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Biochemistry May 2024A central goal of photoprotective energy dissipation processes is the regulation of singlet oxygen (O*) and reactive oxygen species in the photosynthetic apparatus....
A central goal of photoprotective energy dissipation processes is the regulation of singlet oxygen (O*) and reactive oxygen species in the photosynthetic apparatus. Despite the involvement of O* in photodamage and cell signaling, few studies directly correlate O* formation to nonphotochemical quenching (NPQ) or lack thereof. Here, we combine spin-trapping electron paramagnetic resonance (EPR) and time-resolved fluorescence spectroscopies to track in real time the involvement of O* during photoprotection in plant thylakoid membranes. The EPR spin-trapping method for detection of O* was first optimized for photosensitization in dye-based chemical systems and then used to establish methods for monitoring the temporal dynamics of O* in chlorophyll-containing photosynthetic membranes. We find that the apparent O* concentration in membranes changes throughout a 1 h period of continuous illumination. During an initial response to high light intensity, the concentration of O* decreased in parallel with a decrease in the chlorophyll fluorescence lifetime via NPQ. Treatment of membranes with nigericin, an uncoupler of the transmembrane proton gradient, delayed the activation of NPQ and the associated quenching of O* during high light. Upon saturation of NPQ, the concentration of O* increased in both untreated and nigericin-treated membranes, reflecting the utility of excess energy dissipation in mitigating photooxidative stress in the short term (i.e., the initial ∼10 min of high light).
Topics: Electron Spin Resonance Spectroscopy; Photosynthesis; Singlet Oxygen; Thylakoids; Spin Trapping; Chlorophyll; Spinacia oleracea; Light
PubMed: 38679935
DOI: 10.1021/acs.biochem.4c00028 -
Molecular Phylogenetics and Evolution Jul 2024Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These...
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
Topics: Dinoflagellida; Phylogeny; Photosynthesis; Heterotrophic Processes; Biological Evolution; Evolution, Molecular; Plastids
PubMed: 38677354
DOI: 10.1016/j.ympev.2024.108086 -
Genes Apr 2024Tocopherols are secondary metabolites synthesized through the shikimate biosynthetic pathway in the plastids of most plants. It is well known that α-Tocopherol (vitamin... (Review)
Review
Tocopherols are secondary metabolites synthesized through the shikimate biosynthetic pathway in the plastids of most plants. It is well known that α-Tocopherol (vitamin E) has many health benefits for humans and animals; therefore, it is highly used in human and animal diets. Tocopherols vary considerably in most crop (and plant) species and within cultivars of the same species depending on environmental and growth conditions; tocopherol content is a polygenic, complex traits, and its inheritance is poorly understood. The objective of this review paper was to summarize all identified quantitative trait loci (QTL) that control seed tocopherols and related contents identified in maize () during the past two decades (2002-2022). Candidate genes identified within these QTL regions are also discussed. The QTL described here, and candidate genes identified within these genomic regions could be used in breeding programs to develop maize cultivars with high, beneficial levels of seed tocopherol contents.
Topics: Zea mays; Quantitative Trait Loci; Seeds; Tocopherols
PubMed: 38674406
DOI: 10.3390/genes15040472 -
Genes Apr 2024Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported...
Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.
Topics: Republic of Korea; Phylogeny; Genome, Chloroplast; Islands; DNA, Chloroplast; Chloroplasts
PubMed: 38674391
DOI: 10.3390/genes15040457 -
Genes Mar 2024The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering...
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from , revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into evolution and offers potential molecular markers for DNA barcoding.
Topics: Phylogeny; Plastids; Codon Usage; Genome, Plastid; Evolution, Molecular
PubMed: 38674377
DOI: 10.3390/genes15040441 -
Genes Mar 2024Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study,... (Comparative Study)
Comparative Study
Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of using plastid genetic information. We newly sequenced the complete or nearly complete plastomes of four species (, , , and ) and conducted comparative analysis with seventeen published plastomes to examine the evolutionary pattern within this genus. The plastomes of these five newly sequenced species range from 157,093 bp (2) to 160,493 bp (), all exhibiting circular structures when mapped. Nucleotide diversity was observed across the plastomes, leading us to identify 13 mutational hotspot regions, comprising eight intergenic spacer regions and five gene regions. Our phylogenetic analyses based on 77 protein-coding genes generated phylogenetic relationships with high support and resolution for This genus can be divided into three clades, and the previously proposed infrageneric classifications are not supported by our studies. Furthermore, the close affinity between and is supported by the present work, and further studies are necessary to conclude the taxonomic treatment for the latter. These results provide resources for the comparative plastome, breeding, and plastid genetic engineering of Magnoliaceae and flowering plants.
Topics: Genome, Chloroplast; Phylogeny; Evolution, Molecular; Magnoliaceae; High-Throughput Nucleotide Sequencing; Chloroplasts
PubMed: 38674341
DOI: 10.3390/genes15040406 -
Scientific Reports Apr 2024Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and...
