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Chloroplasts: Plant cell inclusion bodies that contain the photosynthetic pigment CHLOROPHYLL, which is associated with the membrane of THYLAKOIDS. Chloroplasts occur in cells of leaves and young stems of plants. They are also found in some forms of PHYTOPLANKTON such as HAPTOPHYTA; DINOFLAGELLATES; DIATOMS; and CRYPTOPHYTA.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Chloroplast Proteins: Proteins encoded by the CHLOROPLAST GENOME or proteins encoded by the nuclear genome that are imported to and resident in the CHOROPLASTS.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Genes, Chloroplast: Those nucleic acid sequences that function as units of heredity which are located within the CHLOROPLAST DNA.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Euglena gracilis: A species of fresh-water, flagellated EUKARYOTES in the phylum EUGLENIDA.Peas: A variable annual leguminous vine (Pisum sativum) that is cultivated for its rounded smooth or wrinkled edible protein-rich seeds, the seed of the pea, and the immature pods with their included seeds. (From Webster's New Collegiate Dictionary, 1973)Photosynthesis: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)Spinacia oleracea: A widely cultivated plant, native to Asia, having succulent, edible leaves eaten as a vegetable. (From American Heritage Dictionary, 1982)Thylakoids: Membranous cisternae of the CHLOROPLAST containing photosynthetic pigments, reaction centers, and the electron-transport chain. Each thylakoid consists of a flattened sac of membrane enclosing a narrow intra-thylakoid space (Lackie and Dow, Dictionary of Cell Biology, 2nd ed). Individual thylakoids are interconnected and tend to stack to form aggregates called grana. They are found in cyanobacteria and all plants.Chlamydomonas reinhardtii: A species of GREEN ALGAE. Delicate, hairlike appendages arise from the flagellar surface in these organisms.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Chloroplast Proton-Translocating ATPases: Proton-translocating ATPases which produce ADENOSINE TRIPHOSPHATE in plants. They derive energy from light-driven reactions that develop high concentrations of protons within the membranous cisternae (THYLAKOIDS) of the CHLOROPLASTS.Chlorophyll: Porphyrin derivatives containing magnesium that act to convert light energy in photosynthetic organisms.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Chloroplast Thioredoxins: A subtype of thioredoxins found primarily in CHLOROPLASTS.Plant Leaves: Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Light: That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.Ribulose-Bisphosphate Carboxylase: A carboxy-lyase that plays a key role in photosynthetic carbon assimilation in the CALVIN-BENSON CYCLE by catalyzing the formation of 3-phosphoglycerate from ribulose 1,5-biphosphate and CARBON DIOXIDE. It can also utilize OXYGEN as a substrate to catalyze the synthesis of 2-phosphoglycolate and 3-phosphoglycerate in a process referred to as photorespiration.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Chlamydomonas: A genus GREEN ALGAE in the order VOLVOCIDA. It consists of solitary biflagellated organisms common in fresh water and damp soil.Chlorophyta: A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.Photosynthetic Reaction Center Complex Proteins: Protein complexes that take part in the process of PHOTOSYNTHESIS. They are located within the THYLAKOID MEMBRANES of plant CHLOROPLASTS and a variety of structures in more primitive organisms. There are two major complexes involved in the photosynthetic process called PHOTOSYSTEM I and PHOTOSYSTEM II.Photophosphorylation: The use of light to convert ADP to ATP without the concomitant reduction of dioxygen to water as occurs during OXIDATIVE PHOSPHORYLATION in MITOCHONDRIA.Photosystem II Protein Complex: A large multisubunit protein complex found in the THYLAKOID MEMBRANE. It uses light energy derived from LIGHT-HARVESTING PROTEIN COMPLEXES to catalyze the splitting of WATER into DIOXYGEN and of reducing equivalents of HYDROGEN.Plants, Medicinal: Plants whose roots, leaves, seeds, bark, or other constituent parts possess therapeutic, tonic, purgative, curative or other pharmacologic attributes, when administered to man or animals.Genes, Plant: The functional hereditary units of PLANTS.Fabaceae: The large family of plants characterized by pods. Some are edible and some cause LATHYRISM or FAVISM and other forms of poisoning. Other species yield useful materials like gums from ACACIA and various LECTINS like PHYTOHEMAGGLUTININS from PHASEOLUS. Many of them harbor NITROGEN FIXATION bacteria on their roots. Many but not all species of "beans" belong to this family.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Galactolipids: A group of GLYCOLIPIDS in which the sugar group is GALACTOSE. They are distinguished from GLYCOSPHINGOLIPIDS in lacking nitrogen. They constitute the majority of MEMBRANE LIPIDS in PLANTS.Euglena: A genus of EUKARYOTES, in the phylum EUGLENIDA, found mostly in stagnant water. Characteristics include a pellicle usually marked by spiral or longitudinal striations.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Algal Proteins: Proteins found in any species of algae.Darkness: The absence of light.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Light-Harvesting Protein Complexes: Complexes containing CHLOROPHYLL and other photosensitive molecules. They serve to capture energy in the form of PHOTONS and are generally found as components of the PHOTOSYSTEM I PROTEIN COMPLEX or the PHOTOSYSTEM II PROTEIN COMPLEX.Cytochrome b6f Complex: A protein complex that includes CYTOCHROME B6 and CYTOCHROME F. It is found in the THYLAKOID MEMBRANE and plays an important role in process of PHOTOSYNTHESIS by transferring electrons from PLASTOQUINONE to PLASTOCYANIN or CYTOCHROME C6. The transfer of electrons is coupled to the transport of PROTONS across the membrane.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Intracellular Membranes: Thin structures that encapsulate subcellular structures or ORGANELLES in EUKARYOTIC CELLS. They include a variety of membranes associated with the CELL NUCLEUS; the MITOCHONDRIA; the GOLGI APPARATUS; the ENDOPLASMIC RETICULUM; LYSOSOMES; PLASTIDS; and VACUOLES.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Proton-Translocating ATPases: Multisubunit enzymes that reversibly synthesize ADENOSINE TRIPHOSPHATE. They are coupled to the transport of protons across a membrane.Cytochromes f: Cytochromes f are found as components of the CYTOCHROME B6F COMPLEX. They play important role in the transfer of electrons from PHOTOSYSTEM I to PHOTOSYSTEM II.Plants, Toxic: Plants or plant parts which are harmful to man or other animals.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Mesophyll Cells: Large and highly vacuolated cells possessing many chloroplasts occuring in the interior cross-section of leaves, juxtaposed between the epidermal layers.Diuron: A pre-emergent herbicide.Plants, Edible: An organism of the vegetable kingdom suitable by nature for use as a food, especially by human beings. Not all parts of any given plant are edible but all parts of edible plants have been known to figure as raw or cooked food: leaves, roots, tubers, stems, seeds, buds, fruits, and flowers. The most commonly edible parts of plants are FRUIT, usually sweet, fleshy, and succulent. Most edible plants are commonly cultivated for their nutritional value and are referred to as VEGETABLES.