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International Review of Cytology 2003Photosynthetic eukaryotes have evolved plastid division mechanisms since acquisition of plastids through endosymbiosis. The emerging evolutionary origin of the plastid... (Review)
Review
Photosynthetic eukaryotes have evolved plastid division mechanisms since acquisition of plastids through endosymbiosis. The emerging evolutionary origin of the plastid division mechanism is remarkably complex. The constituents of the division apparatus of plastids may have complex origins. The one constituent is the plastid FtsZ ring taken over from the cyanobacteria-like ancestral endosymbionts. The second is the doublet of concentric plastid dividing rings (or triplet in red algae), possibly acquired by ancestral host eukaryotes following the primary endosymbiotic event. Placement of the division apparatus at the correct division site may involve a system analogous to the bacterial Min system. Plastid nucleoid partitioning may be mediated by binding to envelope or thylakoid membranes. Multiple copies of plastid DNA and symmetrical distribution of the nucleoids in the plastids may permit faithful transmission to daughter plastids via equal binary plastid divisions. Cyanelles retain peptidoglycan wall and cyanelle division occurs through septum formation such as bacterial cell division. Cyanelle division involves the cyanelle ring analogous to the inner stromal plastid-dividing (PD) ring. According to the prevailing hypothesis that primary endosymbiosis occurred only once, cyanelle division may represent an intermediate stage between cyanobacterial division and the well-known plastid division among extant plants. With the secondary plastids, which are surrounded by three or four membranes, the PD ring also participates in division of the inner two "true" plastid envelope membranes, and the third and the outermost membranes divide by unknown mechanisms.
Topics: Animals; Arabidopsis Proteins; Cell Division; Cyanobacteria; Eukaryota; Evolution, Molecular; Intracellular Membranes; Plant Proteins; Plastids; Symbiosis
PubMed: 12503847
DOI: 10.1016/s0074-7696(02)22012-4 -
Plant Signaling & Behavior Feb 2013Plastid retrograde signaling (chloroplast to nucleus) has been proposed to play an important role in the acclimation of plant function to environmental stress. Although... (Review)
Review
Plastid retrograde signaling (chloroplast to nucleus) has been proposed to play an important role in the acclimation of plant function to environmental stress. Although several pathways and molecular components, as well as some signals, have been identified in recent years, our understanding of the communication between plastid and nucleus under stress remains fragmentary. This mini-review summarizes the properties of currently proposed candidate signals, chief molecular components, and their roles in the plastid retrograde signaling network in a variety of stress responses. We provide special emphasis on the recently characterized AMOS1/EGY1-dependent plastid retrograde signaling pathways engaged during ammonium stress.
Topics: Ammonium Compounds; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Signal Transduction
PubMed: 23299427
DOI: 10.4161/psb.23107 -
International Journal For Parasitology Oct 2011Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the... (Review)
Review
Perkinsus marinus (Phylum Perkinsozoa) is a protozoan parasite that has devastated natural and farmed oyster populations in the USA, significantly affecting the shellfish industry and the estuarine environment. The other two genera in the phylum, Parvilucifera and Rastrimonas, are parasites of microeukaryotes. The Perkinsozoa occupies a key position at the base of the dinoflagellate branch, close to its divergence from the Apicomplexa, a clade that includes parasitic protista, many harbouring a relic plastid. Thus, as a taxon that has also evolved toward parasitism, the Perkinsozoa has attracted the attention of biologists interested in the evolution of this organelle, both in its ultrastructure and the conservation, loss or transfer of its genes. A review of the recent literature reveals mounting evidence in support of the presence of a relic plastid in P. marinus, including the presence of multimembrane structures, characteristic metabolic pathways and proteins with a bipartite N-terminal extension. Further, these findings raise intriguing questions regarding the potential functions and unique adaptation of the putative plastid and/or plastid genes in the Perkinsozoa. In this review we analyse the above-mentioned evidence and evaluate the potential future directions and expected benefits of addressing such questions. Given the rapidly expanding molecular/genetic resources and methodological toolbox for Perkinsus spp., these organisms should complement the currently established models for investigating plastid evolution within the Chromalveolata.
Topics: Alveolata; Amino Acid Sequence; Animals; Evolution, Molecular; Humans; Microscopy, Electron; Models, Biological; Molecular Sequence Data; Ostreidae; Plastids; Sequence Alignment; United States
PubMed: 21889509
DOI: 10.1016/j.ijpara.2011.07.008 -
Cladistics : the International Journal... Dec 2021The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events...
The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.
