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Morphology, ultrastructure, and molecular phylogeny of Wangodinium sinense gen. et sp. nov. (Gymnodiniales, Dinophyceae) and revisiting of Gymnodinium dorsalisulcum and Gymnodinium impudicum

Luo Z, Hu Z, Tang Y, Mertens KN, Leaw CP, Lim PT, et al.

J Phycol, 2018 10;54(5):744-761.
PMID: 30144373 DOI: 10.1111/jpy.12780

The genus Gymnodinium includes many morphologically similar species, but molecular phylogenies show that it is polyphyletic. Eight strains of Gymnodinium impudicum, Gymnodinium dorsalisulcum and a novel Gymnodinium-like species from Chinese and Malaysian waters and the Mediterranean Sea were established. All of these strains were examined with light microscopy, scanning electron microscopy and transmission electron microscopy. SSU, LSU and internal transcribed spacers rDNA sequences were obtained. A new genus, Wangodinium, was erected to incorporate strains with a loop-shaped apical structure complex (ASC) comprising two rows of amphiesmal vesicles, here referred to as a new type of ASC. The chloroplasts of Wangodinium sinense are enveloped by two membranes. Pigment analysis shows that peridinin is the main accessory pigment in W. sinense. Wangodinium differs from other genera mainly in its unique ASC, and additionally differs from Gymnodinium in the absence of nuclear chambers, and from Lepidodinium in the absence of Chl b and nuclear chambers. New morphological information was provided for G. dorsalisulcum and G. impudicum, e.g., a short sulcal intrusion in G. dorsalisulcum; nuclear chambers in G. impudicum and G. dorsalisulcum; and a chloroplast enveloped by two membranes in G. impudicum. Molecular phylogeny was inferred using maximum likelihood and Bayesian inference with independent SSU and LSU rDNA sequences. Our results support the classification of Wangodinium within the Gymnodiniales sensu stricto clade and it is close to Lepidodinium. Our results also support the close relationship among G. dorsalisulcum, G. impudicum, and Barrufeta. Further research is needed to assign these Gymnodinium species to Barrufeta or to erect new genera.

Matched MeSH terms: Chloroplasts/ultrastructure
Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections

Rose JP, Kleist TJ, Löfstrand SD, Drew BT, Schönenberger J, Sytsma KJ

Mol Phylogenet Evol, 2018 05;122:59-79.
PMID: 29410353 DOI: 10.1016/j.ympev.2018.01.014

Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.

Matched MeSH terms: Chloroplasts/genetics
Effect of steam sterilisation on lipophilic nutrient stability in a chloroplast-rich fraction (CRF) recovered from postharvest, pea vine field residue (haulm)

Wattanakul J, Syamila M, Briars R, Ayed C, Price R, Darwish R, et al.

Food Chem, 2021 Jan 01;334:127589.
PMID: 32707366 DOI: 10.1016/j.foodchem.2020.127589

Postharvest, pea vine field residue (haulm) was steam-sterilised and then juiced; a chloroplast-rich fraction (CRF) was recovered from the juice by centrifugation. The stability of selected nutrients (β-carotene, lutein, and α-tocopherol) in the freeze-dried CRF material was measured over 84 days; the impact of temperature (-20 °C, 4 °C, 25 °C and 40 °C), light and air on nutrient stability was established. All three nutrients were stable at -20 °C and 4 °C in the presence or absence of air; this stability was lost at higher temperatures in the presence of air. The extent and rate of nutrient breakdown significantly increased when the CRF samples were exposed to light. β-Carotene appeared to be more susceptible to degradation than lutein and α-tocopherol at 40 °C in the presence of air, but when CRF was exposed to light all three nutrients measured were significantly broken down during storage at 25 °C or 40 °C, whether exposed to air or not.

Matched MeSH terms: Chloroplasts/chemistry*
Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica

Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, et al.

Plant Mol Biol, 2021 Apr;105(6):611-623.
PMID: 33528753 DOI: 10.1007/s11103-020-01113-9

We applied an integrative approach using multiple methods to verify cytosine methylation in the chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.

Matched MeSH terms: Chloroplasts/genetics
PHOTOSYNTHETIC AND RESPIRATORY CHARACTERISTICS OF MALAYAN SUN AND SHADE FERNS

Nasrulhaq-Boyce A, Mohamed MAH

New Phytol, 1987 Jan;105(1):81-88.
PMID: 33874033 DOI: 10.1111/j.1469-8137.1987.tb00112.x

A comparative study of four Malayan ferns, Christensenia aesculifolia (Bl.) Maxon, Tectaria singaporeana (Wall.) Ching, Abacopteris multilineata (Wall.) Ching and Hymenophyllum polyanthos Sw. from shady habitats and another four, Dicranopteris linearis (Burm.) Und., Lygodium scandens (L.) Sw., Blechnum orientate Linn, and Stenochlaena palustris (Burm.) Bedd. from sunlit habitats showed that the total chlorophyll content expressed on a gram fresh weight basis was greater in the shade ferns. There was little difference in the chlorophyll content between the sun and shade ferns when it was expressed on a per unit leaf area basis. The protein and protohaem content was greater in the sun ferns. Measurements of the in vitro photochemical activities of the photosystems I and II in isolated chloroplasts by means of an oxygen electrode showed higher rates in the sun ferns. As determined by spectrophotometric analysis, the photosynthetic cytochrome content from isolated chloroplasts was greater in the sun ferns. The results indicate that the sun ferns have physiological characteristics favouring greater capacity for photosynthesis. Mitochondria isolated from the sun ferns showed faster rates of electron transport using exogenous NADH as substrate.

