What Do We Know about Barley miRNAs?
Abstract
:1. Introduction
2. Plant miRNAs—Biogenesis and Regulatory Potential
3. miRNAs in Barley Physiology and Stress Responses
4. Target Transcripts of Barley miRNAs
5. Conclusions and Future Directions
- (a)
- Showing co-expression of miRNA and target mRNA in vivo;
- (b)
- Proving interaction between miRNA and a specific site within target mRNA;
- (c)
- Demonstrating miRNA-mediated effects on target protein expression;
- (d)
- Demonstrating miRNA effects on biological function.
- (1)
- Are some of the barley miRNAs tissue/developmental, or stage-specific? Are we able to catalog it in some integrative and user-friendly way? For this purpose, it would be beneficial to have something like a barley miRNA atlas (similar to PmiRExAt, where wheat, rice, maize, and Arabidopsis miRNAs in multiple tissues and developmental stages can be found) [171].
- (2)
- Which barley miRNAs have the potential to become a useful stress biomarker? In other words, do some stress-specific miRNAs exist?
- (3)
- Is barley miRNome rather complete, or not? Compared to rice, wheat, and Arabidopsis, the total number of known barley miRNAs is still lack behind, and bona fide many discoveries waiting for us!
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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Title of the Study and Reference | Barley Cultivars Inspected | Year of Publication | Most Important Findings |
---|---|---|---|
Regulation of barley miRNAs upon dehydration stress correlated with target gene expression [79] | Hordeum vulgare | 2010 | A total of 28 potential miRNAs were identified using bioinformatic approaches (BLASTn of known plant miRNAs and barley expressed sequence tags (ESTs), and RNA folding algorithms). |
Discovery of barley miRNAs through deep sequencing of short reads [91] | Hordeum vulgare cultivars Golden Promise and Pallas | 2011 | The first large-scale study of miRNAs in Hordeum Vulgare, 100 miRNAs were identified (only 56 of them had orthologs in wheat, rice, or Brachypodium) and 3 candidates were validated in vitro using a Northern blot assay. |
Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing [92] | Hordeum vulgare L. | 2012 | 126 conserved miRNAs (belonging to 58 families), and 133 novel miRNAs (50 families) were identified in this study. |
miRNA regulation in the early development of barley seed [61] | Hordeum vulgare | 2012 | 84 known miRNAs and 7 new miRNAs together with 96 putative miRNA target genes were identified during the early development of barley seeds (first 15 days post anthesis). |
Developmentally regulated expression and complex processing of barley pri-microRNAs [93] | Hordeum vulgare cultivar Rolap | 2013 | miRNA genes in barley often contain introns which may play important role in miRNA processing. |
A Comprehensive Expression Profile of MicroRNAs and Other Classes of Non-Coding Small RNAs in Barley Under Phosphorous-Deficient and -Sufficient Conditions [84] | Hordeum vulgare L., cultivar Pallas | 2013 | 221 conserved miRNAs and 12 novel miRNAs were identified, many of them were phosphorus condition-specific. A total of 47 miRNAs were significantly differentially expressed between the two phosphorus treatments. |
Boron Stress Responsive MicroRNAs and Their Targets in Barley [83] | Hordeum vulgare L. cultivar Sahara | 2013 | 31 known and 3 new miRNAs were identified in barley, and 25 of them were found to respond to boron treatment. |
Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley [90] | Hordeum vulgare cultivar Rolap | 2014 | Four heat stress up-regulated barley miRNAs were found (miR160a, miR166a, miR167h, and miR5175a). |
Differential expression of microRNAs and other small RNAs in barley between water and drought conditions [80] | Hordeum vulgare cultivar Golden Promise | 2014 | Three novel miRNAs, designated as hvu-miRX33, hvu-miRX34, and hvu-miRX35 were identified. hvu-miRX34 had no homologous miRNA in wheat. |
