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Genes Nov 2022Andr., a member of Paeoniaceae, is native to China. In its 1600 years' cultivation, more than 2000 cultivars for different purposes (ornamental, medicinal and oil use)...
Andr., a member of Paeoniaceae, is native to China. In its 1600 years' cultivation, more than 2000 cultivars for different purposes (ornamental, medicinal and oil use) have been inbred. However, there are still some controversies regarding the provenance of tree peony cultivars and the phylogenetic relationships between and within different cultivar groups. In this study, plastid genome sequencing was performed on 10 representative tree peony cultivars corresponding to 10 different flower types. Structure and comparative analyses of the plastid genomes showed that the total lengths of the chloroplast genome of the 10 cultivars ranged from 152,153 to 152,385 bp and encoded 84-88 protein-coding genes, 8 rRNAs and 31-40 tRNAs. The number of simple sequence repeats and interspersed repeat sequences of the 10 cultivars ranged from 65-68 and 40-42, respectively. Plastid phylogenetic relationships of species/cultivars were reconstructed incorporating data from our newly sequenced plastid genomes and 15 published species, and results showed that subsect. was the closest relative to the central plains cultivar group with robust support, and that it may be involved in the formation of the group. was recovered as a successive sister group to this lineage. Additionally, eleven morphological characteristics of flowers were mapped to the phylogenetic skeleton to reconstruct the evolutionary trajectory of flower architecture in Paeoniaceae.
Topics: Paeonia; Phylogeny; Flowers; Chromosome Mapping; Plastids
PubMed: 36553496
DOI: 10.3390/genes13122229 -
Proceedings of the National Academy of... Aug 2022The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell...
The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of (), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in . We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes () for plastids and mitochondria were ∼ 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria ( ∼ 1.3), potentially because of its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.
Topics: Arabidopsis; Arabidopsis Proteins; DNA, Mitochondrial; DNA, Plant; Genome, Plant; Heteroplasmy; Mitochondria; MutS DNA Mismatch-Binding Protein; Plastids
PubMed: 35969753
DOI: 10.1073/pnas.2206973119 -
Journal of Experimental Botany May 2022Fibrillins (FBNs) are a family of genes in cyanobacteria, algae, and plants. The proteins they encode possess a lipid-binding motif, exist in various types of plastids,... (Review)
Review
Fibrillins (FBNs) are a family of genes in cyanobacteria, algae, and plants. The proteins they encode possess a lipid-binding motif, exist in various types of plastids, and are associated with lipid bodies called plastoglobules, implicating them in lipid metabolism. FBNs present in the thylakoid and stroma are involved in the storage, transport, and synthesis of lipid molecules for photoprotective functions against high-light stress. In this review, the diversity of subplastid locations in the evolution of FBNs, regulation of FBNs expression by various stresses, and the role of FBNs in plastid lipid metabolism are comprehensively summarized and directions for future research are discussed.
Topics: Fibrillins; Lipids; Plants; Plastids; Thylakoids
PubMed: 35560204
DOI: 10.1093/jxb/erac087 -
Journal of Experimental Botany Oct 2022The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change... (Review)
Review
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
Topics: Ribulose-Bisphosphate Carboxylase; Actins; Phylogeny; Plastids; Symbiosis; Evolution, Molecular
PubMed: 35768189
DOI: 10.1093/jxb/erac290 -
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 -
Current Opinion in Plant Biology Dec 2020Stromules are thin tubular extensions of the plastid compartment surrounded by the envelope membrane. A myriad of functions have been proposed for them, and they likely... (Review)
Review
Stromules are thin tubular extensions of the plastid compartment surrounded by the envelope membrane. A myriad of functions have been proposed for them, and they likely have multiple roles. Recent work has illuminated aspects of their formation, especially the important of microtubules in their movement and microfilaments in anchoring. A variety of biotic and abiotic stresses result in induction of stromule formation, and in recent years, stromule formation has been strongly implicated as part of the innate immune response. Both stromules and chloroplasts relocate to surround the nucleus when pathogens are sensed, possibly to supply signaling molecules such as reactive oxygen species. In addition to the nucleus, stromules have been observed in close proximity to other compartments such as mitochondria, endoplasmic reticulum, and the plasma membrane, potentially facilitating exchange of substrates and products to carry out important biosynthetic pathways. Much remains to be learned about the identity of proteins and other molecules released from chloroplasts and stromules and how they function in plant development and defense.
Topics: Actin Cytoskeleton; Chloroplasts; Microtubules; Plant Cells; Plastids
PubMed: 33137706
DOI: 10.1016/j.pbi.2020.10.005 -
Physiologia Plantarum 2023Retrograde signaling conceptually means the transfer of signals from semi-autonomous cell organelles to the nucleus to modulate nuclear gene expression. A generalized... (Review)
Review
Retrograde signaling conceptually means the transfer of signals from semi-autonomous cell organelles to the nucleus to modulate nuclear gene expression. A generalized explanation is that chloroplasts are highly sensitive to environmental stimuli and quickly generate signaling molecules (retrograde signals) and transport them to the nucleus through the cytosol to reprogram nuclear gene expression for cellular/metabolic adjustments to cope with environmental fluctuations. During the past decade, substantial advancements have been made in the area of retrograde signaling, including information on putative retrograde signals. Researchers have also proposed possible mechanisms for generating retrograde signals and their transmission. However, the exact mechanisms and processes responsible for transmitting retrograde signaling from the chloroplast to the nucleus remain elusive, demanding substantial attention. This review highlights strategies employed to detect retrograde signals, their possible modes of signaling to the nucleus, and their implications for cellular processes during stress conditions. The present review also summarizes the role of ROS-mediated retrograde signaling in plastid-nucleus communication and its functional significance in co-coordinating the physiological profile of plant cells.
Topics: Cell Nucleus; Chloroplasts; Plastids; Signal Transduction; Gene Expression Regulation, Plant
PubMed: 37616006
DOI: 10.1111/ppl.13987 -
Molecular Ecology Resources Aug 2023Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately...
Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single-copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short-read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single-molecule, long-read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long-read data. We generated a pipeline, plastid Genome Assembly Using Long-read data (ptGAUL), to address the problem of plastome assembly using long-read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long-read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul.
Topics: Genome, Plastid; Repetitive Sequences, Nucleic Acid; Gene Rearrangement; Plastids; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA
PubMed: 36939021
DOI: 10.1111/1755-0998.13787 -
Methods in Molecular Biology (Clifton,... 2022Studying the stability of a protein dependent on its N-terminal residue requires a mechanism, which selectively exposes the amino acid at the N-terminus. Here, we...
Studying the stability of a protein dependent on its N-terminal residue requires a mechanism, which selectively exposes the amino acid at the N-terminus. Here, we describe the use of the tobacco etch virus (TEV) protease to generate a specific N-terminal amino acid in the stroma of the chloroplast. The established molecular reporter system further allows the quantification of the reporter protein half-life dependent on the identity of the N-terminal residue.
Topics: Amino Acids; Chloroplasts; Plastids; Proteins
PubMed: 35188662
DOI: 10.1007/978-1-0716-1791-5_10 -
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