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Current Biology : CB Apr 2018de Vries and Archibald introduce the topic of plastid genomes - prokaryotic genomes housed within eukaryotic algae and plants. (Review)
Review
de Vries and Archibald introduce the topic of plastid genomes - prokaryotic genomes housed within eukaryotic algae and plants.
Topics: Cyanobacteria; Evolution, Molecular; Genome, Plastid; Phylogeny; Plants; Plastids; Symbiosis
PubMed: 29689202
DOI: 10.1016/j.cub.2018.01.027 -
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 -
Biochimica Et Biophysica Acta Sep 2015Progress in the field of regulated intramembrane proteolysis (RIP) in recent years has not surpassed plant biology. Nevertheless, reports on RIP in plants, and... (Review)
Review
Progress in the field of regulated intramembrane proteolysis (RIP) in recent years has not surpassed plant biology. Nevertheless, reports on RIP in plants, and especially in chloroplasts, are still scarce. Of the four different families of intramembrane proteases, only two have been linked to chloroplasts so far, rhomboids and site-2 proteases (S2Ps). The lack of chloroplast-located rhomboid proteases was associated with reduced fertility and aberrations in flower morphology, probably due to perturbations in jasmonic acid biosynthesis, which occurs in chloroplasts. Mutations in homologues of S2P resulted in chlorophyll deficiency and impaired chloroplast development, through a yet unknown mechanism. To date, the only known substrate of RIP in chloroplasts is a PHD transcription factor, located in the envelope. Upon proteolytic cleavage by an unknown protease, the soluble N-terminal domain of this protein is released from the membrane and relocates to the nucleus, where it activates the transcription of the ABA response gene ABI4. Continuing studies on these proteases and substrates, as well as identification of the genes responsible for different chloroplast mutant phenotypes, are expected to shed more light on the roles of intramembrane proteases in chloroplast biology.
Topics: Membrane Proteins; Peptide Hydrolases; Plastids; Proteolysis
PubMed: 25528366
DOI: 10.1016/j.bbabio.2014.12.006 -
Journal of Experimental Botany Nov 2022Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This... (Review)
Review
Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This requires the coordinated expression of photosynthesis genes encoded in nuclear and plastid genomes. Chloroplast biogenesis needs to be additionally coordinated with the light regulation network that controls seedling development. This coordination is achieved by nucleus to plastid signals called anterograde and plastid to nucleus signals termed retrograde. Retrograde signals sent from plastids during initial chloroplast biogenesis are also called biogenic signals. They have been recognized as highly important for proper chloroplast biogenesis and for seedling development. The molecular nature, transport, targets, and signalling function of biogenic signals are, however, under debate. Several studies disproved the involvement of a number of key components that were at the base of initial models of retrograde signalling. New models now propose major roles for a functional feedback between plastid and cytosolic protein homeostasis in signalling plastid dysfunction as well as the action of dually localized nucleo-plastidic proteins that coordinate chloroplast biogenesis with light-dependent control of seedling development. This review provides a survey of the developments in this research field, summarizes the unsolved questions, highlights several recent advances, and discusses potential new working modes.
