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Biochimica Et Biophysica Acta Sep 2015The development of a repressible chloroplast gene expression system in Chlamydomonas reinhardtii has opened the door for studying the role of essential chloroplast... (Review)
Review
The development of a repressible chloroplast gene expression system in Chlamydomonas reinhardtii has opened the door for studying the role of essential chloroplast genes. This approach has been used to analyze three chloroplast genes of this sort coding for the α subunit of RNA polymerase (rpoA), a ribosomal protein (rps12) and the catalytic subunit of the ATP-dependent ClpP protease (clpP1). Depletion of the three corresponding proteins leads to growth arrest and cell death. Shutdown of chloroplast transcription and translation increases the abundance of a set of plastid transcripts that includes mainly those involved in transcription, translation and proteolysis and reveals multiple regulatory feedback loops in the chloroplast gene circuitry. Depletion of ClpP profoundly affects plastid protein homeostasis and elicits an autophagy-like response with extensive cytoplasmic vacuolization of cells. It also triggers changes in chloroplast and nuclear gene expression resulting in increased abundance of chaperones, proteases, ubiquitin-related proteins and proteins involved in lipid trafficking and thylakoid biogenesis. These features are hallmarks of an unfolded protein response in the chloroplast and raise new questions on plastid protein homeostasis and plastid signaling. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
Topics: Autophagy; Chloroplast Proteins; Gene Expression Regulation, Plant; Genes, Chloroplast; Lipid Metabolism; Plastids; Quality Control; Signal Transduction
PubMed: 25486627
DOI: 10.1016/j.bbabio.2014.11.011 -
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 -
Genome Biology and Evolution Jul 2017Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because...
Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch. placoidea, Cryptomonas curvata, and Storeatula sp. CCMP1868 share a number of features including synteny and gene content with the previously sequenced genomes of Cryptomonas paramecium, Rhodomonas salina, Teleaulax amphioxeia, and Guillardia theta. Our analysis of these plastid genomes reveals examples of gene loss and intron insertion. In particular, the chlB/chlL/chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss and pseudogenization in cryptophytes. Comparison of phylogenetic trees based on plastid and nuclear genome data sets show the introduction, via secondary endosymbiosis, of a red algal derived plastid in a lineage of chlorophyll-c containing algae. This event was followed by additional rounds of eukaryotic endosymbioses that spread the red lineage plastid to diverse groups such as haptophytes and stramenopiles.
Topics: Cryptophyta; Evolution, Molecular; Genome, Plastid; Phylogeny; Plastids; Sequence Analysis, DNA; Symbiosis
PubMed: 28854597
DOI: 10.1093/gbe/evx123 -
International Journal of Molecular... Nov 2023, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and...
, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of and performed comparative plastid genomic analyses with four previously published plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (, , , and ) and two coding genes ( and ). Three protein-coding genes (, , and ) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of . The diagnostic characteristics currently used in may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.
Topics: Phylogeny; Centella; Araliaceae; Genome, Plastid; Plastids; Genome, Chloroplast
PubMed: 38068952
DOI: 10.3390/ijms242316629 -
Plant Physiology Mar 2019Building on recombinant DNA technology, leaps in synthesis, assembly, and analysis of DNA have revolutionized genetics and molecular biology over the past two decades... (Review)
Review
Building on recombinant DNA technology, leaps in synthesis, assembly, and analysis of DNA have revolutionized genetics and molecular biology over the past two decades (Kosuri and Church, 2014). These technological advances have accelerated the emergence of synthetic biology as a new discipline (Cameron et al., 2014). Synthetic biology is characterized by efforts targeted at the modification of existing and the design of novel biological systems based on principles adopted from information technology and engineering (Andrianantoandro et al., 2006; Khalil and Collins, 2010). As in more traditional engineering disciplines such as mechanical, electrical and civil engineering, synthetic biologists utilize abstraction, decoupling and standardization to make the design of biological systems more efficient and scalable. To facilitate the management of complexity, synthetic biology relies on an abstraction hierarchy composed of multiple levels (Endy, 2005): DNA as genetic material, "parts" as elements of DNA encoding basic biological functions (e.g. promoter, ribosome-binding site, terminator sequence), "devices" as any combination of parts implementing a human-defined function, and "systems" as any combination of devices fulfilling a predefined purpose. Parts are designated to perform predictable and modular functions in the context of higher-level devices or systems, which are successively refined through a cycle of designing, building, and testing.
