| the ribosomal rna repeats are non-identical and directly oriented in the chloroplast genome of the red alga porphyra purpurea. | a detailed restriction map of the chloroplast genome of the red alga porphyra purpurea has been constructed. southern hybridization experiments with cloned or gel-purified restriction fragments and pcr products indicate that the p. purpurea chloroplast genome is approximately 188 kb in size. this circular molecule contains two rrna-encoding repeats (approximately 4.9 kb) that separate the genome into single-copy regions of 34 kb and 144 kb. interestingly, these repeats are arranged in a direct o ... | 1993 | 8299161 |
| selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. | in the plant chloroplast genome the codon usage of the highly expressed psba gene is unique and is adapted to the trna population, probably due to selection for translation efficiency. in this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. a method is developed which tests selection on each gene individually by constructing sequences wi ... | 1998 | 9541540 |
| complete sequence of the mitochondrial dna of the red alga porphyra purpurea. cyanobacterial introns and shared ancestry of red and green algae. | the mitochondrial dna (mtdna) of porphyra purpurea, a circular-mapping genome of 36,753 bp, has been completely sequenced. a total of 57 densely packed genes has been identified, including the basic set typically found in animals and fungi, as well as seven genes characteristic of protist and plant mtdnas and specifying ribosomal proteins and subunits of succinate:ubiquinone oxidoreductase. the mitochondrial large subunit rrna gene contains two group ii introns that are extraordinarily similar t ... | 1999 | 10488235 |
| protein translocation into and within cyanelles (review). | the cyanelles of the glaucocystophyte alga cyanophora paradoxa resemble endosymbiotic cyanobacteria in morphology, pigmentation and, especially, in the presence of a peptidoglycan wall situated between the inner and outer envelope membranes. however, it is now clear that cyanelles in fact are primitive plastids. phylogenetic analyses of plastid, nuclear and mitochondrial genes support a single primary endosymbiotic event. in this scenario cyanelles and all other plastid types are derived from an ... | 2005 | 16092530 |
| Determination of Water-Soluble Arsenic Compounds in Commercial Edible Seaweed by LC-ICPMS. | This paper reports arsenic speciation in edible seaweed (from the Galician coast, northwestern Spain) produced for human consumption. Chondrus crispus , Porphyra purpurea , Ulva rigida , Laminaria ochroleuca , Laminaria saccharina , and Undaria pinnatifida were analyzed. The study focused on arsenosugars, the most frequently occurring arsenic species in algae. As(III) and As(V) were also determined in aqueous extracts. Total arsenic in the samples was determined by microwave digestion and ... | 2011 | 22082352 |
| [bioinformatics studies on photosynthetic system genes in cyanobacteria and chloroplasts]. | this study compared homology of base sequences in genes encoding photosynthetic system proteins of cyanobacteria (synechocystics sp. pcc6803, nostoc sp. pcc7120) with these of chloroplasts (from marchantia polymorpha, nicotiana tobacum, oryza sativ, euglena gracilis, pinus thunbergii, zea mays, odentella sinesis, cyanophora paradoxa, porphyra purpurea and arabidopsis thaliana) by blast method. while the gene sequence of synechocystics sp. pcc6803 was considered as the criterion (100%) the homolo ... | 2004 | 15490883 |
| the plastid genome of the cryptophyte alga, guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. | the plastid genome of the cryptophyte alga guillardia theta (121,524 bp) has been completely sequenced. the genome is 33% g+c and contains a short, nonidentical inverted repeat (4.9 kb) encoding the two rrna cistrons. the large and small single-copy regions are 96.3 and 15.4 kb, respectively. forty-six genes encoding proteins for photosynthesis, 5 genes for biosynthetic function, 5 genes involved in replication and division, 30 trna genes, 44 ribosomal protein genes (26 large subunit and 18 smal ... | 1999 | 9929392 |
| pnzip is a novel mesophyll-specific cdna that is regulated by phytochrome and the circadian rhythm and encodes a protein with a leucine zipper motif. | we isolated and characterized a novel light-regulated cdna from the short-day plant pharbitis nil that encodes a protein with a leucine (leu) zipper motif, designated pnzip (pharbitis nil leu zipper). the pnzip cdna is not similar to any other gene with a known function in the database, but it shares high sequence homology with an arabidopsis expressed sequence tag and to two other sequences of unknown function from the cyanobacterium synechocystis spp. and the red alga porphyra purpurea, which ... | 1998 | 9449833 |