Topics: Genome, Plastid; Genomics; High-Throughput Nucleotide Sequencing; Phylogeny; Plastids; Polypodiaceae
PubMed: 34841589
DOI: 10.1111/cla.12461 -
Plant Physiology Apr 2011
Topics: Plant Cells; Plastids
PubMed: 21459978
DOI: 10.1104/pp.111.900408 -
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 -
Annual Review of Plant Biology 2013Plastids (chloroplasts) have long been recognized to have originated by endosymbiosis of a cyanobacterium, but their subsequent evolutionary history has proved complex... (Review)
Review
Plastids (chloroplasts) have long been recognized to have originated by endosymbiosis of a cyanobacterium, but their subsequent evolutionary history has proved complex because they have also moved between eukaryotes during additional rounds of secondary and tertiary endosymbioses. Much of this history has been revealed by genomic analyses, but some debates remain unresolved, in particular those relating to secondary red plastids of the chromalveolates, especially cryptomonads. Here, I examine several fundamental questions and assumptions about endosymbiosis and plastid evolution, including the number of endosymbiotic events needed to explain plastid diversity, whether the genetic contribution of the endosymbionts to the host genome goes far beyond plastid-targeted genes, and whether organelle origins are best viewed as a singular transition involving one symbiont or as a gradual transition involving a long line of transient food/symbionts. I also discuss a possible link between transporters and the evolution of protein targeting in organelle integration.
Topics: Biological Evolution; Chloroplasts; Cyanobacteria; Eukaryota; Plastids; Protein Transport; Symbiosis
PubMed: 23451781
DOI: 10.1146/annurev-arplant-050312-120144 -
Biochimie Jun 1999A unique biochemical machinery is present within the two envelope membranes surrounding plastids (Joyard et al., Plant Physiol. 118 (1998) 715-723) that reflects the... (Review)
Review
A unique biochemical machinery is present within the two envelope membranes surrounding plastids (Joyard et al., Plant Physiol. 118 (1998) 715-723) that reflects the stage of development of the plastid and the specific metabolic requirements of the various tissues. Envelope membranes are the site for the synthesis and metabolism of specific lipids. They are also the site of transport of metabolites, proteins and information between plastids and surrounding cellular compartments. For instance, a complex machinery for the import of nuclear-encoded plastid proteins is rapidly being elucidated. The functional studies of plastid envelope membranes result in the characterization of an increasing number of envelope proteins with unexpected functions. For instance, recent experiments have demonstrated that envelope membranes bind specifically to plastid genetic systems, the nucleoids surrounded by plastid ribosomes. At early stages of plastid differentiation, the inner envelope membrane contains a unique protein (named PEND protein) that binds specifically to plastid DNA. This tight connection suggests that the PEND protein is at least involved in partitioning the plastid DNA to daughter plastids during division. The PEND protein can also provide a physical support for replication and transcription. In addition, factors involved in the control of plastid protein synthesis can become associated to envelope membranes. This was shown for a protein homologous to the E. coli ribosome recycling factor and for the stabilizing factors of some specific chloroplast mRNAs encoding thylakoid membrane proteins. In fact, the envelope membranes together with the plastid DNA are the two essential constituents of plastids that confer identity to plastids and their interactions are becoming uncovered through molecular as well as cytological studies. In this review, we will focus on these recent observations (which are consistent with the endosymbiotic origin of plastids) and we discuss possible roles for the plastid envelope in the expression of plastid genome.
Topics: Animals; DNA, Chloroplast; Gene Expression Regulation, Plant; Genome, Plant; Intracellular Membranes; Plastids; Transcription, Genetic
PubMed: 10433116
DOI: 10.1016/s0300-9084(99)80119-9 -
Molecular Phylogenetics and Evolution Oct 2021Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant...
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
Topics: Base Sequence; Chloroplasts; Fagales; Genome, Plastid; Phylogeny; Plastids
PubMed: 34129935
DOI: 10.1016/j.ympev.2021.107232 -
Journal of Phycology Jun 2021The advent of high-throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used...
The advent of high-throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient diversifications (subphyla, class) and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopogonophyceae, a group with unusual plastid genomes but with low taxon sampling. We use HTS to produce near complete plastid genomes of all genera, and multiple species within some genera, to produce robust phylogenies to investigate character evolution, dating of divergence in the group, and plastid organization, including intron patterns. Our results produce a fully supported phylogeny of the genera in the Erythropeltales and suggest that morphologies (upright versus crustose) have evolved multiple times. Our dated phylogeny also indicates that the order is very old (~800 Ma), with diversification occurring after the ice ages of the Cryogenian period (750-635 Ma). Plastid gene order is congruent with phylogenetic relationships and suggests that genome architecture does not change often. Our data also highlight the abundance of introns in the plastid genomes of this order. We also produce a nearly complete plastid genome of Tsunamia transpacifica (Stylonematophyceae) to add to the taxon sampling of genomes of this class. The use of plastid genomes clearly produces robust phylogenetic relationships that can be used to infer evolutionary events, and increased taxon sampling, especially in less well-known red algal groups, will provide additional insights into their evolution.
Topics: Evolution, Molecular; Introns; Phylogeny; Plastids; Rhodophyta
PubMed: 33657649
DOI: 10.1111/jpy.13159