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Trends in Plant Science Dec 2012Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of... (Review)
Review
Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.
Topics: Gene Expression Regulation, Plant; Plastids; RNA, Untranslated; Transcription Factors
PubMed: 22981395
DOI: 10.1016/j.tplants.2012.08.002 -
Trends in Genetics : TIG Apr 2009The concept of plastid signalling posits that signals originating from chloroplasts modulate nuclear gene expression (NGE). Put simply, it claims that signalling factors... (Review)
Review
The concept of plastid signalling posits that signals originating from chloroplasts modulate nuclear gene expression (NGE). Put simply, it claims that signalling factors are exported from the chloroplast, traverse the cytosol, and act in the nucleus. Pertinent signals are thought to derive from various sources, including the tetrapyrrole pathway, protein synthesis, reactive oxygen species, or the redox state of the organelle. Recent studies have cast doubt on the most popular candidate signalling molecule, the tetrapyrrole pathway intermediate Mg-protoporphyrin IX, indicating that chloroplast activity might control NGE indirectly by affecting cytosolic metabolite levels or redox states (metabolic signalling). Here, we focus on recent developments and confusions in the field of plastid signalling research and highlight alternative scenarios of plastid-nucleus signal transduction. Future analyses of chloroplast-nucleus communication should focus on providing an integrated view of plastid signalling under physiologically relevant conditions.
Topics: Animals; Cell Nucleus; Chlamydomonas reinhardtii; Chloroplasts; Models, Biological; Models, Genetic; Mutation; Oxidation-Reduction; Photosynthesis; Plastids; Reactive Oxygen Species; Signal Transduction; Tetrapyrroles
PubMed: 19303165
DOI: 10.1016/j.tig.2009.02.004 -
Trends in Plant Science Jul 2013Import of most nuclear encoded proteins into plastids is directed by an N-terminal transit peptide. Early studies suggested that transit peptides are interchangeable... (Review)
Review
Import of most nuclear encoded proteins into plastids is directed by an N-terminal transit peptide. Early studies suggested that transit peptides are interchangeable between precursor proteins. However, emerging evidence shows that different transit peptides contain different motifs specifying their preference for certain plastid types or ages. In this opinion article, we propose a 'multi-selection and multi-order' (M&M) model for transit peptide design, describing each transit peptide as an assembly of motifs for interacting with selected translocon components. These interactions determine the preference of the precursor for a particular plastid type or age. Furthermore, the order of the motifs varies among transit peptides, explaining why no consensus sequences have been identified through linear sequence comparison of all transit peptides as one group.
Topics: Amino Acid Sequence; Chloroplast Proteins; Models, Biological; Plastids; Protein Sorting Signals; Protein Transport
PubMed: 23688728
DOI: 10.1016/j.tplants.2013.04.003 -
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 -
International Journal For Parasitology Sep 2000An extrachromosomal genome of between 27 and 35 kb has been described in several apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii.... (Review)
Review
An extrachromosomal genome of between 27 and 35 kb has been described in several apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii. Examination of sequence data proved the genomes to be a remnant plastid genome, from which all genes encoding photosynthetic functions had been lost. Localisation studies had shown that the genome was located within a multi-walled organelle, anterior to the nucleus. This organelle had been previously described in ultrastructural studies of several genera of apicomplexa, but no function had been attributed to it. This invited review describes the evolution of knowledge on the apicomplexan plastid, then discusses current research findings on the likely role of the plastid in the Apicomplexa. How the plastid may be used to effect better drug treatments for apicomplexan diseases, and its potential as a marker for investigating phylogenetic relationships among the Apicomplexa, are discussed.
Topics: Animals; Apicomplexa; Plastids
PubMed: 10996324
DOI: 10.1016/s0020-7519(00)00100-4 -
Archives of Biochemistry and Biophysics Oct 2004Carotenoids are isoprenoid pigmented compounds that are present in representatives from practically all eukaryotic and prokaryotic taxa. In plants, carotenoids are... (Review)
Review
Carotenoids are isoprenoid pigmented compounds that are present in representatives from practically all eukaryotic and prokaryotic taxa. In plants, carotenoids are synthesized and normally sequestered in plastids as lipophilic C40 constituents. However, they are also subjected to oxidative remodeling initiated by specific carotenoid cleavage dioxygenases. Primary products resulting from these reactions undergo modifications involving oxido-reduction, dehydratation rearrangement, and glycosylation. This review focuses on only a few of these derivatives for which the enzymes and genes involved have been characterized. The compartmentation of this metabolism and its significance have also been considered.
