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Current Opinion in Plant Biology Aug 2023Among the eight forms of vitamin E, only tocopherols are essential compounds that are distributed throughout the entire plant kingdom, with α-tocopherol being the most... (Review)
Review
Among the eight forms of vitamin E, only tocopherols are essential compounds that are distributed throughout the entire plant kingdom, with α-tocopherol being the most predominant form in photosynthetic tissues. At the cellular level, α-tocopherol is of special relevance inside the chloroplast, where it eliminates singlet oxygen and modulates lipid peroxidation. This is of utmost relevance since tocopherols are the only antioxidants that counteract lipid peroxidation. Moreover, at the whole-plant level, α-tocopherol appears to modulate several physiological processes from germination to senescence. The antioxidant role of α-tocopherol at the cellular level can have profound effects at the whole-plant level, including the modulation of physiological processes that are apparently not related to redox processes and could be considered non-antioxidant functions. Here, we discuss whether non-antioxidant functions of α-tocopherol at the whole-plant level are mediated by its antioxidant role in chloroplasts and the regulation of redox processes at the cellular level.
Topics: Antioxidants; alpha-Tocopherol; Vitamin E; Tocopherols; Chloroplasts
PubMed: 37311290
DOI: 10.1016/j.pbi.2023.102400 -
Plant Communications Jan 2023Plastid-to-nucleus retrograde signaling coordinates nuclear gene expression with chloroplast developmental status and is essential for the photoautotrophic lifestyle of...
Plastid-to-nucleus retrograde signaling coordinates nuclear gene expression with chloroplast developmental status and is essential for the photoautotrophic lifestyle of plants. Previous studies have established that tetrapyrrole biosynthesis (TPB) and plastid gene expression (PGE) play essential roles in plastid retrograde signaling during early chloroplast biogenesis; however, their functional relationship remains unknown. In this study, we generated a series of rice TPB-related gun (genome uncoupled) mutants and systematically analyzed their effects on nuclear and plastid gene expression under normal conditions or when subjected to treatments with norflurazon (NF; a noncompetitive inhibitor of carotenoid biosynthesis) and/or lincomycin (Lin; a specific inhibitor of plastid translation). We show that under NF treatment, expression of plastid-encoded polymerase (PEP)-transcribed genes is significantly reduced in the wild type but is derepressed in the TPB-related gun mutants. We further demonstrate that the derepressed expression of PEP-transcribed genes may be caused by increased expression of the PEP core subunit and nuclear-encoded sigma factors and by elevated copy numbers of plastid genome per haploid genome. In addition, we show that expression of photosynthesis-associated nuclear genes (PhANGs) and PEP-transcribed genes is correlated in the rice TPB-related gun mutants, with or without NF or Lin treatment. A similar correlation between PhANGs and PGE is also observed in the Arabidopsis gun4 and gun5 mutants. Moreover, we show that increased expression of PEP-transcribed plastid genes is necessary for the gun phenotype in NF-treated TPB-related gun mutants. Further, we provide evidence that these TPB-related GUN genes act upstream of GUN1 in the regulation of retrograde signaling. Taken together, our results suggest that the TPB-related GUN genes control retrograde plastid signaling by regulating the PGE-dependent retrograde signaling pathway.
Topics: Plastids; Arabidopsis; Signal Transduction; Tetrapyrroles; Gene Expression; Arabidopsis Proteins; Intracellular Signaling Peptides and Proteins; DNA-Binding Proteins
PubMed: 35836377
DOI: 10.1016/j.xplc.2022.100411 -
Biochimica Et Biophysica Acta.... Apr 2020The higher plant chloroplast thylakoid membrane system performs the light-dependent reactions of photosynthesis. These provide the ATP and NADPH required for the... (Review)
Review
The higher plant chloroplast thylakoid membrane system performs the light-dependent reactions of photosynthesis. These provide the ATP and NADPH required for the fixation of CO into biomass by the Calvin-Benson cycle and a range of other metabolic reactions in the stroma. Land plants are frequently challenged by fluctuations in their environment, such as light, nutrient and water availability, which can create a mismatch between the amounts of ATP and NADPH produced and the amounts required by the downstream metabolism. Left unchecked, such imbalances can lead to the production of reactive oxygen species that damage the plant and harm productivity. Fortunately, plants have evolved a complex range of regulatory processes to avoid or minimize such deleterious effects by controlling the efficiency of light harvesting and electron transfer in the thylakoid membrane. Generally the regulation of the light reactions has been studied and conceptualised at the microscopic level of protein-protein and protein-ligand interactions, however in recent years dynamic changes in the thylakoid macrostructure itself have been recognised to play a significant role in regulating light harvesting and electron transfer. Here we review the evidence for the involvement of macrostructural changes in photosynthetic regulation and review the techniques that brought this evidence to light.
Topics: Acclimatization; Light; Photosynthesis; Thylakoids
PubMed: 31228404
DOI: 10.1016/j.bbabio.2019.06.011 -
BioMed Research International 2021Species of (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary...
Species of (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of , but the molecular studies of species from this location are lacking. In our study, we assembled four plastid genomes from the Tien Shan Mountains, , , , and , combined with the plastid genome of to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five plastid genomes proved highly similar in overall size (151,691-152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of and the sister relationship between and , . , , and were clustered together, and was clustered with , with our results clearly demonstrating the relationships between these five species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of .