The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling [94] | Hordeum vulgare L. | 2014 | The key role of the miR9863 family in the immune response to the pathogen (powdery mildew fungus, Blumeria graminis f. sp. hordei) was proposed |
Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature [95] | Artificially transformed Hordeum vulgare cultivar Golden Promise | 2015 | Polycistronic artificial miRNA in plasmid vector was successfully transformed into barley embryos and mediated resistance to Wheat dwarf virus. |
Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress [73] | Hordeum vulgare cultivar Morex | 2015 | Authors identified 152 miRNAs (142 conserved and 10 novel ones), and 44 miRNAs (39 conserved and 5 novel ones) were found to be salinity-responsive. |
Characterization of microRNAs and their targets in wild barley (Hordeum vulgare subsp. spontaneum) using deep sequencing [96] | Hordeum vulgare subsp. spontaneum | 2016 | A total of 70 known miRNAs and 18 novel miRNA candidates were identified and many of them were predicted to target mRNAs encoding transcription factors. |
Developmental changes in barley microRNA expression profiles coupled with miRNA target analysis [97] | Hordeum vulgare cultivar Rolap | 2016 | miRNA transcriptomes of five barley developmental stages were inspected. Overall, miR168-3p and miR1432-5p levels increased while the 5′U-miR156-5p level decreased during barley development. |
miR393-Mediated Auxin Signaling Regulation is Involved in Root Elongation Inhibition in Response to Toxic Aluminum Stress in Barley [86] | Hordeum vulgare cultivar Golden Promise | 2017 | Barley miR393 was functionally characterized. It regulates root sensitivity to aluminum through the alteration of auxin signaling. |
Differential expression of microRNAs and potential targets under drought stress in barley [78] | Hordeum vulgare L. cultivars Commander, Fleet, Hindmarsh, and breeding line WI4304 | 2017 | miRNA regulation under drought stress in barley is genotype-specific. |
microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination [98] | Hordeum vulgare cultivar Golden Promise | 2017 | A total of 1324 known miRNAs and 448 novel miRNA candidates were identified. miR393-mediated auxin response regulation significantly affected grain development. |
Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment [99] | Ancient Hordeum vulgare | 2017 | Sequencing of miRNAs obtained from archeological barley samples (600–900 years BP) revealed their local adaptation to an agrarian environment around the river Nile. |
Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley [100] | Hordeum vulgare L. | 2018 | The study identified 17 barley SPL genes, and 7 of them contain a putative miR156 target site. |
Identification of microRNAs in response to aluminum stress in the roots of Tibetan wild barley and cultivated barley [87] | Hordeum vulgare Al-sensitive Golden Promise and Tibetan wild barley (Al-tolerant XZ29) | 2018 | 50 miRNAs responsive to aluminum stress were detected, and some of them were found to be exclusively expressed in Al-tolerant XZ29. |
Identification of microRNAs responding to salt stress in barley by high-throughput sequencing and degradome analysis [76] | Tibetan wild barley accession XZ16; Hordeum vulgare cultivar Golden Promise | 2019 | miR393a, miR156d, and miR172b (regulating HvAFB2/HvTIR1, UGTs, and HvAP2) are responsible for salt tolerance in barley roots. |
Genotypic difference of cadmium tolerance and the associated microRNAs in wild and cultivated barley [88] | Hordeum vulgare cultivar Golden Promise and wild barley WB-1 | 2019 | 216 conserved miRNAs (in 59 miRNA families) and 87 novel miRNAs were identified. Authors suggest that miRNAs may play critical roles underlying the genotypic difference of cadmium tolerance in barley. |
Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley [81] | Tibetan wild barley Hordeum vulgare L. ssp. Spontaneum | 2020 | 69 conserved miRNAs and 1574 novel miRNAs were identified, some of them were differentially expressed in drought conditions. |