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Photosystem I Protein Complex: A large multisubunit protein complex that is found in the THYLAKOID MEMBRANE. It uses light energy derived from LIGHT-HARVESTING PROTEIN COMPLEXES to drive electron transfer reactions that result in either the reduction of NADP to NADPH or the transport of PROTONS across the membrane.Acetabularia: A genus of green algae found in the Mediterranean and other warm seas.Hordeum: A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).Protein PrecursorsPlastoquinone: Polyunsaturated side-chain quinone derivative which is an important link in the electron transport chain of green plants during the photosynthetic conversion of light energy by photophosphorylation into the potential energy of chemical bonds.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.RNA, Algal: Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.Fructose-Bisphosphatase: An enzyme that catalyzes the conversion of D-fructose 1,6-bisphosphate and water to D-fructose 6-phosphate and orthophosphate. EC 3.1.3.11.Plastocyanin: A copper-containing plant protein that is a fundamental link in the electron transport chain of green plants during the photosynthetic conversion of light energy by photophosphorylation into the potential energy of chemical bonds.Group I Chaperonins: A subcategory of chaperonins found in MITOCHONDRIA; CHLOROPLASTS; and BACTERIA. Group I chaperonins form into a barrel-shaped macromolecular structure that is enclosed by a separate lid-like protein component.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Electron Transport: The process by which ELECTRONS are transported from a reduced substrate to molecular OXYGEN. (From Bennington, Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984, p270)Bryopsida: A class of plants within the Bryophyta comprising the mosses, which are found in both damp (including freshwater) and drier situations. Mosses possess erect or prostrate leafless stems, which give rise to leafless stalks bearing capsules. Spores formed in the capsules are released and grow to produce new plants. (Concise Dictionary of Biology, 1990). Many small plants bearing the name moss are in fact not mosses. The "moss" found on the north side of trees is actually a green alga (CHLOROPHYTA). Irish moss is really a red alga (RHODOPHYTA). Beard lichen (beard moss), Iceland moss, oak moss, and reindeer moss are actually LICHENS. Spanish moss is a common name for both LICHENS and an air plant (TILLANDSIA usneoides) of the pineapple family. Club moss is an evergreen herb of the family LYCOPODIACEAE.Protochlorophyllide: A photo-active pigment localized in prolamellar bodies occurring within the proplastids of dark-grown bean leaves. In the process of photoconversion, the highly fluorescent protochlorophyllide is converted to chlorophyll.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Ferredoxins: Iron-containing proteins that transfer electrons, usually at a low potential, to flavoproteins; the iron is not present as in heme. (McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Rhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Plant Physiological Phenomena: The physiological processes, properties, and states characteristic of plants.Thioredoxins: Hydrogen-donating proteins that participates in a variety of biochemical reactions including ribonucleotide reduction and reduction of PEROXIREDOXINS. Thioredoxin is oxidized from a dithiol to a disulfide when acting as a reducing cofactor. The disulfide form is then reduced by NADPH in a reaction catalyzed by THIOREDOXIN REDUCTASE.Cyanobacteria: A phylum of oxygenic photosynthetic bacteria comprised of unicellular to multicellular bacteria possessing CHLOROPHYLL a and carrying out oxygenic PHOTOSYNTHESIS. Cyanobacteria are the only known organisms capable of fixing both CARBON DIOXIDE (in the presence of light) and NITROGEN. Cell morphology can include nitrogen-fixing heterocysts and/or resting cells called akinetes. Formerly called blue-green algae, cyanobacteria were traditionally treated as ALGAE.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Ferredoxin-NADP Reductase: An enzyme that catalyzes the oxidation and reduction of FERREDOXIN or ADRENODOXIN in the presence of NADP. EC 1.18.1.2 was formerly listed as EC 1.6.7.1 and EC 1.6.99.4.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Phototropins: Blue-light receptors that regulate a range of physiological responses in PLANTS. Examples include: PHOTOTROPISM, light-induced stomatal opening, and CHLOROPLAST movements in response to changes in light intensity.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Plant Cells: Basic functional unit of plants.Mustard Plant: Any of several BRASSICA species that are commonly called mustard. Brassica alba is white mustard, B. juncea is brown or Chinese mustard, and B. nigra is black, brown, or red mustard. The plant is grown both for mustard seed from which oil is extracted or used as SPICES, and for its greens used as VEGETABLES or ANIMAL FEED. There is no relationship to MUSTARD COMPOUNDS.Starch: Any of a group of polysaccharides of the general formula (C6-H10-O5)n, composed of a long-chain polymer of glucose in the form of amylose and amylopectin. It is the chief storage form of energy reserve (carbohydrates) in plants.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Mitochondria: Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. They contain distinctive RIBOSOMES, transfer RNAs (RNA, TRANSFER); AMINO ACYL T RNA SYNTHETASES; and elongation and termination factors. Mitochondria depend upon genes within the nucleus of the cells in which they reside for many essential messenger RNAs (RNA, MESSENGER). Mitochondria are believed to have arisen from aerobic bacteria that established a symbiotic relationship with primitive protoeukaryotes. (King & Stansfield, A Dictionary of Genetics, 4th ed)Cytochrome b Group: Cytochromes (electron-transporting proteins) with protoheme (HEME B) as the prosthetic group.Ascorbate Peroxidases: Peroxidases that utilize ASCORBIC ACID as an electron donor to reduce HYDROGEN PEROXIDE to WATER. The reaction results in the production of monodehydroascorbic acid and DEHYDROASCORBIC ACID.Kinetics: The rate dynamics in chemical or physical systems.Molecular Weight: The sum of the weight of all the atoms in a molecule.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Seedling: Very young plant after GERMINATION of SEEDS.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Bryophyta: A division of the plant kingdom. Bryophyta contains the subdivision, Musci, which contains the classes: Andreaeopsida, BRYOPSIDA, and SPHAGNOPSIDA.Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.ATP Synthetase Complexes: Multisubunit enzyme complexes that synthesize ADENOSINE TRIPHOSPHATE from energy sources such as ions traveling through channels.Biological Transport: The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.Phototropism: The directional growth of organisms in response to light. In plants, aerial shoots usually grow towards light. The phototropic response is thought to be controlled by auxin (= AUXINS), a plant growth substance. (From Concise Dictionary of Biology, 1990)Adiantum: A plant genus of the family Pteridaceae. Members contain TRITERPENES. Some species in this genus are called maidenhair fern which is also a common name occasionally used for Lygodium (FERNS) and POLYPODIUM.

