerance in Plants

by Federico Betti, Maria José Ladera-Carmona, Pierdomenico Perata and Elena Loreti

Int. J. Mol. Sci. 2020, 21(24), 9394; https://doi.org/10.3390/ijms21249394 - 10 Dec 2020

Cited by 10 | Viewed by 4075

Abstract

Small RNAs regulate various biological process involved in genome stability, development, and adaptive responses to biotic or abiotic stresses. Small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs). MicroRNAs (miRNAs) are regulators of gene expression that affect the transcriptional and post-transcriptional regulation [...] Read more.

Small RNAs regulate various biological process involved in genome stability, development, and adaptive responses to biotic or abiotic stresses. Small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs). MicroRNAs (miRNAs) are regulators of gene expression that affect the transcriptional and post-transcriptional regulation in plants and animals through RNA interference (RNAi). miRNAs are endogenous small RNAs that originate from the processing of non-coding primary miRNA transcripts folding into hairpin-like structures. The mature miRNAs are incorporated into the RNA-induced silencing complex (RISC) and drive the Argonaute (AGO) proteins towards their mRNA targets. siRNAs are generated from a double-stranded RNA (dsRNA) of cellular or exogenous origin. siRNAs are also involved in the adaptive response to biotic or abiotic stresses. The response of plants to hypoxia includes a genome-wide transcription reprogramming. However, little is known about the involvement of RNA signaling in gene regulation under low oxygen availability. Interestingly, miRNAs have been shown to play a role in the responses to hypoxia in animals, and recent evidence suggests that hypoxia modulates the expression of various miRNAs in plant systems. In this review, we describe recent discoveries on the impact of RNAi on plant responses to hypoxic stress in plants. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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22 pages, 4583 KiB

Open AccessReview

Plant Non-Coding RNAs: Origin, Biogenesis, Mode of Action and Their Roles in Abiotic Stress

by Joram Kiriga Waititu, Chunyi Zhang, Jun Liu and Huan Wang

Int. J. Mol. Sci. 2020, 21(21), 8401; https://doi.org/10.3390/ijms21218401 - 9 Nov 2020

Cited by 69 | Viewed by 6327

Abstract

As sessile species, plants have to deal with the rapidly changing environment. In response to these environmental conditions, plants employ a plethora of response mechanisms that provide broad phenotypic plasticity to allow the fine-tuning of the external cues related reactions. Molecular biology has [...] Read more.

As sessile species, plants have to deal with the rapidly changing environment. In response to these environmental conditions, plants employ a plethora of response mechanisms that provide broad phenotypic plasticity to allow the fine-tuning of the external cues related reactions. Molecular biology has been transformed by the major breakthroughs in high-throughput transcriptome sequencing and expression analysis using next-generation sequencing (NGS) technologies. These innovations have provided substantial progress in the identification of genomic regions as well as underlying basis influencing transcriptional and post-transcriptional regulation of abiotic stress response. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as essential regulators of plants abiotic stress response. However, shared traits in the biogenesis of ncRNAs and the coordinated cross-talk among ncRNAs mechanisms contribute to the complexity of these molecules and might play an essential part in regulating stress responses. Herein, we highlight the current knowledge of plant microRNAs, siRNAs, and lncRNAs, focusing on their origin, biogenesis, modes of action, and fundamental roles in plant response to abiotic stresses. Full article

(This article belongs to the Special Issue Molecular Bases of Stress Adaptation in Plants: The Contribute of Regulation by Small RNAs in Plant Development and Stress Response)

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