scholarly journals The plastid transcription machinery and its coordination with the expression of nuclear genome: Plastid-Encoded Polymerase, Nuclear-Encoded Polymerase and the Genomes Uncoupled 1-mediated retrograde communication

2020 ◽  
Vol 375 (1801) ◽  
pp. 20190399 ◽  
Author(s):  
Luca Tadini ◽  
Nicolaj Jeran ◽  
Carlotta Peracchio ◽  
Simona Masiero ◽  
Monica Colombo ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Higher Plants ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Nuclear Gene Expression ◽  
Retrograde Signalling ◽  
Hsp90 Chaperone ◽  
Plastid Rna Polymerase

Plastid genes in higher plants are transcribed by at least two different RNA polymerases, the plastid-encoded RNA polymerase (PEP), a bacteria-like core enzyme whose subunits are encoded by plastid genes ( rpoA , rpoB , rpoC1 and rpoC2 ), and the nuclear-encoded plastid RNA polymerase (NEP), a monomeric bacteriophage-type RNA polymerase. Both PEP and NEP enzymes are active in non-green plastids and in chloroplasts at all developmental stages. Their transcriptional activity is affected by endogenous and exogenous factors and requires a strict coordination within the plastid and with the nuclear gene expression machinery. This review focuses on the different molecular mechanisms underlying chloroplast transcription regulation and its coordination with the photosynthesis-associated nuclear genes ( PhANGs ) expression. Particular attention is given to the link between NEP and PEP activity and the GUN1- (Genomes Uncoupled 1) mediated chloroplast-to-nucleus retrograde communication with respect to the Δrpo adaptive response, i.e. the increased accumulation of NEP-dependent transcripts upon depletion of PEP activity, and the editing-level changes observed in NEP-dependent transcripts, including rpoB and rpoC1 , in gun1 cotyledons after norflurazon or lincomycin treatment. The role of cytosolic preproteins and HSP90 chaperone as components of the GUN1-retrograde signalling pathway, when chloroplast biogenesis is inhibited in Arabidopsis cotyledons, is also discussed. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

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.

ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control

2021 ◽  
Author(s):  
Søren Lykke-Andersen ◽  
Jérôme O. Rouvière ◽  
Torben Heick Jensen
Keyword(s):  
Quality Control ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nuclear Gene ◽  
Critical Factor ◽  
Central Position ◽  
Pol Ii ◽  
Nuclear Gene Expression ◽  
Exact Function ◽  
Cap Binding Complex

ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.

Flow Cytometry and Cell Sorting in Plant Biotechnology

2005 ◽  
Author(s):  
David W. Galbraith ◽  
Jan BartoŠ
Keyword(s):  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Higher Plants ◽  
Flow Cytometric Analysis ◽  
Nuclear Genome ◽  
Plant Biotechnology ◽  
Biomass Accumulation ◽  
Life Forms ◽  
Dietary Factors ◽  
Eukaryotic Organisms

Higher plants comprise approximately 250,000 described species and represent a critical component of the planetary biomass. They contribute functions essential for life, of which the most important is photosynthesis, as it provides the means for conversion of incident solar radiation into biomass accumulation, as well as the oxygen required by aerobic life forms. Fixed carbon in the form of carbohydrate provides the basis of the food chain, and metabolic interconversions within plants provide a variety of essential dietary factors. Plants also provide biomass in the form of structural materials and are the source of many natural products with important biomedical properties. As a consequence, considerable scientific interest is invested in determining the molecular mechanisms underlying plant growth, development, metabolism, and responses to biotic and abiotic stresses. Investment has also been made in developing tools and resources for biological investigations using plants. Notable advances include the development of genetics, of means for transformation using defined DNA sequences, and most recently, of the entire nuclear genome sequences of two plant species (Arabidopsis thaliana and Oryza sativa). On the basis of information of this type and that from other sources, it is evident that higher plants share many features with other eukaryotic organisms. Shared features can be observed at many levels; for example, the overall method of construction of cells, in which a bilamellar plasma membrane separates the cytoplasm from the external milieu and provides primary homeostatic regulation. Eukaryotic cells of different kingdoms share organelles, as well as overall regulatory mechanisms. Shared, or highly similar, protein sequences are observed, and they perform similar functions as enzymes, regulatory molecules, or structural components . Higher land plants have evident differences from other eukaryotes. They contain unique classes of organelles primarily devoted to energy capture from sunlight (plastids and peroxisomes). Of these, chloroplasts contain highly fluorescent pigments devoted to photosynthesis, which, particularly chlorophyll, provide unique and powerful signals that can be employed for flow cytometric analysis. Higher plants are also essentially immobile in the sporophytic stage and hence must be capable of responding to changes in environmental conditions and to biotic attack.