Topics: Genetic Engineering; Genome, Chloroplast; Plastids; Synthetic Biology
PubMed: 30181342
DOI: 10.1104/pp.18.00767 -
The New Phytologist Feb 2022Plants employ an array of intricate and hierarchical signaling cascades to perceive and transduce informational cues to synchronize and tailor adaptive responses....
Plants employ an array of intricate and hierarchical signaling cascades to perceive and transduce informational cues to synchronize and tailor adaptive responses. Systemic stress response (SSR) is a recognized complex signaling and response network quintessential to plant's local and distal responses to environmental triggers; however, the identity of the initiating signals has remained fragmented. Here, we show that both biotic (aphids and viral pathogens) and abiotic (high light and wounding) stresses induce accumulation of the plastidial-retrograde-signaling metabolite methylerythritol cyclodiphosphate (MEcPP), leading to reduction of the phytohormone auxin and the subsequent decreased expression of the phosphatase PP2C.D1. This enables phosphorylation of mitogen-activated protein kinases 3/6 and the consequential induction of the downstream events ultimately, resulting in biosynthesis of the two SSR priming metabolites pipecolic acid and N-hydroxy-pipecolic acid. This work identifies plastids as a major initiation site, and the plastidial retrograde signal MEcPP as an initiator of a multicomponent signaling cascade potentiating the biosynthesis of SSR activators, in response to biotic and abiotic triggers.
Topics: Arabidopsis; Arabidopsis Proteins; Gene Expression Regulation, Plant; Indoleacetic Acids; Plastids
PubMed: 34859454
DOI: 10.1111/nph.17890 -
Plant Physiology Jun 2018Starch synthesized and stored in amyloplasts serves as the major energy storage molecule in cereal endosperm. To elucidate the molecular mechanisms underlying amyloplast...
Starch synthesized and stored in amyloplasts serves as the major energy storage molecule in cereal endosperm. To elucidate the molecular mechanisms underlying amyloplast development and starch synthesis, we isolated a series of floury endosperm mutants in rice (). We identified the rice mutant (), which exhibited obvious defects in the development of compound starch grains, decreased starch content, and altered starch physicochemical features. Map-based cloning showed that encodes a phospholipase-like protein homologous to phosphatidic acid-preferring phospholipase A was expressed ubiquitously with abundant levels observed in developing seeds and roots. FSE1 was localized to both the cytosol and intracellular membranes. Lipid profiling indicated that total extra-plastidic lipids and phosphatidic acid were increased in plants, suggesting that FSE1 may exhibit in vivo phospholipase A activity on phosphatidylcholine, phosphatidylinositol, phosphatidyl-Ser, phosphatidylethanolamine, and, in particular, phosphatidic acid. Additionally, the total galactolipid content in developing endosperm was significantly reduced, which may cause abnormal amyloplast development. Our results identify FSE1 as a phospholipase-like protein that controls the synthesis of galactolipids in rice endosperm and provide a novel connection between lipid metabolism and starch synthesis in rice grains during endosperm development.
Topics: Cloning, Molecular; Cytoplasm; Endosperm; Gene Expression Regulation, Plant; Genetic Complementation Test; Intracellular Membranes; Mutation; Oryza; Phosphatidic Acids; Phospholipids; Plant Proteins; Plants, Genetically Modified; Plastids; Seeds; Starch
PubMed: 29717019
DOI: 10.1104/pp.17.01826 -
The EMBO Journal Nov 2020The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these...