*  Table 3. TAMU BACs with rDNA or cpDNA
Table 3.TAMU BAC clones containing rDNA and chloroplast DNA sequences identified by hybridization to the YAC probe, EG03G01. ... The YAC EG03G01 has not been sequenced and may contain unique sequence regions in addtion to rDNA and chloroplast DNA. ...
  http://genetics.mgh.harvard.edu/goodman/wang_pj12/table3.shtml
*  Chloroplast DNA - Wikipedia
... a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a ... As in prokaryotes, genes in chloroplast DNA are organized into operons. Interestingly, introns are common in chloroplast DNA ... image Chloroplast DNA Interactive gene map of chloroplast DNA from Nicotiana tabacum. Segments with labels on the inside reside ... but some evidence suggests that chloroplast DNA more commonly takes a linear shape. Over 95% of the chloroplast DNA in corn ...
  https://en.wikipedia.org/wiki/Chloroplast_DNA
*  Clerodendrum - Wikipedia
In 2010, a study of four chloroplast DNA intergenic spacers showed that part of Clerodendrum was closer to the New world genera ... Inferred from Chloroplast DNA". Systematic Botany. 22 (2): 229-243. doi:10.2307/2419455. Dorothy A. Steane; Robert W. Scotland ... and other Ajugoid genera inferred from nuclear and chloroplast DNA sequence data". Molecular Phylogenetics and Evolution. 32 (1 ... In 2004, a study of DNA sequences showed that the monospecific Australian genus Huxleya was embedded in a clade of Clerodendrum ...
  https://en.wikipedia.org/wiki/Clerodendrum
*  Agavoideae - Wikipedia
David J. Bogler and Beryl B. Simpson (1995). "A Chloroplast DNA Study of the Agavaceae". Systematic Botany. 20 (2): 191-205. ...
  https://en.wikipedia.org/wiki/Agavoideae
*  Dipsacales - Wikipedia
Dipsacales phylogeny based on chloroplast DNA sequences. Harvard Papers in Botany 6:481-499. Donoghue, M. J., C. D. Bell, & R. ...
  https://en.wikipedia.org/wiki/Dipsacales
*  Lepidium - Wikipedia
2001). Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae). American Journal of Botany 88(11), 2051-63. ...
  https://en.wikipedia.org/wiki/Lepidium
*  NdhF - Wikipedia
Chloroplast Chloroplast DNA RuBisCO NADPH dehydrogenase (quinone) Neyland, Ray; Lowell E. Urbatsch (1996). "The ndhF ... Its DNA fragment resides in the small single-copy region of the chloroplast genome, and is thought to encode a hydrophobic ... "Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding". PLoS ONE. 7 ... The chloroplast NADH dehydrogenase F (ndhF) gene is found in all vascular plant divisions and is highly conserved. ...
  https://en.wikipedia.org/wiki/NdhF
*  Frangula alnus - Wikipedia
Generic limits in Rhamnus L. s.l. (Rhamnaceae) inferred from nuclear and chloroplast DNA sequence phylogenies. Taxon 53: 383- ...
  https://en.wikipedia.org/wiki/Frangula_alnus
*  Mentha - Wikipedia
Evidence from Chloroplast DNA Sequences". Systematic Botany. 29 (4): 959-64. doi:10.1600/0363644042450973. JSTOR 25064024. ...
  https://en.wikipedia.org/wiki/Mentha
*  Leslie D. Gottlieb - Wikipedia
He continued work on the phylogeny of Clarkia, using restriction site mapping of chloroplast DNA and then in 1996 Ford and ... Systma, K. J.; Gottlieb, L. D. (1986). "Chloroplast DNA evidence for the origin of the genus Heterogaura from a species of ... Subsequent studies confirmed a sister species relationship using chloroplast DNA as well as nucleotide sequences of the gene ... It wasn't until 1986 that he applied a newer molecular technique: chloroplast DNA variation using Restriction fragment length ...
  https://en.wikipedia.org/wiki/Leslie_D._Gottlieb
*  Lathyrus - Wikipedia
March 1998). "Chloroplast DNA characters, phylogeny, and classification of Lathyrus (Fabaceae)". American Journal of Botany. ...
  https://en.wikipedia.org/wiki/Lathyrus
*  Thymelaeaceae - Wikipedia
It was based on 2 regions of chloroplast DNA. These were the rbcL gene and the intergenic spacer between the transfer RNA genes ... Only a sampling of more species and more DNA from each will determine whether these groups are monophyletic or not. ... Stellera, for example, is nested within Wikstroemia, at least (see the phylogenetic tree below). A recent comparison of DNA ... nuclear ribosomal DNA) were used. All of the clades that were strongly supported in the previous study were recovered with even ...
  https://en.wikipedia.org/wiki/Thymelaeaceae
*  Papaver - Wikipedia
Kadereit, J.W.; Sytsma, K.J. (1992). "Disassembling Papaver: a restriction site analysis of chloroplast DNA". Nordic Journal of ... "Phylogenetics of Papaver and related genera based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and ...
  https://en.wikipedia.org/wiki/Papaver
*  Harlan Lewis - Wikipedia
Sytsma, K.J.; Gottlieb, L,D. (1986). "Chloroplast DNA evolution and phylogenetic relationships in Clarkia sect. Peripetasma ( ...
  https://en.wikipedia.org/wiki/Harlan_Lewis
*  Forsythia - Wikipedia
... based on chloroplast DNA variation. P. Syst. Evol. 218: 113-123. Abstract. Germplasm Resources Information Network: Forsythia ...
  https://en.wikipedia.org/wiki/Forsythia
*  Botany - Wikipedia
ISBN 978-0-00-220212-1. Possingham, J. V.; Rose, R. J. (May 18, 1976). "Chloroplast Replication and Chloroplast DNA Synthesis ... ISBN 0-300-08295-9. Heinhorst, S.; Cannon, G. C. (January 1993). "DNA Replication in Chloroplasts". Journal of Cell Science. ... have unique organelles known as chloroplasts. Chloroplasts are thought to be descended from cyanobacteria that formed ... Chloroplasts and cyanobacteria contain the blue-green pigment chlorophyll a. Chlorophyll a (as well as its plant and green ...
  https://en.wikipedia.org/wiki/Botany
*  Spruce - Wikipedia
Aðalsteinn Sigurgeirsson & Alfred E. Szmidt (1993). "Phylogenetic and biogeographic implications of chloroplast DNA variation ... DNA analyses have shown that traditional classifications based on the morphology of needle and cone are artificial. A recent ...
  https://en.wikipedia.org/wiki/Spruce
*  Robert W. Allard - Wikipedia
Wagner, D.B.; Furnier, G.R.; Saghai-Maroof, M.A.; Williams, S.M.; Dancik, B.P.; Allard, R.W. (1987). "Chloroplast DNA ... Neale, D.B.; Saghai-Maroof, M.A.; Allard, R.W.; Zhang, Q.; Jorgensen, R.A. (1988). "Chloroplast DNA diversity in populations of ... Saghai-Maroof, M.A.; Soliman, K.M.; Jorgensen, R.A. (1984). "Ribosomal DNA spacer-length polymorphisms in barley: mendelian ... Cluster, P.D.; Allard, R.W. (1995). "Evolution of ribosomal DNA (rDNA) genetic structure in colonial Californian populations of ...
  https://en.wikipedia.org/wiki/Robert_W._Allard
*  Picea sitchensis - Wikipedia
Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nordic Journal of Botany 13(3): 233-246. ( ... DNA analysis has shown that only Picea breweriana has a more basal position than Sitka spruce to the rest of the spruce. The ...
  https://en.wikipedia.org/wiki/Picea_sitchensis
*  CoRR hypothesis - Wikipedia
Chloroplast DNA Cyanobacteria Mitochondrial DNA Plastids Allen JF (August 2015). "Why chloroplasts and mitochondria retain ... This chloroplast sensor kinase is inherited from cyanobacteria and encoded in plant nuclear DNA. Chloroplast sensor kinase is ... All editions (pgs 868-869 in 5th edition) CoRR seeks to explain why chloroplasts and mitochondria retain DNA, and thus why some ... Chloroplast and mitochondrial genomes also contain genes for components of the chloroplast and mitochondrial genetic systems ...
  https://en.wikipedia.org/wiki/CoRR_hypothesis
*  Picea breweriana - Wikipedia
Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nordic Journal of Botany 13(3): 233-246. ... DNA analyses have shown that Picea breweriana has a basal position in the Picea clade, suggesting that Picea originated in ...
  https://en.wikipedia.org/wiki/Picea_breweriana
*  Bromeliaceae - Wikipedia
Lindmanioideae is the next most basal branch distinguished from the other subfamilies by convolute sepals and chloroplast DNA. ... Navioideae is split from Pitcairnioideae based on its cochlear sepals and chloroplast DNA. Puyoideae has been re-classified ... Hechtioideae is also defined based on analyses of chloroplast DNA; similar morphological adaptations to arid environments also ... multiple times and its monophyly remains controversial according to analyses of chloroplast DNA. Billbergia pyramidalis ...
  https://en.wikipedia.org/wiki/Bromeliaceae
*  Urticaceae - Wikipedia
2003). "Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data" (PDF). Telopea. 10 (1): 235-246. CS1 maint: Multiple ... Hadiah JT, Conn BJ, Quinn CJ (2008). "Infra-familial phylogeny of Urticaceae, using chloroplast sequence data". Australian ... inferred from nuclear and plastid DNA regions". Taxon. 64 (1): 65-78. doi:10.12705/641.20. CS1 maint: Multiple names: authors ...
  https://en.wikipedia.org/wiki/Urticaceae
*  Eremothamnus - Wikipedia
doi:10.1007/s12229-008-9014-8. Bergqvist, Gullevi; Bremer, Birgitta; Bremer, Kåre (1995). "Chloroplast DNA variation and the ...
  https://en.wikipedia.org/wiki/Eremothamnus
*  Caryophyllaceae - Wikipedia
Per Erixon; Bengt Oxelman (2008). "Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)?". Molecular ...
  https://en.wikipedia.org/wiki/Caryophyllaceae