Topics: Biological Evolution; Codon; DNA, Plant; Evolution, Molecular; Gene Order; Genome, Plastid; Genomics; Liliaceae; Microsatellite Repeats; Nucleotides; Phylogeny; Plastids; Polymorphism, Single Nucleotide; Tulipa
PubMed: 34239930
DOI: 10.1155/2021/6648429 -
Molecular Biology and Evolution Apr 2022Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary...
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host-plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
Topics: Ecosystem; Evolution, Molecular; Genome, Plastid; Phylogeny; Plants; Plastids; Stramenopiles
PubMed: 35348760
DOI: 10.1093/molbev/msac065 -
Current Biology : CB Sep 2023Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems...
Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.
Topics: Symbiosis; In Situ Hybridization, Fluorescence; Genome; Plastids; Phylogeny
PubMed: 37536342
DOI: 10.1016/j.cub.2023.07.017 -
Parasites & Vectors Aug 2022The recently discovered Babesia sp. Mymensingh, which causes clinical bovine babesiosis, has a wide geographical distribution. We investigated the phylogenetic position...
BACKGROUND
The recently discovered Babesia sp. Mymensingh, which causes clinical bovine babesiosis, has a wide geographical distribution. We investigated the phylogenetic position of Babesia sp. Mymensingh using its mitochondrial, plastid, and nuclear genes. Based on morphological and molecular data, Babesia sp. Mymensingh is a unique species and we named it as Babesia naoakii n. sp.
METHODS
A blood DNA sample from a Babesia sp. Mymensingh-infected cow was subjected to genome sequencing to obtain the sequences of mitochondrial, plastid, and nuclear genes. Six phylogenetic trees were then constructed with (1) concatenated amino acid sequences of cytochrome oxidase subunit I, cytochrome oxidase subunit III, and cytochrome b genes of the mitochondrial genome; (2) 16S rRNA of the plastid genome; (3) nucleotide sequences of the elongation factor Tu gene of the plastid genome; (4) ITS1-5.8S rRNA-ITS2; (5) concatenated nucleotide sequences of 89 nuclear genes; and (6) concatenated amino acid sequences translated from the 89 nuclear genes.
RESULTS
In all six phylogenetic trees, B. naoakii n. sp. formed a sister clade to the common ancestor of Babesia bigemina and B. ovata. The concatenated nuclear genes of B. naoakii n. sp. and their translated amino acid sequences shared lower identity scores with the sequences from B. bigemina (82.7% and 84.7%, respectively) and B. ovata (83.5% and 85.5%, respectively) compared with the identity scores shared between the B. bigemina and B. ovata sequences (86.3% and 87.9%, respectively).
CONCLUSIONS
Our study showed that B. naoakii n. sp. occupies a unique phylogenetic position distinct from existing Babesia species. Our findings, together with morphological differences, identify B. naoakii n. sp. as a distinct parasite species.
Topics: Animals; Babesia; Babesiosis; Cattle; Cattle Diseases; Female; Phylogeny; Plastids; RNA, Ribosomal, 16S
PubMed: 36002908
DOI: 10.1186/s13071-022-05374-9 -
Proceedings of the National Academy of... Mar 2022SignificanceAlthough plastid division is critical for plant development, how components of the plastid division machinery (PDM) are imported into plastids remains...
SignificanceAlthough plastid division is critical for plant development, how components of the plastid division machinery (PDM) are imported into plastids remains unexplored. A forward genetic screen to identify suppressors of a () mutant deficient in plastid division led us to find dominant gain-of-function (GF) mutations in , which significantly increases the import of PDM components and completely rescues phenotypes. The defective plastid division phenotypes in and mutants and CRL-TIC236 association in a functional complex indicate that the CRL-TIC236 module is vital for plastid division. Hence, we report the first GF translocon mutants and unveil CRL as a novel functional partner of TIC236 for PDM import.
Topics: Arabidopsis; Arabidopsis Proteins; Cell Division; Chloroplast Proteins; Gain of Function Mutation; Membrane Transport Proteins; Plastids; Protein Transport
PubMed: 35275795
DOI: 10.1073/pnas.2123353119 -
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 -
Cell Reports Aug 2020Plastid-nucleus genome coordination is crucial for plastid activity, but the mechanisms remain unclear. By treating Arabidopsis plants with the organellar...
Plastid-nucleus genome coordination is crucial for plastid activity, but the mechanisms remain unclear. By treating Arabidopsis plants with the organellar genome-damaging agent ciprofloxacin, we found that plastid genome instability can alter endoreplication and the cell cycle. Similar results are observed in the plastid genome instability mutants of reca1why1why3. Cell division and embryo development are disturbed in the reca1why1why3 mutant. Notably, SMR5 and SMR7 genes, which encode cell-cycle kinase inhibitors, are upregulated in plastid genome instability plants, and the mutation of SMR7 can restore the endoreplication and growth phenotype of reca1why1why3 plants. Furthermore, we establish that the DNA damage response transcription factor SOG1 mediates the alteration of endoreplication and cell cycle triggered by plastid genome instability. Finally, we demonstrate that reactive oxygen species produced in plastids are important for plastid-nucleus genome coordination. Our findings uncover a molecular mechanism for the coordination of plastid and nuclear genomes during plant growth and development.
Topics: Arabidopsis; Arabidopsis Proteins; Cell Cycle; Cell Cycle Proteins; Cell Nucleus; Endoreduplication; Gene Expression Regulation, Plant; Genome, Plant; Genome, Plastid; Genomic Instability; Plant Development; Plastids; Reactive Oxygen Species; Signal Transduction; Transcription Factors
PubMed: 32783941
DOI: 10.1016/j.celrep.2020.108019