| ccs1, a nuclear gene required for the post-translational assembly of chloroplast c-type cytochromes. | nuclear genes play important regulatory roles in the biogenesis of the photosynthetic apparatus of eukaryotic cells by encoding factors that control steps ranging from chloroplast gene transcription to post-translational processes. however, the identities of these genes and the mechanisms by which they govern these processes are largely unknown. by using glass bead-mediated transformation to generate insertional mutations in the nuclear genome of chlamydomonas reinhardtii, we have generated four ... | 1997 | 9395519 |
| cloning and molecular analyses of the arabidopsis thaliana plastid pyruvate dehydrogenase subunits. | herein we report the first molecular description of the pyruvate dehydrogenase component of the higher plant plastid pyruvate dehydrogenase complex. the full-length cdnas for the e1 alpha (1530 bp) and e1 beta (1441 bp) subunits of the arabidopsis thaliana plastid pyruvate dehydrogenase contain open reading frames that encode polypeptides of 428 and 406 amino acids, respectively, with calculated molecular weight values of 47,120 and 44,208. the deduced amino acid sequences for arabidopsis plasti ... | 1997 | 9393637 |
| the heme oxygenase gene (pbsa) in the red alga rhodella violacea is discontinuous and transcriptionally activated during iron limitation. | heme oxygenase (ho) catalyzes the opening of the heme ring with the release of iron in both plants and animals. in cyanobacteria, red algae, and cryptophyceae, ho is a key enzyme in the synthesis of the chromophoric part of the photosynthetic antennae. in an attempt to study the regulation of this key metabolic step, we cloned and sequenced the pbsa gene encoding this enzyme from the red alga rhodella violacea. the gene is located on the chloroplast genome, split into three distant exons, and is ... | 1997 | 9326680 |
| the plant 2-cys peroxiredoxin bas1 is a nuclear-encoded chloroplast protein: its expressional regulation, phylogenetic origin, and implications for its specific physiological function in plants. | 2-cys peroxiredoxins constitute a family of enzymes which catalyze the transfer of electrons from sulfhydryl residues to peroxides and are ubiquitously distributed among all organisms. this paper characterizes the higher plant 2-cys-peroxiredoxin bas1. (i) escherichia coli over-expressing bas1 exhibit increased tolerance for alkyl hydroperoxides in vivo. this result substantiates the peroxiredoxin function of bas1. (ii) bas1 protein is associated with the soluble chloroplast fraction of mesophyl ... | 1997 | 9263459 |
| the large ribosomal protein gene cluster of a cryptomonad plastid: gene organization, sequence and evolutionary implications. | the complete sequence of the major ribosomal protein gene cluster of the plastid genome of the cryptomonad alga guillardia theta (formerly cryptomonas phi) is presented. the ribosomal protein genes (corresponding to the s10, spc, alpha and l13/s9 operons of e. coli) are found upstream of the previously reported plastid str operon, and transcribed in the same orientation. the genes are very tightly packed with as little as two nucleotides between the rpl14 and rpl24 genes. the gene arrangement is ... | 1997 | 9137835 |
| a 5 s rrna gene is present in the mitochondrial genome of the protist reclinomonas americana but is absent from red algal mitochondrial dna. | except in the case of land plants, mitochondrial ribosomes apparently lack a 5 s rrna species, even though this small rna is a component of all prokaryotic, chloroplast and eukaryotic cytosol ribosomes. in plants, the mitochondrial 5 s rrna is encoded by mtdna and differs in sequence from the 5 s rrna specified by plant nuclear and chloroplast genomes. a distinctive 5 s rrna component has not been found in the mitochondrial ribosomes of non-plant eukaryotes and, with the notable exception of the ... | 1996 | 8800209 |
| elongation factor 1 alpha genes of the red alga porphyra purpurea include a novel, developmentally specialized variant. | the life cycle of the red alga porphyra purpurea alternates between two morphologically distinct phases: a shell-boring, filamentous sporophyte and a free-living, foliose gametophyte. from a subtracted cdna library enriched for sporophyte-specific sequences, we isolated a cdna encoding an unusual elongation factor 1 alpha (ef-1 alpha) that is expressed only in the sporophyte. a second ef-1 alpha gene that is expressed equally in the sporophyte and the gametophyte was isolated from a genomic libr ... | 1996 | 8704161 |
