scholarly journals Impact of small RNAs in retrograde signalling pathways in Arabidopsis thaliana

2019 ◽  
Author(s):  
Kristin Habermann ◽  
Bhavika Tiwari ◽  
Maria Krantz ◽  
Stephan O. Adler ◽  
Edda Klipp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nuclear Gene ◽  
Signalling Pathways ◽  
Wild Type ◽  
Nuclear Gene Expression ◽  
Non Coding Rna ◽  
Retrograde Signalling ◽  
Transcriptional Changes ◽  
Non Coding Rnas

SummaryChloroplast perturbations activate retrograde signalling pathways causing dynamic changes of gene expression. Besides transcriptional control of gene expression different classes of small non-coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling is lacking. We performed sRNA profiling in response to norflurazon (NF) that provokes retrograde signals in A. thaliana wild type and the two retrograde signalling mutants gun1 and gun5. The RNA samples were also used for mRNA and long non-coding RNA (lncRNA) profiling to link altered sRNA levels to changes of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in wild type. Strikingly, 140 and 213 sRNAs were found to be differentially regulated in both mutants indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression we detected about 1500 differentially expressed mRNAs in the NF treated wild type and around 900 and 1400 mRNAs that were differentially regulated in the gun1 and gun5 mutant with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid localised proteins. The analyses of sRNA-target pairs identified pairs with an anticorrelated expression as well pairs showing other expressional relations pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression we assume a considerable impact of sRNAs in retrograde-dependent transcriptional changes to adjust plastidic and nuclear gene expression.Significance statementPerturbations of plastid functions trigger retrograde signalling to adjust plastidic and nuclear gene expression, however, the role of small non-coding RNAs acting as regulators in these pathways is not well understood. We analysed small non-coding RNA expression in response to retrograde signals in A. thaliana wild type and two retrograde signalling mutants and identified members of all known small non-coding RNA classes pointing to a functional role of these RNA classes in retrograde pathways.

scholarly journals Overexpression of chloroplast-targeted ferrochelatase 1 results in a genomes uncoupled chloroplast-to-nucleus retrograde signalling phenotype

2020 ◽  
Vol 375 (1801) ◽  
pp. 20190401 ◽  
Author(s):  
Mike T. Page ◽  
Tania Garcia-Becerra ◽  
Alison G. Smith ◽  
Matthew J. Terry
Keyword(s):  
Gene Expression ◽  
Feedback Inhibition ◽  
Nuclear Gene ◽  
Signalling Pathway ◽  
Chloroplast Genes ◽  
Nuclear Gene Expression ◽  
Retrograde Signalling ◽  
Genes Encoding ◽  
Retrograde Signal

Chloroplast development requires communication between the progenitor plastids and the nucleus, where most of the genes encoding chloroplast proteins reside. Retrograde signals from the chloroplast to the nucleus control the expression of many of these genes, but the signalling pathway is poorly understood. Tetrapyrroles have been strongly implicated as mediators of this signal with the current hypothesis being that haem produced by the activity of ferrochelatase 1 (FC1) is required to promote nuclear gene expression. We have tested this hypothesis by overexpressing FC1 and specifically targeting it to either chloroplasts or mitochondria, two possible locations for this enzyme. Our results show that targeting of FC1 to chloroplasts results in increased expression of the nuclear-encoded chloroplast genes GUN4 , CA1 , HEMA1 , LHCB2.1, CHLH after treatment with Norflurazon (NF) and that this increase correlates to FC1 gene expression and haem production measured by feedback inhibition of protochlorophyllide synthesis. Targeting FC1 to mitochondria did not enhance the expression of nuclear-encoded chloroplast genes after NF treatment. The overexpression of FC1 also increased nuclear gene expression in the absence of NF treatment, demonstrating that this pathway is operational in the absence of a stress treatment. Our results therefore support the hypothesis that haem synthesis is a promotive chloroplast-to-nucleus retrograde signal. However, not all FC1 overexpression lines enhanced nuclear gene expression, suggesting there is still a lot we do not understand about the role of FC1 in this signalling pathway. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

scholarly journals Linking mitochondrial and chloroplast retrograde signalling in plants

