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At least 19 recordsLinked to original sources
PubMed1992

Structure and organization of rhodophyte and chromophyte plastid genomes: implications for the ancestry of plastids.

Plastid genomes of two rhodophytes (Porphyra yezoensis and Griffithsia pacifica) and two chromophytes (Olisthodiscus luteus and Ochromonas danica) were compared with one another and with green plants in terms of overall structure, gene complement and organization. The rhodophyte genomes are moderately colinear in terms of gene organization, and are distinguished by three rearrangements that can most simply be explained by transpositions and a large (approximately 40 kb) inversion. Porphyra contains two loci for ppcBA and Griffithsia has two loci for rpoA. Although there is little similarity in gene organization between the rhodophytes and consensus green plant genome, certain gene clusters found in green plants appear to be conserved in the rhodophytes. The chromophytes Olisthodiscus and Ochromonas contain relatively large plastid inverted repeats that encode several photosynthetic genes in addition to the rRNA genes. With the exception of rbcS, the plastid gene complement in Olisthodiscus is similar to that of green plants, at least for the subset of genes tested. The Ochromonas genome, in contrast, appears unusual in that several of the green plant gene probes hybridizing to Olisthodiscus DNA did not detect similar sequences in Ochromonas DNA. Gene organization within the chromophytes is scrambled relative to each other and to green plants, despite the presence of putatively stabilizing inverted repeats. However, some gene clusters conserved in green plants and rhodophytes are also present in the chromophytes. Comparison of the entire rhodophyte, chromophyte and green plant plastid genomes suggests that despite differences in gene organization, there remain overall similarities in architecture, gene content, and gene sequences among in three lineages. These similarities are discussed with reference to the ancestry of the different plastid types.

Biological Evolution↗
PubMed1975

Plastid development in primary leaves of Phaseolus vulgaris. Development of plastid adenosine triphosphatase activity during greening.

The etioplasts of dark-grown bean leaves showed ATPase (adenosine triphosphatase) activity which had a pH optimum of 8.5, was stimulated by dithiothreitol and unaffected by light-triggering. Bean chloroplasts showed a low activity of dark-induced ATPase with a pH optimum of 8.5 and a substantial amount of light-triggered activity with a pH optimum of 8.0. The light-triggered activity depended on dithiothreitol and Mg2+ and was promoted by phenazine methosulphate. Light-triggered ATPase activity was completely inhibited by 20mum-dicyclohexylcarbodi-imide. Etioplasts developed light-triggered ATPase activity in response to 30 min illumination of the etiolated leaves. During the 48 h of light-induced greening of dark-grown leaves there was a 70% increase of the chloroplast ATPase activity found after light-triggering and a 30% fall in the dark-induced activity, both expressed on a per leaf basis. As the larger part of these changes occurred during the first 30 min of illumination, it is concluded that most or all of the chloroplast ATPase was present in the etioplast, a conclusion identical with that of Lockshin et al. (1971) for maize. During 48 h of greening there was a tenfold increase in the amount of thylakoid membrane in the leaf together with an 83% fall in the ATPase activity per m2 of thylakoid membrane, measured after light-triggering.

Adenosine Triphosphatases↗
PubMed1979

Events surrounding the early development of Euglena chloroplasts. 15. Origin of plastid thylakoid polypeptides in wild-type and mutant cells.

