Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

Djami-Tchatchou, Arnaud T.; Sanan-Mishra, Neeti; Ntushelo, Khayalethu; Dubery, Ian A.

doi:10.3389/fpls.2017.00378

Cited by 180 publications

(88 citation statements)

References 193 publications

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“…Transcription factors (TFs) and miRNAs are both considered as key regulators and have been well characterized in controlling the transcriptional events and ultimately the plant metabolic process (Djami‐Tchatchou et al ., ; Nigam et al ., ). TFs regulate gene expression by translating cis‐regulatory codes into specific gene‐regulatory events (Rothenberg, ).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Tyagi

Nigam

Mithra

et al. 2018

Plant Biotechnology Journal

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SummaryOwing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC‐936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP‐ D‐glucose 4‐epimerase) and validated as targets for three novel miRNAs, that is Ct‐miR3130, Ct‐miR3135 and Ct‐miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan‐producing species.

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Section: Discussionmentioning

confidence: 99%

Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Tyagi

Nigam

Mithra

et al. 2018

Plant Biotechnology Journal

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“…It was suggested that the function of HXK1 is dependent on the presence of brassinosteroids, which might act downstream of HXK1 to regulate hypocotyl elongation in A. thaliana in darkness (in a glucose-dependent reaction) [104]. Recent studies have indicated the involvement of several miRNAs in phytohormone signaling pathways [105] and in sugar responses in plants [106], but more research is needed to fill in some gaps in knowledge.…”

Section: Receiving and Transmitting The Signals Triggered By Sugarsmentioning

confidence: 99%

Regulatory roles of sugars in plant growth and development

Ciereszko

2018

Acta Soc Bot Pol

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In recent years, several studies have focused on the factors and mechanisms that regulate plant growth and development, as well as the functioning of signaling pathways in plant cells, unraveling the involvement of sugars in the processes regulating such growth and development. Saccharides play an important role in the life of plants: they are structural and storage substances, respiratory substrates, and intermediate metabolites of many biochemical processes. Sucrose is the major transport form of assimilates in plants. Sugars can also play an important role in the defense reactions of plants. However, it has been shown that glucose, sucrose, or trehalose-6-phosphate (Tre6P) can regulate a number of growth and metabolic processes, acting independently of the basal functions; they can also act as signaling molecules. Changes in the concentration, qualitative composition, and transport of sugars occur continuously in plant tissues, during the day and night, as well as during subsequent developmental stages. Plants have developed an efficient system of perception and transmission of signals induced by lower or higher sugar availability. Changes in their concentration affect cell division, germination, vegetative growth, flowering, and aging processes, often independently of the metabolic functions. Currently, the mechanisms of growth regulation in plants, dependent on the access to sugars, are being increasingly recognized. The plant growth stimulating system includes hexokinase (as a glucose sensor), trehalose-6-phosphate, and TOR protein kinase; the lack of Tre6P or TOR kinase inhibits the growth of plants and their transition to the generative phase. It is believed that the plant growth inhibition system consists of SnRK1 protein kinases and C/S1 bZIP transcription factors. The signal transduction routes induced by sugars interact with other pathways in plant tissues (for example, hormonal pathways) creating a complex communication and signaling network in plants that precisely controls plant growth and development.

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“…MicroRNAs (miRNAs) are approximately 20-25 nt long and are important post-transcriptional regulators that modulate gene expression by targeting mRNAs for translational repression or cleavage [10,11]. An increasing number of miRNAs have been identified and their sequences have been deposited in a publicly available database (http://www.mirbase.org/).…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

Cao

Zhai

Zhang

et al. 2018

Forests

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Paulownia witches' broom (PaWB), caused by phytoplasma, is an important disease of Paulownia. To further identify the key miRNAs associated with the formation of PaWB symptoms, miRNA and degradome sequencing were performed to explore important miRNAs-target regulation in healthy and diseased Paulownia tomentosa, Paulownia fortunei, and P. tomentosa × P. fortunei seedlings, and the corresponding diseased seedlings treated with 75 mg L −1 dimethyl sulfate. A total of 212, 111, and 197 differentially expressed miRNAs (DEMs) were obtained in P. tomentosa, P. fortunei, and P. tomentosa × P. fortunei, respectively. Degradome sequencing detected 559, 251, and 568 target genes of the DEMs in P. tomentosa, P. fortunei, and P. tomentosa × P. fortunei, respectively. The expression patterns of selected miRNAs and the target genes were verified be qRT-PCR. Through analysis of the expression level of the DEMs in this study, combined with the results in our previous studies, as well as with those reported in other phytoplasma-infected plants, we concluded that miR156 is an important miRNA related to witches' broom. According to the functions of the target genes of DEMs, we constructed a co-regulatory network of the DEMs-target genes interaction. These results will help to advance the understanding of the mechanism of PaWB.

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Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

Cited by 180 publications

References 193 publications

Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Regulatory roles of sugars in plant growth and development

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

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