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Current Opinion in Plant Biology Oct 2021Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from... (Review)
Review
Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.
Topics: Biological Evolution; Eukaryota; Photosynthesis; Phylogeny; Plastids; Symbiosis
PubMed: 34390927
DOI: 10.1016/j.pbi.2021.102093 -
Current Opinion in Biotechnology Oct 2019Plastids are interesting targets for metabolic engineering using the tools of synthetic biology. Plastids carry their own genome, which can be manipulated genetically in... (Review)
Review
Plastids are interesting targets for metabolic engineering using the tools of synthetic biology. Plastids carry their own genome, which can be manipulated genetically in many algae and plants. Incorporating foreign genes into the plastid genome offers valuable benefits, such as high-level foreign protein expression and the absence of gene silencing. Here, we review progress in bioengineering of chloroplasts to produce valuable metabolites and proteins. Various strategies for enhancing yields of desired products, including design of operons, fusion proteins for improved translational efficiency, protein scaffolding, metabolic channeling and storage, are described. Efforts to control plastid differentiation also offer promising ways of turning plastids into controllable bio-factories, and the construction of synthetic plastids optimized for specific functions would be a major advance.
Topics: Chloroplasts; Metabolic Engineering; Plants, Genetically Modified; Plastids; Synthetic Biology
PubMed: 30798145
DOI: 10.1016/j.copbio.2019.01.009 -
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 -
Plant Molecular Biology Mar 2022Mutation of the BEIIb gene in an isa1 mutant background mitigates the negative effect of the ISA1 mutation on grain filling, and facilitates recovery of amyloplast...
Mutation of the BEIIb gene in an isa1 mutant background mitigates the negative effect of the ISA1 mutation on grain filling, and facilitates recovery of amyloplast formation in rice endosperm. In this study, the effect of branching enzyme IIb and isoamylase 1 deficiency on starch properties was demonstrated using high resistant starch rice lines, Chikushi-kona 85 and EM129. Both lines harbored a mutation in the BEIIb and ISA1 genes and showed no BEIIb and ISA1 activity, implying that both lines are beIIb isa1 double mutants. The amylopectin long chain and apparent amylose content of both mutant lines were higher than those of the wild-type. While both mutants contained loosely packed, round starch grains, a trait specific to beIIb mutants, they also showed collapsed starch grains at the center of the endosperm, a property specific to isa1 mutants. Furthermore, beIIb isa1 double mutant F lines derived from a cross between Chikushi-kona 85 and Nishihomare (wild-type cultivar) showed significantly heavier seed weight than the beIIb and isa1 single mutant lines. These results suggest that co-occurrence of beIIb and isa1 mutant alleles in a single genetic background mitigates the negative effect of the isa1 allele on grain filling, and contributes to recovery of the amyloplast formation defect in the isa1 single mutant.
Topics: 1,4-alpha-Glucan Branching Enzyme; Edible Grain; Genotype; Isoamylase; Mutation; Oryza; Plastids
PubMed: 35083581
DOI: 10.1007/s11103-022-01242-3 -
Plant Cell Reports Aug 2023Iron-sulfur (Fe-S) clusters are ancient protein cofactors ubiquitously exist in organisms. They are involved in many important life processes. Plastids are... (Review)
Review
Iron-sulfur (Fe-S) clusters are ancient protein cofactors ubiquitously exist in organisms. They are involved in many important life processes. Plastids are semi-autonomous organelles with a double membrane and it is believed to originate from a cyanobacterial endosymbiont. By learning form the research in cyanobacteria, a Fe-S cluster biosynthesis and delivery pathway has been proposed and partly demonstrated in plastids, including iron uptake, sulfur mobilization, Fe-S cluster assembly and delivery. Fe-S clusters are essential for the downstream Fe-S proteins to perform their normal biological functions. Because of the importance of Fe-S proteins in plastid, researchers have made a lot of research progress on this pathway in recent years. This review summarizes the detail research progress made in recent years. In addition, the scientific problems remained in this pathway are also discussed.
Topics: Iron; Plastids; Biological Transport; Sulfur; Iron-Sulfur Proteins
PubMed: 37160773
DOI: 10.1007/s00299-023-03024-7 -
Molecular Phylogenetics and Evolution May 2023Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of...
Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.
Topics: Phylogeny; Genome, Plant; Cyperaceae; Genome, Mitochondrial; Evolution, Molecular; Magnoliopsida; Plastids; Genome, Plastid
PubMed: 36921696
DOI: 10.1016/j.ympev.2023.107760 -
The New Phytologist Aug 2022Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have...
Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have examined these patterns in microalgae or the discordance between the two organelles. Here we investigated the nuclear-mitochondrial-plastid phylogenomic incongruence in Emiliania-Gephyrocapsa, a group of cosmopolitan calcifying phytoplankton with enormous populations and recent speciations. We assembled mitochondrial and plastid genomes of 27 strains from across global oceans and temperature regimes, and analyzed the phylogenomic histories of the three compartments using concatenation and coalescence methods. Six major clades with varying morphology and distribution are well recognized in the nuclear phylogeny, but such relationships are absent in the mitochondrial and plastid phylogenies, which also differ substantially from each other. The rampant phylogenomic discordance is due to a combination of organellar capture (introgression), organellar genome recombination, and incomplete lineage sorting of ancient polymorphic organellar genomes. Hybridization can lead to replacements of whole organellar genomes without introgression of nuclear genes and the two organelles are not inherited as a single cytoplasmic unit. This study illustrates the convoluted evolution and inheritance of organellar genomes in isogamous haplodiplontic microalgae and provides a window into the phylogenomic complexity of marine unicellular eukaryotes.
Topics: Animals; Genome, Mitochondrial; Genome, Plastid; Microalgae; Phylogeny; Plastids
PubMed: 35556250
DOI: 10.1111/nph.18219 -
Biomolecules Jul 2019Plastid genome sequences are becoming more readily available with the increase in high-throughput sequencing, and whole-organelle genetic data is available for algae and... (Review)
Review
Plastid genome sequences are becoming more readily available with the increase in high-throughput sequencing, and whole-organelle genetic data is available for algae and plants from across the diversity of photosynthetic eukaryotes. This has provided incredible opportunities for studying species which may not be amenable to in vivo study or genetic manipulation or may not yet have been cultured. Research into plastid genomes has pushed the limits of what can be deduced from genomic information, and in particular genomic information obtained from public databases. In this Review, we discuss how research into plastid genomes has benefitted enormously from the explosion of publicly available genome sequence. We describe two case studies in how using publicly available gene data has supported previously held hypotheses about plastid traits from lineage-restricted experiments across algal and plant diversity. We propose how this approach could be used across disciplines for inferring functional and biological characteristics from genomic approaches, including integration of new computational and bioinformatic approaches such as machine learning. We argue that the techniques developed to gain the maximum possible insight from plastid genomes can be applied across the eukaryotic tree of life.
Topics: Big Data; Computational Biology; Evolution, Molecular; Genome Size; Genome, Plastid; Genomics; High-Throughput Nucleotide Sequencing; Machine Learning; Phylogeny; Plants; Plastids
PubMed: 31344945
DOI: 10.3390/biom9080299 -
Microbiology (Reading, England) Sep 2022is a unicellular photosynthetic eukaryotic flagellate of the Discoba supergroup, which also encompasses Kinetoplastida and Diplonema. Plastids have green algal origin...
is a unicellular photosynthetic eukaryotic flagellate of the Discoba supergroup, which also encompasses Kinetoplastida and Diplonema. Plastids have green algal origin and are secondarily acquired. The nuclear genome is extremely large and many genes suggest multiple endosymbiotic/gene transfer events, i.e. derivation from prokaryotes of various lineages. is remarkably robust and can proliferate in environments contaminated with heavy metals and acids. Extraordinary metabolic plasticity and a mixotrophic lifestyle confers an ability to thrive in a broad range of environments, as well as facilitating production of many novel metabolites, making of considerable biotechnological importance.
Topics: Chlorophyta; Euglena gracilis; Photosynthesis; Plastids; Symbiosis
PubMed: 36178464
DOI: 10.1099/mic.0.001241 -
ACS Nano Feb 2022Mitochondria and chloroplasts not only are cellular energy sources but also have important regulatory and developmental roles in cell function. CeO, FeOx ENMs, ZnS, CdS...
Mitochondria and chloroplasts not only are cellular energy sources but also have important regulatory and developmental roles in cell function. CeO, FeOx ENMs, ZnS, CdS QDs, and relative metal salts were utilized in Murashige-Skoog (MS) synthetic growth medium at different concentrations (80-500 mg L) and times of exposures (0-20 days). Analysis of physiological and molecular response of chloroplasts and mitochondrion demonstrates that ENMs increase or decrease functionality and organelle genome replication. Exposure to nanoscale CeO and FeOx causes an 81-105% increase in biomass, whereas ZnS and CdS QDs yielded neutral or a 59% decrease in growth, respectively. Differential effects between ENMs and their corresponding metal salts highlight nanoscale-specific response pathways, which include energy production and oxidative stress response. Differences may be ascribed to ENM and the metal salt dissolution rate and the toxicity of the metal ion, which suggests eventual biotransformation processes occurring within the plant. With regard to specific effects on plastid (pt) and mitochondrial (mt) DNA, CdS QD exposure triggered potential variations at the substoichiometric level in the two organellar genomes, while nanoscale FeOx and ZnS QDs caused a 1- to 3-fold increase in ptDNA and mtDNA copy numbers. Nanoparticle CeO exposure did not affect ptDNA and mtDNA stoichiometry. These findings suggest that modification in stoichiometry is a potential morpho-functional adaptive response to ENM exposure, triggered by modifications of bioenergetic redox balance, which leads to reducing the photosynthesis or cellular respiration rate.
Topics: Arabidopsis; Chloroplasts; Mitochondria; Nanostructures; Plastids
PubMed: 35048688
DOI: 10.1021/acsnano.1c08367