LeucoplastGroup III intron: Group III intron is a class of introns found in mRNA genes of chloroplasts in euglenid protists. They have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus.Mushy peasPhotosynthesis: Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy that can be later released to fuel the organisms' activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek [phōs, "light", and σύνθεσις], synthesis, "putting together".ThylakoidD66 Strain of Chlamydomonas reinhardtii: The D66 strain of Chlamydomonas reinhardtii, a single-celled green alga, is a cell-wall-deficient strain of algae that exhibits normal photosynthetic characteristics, but requires ammonia as a source of nitrogen for growth. This strain of Green Algae is becoming an increasingly popular research organism due to its potential to be used as a source of biofuels.Stromule: A stromule is a microscopic structure found in plant cells. Stromules (stroma-filled tubules) are highly dynamic structures extending from the surface of all plastid types, including proplastids, chloroplasts, etioplasts, leucoplasts, amyloplasts, and chromoplasts.Red chlorophyll catabolite reductase: In molecular biology, the red chlorophyll catabolite reductase (RCC reductase) family of proteins consists of several red chlorophyll catabolite reductase (RCC reductase) proteins. Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyse the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC).GAI (Arabidopsis thaliana gene)Canna Leaf Roller: Cannas are largely free of pests, but in the USA plants sometimes fall victim the Canna Leaf Roller, which can actually be two different insects. Larva of the Brazilian skipper butterfly (Calpodes ethlius), also known as the Larger Canna Leaf Roller, cut the leaves and roll them over to live inside while pupating and eating the leaf.Grow lightRubiscolin: The rubiscolins are a group of opioid peptides that are formed during digestion of the ribulose bisphosphate carboxylase/oxygenase (Rubisco) protein from spinach leaves. Rubiscolins mimic the effects of opiates and, therefore, influence the brain.Coles PhillipsHaematococcus pluvialis: Haematococcus pluvialis is a freshwater species of Chlorophyta from the family Haematococcaceae. This species is well known for its high content of the strong antioxidant astaxanthin, which is important in aquaculture, and cosmetics.Oxygen evolution: Oxygen evolution is the process of generating molecular oxygen through chemical reaction. Mechanisms of oxygen evolution include the oxidation of water during oxygenic photosynthesis, electrolysis of water into oxygen and hydrogen, and electrocatalytic oxygen evolution from oxides and oxoacids.Medicinal plants of the American West: Many plants that grow in the American West have use in traditional and herbal medicine.Lonchocarpus: Lonchocarpus is a plant genus in the legume family (Fabaceae). The species are called lancepods due to their fruit resembling an ornate lance tip or a few beads on a string.Nicotiana glauca: Nicotiana glauca is a species of wild tobacco known by the common name tree tobacco. Its leaves are attached to the stalk by petioles (many other Nicotiana species have sessile leaves), and its leaves and stems are neither [nor sticky like Nicotiana tabacum].Galactolipid: Galactolipids are a type of glycolipid whose sugar group is galactose. They differ from glycosphingolipids in that they do not have nitrogen in their composition.EuglenophycinSquamosa promoter binding protein: The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Plant perception (physiology): Plant perception is the ability of plants to sense and respond to the environment to adjust their morphology, physiology and phenotype accordingly. Other disciplines such as plant physiology, ecology and molecular biology are used to assess this ability.Southern corn leaf blight: Southern corn leaf blight (SCLB) is a fungal disease of maize caused by the plant pathogen Bipolaris maydis (also known as Cochliobolus heterostrophus in its teleomorph state).Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Oxymonad: The Oxymonads are a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Along with the similar parabasalid flagellates, they harbor the symbiotic bacteria that are responsible for breaking down cellulose.Bradford LeslieCytochrome f: Cytochrome f is the largest subunit of cytochrome b6f complex (plastoquinol—plastocyanin reductase; ). In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria.Palisade cell: Palisade cells are plant cells found within the mesophyll in leaves, right below the upper epidermis and cuticle. They are vertically elongated, a different shape from spongy mesophyll cells beneath them in the leaf.DimethylureaTropical Asia: Through a crop-based biodiversity, natural resources and animals (birds, fruits, and forests), Tropical Asia is economically and physiogeographically rich. There are 16 countries of Tropical Asia ranging in size from around 610 km² (Singapore) to 3,000,000 km² (India).Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Photosystem IBrian Goodwin: Brian Carey Goodwin (25 March 1931 – 15 July 2009) was a Canadian mathematician and biologist, a Professor Emeritus at the Open University and a key founder of the field of theoretical biology. He made key contributions to the foundations of biomathematics, complex systems and generative models in developmental biology.Leaf rust (barley): Leaf rust is a fungal disease of barley caused by Puccinia hordei. It is also known as brown rust and it is the most important rust disease on barley.Plastid terminal oxidase: Plastid terminal oxidase or plastoquinol terminal oxidase (PTOX) is an enzyme that resides on the thylakoid membranes of plant and algae chloroplasts and on the membranes of cyanobacteria. The enzyme was hypothesized to exist as a photosynthetic oxidase in 1982 and was verified by sequence similarity to the mitochondrial alternative oxidase (AOX).Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.AmborellaFructose bisphosphatase deficiencyPlastocyanin: Plastocyanin is a copper-containing protein involved in electron-transfer. The protein is monomeric, with a molecular weight around 10,500 Daltons, and 99 amino acids in most vascular plants.CS-BLASTElectron transfer: Electron transfer (ET) occurs when an electron moves from an atom or a chemical species (e.g.International Moss Stock CenterFerredoxin:protochlorophyllide reductase (ATP-dependent): Ferredoxin:protochlorophyllide reductase (ATP-dependent) (, light-independent protochlorophyllide reductase) is an enzyme with system name ATP-dependent ferredoxin:protochlorophyllide-a 7,8-oxidoreductase. This enzyme catalyses the following chemical reactionMT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.Membrane protein: Membrane proteins are proteins that interact with biological membranes. They are one of the common types of protein along with soluble globular proteins, fibrous proteins, and disordered proteins.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Ferredoxin: Ferredoxins (from Latin ferrum: iron + redox, often abbreviated "fd") are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.Cyanidioschyzon merolae: C. merolae is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments (pH 1.Translational regulation: Translational regulation refers to the control of the levels of protein synthesized from its mRNA. The corresponding mechanisms are primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of the elongation or termination of protein synthesis.Ferredoxin-thioredoxin reductase: Ferredoxin-thioredoxin reductase , systematic name ferredoxin:thioredoxin disulfide oxidoreductase, is a [4Fe-4S] protein that plays an important role in the ferredoxin/thioredoxin regulatory chain. It catalyzes the following reaction:Planktothrix: Planktothrix is a genus of filamentous cyanobacteria (often called blue-green algae). P.FnrS RNA: FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named FnrS because its expression is strongly dependent on fumarate and nitrate reductase regulator (FNR), a direct oxygen availability sensor.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Phototropin: Phototropins are photoreceptor proteins (more specifically, flavoproteins) that mediate phototropism responses in higher plants. Along with cryptochromes and phytochromes they allow plants to respond and alter their growth in response to the light environment.RMF RNA motif: The rmf RNA motif is a conserved RNA structure that was originally detected using bioinformatics. rmf RNAs are consistently foundwithin species classified into the genus Pseudomonas, and is located potentially in the 5' untranslated regions (5' UTRs) of rmf genes.Brassica nigra: Brassica nigra (black mustard) ( Sanskrit : राजक्षवक, rajakshavak ; Marathi :काळी मोहरी, Kali Mohari ) is an annual weedy plant cultivated for its seeds, which are commonly used as a spice.Starch gelatinization: Starch gelatinization is a process of breaking down the intermolecular bonds of starch molecules in the presence of water and heat, allowing the hydrogen bonding sites (the hydroxyl hydrogen and oxygen) to engage more water. This irreversibly dissolves the starch granule in water.Table of standard reduction potentials for half-reactions important in biochemistry: The values below are standard reduction potentials for half-reactions measured at 25°C, 1 atmosphere and a pH of 7 in aqueous solution.Mitochondrion: The mitochondrion (plural mitochondria) is a double membrane-bound organelle found in most eukaryotic cells. The word mitochondrion comes from the Greek , , i.Burst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".Molar mass distribution: In linear polymers the individual polymer chains rarely have exactly the same degree of polymerization and molar mass, and there is always a distribution around an average value. The molar mass distribution (or molecular weight distribution) in a polymer describes the relationship between the number of moles of each polymer species (Ni) and the molar mass (Mi) of that species.