Techniques are described for the isolation of plastid thylakoid membranes from light-grown and dark-grown cells of Euglena gracilis var. bacillaris, and from mutants affecting plastid development. These membranes, which have minimal contamination with other cell fractions, are localized in sucrose gradients by using the thylakoid membrane sulfolipid as a specific marker. The plastid thylakoid membrane polypeptides isolated from these membranes were separated on SDS polyacrylamide gels and yielded patterns containing 30-40 polypeptides. Light-grown strain Z gave patterns identical with bacillaris. Since the plastid thylakoid polypeptide patterns obtained from dark-grown wild-type cells and from a bleached mutant W3BUL in which plastid DNA is undetectable are identical, it appears that the proplastid thylakoid polypeptides of wild-type cannot be coded in plastid DNA and are probably coded in nuclear DNA. The plastid thylakoid polypeptide patterns obtained from various dark-grown mutants, making large but abnormal chloroplasts, show a correlation between the amount of chlorophyll formed and the amount of a plastid thylakoid polypeptide thought to be associated wtth one of the pigment-protein light-harvesting complexes. Treatment with SAN 9789 (4-chloro-5-(methylamino)-2(alpha, alpha, alpha,-trifluoro-m-tolyl)-3-(2H(pyridazinone) known to block carotenoid synthesis at the level of phytoene, causes a progressive loss of all plastid thylakoid polypeptides during growth in darkness and results in the establishment of a new, lowere steady-state level of sulfolipid. At least ten of the plastid thylakoid polypeptides become labeled when isolated chloroplasts are supplied with radioactive amono acids; of these six are undectable in W3BUL and are, therefore, candidates for coding by plastid DNA.

Chloroplasts↗
PubMed1992

Gene phylogenies and the endosymbiotic origin of plastids.

The endosymbiotic origin of chloroplasts from cyanobacteria has long been suspected and has been confirmed in recent years by many lines of evidence. Debate now is centered on whether plastids are derived from a single endosymbiotic event or from multiple events involving several photosynthetic prokaryotes and/or eukaryotes. Phylogenetic analysis was undertaken using the inferred amino acid sequences from the genes psbA, rbcL, rbcS, tufA and atpB and a published analysis (Douglas and Turner, 1991) of nucleotide sequences of small subunit (SSU) rRNA to examine the relationships among purple bacteria, cyanobacteria and the plastids of non-green algae (including rhodophytes, chromophytes, a cryptophyte and a glaucophyte), green algae, euglenoids and land plants. Relationships within and among groups are generally consistent among all the trees; for example, prochlorophytes cluster with cyanobacteria (and not with green plastids) in each of the trees and rhodophytes are ancestral to or the sister group of the chromophyte algae. One notable exception is that Euglenophytes are associated with the green plastid lineage in psbA, rbcL, rbcS and tufA trees and with the non-green plastid lineage in SSU rRNA trees. Analysis of psbA, tufA, atpB and SSU rRNA sequences suggests that only a single bacterial endosympbiotic event occurred leading to plastids in the various algal and plant lineages. In contrast, analysis of rbcL and rbcS sequences strongly suggests that plastids are polyphyletic in origin, with plastids being derived independently from both purple bacteria and cyanobacteria. A hypothesis consistent with these discordant trees is that a single bacterial endosymbiotic event occurred leading to all plastids, followed by the lateral transfer of the rbcLS operon from a purple bacterium to a rhodophyte.

Amino Acid Sequence↗
PubMed1992

Cell type determines plastid transmission in tomato intergeneric somatic hybrids.

Mesophyll (M)- and suspension culture (S)-derived protoplasts of both Lycopersicon esculentum, tomato, and its wild relative Solanum lycopersicoides were fused as S + M, M + M and S + S combinations, respectively, to resolve the role of parental cell types in determining cpDNA transmission to intergeneric somatic hybrid plants. The mesophyll cpDNA was preferentially transmitted to 96% of the plants, each regenerated from a separate callus, in M + S and S + M fusion combinations. In contrast, for the M + M combination there was an equable distribution of either tomato cpDNA or that of S. lycopersicoides among the 34 hybrid plants. The number of plastids or proplastids in mesophyll or suspension protoplasts was not a factor regulating cpDNA transmission. Mesophyll or suspension protoplasts of both fusion partners had comparable frequencies of either plastid type with a mean of 23. The biased transmission of plastids from the mesophyll parent in somatic hybrid plants of S + M and M + S combinations appears to be due to differential multiplication of plastids, possibly conditioned by an unequal input of the nucleoids found in plastids versus proplastids. In the M + M fusion, plastid and nucleotide input and subsequent plastid multiplication are apparently equal, and when combined with random sorting out leads to an equal distribution of parental cpDNAs in the regenerated somatic hybrid plants. For the S+S combination, 22 somatic hybrid plants have exclusively tomato cpDNA, an outcome that is not readily explained by donor cell input.