2020 ◽  
Vol 375 (1801) ◽  
pp. 20190410 ◽  
Author(s):  
Yan Wang ◽  
Jennifer Selinski ◽  
Chunli Mao ◽  
Yanqiao Zhu ◽  
Oliver Berkowitz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nuclear Gene ◽  
Signalling Pathways ◽  
Theme Issue ◽  
Functional Changes ◽  
Nuclear Gene Expression ◽  
Retrograde Signalling ◽  
Energy Converting

Retrograde signalling refers to the regulation of nuclear gene expression in response to functional changes in organelles. In plants, the two energy-converting organelles, mitochondria and chloroplasts, are tightly coordinated to balance their activities. Although our understanding of components involved in retrograde signalling has greatly increased in the last decade, studies on the regulation of the two organelle signalling pathways have been largely independent. Thus, the mechanism of how mitochondrial and chloroplastic retrograde signals are integrated is largely unknown. Here, we summarize recent findings on the function of mitochondrial signalling components and their links to chloroplast retrograde responses. From this, a picture emerges showing that the major regulators are integrators of both organellar retrograde signalling pathways. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

Plastid Signals Confer Arabidopsis Tolerance to Water Stress

2011 ◽  
Vol 66 (1-2) ◽  
pp. 47-54 ◽  
Author(s):  
Jian Cheng ◽  
Chun-Xia He ◽  
Zhong-Wei Zhang ◽  
Fei Xu ◽  
Da-Wei Zhang ◽  
...  
Keyword(s):  
Water Stress ◽  
Photosynthetic Apparatus ◽  
Nuclear Gene ◽  
Stress Adaptation ◽  
Wild Type ◽  
Oxidative Damages ◽  
Nuclear Gene Expression ◽  
Retrograde Signalling ◽  
The Relationship ◽  
Mutant Cells

Plastid-to-nucleus retrograde signalling coordinates nuclear gene expression with chloroplast function and is essential for the photoautotrophic life-style of plants. The relationship between plastid signalling and water stress response was investigated with genome uncoupled (gun) mutants, gun1, gun3, and gun5, and an abscisic acid (ABA)-responsible transcription factor mutant, abi4. The results showed that gun1, gun3, gun5, and abi4 mutants suffered from more oxidative damages than the wild-type plants under the water stress and the water stress + herbicide (norflurazon, NF) co-treatment. Superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX) activities could not be prompted in the plastidsignalling defective mutants under the stress conditions. At the same time, Lhcb expression was not repressed in the plastid-signalling defective mutants by the NF treatment or water stress. Therefore, the photosynthetic apparatus in the mutant cells could not be closed during the stresses and the excessive light caused more photodamages on the mutant leaves. The roles of GUN1, GUN3, GUN5 and ABI4 proteins in environmental stress adaptation have been discussed.

scholarly journals The role of m6A, m5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Paz Nombela ◽  
Borja Miguel-López ◽  
Sandra Blanco
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Therapeutic Potential ◽  
Biological Processes ◽  
Rna Modifications ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
Made In

AbstractRNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.

scholarly journals CIRCULAR RNA – miRNA MEDIATED INTERACTION IN MYOCARDIAL INFARCTION

2021 ◽  
Vol 27 (2) ◽  
pp. 3793-3798
Author(s):  
Yordanka Doneva ◽  
◽  
Veselin Valkov ◽  
Yavor Kashlov ◽  
Galya Mihaylova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Infarction ◽  
Circular Rna ◽  
Biological Functions ◽  
Non Coding Rna ◽  
Circular Structure ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Circular RNA (circRNAs) belong to the long non-coding RNA family, but unlike the linear RNA in circular RNA, the 3’ and 5’ end in the RNA molecule are joined together, forming their circular structure. Until recently, circRNAs have been believed to be a side product of splicing, but now it is known that they have a wide range of biological functions, from regulators of gene expression to regulators of other non-coding RNAs - microRNAs (miRNAs). CircRNAs have the potential of being therapeutic targets and biomarkers for diseases. There are little data and only several investigations about this type of RNAs in myocardial infarction in humans. This review summarizes the role of some new circRNA – miRNA interactions in the development of Myocardial Infarction.

scholarly journals Small non-coding RNA CjNC110 influences motility, autoagglutination, AI-2 localization, hydrogen peroxide sensitivity and chicken colonization in Campylobacter jejuni

