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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 -
Plant & Cell Physiology May 2024Chloroplasts/plastids are unique organelles found in plant cells and some algae and are responsible for performing essential functions such as photosynthesis. The... (Review)
Review
Chloroplasts/plastids are unique organelles found in plant cells and some algae and are responsible for performing essential functions such as photosynthesis. The plastid genome, consisting of circular and linear DNA molecules, is packaged and organized into specialized structures called nucleoids. The composition and dynamics of these nucleoids have been the subject of intense research, as they are critical for proper plastid functions and development. In this mini-review, recent advances in understanding the organization and regulation of plastid nucleoids are overviewed, with a focus on the various proteins and factors that regulate the shape and dynamics of nucleoids, including DNA-binding proteins and membrane anchorage proteins. The dynamic nature of nucleoid organization, which is influenced by a variety of developmental cues and the cell cycle, is also examined.
Topics: Plastids; Chloroplasts; Plant Proteins; Plants
PubMed: 37542434
DOI: 10.1093/pcp/pcad090 -
International Journal of Molecular... Jul 2020In recent years, plant genetic engineering has advanced agriculture in terms of crop improvement, stress and disease resistance, and pharmaceutical biosynthesis. Cells... (Review)
Review
In recent years, plant genetic engineering has advanced agriculture in terms of crop improvement, stress and disease resistance, and pharmaceutical biosynthesis. Cells from land plants and algae contain three organelles that harbor DNA: the nucleus, plastid, and mitochondria. Although the most common approach for many plant species is the introduction of foreign DNA into the nucleus (nuclear transformation) via Agrobacterium- or biolistics-mediated delivery of transgenes, plastid transformation offers an alternative means for plant transformation. Since there are many copies of the chloroplast genome in each cell, higher levels of protein accumulation can often be achieved from transgenes inserted in the chloroplast genome compared to the nuclear genome. Chloroplasts are therefore becoming attractive hosts for the introduction of new agronomic traits, as well as for the biosynthesis of high-value pharmaceuticals, biomaterials and industrial enzymes. This review provides a comprehensive historical and biological perspective on plastid transformation, with a focus on current and emerging approaches such as the use of single-walled carbon nanotubes (SWNTs) as DNA delivery vehicles, overexpressing morphogenic regulators to enhance regeneration ability, applying genome editing techniques to accelerate double-stranded break formation, and reconsidering protoplasts as a viable material for plastid genome engineering, even in transformation-recalcitrant species.
Topics: Animals; Chloroplasts; Crops, Agricultural; Gene Editing; Genetic Engineering; Genome, Chloroplast; Humans; Nanotubes, Carbon; Plants, Genetically Modified; Plastids; Transformation, Genetic; Transgenes
PubMed: 32659946
DOI: 10.3390/ijms21144854 -
International Journal of Molecular... Nov 2021The polypeptides encoded by the chloroplast genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I.... (Review)
Review
The polypeptides encoded by the chloroplast genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack genes. Among vascular plants, the genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid genes allows comparison on phylogenetic trees and functional investigations of the genes. The genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without genes at risk of extinction and, probably, most extant ones may have lost genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking genes challenge models about the role of genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of genes.
Topics: Charophyceae; Chloroplasts; Genes, Chloroplast; NADH Dehydrogenase; Photosynthesis; Plant Senescence; Plastids; Thylakoids
PubMed: 34830386
DOI: 10.3390/ijms222212505 -
American Journal of Botany Apr 2023Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and...
PREMISE
Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome.
METHODS
We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω).
RESULTS
Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK.
CONCLUSIONS
We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.
Topics: Phylogeny; Evolution, Molecular; Heterotrophic Processes; Genome, Plastid; Plastids
PubMed: 36779918
DOI: 10.1002/ajb2.16141 -
Genes Jul 2022Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient...
Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.
Topics: Base Composition; Evolution, Molecular; Genome, Plastid; Humans; Phylogeny; Plastids; Tracheophyta
PubMed: 35886063
DOI: 10.3390/genes13071280 -
Cell Feb 2024Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex...
Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.
Topics: Arabidopsis Proteins; Chloroplasts; Cryoelectron Microscopy; DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Transcription, Genetic
PubMed: 38428394
DOI: 10.1016/j.cell.2024.01.036 -
PLoS Biology Nov 2022Kleptoplasty, the process by which a host organism sequesters and retains algal chloroplasts, is relatively common in protists. The origin of the plastid varies, as do...
Kleptoplasty, the process by which a host organism sequesters and retains algal chloroplasts, is relatively common in protists. The origin of the plastid varies, as do the length of time it is retained in the host and the functionality of the association. In metazoa, the capacity for long-term (several weeks to months) maintenance of photosynthetically active chloroplasts is a unique characteristic of a handful of sacoglossan sea slugs. This capability has earned these slugs the epithets "crawling leaves" and "solar-powered sea slugs." This Unsolved Mystery explores the basis of chloroplast maintenance and function and attempts to clarify contradictory results in the published literature. We address some of the mysteries of this remarkable association. Why are functional chloroplasts retained? And how is the function of stolen chloroplasts maintained without the support of the algal nucleus?
Topics: Animals; Photosynthesis; Chloroplasts; Plastids; Gastropoda
PubMed: 36346789
DOI: 10.1371/journal.pbio.3001857 -
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 -
Plant Biology (Stuttgart, Germany) Sep 2021Reactive oxygen species (ROS) generation within a cell is a natural process of specific subcellular components involved in redox reactions. Within a plant cell,... (Review)
Review
Reactive oxygen species (ROS) generation within a cell is a natural process of specific subcellular components involved in redox reactions. Within a plant cell, chloroplasts are one of the major sources of ROS generation. Plastid-generated ROS molecules include singlet oxygen ( O ), superoxide radical (O ), hydroxyl radical (OH ) and hydrogen peroxide (H O ), which are produced mainly during photochemical reactions of photosynthesis and chlorophyll biosynthetic process. Under normal growth and developmental, generated ROS molecules act as a secondary messenger controlling several metabolic reactions; however, perturbed environmental conditions lead to multi-fold amplification of cellular ROS that eventually kill the target cell. To maintain homeostasis between production and scavenging of ROS, the cell has instituted several enzymatic and non-enzymatic antioxidant machineries to maintain ROS at a physiological level. Among chloroplastic ROS molecules, excess generation of singlet oxygen ( O ) is highly deleterious to the cell metabolic functions and survival. Interestingly, within cellular antioxidant machinery, enzymes involved in detoxification of O are lacking. Recent studies suggest that under optimal concentrations, O acts as a signalling molecule and drives the cell to either the acclimation pathway or regulated cell death (RCD). Stress-induced RCD is a survival mechanism for the whole plant, while the involvement of chloroplasts and chloroplast-localized molecules that execute RCD are not well understood. In this review, we advocate for participation of chloroplasts-generated O in signalling and RCD in plants.
Topics: Chloroplasts; Plastids; Reactive Oxygen Species; Regulated Cell Death; Singlet Oxygen
PubMed: 33768665
DOI: 10.1111/plb.13260