The complexity of gene expression in higher plants

1986 ◽  
Vol 314 (1166) ◽  
pp. 481-492 ◽  
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Higher Plants ◽  
Nuclear Gene ◽  
Nuclear Genes ◽  
High Concentration ◽  
Plastid Gene ◽  
Plastid Gene Expression ◽  
Nuclear Gene Expression ◽  
Chloroplast Formation

During light-induced chloroplast formation in higher plants the synthesis of several nuclear encoded plastid proteins is under the control of phytochrome. Light acting through the phytochrome system is able both to increase the transcription of certain nuclear genes and to decrease the transcription of others. It has been generally assumed that regulation by phytochrome alone would be sufficient to account for the observed light-dependent changes in nuclear gene expression during chloroplast formation. However, it has recently become evident that the light-dependent control of nuclear gene expression may be far more complex than originally expected. There are at least two other factors that in addition to phytochrome may affect nuclear gene expression: (1) changes in chromatin organization from an inactive to a transcriptionally active state, and (2) a plastid-derived factor that seems to be involved in the transcriptional control of some nuclear genes encoding plastid-specific proteins. Although the light-dependent control of transcription has been studied intensively for nuclear genes, much less is known about the light-dependent control of plastid gene expression. The P700 chlorophyll a protein of photosystem I is a major membrane protein whose massive accumulation is induced by light and whose genes have been located on the plastid DNA. In barley a high concentration of mRNA for the P700 chlorophyll a protein was detected within the total RNA as well as within the polysomal fraction of etioplasts and remained almost constant during greening. Based on these results it can be inferred that the accumulation of the P700 chlorophyll a protein during light-dependent chloroplast development in barley is not coupled to its transcript concentration but is controlled at a translational — or post-translational - level. The possible function of protochlorophyllide as photoreceptor in this light-dependent control of plastid gene expression is discussed.

scholarly journals Light-Mediated Regulation of Leaf Senescence

2021 ◽  
Vol 22 (7) ◽  
pp. 3291
Author(s):  
Yasuhito Sakuraba
Keyword(s):  
Leaf Senescence ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Current Knowledge ◽  
Red Light ◽  
Nuclear Gene ◽  
Nuclear Gene Expression ◽  
Transcriptional Regulatory ◽  
Plant Life Cycle

Light is the primary regulator of various biological processes during the plant life cycle. Although plants utilize photosynthetically active radiation to generate chemical energy, they possess several photoreceptors that perceive light of specific wavelengths and then induce wavelength-specific responses. Light is also one of the key determinants of the initiation of leaf senescence, the last stage of leaf development. As the leaf photosynthetic activity decreases during the senescence phase, chloroplasts generate a variety of light-mediated retrograde signals to alter the expression of nuclear genes. On the other hand, phytochrome B (phyB)-mediated red-light signaling inhibits the initiation of leaf senescence by repressing the phytochrome interacting factor (PIF)-mediated transcriptional regulatory network involved in leaf senescence. In recent years, significant progress has been made in the field of leaf senescence to elucidate the role of light in the regulation of nuclear gene expression at the molecular level during the senescence phase. This review presents a summary of the current knowledge of the molecular mechanisms underlying light-mediated regulation of leaf senescence.

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.

Perception and Signaling of Ultraviolet-B Radiation in Plants

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Roman Podolec ◽  
Emilie Demarsy ◽  
Roman Ulm
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Nuclear Gene ◽  
Feedback Regulation ◽  
Ultraviolet B ◽  
Photon Absorption ◽  
Annual Review ◽  
Publication Date ◽  
Negative Feedback Regulation ◽  
Nuclear Gene Expression

Ultraviolet-B (UV-B) radiation is an intrinsic fraction of sunlight that plants perceive through the UVR8 photoreceptor. UVR8 is a homodimer in its ground state that monomerizes upon UV-B photon absorption via distinct tryptophan residues. Monomeric UVR8 competitively binds to the substrate binding site of COP1, thus inhibiting its E3 ubiquitin ligase activity against target proteins, which include transcriptional regulators such as HY5. The UVR8–COP1 interaction also leads to the destabilization of PIF bHLH factor family members. Additionally, UVR8 directly interacts with and inhibits the DNA binding of a different set of transcription factors. Each of these UVR8 signaling mechanisms initiates nuclear gene expression changes leading to UV-B-induced photomorphogenesis and acclimation. The two WD40-repeat proteins RUP1 and RUP2 provide negative feedback regulation and inactivate UVR8 by facilitating redimerization. Here, we review the molecular mechanisms of the UVR8 pathway from UV-B perception and signal transduction to gene expression changes and physiological UV-B responses. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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