Barley microRNAs as metabolic sensors for soil nitrogen availability [82] | Hordeum vulgare cultivar Golden Promise | 2020 | Authors identified 13 barley miRNAs that are nitrogen excess responsive with the possible function of metabolic sensors for soil nitrogen availability. |
The Impact of Zinc Oxide Nanoparticles on Cytotoxicity, Genotoxicity, and miRNA Expression in Barley (Hordeum vulgare L.) Seedlings [101] | Hordeum vulgare L. var. Abava | 2020 | ZnO nanoparticles significantly changed the expression of barley miR156a, miR159a, and miR159c in a dosage-dependent manner. |
Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated [102] | A Tibetan wild barley accession (XZ153) and a cultivar (ZD9) differing in low K tolerance | 2021 | A total of 1088 miRNAs were identified in the two barley genotypes under low potassium conditions. 65 of them were significantly differentially expressed. |
Barley Seeds miRNome Stability during Long-Term Storage and Aging [103] | Hordeum vulgare cultivar Damazy | 2021 | miRNome of barley seeds harvested in 1972 was inspected. 61 known and 81 novel miRNA were identified pointing to the fact that miRNAs in dry seeds are extremely stable. |
Identification microRNAs and target genes in Tibetan hulless barley to BLS infection [104] | Hordeum vulgare L. variety nudum Hook. f. | 2021 | A total of 36 conserved and 56 novel miRNAs were identified, some of them were differentially expressed between BLS (barley leaf stripe fungal disease)-sensitive and BLS-tolerant barley genotypes. |
Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses [85] | Hordeum vulgare L. | 2021 | Authors suggest that barley adapts to inorganic phosphate (Pi)-starvation also via differential expression of several miRNAs. |
Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots [74] | Hordeum vulgare cultivar Golden Promise | 2021 | 525 miRNAs (198 known and 327 novel miRNAs) were identified through high-throughput sequencing. 31 miRNAs were differentially expressed under inspected stresses. |
An miR156-regulated nucleobase-ascorbate transporter 2 confers cadmium tolerance via enhanced anti-oxidative capacity in barley [105] | Hordeum vulgare genotypes Zhenong8 (ZN8) (Cd-tolerant genotype) and W6nk2 (Cd-sensitive genotype) | 2022 | miR156g-3p_3 targets a novel nucleobase-ascorbate transporter gene (HvNAT2). HvNAT2 evolved from the Zygnematales in Streptophyte algae and positively regulates cadmium tolerance → genetic engineering of NAT in plants may have potential in the remediation of soil/water cadmium pollution |
Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance [21] | Hordeum vulgare L. cultivar Bojos | 2022 | Several barley miRNAs were differentially expressed in response to the spectral quality of incident light. |
Database Name | Direct Link | The Overall Count of Barley miRNAs | Notes |
---|---|---|---|
Plant Non-coding RNA Database (PNRD) | http://structuralbiology.cau.edu.cn/PNRD/index.php | 71 | 58 of them were experimentally validated |
Plant MicroRNA Encyclopedia (PmiREN) | https://www.pmiren.com/ | 178 | Divided into 94 miRNA families |
miRBase | https://www.mirbase.org/summary.shtml?org=hvu | 69 | / |
Plant small RNA genes | https://plantsmallrnagenes.science.psu.edu/ | 49 | Contain also 118 entities similar to miRNAs |
miRNEST | http://rhesus.amu.edu.pl/mirnest/copy/browse.php | 398 | An integrative miRNA resource |
miRNA | mRNA Target(s) in Hordeum vulgare | Known Biological Function(s) of miRNA in Plant Species and Further Notes | References |
---|---|---|---|
miR156a | SBP-box gene family member | Inflorescence morphogenesis regulation in tomato (Solanum lycopersicum) plants; male fertility regulation in thale cress (Arabidopsis thaliana) plants | [114,115,116] |
miR156b | |||
miR159a | MYB family transcription factor;lectin-like receptor kinase | Ensure normal growth via regulation of GAMYB genes | [117,118,119] |
miR159b | MYB family transcription factor; | ||