(1/448) Structural and kinetic properties of adenylyl sulfate reductase from Catharanthus roseus cell cultures.

A cDNA encoding a plant-type APS reductase was isolated from an axenic cell suspension culture of Catharanthus roseus (Genbank/EMBL-databank accession number U63784). The open reading frame of 1392 bp (termed par) encoded for a protein (Mr=51394) consisting of a N-terminal transit peptide, a PAPS reductase-like core and a C-terminal extension with homology to the thioredoxin-like domain of protein disulfide isomerase. The APS reductase precursor was imported into pea chloroplasts in vitro and processed to give a mature protein of approximately 45 kDa. The homologous protein from pea chloroplast stroma was detected using anti:par polyclonal antibodies. To investigate the catalytical function of the different domains deleted par proteins were purified. ParDelta1 lacking the transit sequence liberated sulfite from APS (Km 2.5+/-0.23 microM) in vitro with glutathione (Km 3+/-0.64 mM) as reductant (Vmax 2.6+/-0.14 U mg-1, molecular activity 126 min-1). ParDelta2 lacking the transit sequence and C-terminal domain had to be reconstituted with exogenous thioredoxin as reductant (Km 15. 3+/-1.27 microM, Vmax 0.6+/-0.014 U mg-1). Glutaredoxin, GSH or DTT were ineffective substitutes. ParDelta1 (35.4%) and parDelta2 (21. 8%) both exhibited insulin reductase activity comparable to thioredoxin (100%). Protein disulfide isomerase activity was observed for parDelta1.  (+info)