Cell Fusion↗
PubMed1979

Events surrounding the early development of Euglena chloroplasts. 16. Plastid thylakoid polypeptides during greening.

Using sulfolipid to locate plastid thylakoid membranes in gradients from dark-grown resting cells it has been possible to study the plastid thylakoid membrane polypeptides of Euglena gracilis var. bacillaris undergoing light-induced chloroplast development. All plastid thylakoid bands seen in dark-growing wild-type cells and in mutant W3BUL in which plastid DNA is undetectable, are observed to increase in amount during plastid development. Others, which are undetectable in dark-grown wild-type and W3BUL increase greatly during plastid development and appear to be those associated with pigment-protein complexes. The data obtained from experiments where the polypeptides were labeled with 35S during development, either continuously or in pulses, were consistent with these findings. Cycloheximide strongly inhibited the increases in amount in all bands and chloramphenicol or streptomycin produced a lower level of inhibition in all bands indicating tight control of theformation of each plastid membrane constituent by the others. The formation of a polypeptide band of 25 000 molecular weight, thought to be a part of a pigment-protein complex of the thylakoid, and chlorophyll synthesis were inhibited identically by these antibiotics.

Chloramphenicol↗
PubMed2024

Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes.

Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.

Iris Plant↗
PubMed1992

Plastid DNA sequence homologies in the tobacco nuclear genome.

The tobacco (Nicotiana tabacum) nuclear genome contains long tracts of DNA (i.e. in excess of 18 kb) with high sequence homology to the tobacco plastid genome. Five lambda clones containing these nuclear DNA sequences encompass more than one-third of the tobacco plastid genome. The absolute size of these five integrants is unknown but potentially includes uninterrupted sequences that are as large as the plastid genome itself. An additional sequence was cloned consisting of both nuclear and plastid-derived DNA sequences. The nuclear component of the clone is part of a family of repeats, which are present in about 400 locations in the nuclear genome. The homologous sequences present in chromosomal DNA were very similar to those of the corresponding sequences in the plastid genome. However significant sequence divergence, including base substitutions, insertions and deletions of up to 41 bp, was observed between these nuclear sequences and the plastid genome. Associated with the larger deletions were sequence motifs suggesting that processes such as DNA replication slippage and excision of hairpin loops may have been involved in deletion formation.

Base Sequence↗
PubMed1979

Plastid ultrastructural features in the various tissues of sunflower leaves.

In young sunflower leaves a cell differentiation gradient has been observed along the major leaf where the leaf basal cells are less differentiated than the apical ones. The tip-base gradient also affects plastid differentiation. Moreover, diverse differentiation speeds are observed among the plastids of the various leaf tissues. The first plastids to take on a well-differentiated appearance are those of the mesophyll. In both the epidermis and vein regions (i.e. in a monocellular sheath round the bundle) one can observe plastids with electron-dense intrathylakoid compartments and lightly stained membranes which, however, are numerous and well-arranged in the grana. The latter membranes have a definite appearance for some plastids. It is assumed that the cell's internal environment is able to control the rate of plastid differentiation.

Chlorophyll↗
PubMed1992

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.

Complete nucleotide sequencing shows that the plastid genome of Epifagus virginiana, a nonphotosynthetic parasitic flowering plant, lacks all genes for photosynthesis and chlororespiration found in chloroplast genomes of green plants. The 70,028-base-pair genome contains only 42 genes, at least 38 of which specify components of the gene-expression apparatus of the plastid. Moreover, all chloroplast-encoded RNA polymerase genes and many tRNA and ribosomal protein genes have been lost. Since the genome is functional, nuclear gene products must compensate for some gene losses by means of previously unsuspected import mechanisms that may operate in all plastids. At least one of the four unassigned protein genes in Epifagus plastid DNA must have a nongenetic and nonbioenergetic function and, thereby, serve as the reason for the maintenance of an active genome. Many small insertions in the Epifagus plastid genome create tandem duplications and presumably arose by slippage mispairing during DNA replication. The extensive reduction in genome size in Epifagus reflects an intensification of the same processes of length mutation that govern the amount of noncoding DNA in chloroplast genomes. Remarkably, this massive pruning occurred with a virtual absence of gene order change.

