The Crosstalk between MicroRNAs and Gibberellin Signaling in Plants

2020 ◽  
Vol 61 (11) ◽  
pp. 1880-1890 ◽  
Author(s):  
Sha Yu ◽  
Jia-Wei Wang
Keyword(s):  
Target Genes ◽  
Floral Induction ◽  
Stem Elongation ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Master Regulators ◽  
The Past ◽  
Della Proteins ◽  
Wide Range ◽  
Ga Response

Abstract Gibberellin (GA) is an integral phytohormone that plays prominent roles in controlling seed germination, stem elongation, leaf development and floral induction. It has been shown that GA regulates these diverse biological processes mainly through overcoming the suppressive effects of the DELLA proteins, a family of nuclear repressors of GA response. MicroRNAs (miRNAs), which have been identified as master regulators of gene expression in eukaryotes, are also involved in a wide range of plant developmental events through the repression of their target genes. The pathways of GA biosynthesis and signaling, as well as the pathways of miRNA biogenesis and regulation, have been profoundly delineated in the past several decades. Growing evidence has shown that miRNAs and GAs are coordinated in regulating plant development, as several components in GA pathways are targeted by miRNAs, and GAs also regulate the expression of miRNAs or their target genes vice versa. Here, we review the recent advances in our understanding of the molecular connections between miRNAs and GA, with an emphasis on the two miRNAs, miR156 and miR159.

scholarly journals Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yaqiong Wu ◽  
Jing Guo ◽  
Tongli Wang ◽  
Fuliang Cao ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Leaf Color ◽  
Wide Range ◽  
Color Mutation

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood. Results In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks. Conclusions This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.

scholarly journals Spatiotemporal Control of Intracellular Membrane Trafficking by Rho GTPases

Cells ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1478 ◽  
Author(s):  
Monilola A. Olayioye ◽  
Bettina Noll ◽  
Angelika Hausser
Keyword(s):  
Membrane Trafficking ◽  
Rho Gtpases ◽  
Rho Gtpase ◽  
Regulatory Proteins ◽  
Biological Processes ◽  
Intracellular Membrane ◽  
Master Regulators ◽  
Cytoskeletal Remodeling ◽  
Wide Range ◽  
Spatiotemporal Control

As membrane-associated master regulators of cytoskeletal remodeling, Rho GTPases coordinate a wide range of biological processes such as cell adhesion, motility, and polarity. In the last years, Rho GTPases have also been recognized to control intracellular membrane sorting and trafficking steps directly; however, how Rho GTPase signaling is regulated at endomembranes is still poorly understood. In this review, we will specifically address the local Rho GTPase pools coordinating intracellular membrane trafficking with a focus on the endo- and exocytic pathways. We will further highlight the spatiotemporal molecular regulation of Rho signaling at endomembrane sites through Rho regulatory proteins, the GEFs and GAPs. Finally, we will discuss the contribution of dysregulated Rho signaling emanating from endomembranes to the development and progression of cancer.

Subsite cooperativity in protease specificity

2009 ◽  
Vol 390 (5/6) ◽  
Author(s):  
Natasha M. Ng ◽  
Robert N. Pike ◽  
Sarah E. Boyd
Keyword(s):  
Cell Cycle ◽  
Active Site ◽  
Negative Influence ◽  
Biological Processes ◽  
The Past ◽  
Wide Range ◽  
Cell Growth And Differentiation ◽  
Protease Specificity ◽  
Potential Methods ◽  
Protease Action

Abstract Proteases play vital roles in a range of biological processes, such as cell cycle, cell growth and differentiation, apoptosis, haemostasis and signalling. Fundamental to our knowledge of protease action is an understanding of how the active site operates; this has been examined through extensive studies of the substrate specificity of the enzymes. Kinetic and structural analyses have shown that the binding of a particular substrate residue at a protease subsite can have either a positive or negative influence on the binding of particular residues at other subsites. This phenomenon has been termed subsite cooperativity and has been observed in a wide range of proteases, often between non-adjacent subsites. This review aims to highlight studies where subsite cooperativity has been observed, experimental techniques used in the past and potential methods that can be employed to comprehensively examine this phenomenon. Further understanding of how the protease active site recognises and chooses its substrates for cleavage will have a significant impact on the development of pharmaceuticals that target these enzymes.