(2/448) Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis.

It is shown that the two strands of the chloroplast genome from Euglena gracilis are asymmetric with regards to nucleotide composition. This asymmetry switches at both the origin of replication and a location that is halfway around the circular genome from the origin. In both halves of the genome the leading strand is G+T-rich, having a bias toward G over C and T over A, and the lagging strand is A+C-rich. This asymmetry is probably the result of a difference in mutation dynamics between the leading and lagging strands. In addition to composition asymmetry, the two strands differ with regards to coding content. In both halves of the genome the vast majority of genes are coded by the leading strand. These two aspects of strand asymmetry are then applied to a statistical test for selection on codon usage. The results indicate that selection on codon usage is limited to genes on the leading strand; no gene on the A+C-rich lagging strand shows evidence for selection, suggesting that highly expressed genes are coded predominantly on the strand of DNA that is the leading strand during replication. On the basis of these observations it is proposed that the coding strand bias is generated by selection to code highly expressed genes on the leading strand to coordinate the direction of replication and transcription, thereby increasing the potential rate of both reactions.  (+info)

(3/448) The active digestion of uniparental chloroplast DNA in a single zygote of Chlamydomonas reinhardtii is revealed by using the optical tweezer.

The non-Mendelian inheritance of organelle genes is a phenomenon common to almost all eukaryotes, and in the isogamous alga Chlamydomonas reinhardtii, chloroplast (cp) genes are transmitted from the mating type positive (mt(+)) parent. In this study, the preferential disappearance of the fluorescent cp nucleoids of the mating type negative (mt(-)) parent was observed in living young zygotes. To study the change in cpDNA molecules during the preferential disappearance, the cpDNA of mt(+) or mt(-) origin was labeled separately with bacterial aadA gene sequences. Then, a single zygote with or without cp nucleoids was isolated under direct observation by using optical tweezers and investigated by nested PCR analysis of the aadA sequences. This demonstrated that cpDNA molecules are digested completely during the preferential disappearance of mt(-) cp nucleoids within 10 min, whereas mt(+) cpDNA and mitochondrial DNA are protected from the digestion. These results indicate that the non-Mendelian transmission pattern of organelle genes is determined immediately after zygote formation.  (+info)

(4/448) Chloroplast ribonucleoproteins are associated with both mRNAs and intron-containing precursor tRNAs.