Chromosomes↗
PubMed1992

Long regions of homologous DNA are incorporated into the tobacco plastid genome by transformation.

We investigated the size of flanking DNA incorporated into the tobacco plastid genome alongside a selectable antibiotic resistance mutation. The results showed that integration of a long uninterrupted region of homologous DNA, rather than of small fragments as previously thought, is the more likely event in plastid transformation of land plants. Transforming plasmid pJS75 contains a 6.2-kb DNA fragment from the inverted repeat region of the tobacco plastid genome. A spectinomycin resistance mutation is encoded in the gene of the 16S rRNA and, 3.2 kb away, a streptomycin resistance mutation is encoded in exon II of the ribosomal protein gene rps12. Transplastomic lines were obtained after introduction of pJS75 DNA into leaf cells by the biolistic process and selection for the spectinomycin resistance marker. Homologous replacement of resident wild-type sequences resulted in integration of all, or almost all, of the 6.2-kb plastid DNA sequence from pJS75. Plasmid pJS75, which contains engineered cloning sites between two selectable markers, can be used as a plastid insertion vector.

Base Sequence↗
PubMed1975

Rifampicin inhibition of the plastid rRNA synthesis of Marchantia polymorpha.

The effect of rifampicin on the synthesis of plastid rRNA in Marchantia polymorpha was studied in vivo. As bacterial rRNA and plastid rRNA have the same electrophoretic mobilities, this study was possible only after a method for inhibiting bacterial contamination was developed. It was established that 91-100% of the rRNA synthesized by cultures of bacteria from Marchantia, after a labelling period of 3 and 9 h by 32-P, is inhibited by 10 mug/ml of rifampicin. The same inhibition was observed when Marchantia was labelled for 3 h in the presence of 10 mug/ml of rifampicin, showing that no plastid rRNA was synthesized under out conditions, but only bacterial RNA. However, when labelling was continued for 9 h two important peaks of rRNA (23 and 19 s) were labelled in the presence of 10 or 20 mug/ml of rifampicin. These peaks are of chlorophastic origin as confirmed by the following facts: the labelling is light-activated; plastids isolated from thalli labelled for 12 h also show these two radioactive peaks. Cytoplasmic rRNA is synthesized under certain conditions. The synthesis of plastid rRNA is inhibited by higher concentrations of rifampicin, a concentration of 250 mug/ml producing at least 75% inhibition. Marchantia, a primitive multicellular plant, differs in this respect from higher plants, which seem to be, in most cases, insensitive to rifampicin

Bacteria↗
PubMed1975

Use of plastome and nuclear mutants of higher plants to study the genetic control of plastid formation and function.

We conducted comparative biochemical and electron-microscopic studies of several types of plastome and nuclear mutants of Antirrhinum majus and Pelargonium zonale. It was shown that specific blocking of the photosynthetic reaction occurs in plastome mutants of A. majus; Photosystem II was found to be damaged in the en:alba-1 mutant and photo-system I was affected in the en:viridis-1 mutant. The plastid mutations in these mutants caused loss of certain soluble lamellar proteins and pigment--protein complexes or a reduction in their content, which led to disappearance of photosynthetic activity. When the content of high-molecular ribosomal RNA in the leaves of normal and mutant P. zonale plants was compared, the normal plants were found to have four types of RNA: two types of cytoplasmic-ribosome RNA and two types of plastid-ribosome RNA. No plastid-ribosome RNA was detected in the mutant. These results were confirmed by electron-microscopic examination: no ribosomes were detected in the mutant plastids. Thus, use of plastome mutants made it possible to establish that the genetic information concentrated in the plastid DNA controls formation of ribosomes and lamellae in the chloroplasts and thus affects chloroplast photosynthetic function.