scholarly journals Complexity in regulating microRNA biogenesis in cancer

2020 ◽  
Vol 245 (5) ◽  
pp. 395-401
Author(s):  
Pai-Sheng Chen ◽  
Shao-Chieh Lin ◽  
Shaw-Jenq Tsai
Keyword(s):  
Noncoding Rna ◽  
Target Genes ◽  
Mirna Biogenesis ◽  
Transcriptional Level ◽  
Cellular Processes ◽  
Wide Range ◽  
Mirnas Expression ◽  
Cellular Phenotypes ◽  
Fine Tune ◽  
Processing Factors

The discovery of microRNA (miRNA) significantly extends our knowledge on gene regulation and noncoding gene functions. MiRNAs are important post-transcriptional regulators involve in a wide range of biological functions and diseases, including cancer. MiRNAs are produced by a unique biogenesis pathway involving the two-step sequential nuclear and cytoplasmic RNase-dependent processing at post-transcriptional level. However, a specific (set) of miRNA(s) is (are) synthesized under certain circumstance or developmental/pathological stage to fine-tune the gene expression profile. In this minireview, we will discuss the mechanism of miRNA biogenesis in cancer, mainly focusing on how Drosha and Dicer, two critical molecules controlling miRNA biogenesis, are modulated and which factor contributes to the specificity of selected miRNA maturation. Impact statement The canonical maturation pathway of miRNAs is highly conserved, indicating the crucial roles of these mini-regulators in most cellular processes. Dysregulation of specific miRNAs or imbalance of miRNA abundance has been observed in cancers. Accumulating evidence has shown that the interplay between miRNA processing factors and regulatory proteins previously known as key players in cancer malignancy regulates the biogenesis of miRNAs, expression of target genes, and eventually the alteration of cellular phenotypes. This minireview summarizes the current findings in the modulation of miRNA biogenesis in cancer to advance the understanding of how noncoding RNA contributes to cancer development and malignancy.

scholarly journals Discovery, Identification, and Functional Characterization of Long Noncoding RNAs in Arachis hypogaea L.

2020 ◽  
Author(s):  
Haiying Tian ◽  
Feng Guo ◽  
Zhimeng Zhang ◽  
Hong Ding ◽  
Jingjing Meng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Arachis Hypogaea ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Occurrence Rate ◽  
Biological Processes ◽  
Arachis Hypogaea L ◽  
A Genome ◽  
Wide Range

Abstract Background Long noncoding RNAs (lncRNAs), which are typically >200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Results A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1,442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. The majority of the lncRNAs featured an exon/intron structure, and approximately 44.17% were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

scholarly journals LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat

2019 ◽  
Author(s):  
Beata Orman-Ligeza ◽  
Philippa Borrill ◽  
Tansy Chia ◽  
Marcella Chirico ◽  
Jaroslav Doležel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
List Type ◽  
Biological Processes ◽  
Organ Development ◽  
Starch Metabolism ◽  
Embryo Size ◽  
Binding Factor ◽  
Wide Range ◽  
Endosperm Starch

ABSTRACTMutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks.HIGHLIGHTSLYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only.Wheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth.The down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism.

Cytoplasmic HYL1 modulates miRNA-mediated translational repression

2021 ◽  
Author(s):  
Xi Yang ◽  
Weiguo Dong ◽  
Wenqing Ren ◽  
Qiuxia Zhao ◽  
Feijie Wu ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Mrna Translation ◽  
Gene Repression ◽  
Translational Repression ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Core Component ◽  
Plant Gene Regulation ◽  
Insight Into

Abstract MicroRNAs (miRNAs) control various biological processes by repressing target mRNAs. In plants, miRNAs mediate target gene repression via both mRNA cleavage and translational repression. However, the mechanism underlying this translational repression is poorly understood. Here, we found that Arabidopsis thaliana HYPONASTIC LEAVES1 (HYL1), a core component of the miRNA processing machinery, regulates miRNA-mediated mRNA translation but not miRNA biogenesis when it localized in the cytoplasm. Cytoplasmic HYL1 localizes to the endoplasmic reticulum and associates with ARGONAUTE1 (AGO1) and ALTERED MERISTEM PROGRAM1 (AMP1). In the cytoplasm, HYL1 monitors the distribution of AGO1 onto polysomes, binds to the mRNAs of target genes, represses their translation, and partially rescues the phenotype of the hyl1 null mutant. This study uncovered another function of HYL1 and provides insight into the mechanism of plant gene regulation.

