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Molecular Phylogenetics and Evolution Aug 2021The establishment of a segregate lepisoroid fern genus Ellipinema was mainly to accommodate the isolated position of Lepisorus jakonensis (Polypodiaceae) recovered in...
The establishment of a segregate lepisoroid fern genus Ellipinema was mainly to accommodate the isolated position of Lepisorus jakonensis (Polypodiaceae) recovered in plastid gene tree. Using newly obtained nuclear data, we recovered that Ellipinema and allied genera, such as Lepidomicrosorium, Lemmaphyllum, Neolepisorus, Paragramma, Tricholepidium and Weatherbya are deeply nested within Lepisorus. The nuclear phylogeny showing incongruent phylogenetic placement in comparison with plastid results perhaps indicated ancient hybridization events. The diagnostic morphology characterizing Ellipinema - elliptic scale-like paraphyses, which is shared by all the taxa of sect. Lepisorus and sect. Hymenophyton - falls within the range of continuous variation in the type species Ellipinema jakonense (=Lepisorus jakonensis). Our study, which integrated molecular and morphological data, demonstrates that the segregation of Ellipinema and ×Ellipisorus (= ×Lepinema Li Bing Zhang & Liang Zhang, nom. illeg.) from Lepisorus should be rejected.
Topics: DNA, Plant; Phylogeny; Plastids; Polypodiaceae
PubMed: 33866009
DOI: 10.1016/j.ympev.2021.107176 -
The New Phytologist May 2021The transition from an engulfed autonomous unicellular photosynthetic bacterium to a semiautonomous endosymbiont plastid was accompanied by the transfer of genetic... (Review)
Review
The transition from an engulfed autonomous unicellular photosynthetic bacterium to a semiautonomous endosymbiont plastid was accompanied by the transfer of genetic material from the endosymbiont to the nuclear genome of the host, followed by the establishment of plastid-to-nucleus (retrograde) signaling. The retrograde coordinated activities of the two subcellular genomes ensure chloroplast biogenesis and function as the photosynthetic hub and sensing and signaling center that tailors growth-regulating and adaptive processes. This review specifically focuses on the current knowledge of selected stress-induced retrograde signals, genomes uncoupled 1 (GUN1), methylerythritol cyclodiphosphate (MEcPP), apocarotenoid and β-cyclocitral, and 3'-phosphoadenosine 5'-phosphate (PAP), which evolved to establish the photoautotrophic lifestyle and are instrumental in the integration of light and hormonal signaling networks to ultimately fashion adaptive responses in an ever-changing environment.
Topics: Arabidopsis; Arabidopsis Proteins; Chloroplasts; DNA-Binding Proteins; Gene Expression Regulation, Plant; Plastids; Signal Transduction
PubMed: 33452833
DOI: 10.1111/nph.17192 -
Cells Oct 2020GUN1 (genomes uncoupled 1), a chloroplast-localized pentatricopeptide repeat (PPR) protein with a C-terminal small mutS-related (SMR) domain, plays a central role in the... (Review)
Review
GUN1 (genomes uncoupled 1), a chloroplast-localized pentatricopeptide repeat (PPR) protein with a C-terminal small mutS-related (SMR) domain, plays a central role in the retrograde communication of chloroplasts with the nucleus. This flow of information is required for the coordinated expression of plastid and nuclear genes, and it is essential for the correct development and functioning of chloroplasts. Multiple genetic and biochemical findings indicate that GUN1 is important for protein homeostasis in the chloroplast; however, a clear and unified view of GUN1's role in the chloroplast is still missing. Recently, GUN1 has been reported to modulate the activity of the nucleus-encoded plastid RNA polymerase (NEP) and modulate editing of plastid RNAs upon activation of retrograde communication, revealing a major role of GUN1 in plastid RNA metabolism. In this opinion article, we discuss the recently identified links between plastid RNA metabolism and retrograde signaling by providing a new and extended concept of GUN1 activity, which integrates the multitude of functional genetic interactions reported over the last decade with its primary role in plastid transcription and transcript editing.
Topics: Gene Expression Regulation, Plant; Plant Proteins; Plastids; Protein Binding; RNA, Chloroplast; Stress, Physiological
PubMed: 33081381
DOI: 10.3390/cells9102307 -
Molecular Cell Mar 2024Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a...
Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
Topics: RNA, Chloroplast; DNA-Directed RNA Polymerases; Chloroplasts; Plastids; Gene Expression Regulation, Plant; Transcription, Genetic
PubMed: 38428434
DOI: 10.1016/j.molcel.2024.02.003 -
Plant Science : An International... Apr 2021Cereal crops accumulate large amounts of starch which is synthesized and stored in amyloplasts in the form of starch grains (SGs). Despite significant progress in... (Comparative Study)
Comparative Study
Cereal crops accumulate large amounts of starch which is synthesized and stored in amyloplasts in the form of starch grains (SGs). Despite significant progress in deciphering starch biosynthesis, our understanding of amyloplast development in rice (Oryza sativa) endosperm remains largely unknown. Here, we report a novel rice floury mutant named enlarged starch grain1 (esg1). The mutant has decreased starch content, altered starch physicochemical properties, slower grain-filling rate and reduced 1000-grain weight. A distinctive feature in esg1 endosperm is that SGs are much larger, mainly due to an increased number of starch granules per SG. Spherical and loosely assembled granules, together with those weakly stained SGs may account for decreased starch content in esg1. Map-based cloning revealed that ESG1 encodes a putative permease subunit of a bacterial-type ABC (ATP-binding cassette) lipid transporter. ESG1 is constitutively expressed in various tissues. It encodes a protein localized to the chloroplast and amyloplast membranes. Mutation of ESG1 causes defective galactolipid synthesis. The overall study indicates that ESG1 is a newly identified protein affecting SG development and subsequent starch biosynthesis, which provides novel insights into amyloplast development in rice.
Topics: Edible Grain; Endosperm; Gene Expression Regulation, Plant; Genes, Plant; Genetic Variation; Genotype; Mutation; Oryza; Plastids; Starch
PubMed: 33691965
DOI: 10.1016/j.plantsci.2021.110831 -
Biochimica Et Biophysica Acta. Gene... Mar 2021The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted... (Review)
Review
The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.
Topics: DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Transcription Initiation, Genetic
PubMed: 33561560
DOI: 10.1016/j.bbagrm.2021.194689 -
BioEssays : News and Reviews in... Jan 2023
Topics: Biological Evolution; Phylogeny; Plastids; Symbiosis
PubMed: 36385390
DOI: 10.1002/bies.202200217 -
Nature Plants Sep 2022Engineering the plastid genome based on homologous recombination is well developed in a few model species. Homologous recombination is also the rule in mitochondria, but... (Review)
Review
Engineering the plastid genome based on homologous recombination is well developed in a few model species. Homologous recombination is also the rule in mitochondria, but transformation of the mitochondrial genome has not been realized in the absence of selective markers. The application of transcription activator-like (TAL) effector-based tools brought about a dramatic change because they can be deployed from nuclear genes and targeted to plastids or mitochondria by an N-terminal targeting sequence. Recognition of the target site in the organellar genomes is ensured by the modular assembly of TALE repeats. In this paper, I review the applications of TAL effector nucleases and TAL effector cytidine deaminases for gene deletion, base editing and mutagenesis in plastids and mitochondria. I also review emerging technologies such as post-transcriptional RNA modification to regulate gene expression, Agrobacterium- and nanoparticle-mediated organellar genome transformation, and self-replicating organellar vectors as production platforms.
Topics: Cytidine; Genome, Mitochondrial; Genome, Plant; Magnoliopsida; Plastids; Transcription Activator-Like Effectors
PubMed: 36038655
DOI: 10.1038/s41477-022-01227-6 -
The New Phytologist Jun 2021Plants are able to adjust phenotype in response to changes in the environment. This system depends on an internal capacity to sense environmental conditions and to... (Review)
Review
Plants are able to adjust phenotype in response to changes in the environment. This system depends on an internal capacity to sense environmental conditions and to process this information to plant response. Recent studies have pointed to mitochondria and plastids as important environmental sensors, capable of perceiving stressful conditions and triggering gene expression, epigenomic, metabolic and phytohormone changes in the plant. These processes involve integrated gene networks that ultimately modulate the energy balance between growth and plant defense. This review attempts to link several unusual recent findings into a comprehensive hypothesis for the regulation of plant phenotypic plasticity.
Topics: Gene Expression Regulation, Plant; Mitochondria; Phenotype; Plants; Plastids
PubMed: 33704791
DOI: 10.1111/nph.17333 -
Current Opinion in Plant Biology Dec 2020Stromules are thin tubular extensions of the plastid compartment surrounded by the envelope membrane. A myriad of functions have been proposed for them, and they likely... (Review)
Review
Stromules are thin tubular extensions of the plastid compartment surrounded by the envelope membrane. A myriad of functions have been proposed for them, and they likely have multiple roles. Recent work has illuminated aspects of their formation, especially the important of microtubules in their movement and microfilaments in anchoring. A variety of biotic and abiotic stresses result in induction of stromule formation, and in recent years, stromule formation has been strongly implicated as part of the innate immune response. Both stromules and chloroplasts relocate to surround the nucleus when pathogens are sensed, possibly to supply signaling molecules such as reactive oxygen species. In addition to the nucleus, stromules have been observed in close proximity to other compartments such as mitochondria, endoplasmic reticulum, and the plasma membrane, potentially facilitating exchange of substrates and products to carry out important biosynthetic pathways. Much remains to be learned about the identity of proteins and other molecules released from chloroplasts and stromules and how they function in plant development and defense.
Topics: Actin Cytoskeleton; Chloroplasts; Microtubules; Plant Cells; Plastids
PubMed: 33137706
DOI: 10.1016/j.pbi.2020.10.005