Tobacco chloroplasts possess five conserved ribonucleoproteins (cpRNPs). To elucidate the function of cpRNPs we analyzed their localization and target nucleic acid molecules in chloroplasts. Immunoprecipitation of the stromal extract and Northern analysis revealed that cpRNPs are associated in vivo with not only various species of chloroplast mRNAs but also intron-containing precursor (pre-) tRNAs. This observation strongly suggests that cpRNPs are involved in RNA processing, including mRNA stability and pre-tRNA splicing.  (+info)

(5/448) Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses.

We sequenced the first ca. 900 bp of the 5'-trnL(UAA)-trnV(UAC)/ndhJ region of the chloroplast DNA of different Microseris accessions in order to resolve homoplasious length variation detected in the trnL(UAA)-trnF(GAA) region. We found two to four tandemly repeated trnF genes in the species of Microseris (Asteraceae, Lactuceae) and two in their sister genus Uropappus. Sequences indicated nonhomologous transitions between two, three, and four trnF genes in different Microseris taxa. Independent origins of similar trnF copy numbers were inferred from a chloroplast phylogeny of Microseris. The taxa involved grow on separate continents, supporting parallel origins of similar length variants. The changes in trnF copy numbers were best explained by interchromosomal recombination with unequal crossing over. The 5' copies of the repeats showed the highest sequence conservation, suggesting that these copies are likely to be functional trnF genes, whereas the other ones probably represent pseudogenes. Our results show that length polymorphisms accumulate once a duplicated sequence has become incorporated. Due to parallel gains of similar trnF copy numbers, homoplasious length variation was introduced into the data matrix. The data demonstrate that length polymorphisms cannot be used as indicators for phylogenetic distance unless they can be analyzed at the sequence level.  (+info)

(6/448) Protease activity of CND41, a chloroplast nucleoid DNA-binding protein, isolated from cultured tobacco cells.

CND41 is a 41 kDa DNA-binding protein isolated from chloroplast nucleoids of cultured tobacco cells. The presence of the active domain of aspartic protease in the deduced amino acid sequence of CND41 suggests that it has proteolytic activity. To confirm this, CND41 was highly purified from cultured tobacco cells and its proteolytic activity was characterized with fluorescein isothiocyanate-labeled hemoglobin as the substrate. The purified CND41 had strong proteolytic activity at an acidic pH (pH 2-4). This activity was inhibited by various chemicals, including the nucleoside triphosphates, NADPH, Fe(3+) and sodium dodecyl sulfate.  (+info)

(7/448) Cryptosporidium parvum appears to lack a plastid genome.

Surprisingly, unlike most Apicomplexa, Cryptosporidium parvum appears to lack a plastid genome. Primers based upon the highly conserved plastid small- or large-subunit rRNA (SSU/LSU rRNA) and the tufA-tRNAPhe genes of other members of the phylum Apicomplexa failed to amplify products from intracellular stages of C. parvum, whereas products were obtained from the plastid-containing apicomplexans Eimeria bovis and Toxoplasma gondii, as well as the plants Allium stellatum and Spinacia oleracea. Dot-blot hybridization of sporozoite genomic DNA (gDNA) supported these PCR results. A T. gondii plastid-specific set of probes containing SSU/LSU rRNA and tufA-tRNA(Phe) genes strongly hybridized to gDNA from a diverse group of plastid-containing organisms including three Apicomplexa, two plants, and Euglena gracilis, but not to those without this organelle including C. parvum, three kinetoplastids, the yeast Saccharomyces cerevisiae, mammals and the eubacterium Escherichia coli. Since the origin of the plastid in other apicomplexans is postulated to be the result of a secondary symbiogenesis of either a red or a green alga, the most parsimonious explanation for its absence in C. parvum is that it has been secondarily lost. If confirmed, this would indicate an alternative evolutionary fate for this organelle in one member of the Apicomplexa. It also suggests that unlike the situation with other diseases caused by members of the Apicomplexa, drug development against cryptosporidiosis targeting a plastid genome or metabolic pathways associated with it may not be useful.  (+info)

(8/448) Molecular analysis of plant migration and refugia in the Arctic.

The arctic flora is thought to have originated during the late Tertiary, approximately 3 million years ago. Plant migration routes during colonization of the Arctic are currently unknown, and uncertainty remains over where arctic plants survived Pleistocene glaciations. A phylogenetic analysis of chloroplast DNA variation in the purple saxifrage (Saxifraga oppositifolia) indicates that this plant first occurred in the Arctic in western Beringia before it migrated east and west to achieve a circumpolar distribution. The geographical distribution of chloroplast DNA variation in the species supports the hypothesis that, during Pleistocene glaciations, some plant refugia were located in the Arctic as well as at more southern latitudes.  (+info)