Matched MeSH terms: Chloroplasts
Fulltext Complete chloroplast genome sequence of Gigantochloa verticillata (Bambusodae)

Zhang YY, Fan LL, Zheng FY, Zhao T, Rong JD, Chen LG, et al.

Mitochondrial DNA B Resour, 2020 Feb 06;5(1):306-307.
PMID: 33366532 DOI: 10.1080/23802359.2019.1702484

Gigantochloa verticillata is produced in Mengla and Jinghong, Yunnan Province, China, and cultivated in Hong Kong. Vietnam, Thailand, India, Indonesia, and Malaysia are distributed and cultivated. We determined the complete chloroplast genome sequence for G. verticillata using Illumina sequencing data. The complete chloroplast sequence is 139,489 bp, including large single-copy (LSC) region of 83,062 bp, small single-copy (SSC) region of 12,877 bp, and a pair of invert repeats (IR) regions of 21,775 bp. Plastid genome contain 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 23 chloroplast genomes indicates that G. verticillata is closely related to Dendrocalamus latiflorus in Bambusodae.

Matched MeSH terms: Chloroplasts
Fulltext Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis

Fadzil NF, Wagiran A, Mohd Salleh F, Abdullah S, Mohd Izham NH

Genes (Basel), 2018 Aug 12;9(8).
PMID: 30103564 DOI: 10.3390/genes9080408

The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues.

Matched MeSH terms: Chloroplasts
The chloroplast-associated protein degradation pathway controls chromoplast development and fruit ripening in tomato

Ling Q, Sadali NM, Soufi Z, Zhou Y, Huang B, Zeng Y, et al.

Nat Plants, 2021 05;7(5):655-666.
PMID: 34007040 DOI: 10.1038/s41477-021-00916-y

The maturation of green fleshy fruit to become colourful and flavoursome is an important strategy for plant reproduction and dispersal. In tomato (Solanum lycopersicum) and many other species, fruit ripening is intimately linked to the biogenesis of chromoplasts, the plastids that are abundant in ripe fruit and specialized for the accumulation of carotenoid pigments. Chromoplasts develop from pre-existing chloroplasts in the fruit, but the mechanisms underlying this transition are poorly understood. Here, we reveal a role for the chloroplast-associated protein degradation (CHLORAD) proteolytic pathway in chromoplast differentiation. Knockdown of the plastid ubiquitin E3 ligase SP1, or its homologue SPL2, delays tomato fruit ripening, whereas overexpression of SP1 accelerates ripening, as judged by colour changes. We demonstrate that SP1 triggers broader effects on fruit ripening, including fruit softening, and gene expression and metabolism changes, by promoting the chloroplast-to-chromoplast transition. Moreover, we show that tomato SP1 and SPL2 regulate leaf senescence, revealing conserved functions of CHLORAD in plants. We conclude that SP1 homologues control plastid transitions during fruit ripening and leaf senescence by enabling reconfiguration of the plastid protein import machinery to effect proteome reorganization. The work highlights the critical role of chromoplasts in fruit ripening, and provides a theoretical basis for engineering crop improvements.

Matched MeSH terms: Chloroplasts/metabolism
Characterization of Chlamydomonas Ribulose-1,5-bisphosphate carboxylase/oxygenase variants mutated at residues that are post-translationally modified

Rasineni GK, Loh PC, Lim BH

Biochim Biophys Acta Gen Subj, 2017 Feb;1861(2):79-85.
PMID: 27816753 DOI: 10.1016/j.bbagen.2016.10.027