miR166a | START domain-containing protein; MATE domain-containing protein; class III HD-Zip protein 8 | Shoot apical meristem and vascular differentiation, leaf and root development; evolutionarily conserved stress biomarker in land plants—drought, salinity, temperature, biotic stress | [120,121] |
miR166b | |||
miR166c | |||
miR168-5p | receptor-like protein kinase 5 precursor | Function in plants is unclear but targets many important mammalian transcripts (123 in total), including the gene for Low-density lipoprotein receptor adaptor protein 1 (LDLRAP1, also known as ARH)) | [122] |
miR171-3p | scarecrow transcription factor family protein | Regulation of germination and seedling growth in Tibetan hull-less barley (Hordeum vulgare L. var. nudum); drought tolerance by regulation of flavonoid biosynthesis genes in rice | [113,123] |
miR397a | laccase precursor protein; transporter family protein; | Plant development; circadian regulation and plant flowering; cold response in thale cress (Arabidopsis thaliana) | [124,125] |
miR399 | rp1; ubiquitin-conjugating enzyme protein; pentatricopeptide | Salt stress response and flowering regulation in thale cress (Arabidopsis thaliana) | [126,127] |
miR444a | FAD-binding domain of DNA photolyase domain-containing protein; DnaK family protein; alpha-taxilin; MADS-box family gene with MIKCc type-box; pentatricopeptide; WD domain, G-beta repeat domain-containing protein | Regulation of nitrate signaling pathway in nitrate-dependent root growth, nitrate accumulation, and phosphate-starvation responses in rice (Oryza sativa); antiviral pathway in rice; regulation of brassinosteroids synthesis in rice | [128,129,130] |
miR444b | MADS-box family gene with MIKCc type-box; methyltransferase; zinc finger, C3HC4 type domain-containing protein | ||
miR1120 | An enzyme of the cupin superfamily protein; retrotransposon protein; tesmin/TSO1-like CXC domain-containing protein; WD domain, G-beta repeat domain-containing protein; CCR4-NOT transcription factor; glycosyltransferase family 43 protein; amine oxidase-related; Divergent PAP2 family domain-containing protein | Early anther development in wheat (Triticum aestivum). miR1120 in barley has many diverse mRNA targets, however, it is questionable, if this miR1120 is a true miRNA (originating from hairpin RNA precursor), as the miR1120 gene region in barley displays almost 80% sequence similarity to the short transposon element DNA/TcMar-Stowaway | [93,131] |
miR1436 | pseudogene | Various stress responses in Cestrum nocturnum L. and Cestrum diurnum L. | [132] |
miR5048a | cysteine-rich receptor-like protein kinase precursor | Wheat (Triticum aestivum) grains development regulation | [133] |
miR5049c | modifier of rudimentary protein; auxin-induced protein 5NG4; Spc97/Spc98 family protein; protein kinase domain-containing protein; OsWAK receptor-like protein kinase | Hormone, stress (heat, drought, salinity, and excess boron), and light responsiveness in barley (Hordeum vulgare L.) | [67] |
miR5049f | resistance protein; transcription factor-related; WD domain, G-beta repeat domain-containing protein; TBC domain-containing protein; | Regulation of salt adaptation in Hordeum bulbosum | [75] |
miR6197 | DUF26 kinase; exosome complex exonuclease rrp4 | Boron stress response regulation in barley (Hordeum vulgare) | [83] |
miR6201 | C4-dicarboxylate transporter/malic acid transport protein | Cadmium stress response regulation in wheat (Triticum aestivum) | [134] |
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Volná, A.; Bartas, M.; Pečinka, P.; Špunda, V.; Červeň, J. What Do We Know about Barley miRNAs? Int. J. Mol. Sci. 2022, 23, 14755. https://doi.org/10.3390/ijms232314755
Volná A, Bartas M, Pečinka P, Špunda V, Červeň J. What Do We Know about Barley miRNAs? International Journal of Molecular Sciences. 2022; 23(23):14755. https://doi.org/10.3390/ijms232314755
Chicago/Turabian StyleVolná, Adriana, Martin Bartas, Petr Pečinka, Vladimír Špunda, and Jiří Červeň. 2022. "What Do We Know about Barley miRNAs?" International Journal of Molecular Sciences 23, no. 23: 14755. https://doi.org/10.3390/ijms232314755