  • species
  • The adaptations necessary for long-term chloroplast survival arose independently in species feeding on different algal hosts, providing a valuable study system for examining the parallel evolution of this unique trophic strategy. (beds.ac.uk)
  • DNA barcoding can be used to elucidate plant relationships at the species level. (frontiersin.org)
  • sequences
  • A recent comparison of DNA sequences has established the monophyly of Thymelaea and the polyphyly of Diarthron, but there was not sufficient sampling in Wikstroemia and Daphne to exclude the possibility that Thymelaea, Diarthron, and others might be embedded in them. (wikipedia.org)
  • In the last two decades of the 20th century, botanists exploited the techniques of molecular genetic analysis, including genomics and proteomics and DNA sequences to classify plants more accurately. (wikipedia.org)
  • genes
  • Each minicircle contains one to three genes, but blank plasmids, with no coding DNA, have also been found. (wikipedia.org)
  • Using five trees to represent each major genetic group in the complex, 667 bp of the intergenic region between the chloroplast genes rbcL and atpB were amplified via the polymerase chain reaction and directly sequenced. (oregonstate.edu)
  • This region is more variable than other chloroplast loci that have been sequenced for members of Acanthaceae (rbcL and ndhF), is more prone to length mutations, and is less homoplasious than these genes. (semanticscholar.org)
  • Most genes for proteins of chloroplasts and mitochondria are, however, now located on chromosomes in the nuclei of eukaryotic cells. (wikipedia.org)
  • CoRR states that chloroplasts and mitochondria contain those genes whose expression is required to be under the direct, regulatory control of the redox state of their gene products, or of electron carriers with which those gene products interact. (wikipedia.org)
  • Genes in chloroplasts are selected for transcription according to the redox state of the electron carrier plastoquinone. (wikipedia.org)

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  • species
  • Since then, hundreds of chloroplast DNAs from various species have been sequenced, but they are mostly those of land plants and green algae-glaucophytes, red algae, and other algal groups are extremely underrepresented, potentially introducing some bias in views of "typical" chloroplast DNA structure and content. (wikipedia.org)
  • plant
  • Plant cotyledons are a tissue that is particularly active in plastid gene expression in order to develop functional chloroplasts from pro-plastids, the plastid precursor stage in plant embryos. (frontiersin.org)
  • Plant chloroplasts are semiautonomous cell organelles of endosymbiotic origin that emerged from a cyanobacteria-like ancestor ( Lopez-Juez and Pyke, 2005 ). (frontiersin.org)
  • The chloroplast NADH dehydrogenase F (ndhF) gene is found in all vascular plant divisions and is highly conserved. (wikipedia.org)
  • cytoplasm
  • Chloroplasts and mitochondria are energy-converting organelles in the cytoplasm of eukaryotic cells. (wikipedia.org)
  • All editions (pgs 868-869 in 5th edition) CoRR seeks to explain why chloroplasts and mitochondria retain DNA, and thus why some characters are inherited through the cytoplasm in the phenomenon of cytoplasmic, non-Mendelian, uniparental, or maternal inheritance. (wikipedia.org)
  • Study
  • Here, we present a pilot study that uses heparin-Sepharose and phospho-cellulose chromatography in combination with isoelectric focussing and denaturing SDS gel electrophoresis (two-dimensional gel electrophoresis) for investigating the nucleic acids binding sub-proteome of mustard chloroplasts purified from cotyledons. (frontiersin.org)
  • small
  • Doyle, J. J., Doyle, J. L. , 1987: A rapid DNA isolation procedure for small quantities of fresh leaf material. (springer.com)
  • species
  • The adaptations necessary for long-term chloroplast survival arose independently in species feeding on different algal hosts, providing a valuable study system for examining the parallel evolution of this unique trophic strategy. (beds.ac.uk)
  • DNA barcoding can be used to elucidate plant relationships at the species level. (frontiersin.org)
  • Brassicaceae
  • Early DNA-analysis showed that the Capparaceae - as defined at that moment - were paraphyletic, and it was suggested to assign the genera closest to the Brassicaceae to the Cleomaceae. (wikipedia.org)
  • Current insights in the relationships of the Brassicaceae, based on a 2012 DNA-analysis, are summarized in the following tree. (wikipedia.org)
  • Probes
  • In biomedical research and recombinant DNA technology it is often useful to have indicator probes which allow the user to detect, monitor, localize or isolate nucleic acids when present in any amount. (google.com)
  • phylogenetic analyses
  • As a result of modern investigations (ultrastructural and biochemical studies and, more recently, phylogenetic analyses based on DNA sequencing), we now know that the differences among these three groups run far deeper than the color differences suggested by their names. (eol.org)
  • sequence
  • These clones were prepared by synthesizing cDNA from an mRNA mix containing mRNA coding for the desired HLA antigen, inserting the cDNA into a vector, transforming a bacterial host and isolating transformant clones that contain the desired DNA segment by probing with an oligonucleotide probe that is specific for the desired DNA sequence. (google.com)
  • cell
  • The three seaweed groups differ considerably in many ultrastructural and biochemical features, including what photosynthetic pigments they contain, what chemical compounds they use for energy storage, the composition of their cell walls, the presence/absence of flagella , details of mitosis , the types of connections between adjacent cells, and the fine structure of the chloroplasts . (eol.org)
  • The goal of this section is for students to see the link knowledge of the cell and DNA to a more in depth study of heredity over the course of the next few weeks. (livebinders.com)
  • consists
  • DNA consists of a sugar (fruit pastille) and phosphate (marshmallow) backbone and pairs of nitrogenous bases (jelly joiners), arranged in a double helix. (edublogs.org)
  • proteins
  • These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. (wikipedia.org)
  • regions
  • This is usually accomplished on human mitochondrial DNA by sequencing the hypervariable control regions (HVR1 or HVR2), and sometimes the complete molecule of the mitochondrial DNA, as a genealogical DNA test. (wikipedia.org)
  • thought
  • Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. (wikipedia.org)
  • larger
  • Cloning of large inserts was favored by including two successive size fractionation steps (after partial EcoRI digestion and after ligation with the vector arms), which selected DNA fragments larger than 350 kb. (harvard.edu)
  • separate
  • In the fertilized daughter, DNA is then replicated in the two separate pronuclei derived from the sperm and ovum, making the zygote's chromosome number temporarily 4n diploid. (wikipedia.org)
  • library
  • Both the DNA capture and library preparation was carried out as outlined in the protocols supplied by Agilent (protocol version 1.1.1) and Roche/nimblegen (NimbleGen SeqCap User's Guide, version 1.0, Illumina optimized), except that a Bioruptor (Diagenode) was used for fragmentation of the DNA. (g3journal.org)
  • provide
  • Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for ( i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and ( ii) millet landrace conservation. (ebscohost.com)