Topics: Carotenoids; Oxidation-Reduction; Plant Physiological Phenomena; Plants; Plastids
PubMed: 15325907
DOI: 10.1016/j.abb.2004.06.028 -
Molekuliarnaia Biologiia 2005Plastids have a very interesting transcription apparatus that gives us an opportunity to investigate mono- and multisubunut RNA polymerase interaction under conditions... (Review)
Review
Plastids have a very interesting transcription apparatus that gives us an opportunity to investigate mono- and multisubunut RNA polymerase interaction under conditions of complex biogenesis of the organelles and the necessity to coordinate the expression of genes located in different cell compartments. The last decade has been a breakthrough in the study of chloroplast RNA polymerases. The most important advances are the discovery of nucleus-encoded RNA polymerase and nuclear gene family for sigma subunits of plastid-encoded RNA polymerase, the obtaining of knockout-mutants on the subunits of plastid-encoded RNA polymerase, and the revelation of this RNA polymerase reorganization during plastid biogenesis. The hypothesis concerning labor division between two plastid RNA polymerases has been proposed. The review focuses on the analysis of modern information about organization, function and evolution of plastid RNA polymerases.
Topics: Cell Nucleus; DNA-Directed RNA Polymerases; Phylogeny; Plastids; Protein Subunits
PubMed: 16240710
DOI: No ID Found -
Nature Reviews. Genetics Jul 2009The eukaryotic organelles mitochondrion and plastid originated from eubacterial endosymbionts. Here we propose that, in both cases, prokaryote-to-organelle conversion... (Review)
Review
The eukaryotic organelles mitochondrion and plastid originated from eubacterial endosymbionts. Here we propose that, in both cases, prokaryote-to-organelle conversion was driven by the internalization of host-encoded factors progressing from the outer membrane of the endosymbionts towards the intermembrane space, inner membrane and finally the organelle interior. This was made possible by an outside-to-inside establishment in the endosymbionts of host-controlled protein-sorting components, which enabled the gradual integration of organelle functions into the nuclear genome. Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis.
Topics: Animals; Eukaryotic Cells; Evolution, Molecular; Humans; Plants; Plastids; Protein Transport
PubMed: 19506574
DOI: 10.1038/nrg2610 -
Bioscience, Biotechnology, and... 2010Plastids are a diverse group of organelles found in plants and some parasites. Chloroplasts are the archetypical plastids and are present in photosynthetic plant cells.... (Review)
Review
Plastids are a diverse group of organelles found in plants and some parasites. Chloroplasts are the archetypical plastids and are present in photosynthetic plant cells. Because most plastid proteins are encoded by the nuclear genome, plastid biogenesis relies on importing these proteins into the plastid. On the other hand, changes in functional or metabolic states of plastids have been known to affect the expression of nuclear genes encoding plastid proteins, and are collectively called "plastid signals." This regulation is also important for maintaining plastid function. This review focuses on the roles of these anterograde and retrograde pathways in plastid biogenesis and environmental adaptation.
Topics: Active Transport, Cell Nucleus; Adaptation, Physiological; Algal Proteins; Cell Nucleus; Gene Expression Regulation; Plant Proteins; Plastids; Protein Transport; Reactive Oxygen Species; Secretory Pathway; Signal Transduction; Tetrapyrroles
PubMed: 20208345
DOI: 10.1271/bbb.90842 -
Journal of Experimental Botany Apr 2005Plastids are essential plant organelles vital for life on earth, responsible not only for photosynthesis but for many fundamental intermediary metabolic reactions.... (Review)
Review
Plastids are essential plant organelles vital for life on earth, responsible not only for photosynthesis but for many fundamental intermediary metabolic reactions. Plastids are not formed de novo but arise by binary fission from pre-existing plastids, and plastid division therefore represents an important process for the maintenance of appropriate plastid populations in plant cells. Plastid division comprises an elaborate pathway of co-ordinated events which include division machinery assembly at the division site, the constriction of envelope membranes, membrane fusion and, ultimately, the separation of the two new organelles. Because of their prokaryotic origin bacterial cell division has been successfully used as a paradigm for plastid division. This has resulted in the identification of the key plastid division components FtsZ, MinD, and MinE, as well as novel proteins with similarities to prokaryotic cell division proteins. Through a combination of approaches involving molecular genetics, cell biology, and biochemistry, it is now becoming clear that these proteins act in concert during plastid division, exhibiting both similarities and differences compared with their bacterial counterparts. Recent efforts in the cloning of the disrupted loci in several of the accumulation and replication of chloroplasts mutants has further revealed that the division of plastids is controlled by a combination of prokaryote-derived and host eukaryote-derived proteins residing not only in the plastid stroma but also in the cytoplasm. Based on the available data to date, a working model is presented showing the protein components involved in plastid division, their subcellular localization, and their protein interaction properties.
Topics: Cell Division; Chloroplasts; Organelles; Plant Cells; Plastids
PubMed: 15753112
DOI: 10.1093/jxb/eri118