The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these semi-autonomous organelles, construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here, we show that the expression of PAP8, an essential subunit of the plastid-encoded RNA polymerase (PEP) in Arabidopsis thaliana, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 protein is localized and active in both plastids and the nucleus, and particularly required for the formation of late photobodies. In the pap8 albino mutant, phytochrome-mediated signalling is altered, degradation of the chloroplast development repressors PIF1/PIF3 is disrupted, HY5 is not stabilized, and the expression of the photomorphogenesis regulator GLK1 is impaired. PAP8 translocates into plastids via its targeting pre-sequence, interacts with the PEP and eventually reaches the nucleus, where it can interact with another PEP subunit pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome B-mediated signalling cascade and the reshaping of the PEP activity, it may coordinate nuclear gene expression with PEP-driven chloroplastic gene expression during chloroplast biogenesis.
Topics: Acid Phosphatase; Arabidopsis; Arabidopsis Proteins; Cell Nucleus; Chloroplasts; DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Light; Morphogenesis; Organelle Biogenesis; Phytochrome; Plants, Genetically Modified; Plastids; Signal Transduction; Transcription Factors; Transcription, Genetic
PubMed: 33001465
DOI: 10.15252/embj.2020104941 -
Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions.The New Phytologist Dec 2014Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host... (Review)
Review
Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host cell reprogramming. Cell-autonomous defense reactions are typically polarized to the plant cell periphery underneath microbial contact sites, including de novo cell wall biosynthesis. Alternatively, host cell reprogramming converges in the biogenesis of membrane-enveloped compartments for accommodation of beneficial bacteria or invasive infection structures of filamentous microbes. Recent advances have revealed that, in response to microbial encounters, plasma membrane symmetry is broken, membrane tethering and SNARE complexes are recruited, lipid composition changes and plasma membrane-to-cytoskeleton signaling is activated, either for pre-invasive defense or for microbial entry. We provide a critical appraisal on recent studies with a focus on how plant cells re-structure membranes and the associated cytoskeleton in interactions with microbial pathogens, nitrogen-fixing rhizobia and mycorrhiza fungi.
Topics: Cell Membrane; Cytoskeleton; Host-Pathogen Interactions; Lipids; Plant Cells; Plastids
PubMed: 25168837
DOI: 10.1111/nph.12978 -
Genome Biology and Evolution Jun 2023The chloroplast (plastid) arose via the endosymbiosis of a photosynthetic cyanobacterium by a nonphotosynthetic eukaryotic cell ∼1.5 billion years ago. Although the...
The chloroplast (plastid) arose via the endosymbiosis of a photosynthetic cyanobacterium by a nonphotosynthetic eukaryotic cell ∼1.5 billion years ago. Although the plastid underwent rapid evolution by genome reduction, its rate of molecular evolution is low and its genome organization is highly conserved. Here, we investigate the factors that have constrained the rate of molecular evolution of protein-coding genes in the plastid genome. Through phylogenomic analysis of 773 angiosperm plastid genomes, we show that there is substantial variation in the rate of molecular evolution between genes. We demonstrate that the distance of a plastid gene from the likely origin of replication influences the rate at which it has evolved, consistent with time and distance-dependent nucleotide mutation gradients. In addition, we show that the amino acid composition of a gene product constraints its substitution tolerance, limiting its mutation landscape and its corresponding rate of molecular evolution. Finally, we demonstrate that the mRNA abundance of a gene is a key factor in determining its rate of molecular evolution, suggesting an interaction between transcription and DNA repair in the plastid. Collectively, we show that the location, the composition, and the expression of a plastid gene can account for >50% of the variation in its rate of molecular evolution. Thus, these three factors have exerted a substantial limitation on the capacity for adaptive evolution in plastid-encoded genes and ultimately constrained the evolvability of the chloroplast.
Topics: Magnoliopsida; Chloroplasts; Phylogeny; Evolution, Molecular; Genome; Plastids; Genome, Plastid
PubMed: 37279504
DOI: 10.1093/gbe/evad101