| genes encoding the same three subunits of respiratory complex ii are present in the mitochondrial dna of two phylogenetically distant eukaryotes. | although mitochondrial dna is known to encode a limited number (<20) of the polypeptide components of respiratory complexes i, iii, iv, and v, genes for components of complex ii [succinate dehydrogenase (ubiquinone); succinate:ubiquinone oxidoreductase, ec 1.3.5.1] are conspicuously lacking in mitochondrial genomes so far characterized. here we show that the same three subunits of complex ii are encoded in the mitochondrial dna of two phylogenetically distant eukaryotes, porphyra purpurea (a pho ... | 1996 | 8637872 |
| similarity between putative atp-binding sites in land plant plastid orf2280 proteins and the ftsh/cdc48 family of atpases. | plastid orf2280 proteins from five species of land plant are shown to have limited amino-acid sequence similarity to a family of proteins that includes the yeast cdc48, sec18, pas1 and sug1 proteins, three subunits of the mammalian 26s protease, and the escherichia coli ftsh protein. these proteins all contain one or two atpase domains and many are involved in cell division, transport of proteins across membranes, or proteolysis. similarity with the orf2280 proteins is restricted to a single reg ... | 1994 | 8082182 |
| isolation of a gametophyte-specific cdna encoding a lipoxygenase from the red alga porphyra purpurea. | a cdna clone encoding a lipoxygenase was obtained from a subtracted cdna library specific for the gametophyte of porphyra purpurea. the amino acid sequence of the p. purpurea lipoxygenase is most similar to the sequences of animals and plants in the iron-binding, catalytic region located in the c-terminal half of the enzymes. northern hybridization confirmed that the gene represented by this cdna is expressed only in the gametophyte. | 1994 | 7528079 |
| recent horizontal intron transfer to a chloroplast genome. | evidence is presented for the recent, horizontal transfer of a self-splicing, homing group ii intron from a cyanobacteria to the chloroplast genome of euglena myxocylindracea. the psba gene of e.myxocylindracea was found to contain a single 2566 nt group ii intron with a gene in domain 4 for a 575 amino acid maturase. the predicted secondary structure and tertiary interactions of the group ii intron, as well as the derived maturase primary sequence, most closely resemble the homing intron of the ... | 2004 | 14762207 |
| a structural and functional study of plastid rnas homologous to catalytic bacterial rnase p rna. | ribonuclease p (rnase p), the ubiquitous enzyme required for 5' maturation of transfer rna, is a ribonucleoprotein containing an essential rna subunit. this rna (p rna) is the catalytic component of rnase p in bacteria and some archaea. a putative p rna is encoded in the chloroplast genome of three algae: cyanophora paradoxa, porphyra purpurea and nephroselmis olivacea. in no case, the p rnas from the plastids were active in vitro in conditions where bacterial and some archaeal p rnas are functi ... | 2003 | 14636991 |
| a high-resolution gene map of the chloroplast genome of the red alga porphyra purpurea. | extensive dna sequencing of the chloroplast genome of the red alga porphyra purpurea has resulted in the detection of more than 125 genes. fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. these include genes encoding 17 photosynthetic proteins, three trnas, and nine ribosomal proteins. in addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes ... | 1993 | 12271072 |
| [identification and tissue-specific expression of a full length cdna encoding zip protein in arabidopsis]. | a full-length cdna encoding a putative zip proteins, has been isolated from arabidopsis cdna library using a heterologous dna probe. sequence analysis showed that the deduced protein contained a leucine zipper and a possible nuclear localization signal domain. there was no identical proteins in the database we searched, but it shared high sequence homology with pnzip from pharbitis nil and two other open reading frames (orf) of unknown function from synechocystis spp and porphyra purpurea. these ... | 2002 | 11958125 |
| the structure and gene repertoire of an ancient red algal plastid genome. | photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. to extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of cyanidium caldarium rk1, a unicellular red alga (af022186). the analysis revealed that this genome shows several unusual structural features, such as a hypothetical hairpin structure in a gene-free region a ... | 2000 | 11040290 |