scholarly journals MicroRNAs: crucial regulators of placental development

Reproduction ◽  
2018 ◽  
Vol 155 (6) ◽  
pp. R259-R271 ◽  
Author(s):  
Heyam Hayder ◽  
Jacob O’Brien ◽  
Uzma Nadeem ◽  
Chun Peng
Keyword(s):  
Mrna Stability ◽  
Target Genes ◽  
Current Knowledge ◽  
Mirna Biogenesis ◽  
Placental Development ◽  
Future Directions ◽  
Cellular Processes ◽  
Wide Range ◽  
Canonical Pathways

MicroRNAs (miRNAs) are small non-coding single-stranded RNAs that are integral to a wide range of cellular processes mainly through the regulation of translation and mRNA stability of their target genes. The placenta is a transient organ that exists throughout gestation in mammals, facilitating nutrient and gas exchange and waste removal between the mother and the fetus. miRNAs are expressed in the placenta, and many studies have shown that miRNAs play an important role in regulating trophoblast differentiation, migration, invasion, proliferation, apoptosis, vasculogenesis/angiogenesis and cellular metabolism. In this review, we provide a brief overview of canonical and non-canonical pathways of miRNA biogenesis and mechanisms of miRNA actions. We highlight the current knowledge of the role of miRNAs in placental development. Finally, we point out several limitations of the current research and suggest future directions.

Enhancing our understanding of the molecular responses to hypoxia in mammals using Drosophila melanogaster

2000 ◽  
Vol 88 (4) ◽  
pp. 1481-1487 ◽  
Author(s):  
Gabriel G. Haddad
Keyword(s):  
Drosophila Melanogaster ◽  
Neural Development ◽  
Genetic Model ◽  
Alcohol Intoxication ◽  
Biological Processes ◽  
Loss Of Function ◽  
Mutagenesis Screen ◽  
The Past ◽  
Wide Range ◽  
Or Gene

Drosophila melanogaster has been used as a genetic model, especially in the past decade, to examine normative biological processes and disease conditions very effectively. These span a wide range of major issues such as aging, cancer, embryogenesis, neural development, apoptosis, and alcohol intoxication. Here, we detail how the Drosophila melanogaster can be used as a genetic model to study the molecular and genetic underpinnings of the response to hypoxia. In our study of the basis of anoxia tolerance, one of the potent approaches that we use is a mutagenesis screen to identify loss-of-function mutants that are anoxia sensitive. The major advantage of this approach is that it is not biased for any particular gene or gene product. Although our screen is in progress, we already have evidence that this approach is useful.

scholarly journals Selection and validation of reference genes by RT-qPCR under photoperiodic induction of flowering in sugarcane (Saccharum spp.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paulo H. da Silva Santos ◽  
João R. Vieira Manechini ◽  
Michael S. Brito ◽  
Elisson Romanel ◽  
Renato Vicentini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Reference Genes ◽  
Target Genes ◽  
Floral Induction ◽  
Photoperiodic Induction ◽  
Experimental Conditions ◽  
Wide Range ◽  
The Stability ◽  
Stability And Consistency

AbstractAlthough reference genes have previously been used in the expression analysis of genes involved in sugarcane flowering they had not been experimentally validated for stability and consistency of expression between different samples over a wide range of experimental conditions. Here we report the analysis of candidate reference genes in different tissue types, at different temporal time-points, in both short and long day photoperiodic treatments. The stability of the candidate reference genes in all conditions was evaluated with NormFinder, BestKeeper, and RefFinder algorithms that complement each other for a more robust analysis. As the Normfinder algorithm was more appropriate for our experimental conditions, greater emphasis was placed on Normfinder when choosing the most stable genes. UBQ1 and TUB were shown to be the most stable reference genes to use for normalizing RT-qPCR gene expression data during floral induction, whilst 25SrRNA1 and GAPDH were the least stable. Their use as a reference gene pair was validated by analyzing the expression of two differentially expressed target genes (PIL5 and LHP1). The UBQ1/TUB reference genes combination was able to reveal small significant differences in gene expression of the two target genes that were not detectable when using the least stable reference gene combination. These results can be used to inform the choice of reference genes to use in the study of the sugarcane floral induction pathway. Our work also demonstrates that both PIL5 and LHP1 are significantly up-regulated in the initial stages of photoperiodic induction of flowering in sugarcane.

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