Topics: Plastids; Chloroplasts; Genome, Plastid; Chloroplast Proteins; Photosynthesis
PubMed: 36002302
DOI: 10.1093/jxb/erac344 -
Plant Cell Reports Jul 2019Plant cells are characterized by a unique group of interconvertible organelles called plastids, which are descended from prokaryotic endosymbionts. The most studied... (Review)
Review
Plant cells are characterized by a unique group of interconvertible organelles called plastids, which are descended from prokaryotic endosymbionts. The most studied plastid type is the chloroplast, which carries out the ancestral plastid function of photosynthesis. During the course of evolution, plastid activities were increasingly integrated with cellular metabolism and functions, and plant developmental processes, and this led to the creation of new types of non-photosynthetic plastids. These include the chromoplast, a carotenoid-rich organelle typically found in flowers and fruits. Here, we provide an introduction to non-photosynthetic plastids, and then review the structures and functions of chromoplasts in detail. The role of chromoplast differentiation in fruit ripening in particular is explored, and the factors that govern plastid development are examined, including hormonal regulation, gene expression, and plastid protein import. In the latter process, nucleus-encoded preproteins must pass through two successive protein translocons in the outer and inner envelope membranes of the plastid; these are known as TOC and TIC (translocon at the outer/inner chloroplast envelope), respectively. The discovery of SP1 (suppressor of ppi1 locus1), which encodes a RING-type ubiquitin E3 ligase localized in the plastid outer envelope membrane, revealed that plastid protein import is regulated through the selective targeting of TOC complexes for degradation by the ubiquitin-proteasome system. This suggests the possibility of engineering plastid protein import in novel crop improvement strategies.
Topics: Chloroplast Proteins; Chloroplasts; Organelles; Plant Proteins; Plasmids; Plastids; Protein Transport
PubMed: 31079194
DOI: 10.1007/s00299-019-02420-2 -
Biochimica Et Biophysica Acta Sep 2015Plastids, such as chloroplasts, are widely distributed endosymbiotic organelles in plants and algae. Apart from their well-known functions in photosynthesis, they have... (Review)
Review
Plastids, such as chloroplasts, are widely distributed endosymbiotic organelles in plants and algae. Apart from their well-known functions in photosynthesis, they have roles in processes as diverse as signal sensing, fruit ripening, and seed development. As most plastid proteins are produced in the cytosol, plastids have developed dedicated translocon machineries for protein import, comprising the TOC (translocon at the outer envelope membrane of chloroplasts) and TIC (translocon at the inner envelope membrane of chloroplasts) complexes. Multiple lines of evidence reveal that protein import via the TOC complex is actively regulated, based on the specific interplay between distinct receptor isoforms and diverse client proteins. In this review, we summarize recent advances in our understanding of protein import regulation, particularly in relation to control by the ubiquitin-proteasome system (UPS), and how such regulation changes plastid development. The diversity of plastid import receptors (and of corresponding preprotein substrates) has a determining role in plastid differentiation and interconversion. The controllable turnover of TOC components by the UPS influences the developmental fate of plastids, which is fundamentally linked to plant development. Understanding the mechanisms by which plastid protein import is controlled is critical to the development of breakthrough approaches to increase the yield, quality and stress tolerance of important crop plants, which are highly dependent on plastid development. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
Topics: Chloroplast Proteins; Plastids; Proteasome Endopeptidase Complex; Protein Transport; Ubiquitin; Ubiquitination
PubMed: 25762164
DOI: 10.1016/j.bbabio.2015.02.017 -
The New Phytologist Oct 2019Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered... (Review)
Review
Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, the analysis of nuclear genomes of plastid-bearing lineages has revealed a mosaic origin of plastid-related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of noncyanobacterial origin. Therefore, plastid proteins and plastid-localised metabolic pathways evolved by tinkering and using gene toolkits from different sources. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the 'red carpet hypothesis').
Topics: Biological Evolution; Gene Expression Regulation; Gene Transfer, Horizontal; Photosynthesis; Plastids; Symbiosis
PubMed: 31135958
DOI: 10.1111/nph.15965 -
Cellular and Molecular Life Sciences :... Apr 2011Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid-the apicoplast. Although its tiny genome and even the entire nuclear... (Review)
Review
Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid-the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle's unique symbiotic origin.
Topics: Apicomplexa; Evolution, Molecular; Phylogeny; Plastids
PubMed: 21380560
DOI: 10.1007/s00018-011-0646-1 -
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 -
Scientific Reports Aug 2022Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in...
Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.
Topics: Artemisia; Evolution, Molecular; Genome, Mitochondrial; Genome, Plastid; Phylogeny; Plastids
PubMed: 35978085
DOI: 10.1038/s41598-022-18387-2