2020 ◽  
Author(s):  
Amanda J. Kreuder ◽  
Brandon Ruddell ◽  
Kathy Mou ◽  
Alan Hassall ◽  
Qijing Zhang ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Quorum Sensing ◽  
Campylobacter Jejuni ◽  
Wild Type ◽  
Zoonotic Pathogen ◽  
Autoinducer 2 ◽  
Energy Taxis ◽  
Non Coding Rna ◽  
Non Coding Rnas

ABSTRACTSmall non-coding RNAs are involved in many important physiological functions in pathogenic microorganisms. Previous studies have identified the presence of non-coding RNAs in the major zoonotic pathogen Campylobacter jejuni, however, few have been functionally characterized to date. CjNC110 is a conserved ncRNA in C. jejuni, located downstream of the luxS gene which is responsible for the production of the quorum-sensing molecule autoinducer-2 (AI-2). In this study, we utilized strand specific high-throughput RNAseq to identify potential targets or interactive partners of CjNC110 in a sheep abortion clone of C. jejuni. This data was then utilized to focus further phenotypic evaluation of the role of CjNC110 in motility, autoagglutination, quorum sensing, hydrogen peroxide sensitivity and chicken colonization in C. jejuni. Inactivation of the CjNC110 ncRNA led to a statistically significant decrease in autoagglutination ability as well as increased motility and hydrogen peroxide sensitivity when compared to wild-type. Extracellular AI-2 detection was decreased in ΔCjNC110, however, intracellular AI-2 accumulation was significantly increased, suggesting a key role of CjNC110 in modulating the transport of AI-2. Notably, ΔCjNC110 also showed a decreased ability to colonize chickens. Complementation of CjNC110 restored all phenotypic changes back to wild-type levels. The collective results of the phenotypic and transcriptomic changes observed in our data provide valuable insights into the pathobiology of C. jejuni sheep abortion clone and strongly suggest that CjNC110 plays an important role in regulation of energy taxis, flagellar glycosylation, cellular communication via quorum sensing, oxidative stress tolerance and chicken colonization in this important zoonotic pathogen.

A Review on Theragnostic Applications of Micrornas and Long Non- Coding RNAs in Colorectal Cancer

2019 ◽  
Vol 18 (30) ◽  
pp. 2614-2629 ◽  
Author(s):  
Ganesan Jothimani ◽  
Sushmitha Sriramulu ◽  
Yashna Chabria ◽  
Xiao-Feng Sun ◽  
Antara Banerjee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Cell Fate ◽  
Target Identification ◽  
Vital Role ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Median Survival Rate

Colorectal cancer (CRC) is a heterogeneous malignancy leading to increased mortality and poor prognosis due to the lack of efficient early diagnostics. Metastasis of the tumor being the most common cause of mortality is accountable for almost 90% of CRC associated deaths. Intensified screening procedures and molecular target identification has inflated the median survival rate of in CRC patients. microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have come forward as potential targets for developing a novel approach in CRC theragnostics. Non-coding RNA (ncRNAs) sequences are abundantly present and thereby play a vital role in several biological processes such as cellular organization, cell fate determination, proliferation, apoptosis, tissue homeostasis maintenance as well as pathological conditions such as cancer by acting as post transcriptional regulators of gene expression. Several studies have highlighted the involvement of these ncRNAs in CRC development. However, the molecular mechanism involved in regulating CRC has not been clearly elucidated. This review, throws light upon the several non-coding RNAs involved in CRC with a focus on novel mechanisms of action, recent advances in the regulatory mechanisms that control the gene expression related to carcinogenesis. Furthermore, the potential role of ncRNAs as diagnostic as well as therapeutic targets has been reviewed.

Chloroplast Redox Control of Nuclear Gene Expression—A New Class of Plastid Signals in Interorganellar Communication

2003 ◽  
Vol 5 (1) ◽  
pp. 95-101 ◽  
Author(s):  
Thomas Pfannschmidt ◽  
Katia Schütze ◽  
Vidal Fey ◽  
Irena Sherameti ◽  
Ralf Oelmüller
Keyword(s):  
Gene Expression ◽  
Nuclear Gene ◽  
Redox Control ◽  
New Class ◽  
Nuclear Gene Expression
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