Calendula officinalis L.is a versatile medicinal plant with numerous applications in various fields. However, its chloroplast genome structure, features, phylogeny, and patterns of evolution and mutation remain largely unexplored. This study examines the chloroplast genome, phylogeny, codon usage bias, and divergence time of C. officinalis, enhancing our understanding of its evolution and adaptation. The chloroplast genome of C. officinalis is a 150,465 bp circular molecule with a G + C content of 37.75% and comprises 131 genes. Phylogenetic analysis revealed a close relationship between C. officinalis, C. arvensis, and Osteospermum ecklonis. A key finding is the similarity in codon usage bias among these species, which, coupled with the divergence time analysis, supports their close phylogenetic proximity. This similarity in codon preference and divergence times underscores a parallel evolutionary adaptation journey for these species, highlighting the intricate interplay between genetic evolution and environmental adaptation in the Asteraceae family. Moreover unique evolutionary features in C. officinalis, possibly associated with certain genes were identified, laying a foundation for future research into the genetic diversity and medicinal value of C. officinalis.
Topics: Genome, Chloroplast; Plants, Medicinal; Phylogeny; Evolution, Molecular; Calendula; Codon Usage; Base Composition; Chloroplasts
PubMed: 38671173
DOI: 10.1038/s41598-024-60455-2 -
Chemosphere Jun 2024Microcystin-LR (MC-LR) is a harmful cyanotoxin that inhibits 1 and 2A serine-threonine protein phosphatases. This study examines the influence of MC-LR on chloroplast...
Microcystin-LR (MC-LR) is a harmful cyanotoxin that inhibits 1 and 2A serine-threonine protein phosphatases. This study examines the influence of MC-LR on chloroplast division and the underlying mechanisms and consequences in Arabidopsis. MC-LR increased the frequency of dividing chloroplasts in hypocotyls in a time range of 1-96 h. At short-term exposures to MC-LR, small-sized chloroplasts (longitudinal diameters ≤6 μm) were more sensitive to these stimulatory effects, while both small and large chloroplasts showed stimulations at long-term exposure. After 48 h, the cyanotoxin increased the frequency of small-sized chloroplasts, indicating the stimulation of division. MC-LR inhibited protein phosphatases in whole hypocotyls and isolated chloroplasts, while it did not induce oxidative stress. We show for the first time that total cellular phosphatases play important roles in chloroplast division and that particular chloroplast phosphatases may be involved in these processes. Interestingly, MC-LR has a protective effect on cyanobacterial division during methyl-viologen (MV) treatments in Synechococcus PCC6301. MC-LR production has harmful effects on ecosystems and it may have an ancient cell division regulatory role in stressed cyanobacterial cells, the evolutionary ancestors of chloroplasts. We propose that cytoplasmic (eukaryotic) factors also contribute to the relevant effects of MC-LR in plants.
Topics: Microcystins; Chloroplasts; Marine Toxins; Phosphoprotein Phosphatases; Arabidopsis; Cyanobacteria; Cell Division; Synechococcus
PubMed: 38670509
DOI: 10.1016/j.chemosphere.2024.142125 -
Plant Physiology and Biochemistry : PPB May 2024Glutamine synthetase (GS), an initial enzyme in nitrogen (N) plant metabolism, exists as a group of isoenzymes found in both cytosolic (GS1) and plastids (GS2) and has...
Glutamine synthetase (GS), an initial enzyme in nitrogen (N) plant metabolism, exists as a group of isoenzymes found in both cytosolic (GS1) and plastids (GS2) and has gathered significant attention for enhancing N use efficiency and crop yield. This work focuses on the A. thaliana GLN1;3 and GLN1;5 genes, the two predicted most expressed genes in seeds, among the five isogenes encoding GS1 in this species. The expression patterns were studied using transgenic marker line plants and qPCR during seed development and germination. The observed patterns highlight distinct functions for the two genes and confirm GLN1;5 as the most highly expressed GS1 gene in seeds. The GLN1;5, expression, oriented towards hypocotyl and cotyledons, suggests a role in protein turnover during germination, while the radicle-oriented expression of GLN1;3 supports a function in early external N uptake. While the single mutants exhibited a normal phenotype, except for a decrease in seed parameters, the double gln1;3/gln1;5 mutant displayed a germination delay, substantial impairment in growth, nitrogen metabolism, and number and quality of the seeds, as well as a diminishing in flowering. Although seed and pollen-specific, GLN1;5 expression is upregulated in the meristems of the gln1;3 mutants, filling the lack of GLN1;3 and ensuring the normal functioning of the gln1;3 mutants. These findings validate earlier in silico data on the expression patterns of GLN1;3 and GL1;5 genes in seeds, explore their different functions, and underscore their essential role in plant growth, seed production, germination, and early stages of plant development.
Topics: Arabidopsis; Seeds; Germination; Glutamate-Ammonia Ligase; Arabidopsis Proteins; Gene Expression Regulation, Plant; Cytosol; Nitrogen; Plants, Genetically Modified; Isoenzymes
PubMed: 38657550
DOI: 10.1016/j.plaphy.2024.108631 -
BMC Bioinformatics Apr 2024The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in...
BACKGROUND
The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained.
RESULTS
To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers.
CONCLUSIONS
The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.
Topics: Terminology as Topic; Evolution, Molecular; Genes, Chloroplast; Genes, Mitochondrial; Databases, Genetic; Chloroplasts; Internet; Software
PubMed: 38649820
DOI: 10.1186/s12859-024-05781-y