BACKGROUND: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the chloroplast enzyme that fixes CO2 in photosynthesis, but the enzyme also fixes O2, which leads to the wasteful photorespiratory pathway. If we better understand the structure-function relationship of the enzyme, we might be able to engineer improvements. When the crystal structure of Chlamydomonas Rubisco was solved, four new posttranslational modifications were observed which are not present in other species. The modifications were 4-hydroxylation of the conserved Pro-104 and 151 residues, and S-methylation of the variable Cys-256 and 369 residues, which are Phe-256 and Val-369 in land plants. Because the modifications were only observed in Chlamydomonas Rubisco, they might account for the differences in kinetic properties between the algal and plant enzymes.
METHODS: Site-directed mutagenesis and chloroplast transformation have been used to test the essentiality of these modifications by replacing each of the residues with alanine (Ala). Biochemical analyses were done to determine the specificity factors and kinetic constants.
RESULTS: Replacing the modified-residues in Chlamydomonas Rubisco affected the enzyme's catalytic activity. Substituting hydroxy-Pro-104 and methyl-Cys-256 with alanine influenced Rubisco catalysis.
CONCLUSION: This is the first study on these posttranslationally-modified residues in Rubisco by genetic engineering. As these forms of modifications/regulation are not available in plants, the modified residues could be a means to modulate Rubisco activity.
GENERAL SIGNIFICANCE: With a better understanding of Rubisco structure-function, we can define targets for improving the enzyme.

Matched MeSH terms: Chloroplasts/genetics
Genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice ( Oryza rufipogon Griff.) and cultivated rice ( Oryza sativa L.)

Sun Q, Wang K, Yoshimura A, Doi K

Theor Appl Genet, 2002 Jun;104(8):1335-1345.
PMID: 12582589

The genetic differentiation of nuclear, mitochondrial (mt) and chloroplast (cp) genomes was investigated by Southern and PCR analysis using 75 varieties of cultivated rice ( Oryza sativa L.) and 118 strains of common wild rice (CWR, Oryza rufipogon Griff.) from ten countries of Asia. The distinguishing differences between the Indica and Japonica cultivars were detected both in the nuclear genome and the cytoplasmic genome, confirming that the Indica-Japonica differentiation is of major importance for the three different classes of genome in cultivated rice. This differentiation was also detected in common wild rice with some differences among the genome compartments and the various regions. For nuclear DNA variation, both Indica-like and Japonica-like types were observed in the Chinese CWR, with the latter more-frequent than the former. No Japonica-like type was found in South Asia, and only two strains of the Japonica-like type were detected in Southeast Asia, thus the Indica-like type is the major type among South and Southeast Asian CWR. For mtDNA, only a few strains of the Japonica-like type were detected in CWR. For cpDNA, the Japonica type was predominant among the CWR strains from China, Bangladesh and Burma, while the Indica type was predominant among the CWR strains from Thailand, Malaysia, Cambodia and Sri Lanka, and both types were found in similar frequencies among the Indian CWR. Altogether, however, the degree of Indica-Japonica differentiation in common wild rice was much-less important than that in cultivated rice. Cluster analyses for nuclear and mitochondrial DNA variation revealed that some CWR strains showed large genetic distances from cultivated rice and formed clusters distinct from cultivated rice. Coincidence in the genetic differentiation between the three different classes of genome was much higher in cultivated rice than in CWR. Among the 75 cultivars, about 3/4 entries were "homoeotype" showing congruent results for nuclear, mt and cpDNA regarding the Indica-Japonica differentiation. In CWR, the proportions of homoeotypes were 5.7%, 15% and 48.8% in China, South Asia and Southeast Asia, respectively. Based on the average genetic distance among all the strains of CWR and cultivated rice for nuclear and mitochondrial genomes, the variability of the nuclear genome was found to be higher than that of the mitochondrial genome. The global pattern based on all genomes shows much-more diversification in CWR than that in cultivated rice.

Matched MeSH terms: Chloroplasts
Rational Design Principles for the Transport and Subcellular Distribution of Nanomaterials into Plant Protoplasts

Lew TTS, Wong MH, Kwak SY, Sinclair R, Koman VB, Strano MS

Small, 2018 Nov;14(44):e1802086.
PMID: 30191658 DOI: 10.1002/smll.201802086

The ability to control the subcellular localization of nanoparticles within living plants offers unique advantages for targeted biomolecule delivery and enables important applications in plant bioengineering. However, the mechanism of nanoparticle transport past plant biological membranes is poorly understood. Here, a mechanistic study of nanoparticle cellular uptake into plant protoplasts is presented. An experimentally validated mathematical model of lipid exchange envelope penetration mechanism for protoplasts, which predicts that the subcellular distribution of nanoparticles in plant cells is dictated by the particle size and the magnitude of the zeta potential, is advanced. The mechanism is completely generic, describing nanoparticles ranging from quantum dots, gold and silica nanoparticles, nanoceria, and single-walled carbon nanotubes (SWNTs). In addition, the use of imaging flow cytometry to investigate the influence of protoplasts' morphological characteristics on nanoparticle uptake efficiency is demonstrated. Using DNA-wrapped SWNTs as model nanoparticles, it is found that glycerolipids, the predominant lipids in chloroplast membranes, exhibit stronger lipid-nanoparticle interaction than phospholipids, the major constituent in protoplast membrane. This work can guide the rational design of nanoparticles for targeted delivery into specific compartments within plant cells without the use of chemical or mechanical aid, potentially enabling various plant engineering applications.

Matched MeSH terms: Chloroplasts

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