Cell Nucleus↗
PubMed1978

[Comparative analysis of ultrastructure and lipid composition of plastids from sun and shade plants (author's transl)].

The ultrastructure and lipid composition of chloroplasts, isolated from various shade and sun plants, were compared. Depending on the origin of the plastid, significant differences were observed in the percentage of appressed thylakoids. Accordingly, plastids could be classified into three different types: Type I chloroplasts, from mesophyll cells of sun plants (barley, corn, spinach, bean), display well-developed grana and intergrana thylakoid membranes. Type II chloroplasts, typical of shade plant (Arum), show giant grana stacks with few interconnecting thylakoids. Type III chloroplasts, from bundle sheath cells of leaves from C4-plants (corn), are characterized by an extensive development of stroma thylakoids with only occasional rudimentary grana. The percentages of appressed membranes are in the ranges of 50 to 60%, 80% and 2% for type I, II and III plastids respectively. Striking differences are observed in the fatty acid composition of phosphatidylglycerol molecules. Trans-delta3-hexadecenoic acid is found only in this phospholipid and amounts to 30 to 40%, 50% and less than 8% of total fatty acids in type I, II and III plastids respectively. The comparison of ultrastructural and biochemical data suggests a strong correlation between the amounts of phosphatidylglycerol molecules containing trans-delta3-hexadecenoic acid and the percentages of appressed membranes (grana stacks) within plastid stroma.

Chloroplasts↗
PubMed2025

The evolution of the plastid genomes in the holoparasitic Balanophoraceae.

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions in their plastomes. The characteristics of the minimum plastome required for survival, if they exist, remain a topic of debate. The holoparasitic family Balanophoraceae was initially presumed to have entirely lost their plastids, however, recent reports revealed the presence of reduced and aberrant plastids with odd genomes. Among the outstanding features of these genomes are the highest nucleotide composition bias across the tree of life and the only two genetic code changes ever recorded among plants. In this study, we assembled the plastomes from five genera, four of which had never been studied. Major common features include extremely high AT content, the lack of a typical quadripartite structure and extensive size reduction due to gene elimination and genome compaction. The family exhibits multiple gene and intron losses, and a broad range of scenarios regarding the evolution of the plastid trnE, a gene considered essential because of its dual function in tetrapyrrole biosynthesis and translation within the plastid. In addition, phylogenetic analyses suggest that the genus Scybalium is not monophyletic. An evolutionary model for the plastomes of the Balanophoraceae is proposed.

Genome, Plastid↗
PubMed2026

Identification of a plastid-targeted RecQ-like helicase in the red alga Cyanidioschyzon merolae.

Plastids retain their own genomic DNA (plastid DNA, ptDNA) which must be faithfully maintained for proper organelle function. However, the molecular mechanisms responsible for ptDNA maintenance remain poorly understood, particularly in red algae. Here, we identified a plastid-targeted RecQ-like helicase (ptRECQ) in the unicellular red alga Cyanidioschyzon merolae. Biochemical assays demonstrated that ptRECQ possesses ATP-dependent helicase activity and preferentially unwinds splayed DNA substrates that mimic replication fork structures. ptrecQ mutant cells were hypersensitive to nalidixic acid, a ptDNA gyrase inhibitor that induces replication stress, indicating a role for ptRECQ in plastid genome maintenance under replication stress. Phylogenetic analyses showed that ptRECQ is broadly conserved in red algae, absent from green algae and land plants, and phylogenetically distinct from cyanobacterial RecQ proteins. These results suggest that red algae employ a ptDNA maintenance system that differs from that of the green lineage.

Rhodophyta↗
PubMed2026

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae.

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (accD, ycf1, clpP, ndhF, and rpl22) and intergenic spacers (rpl33-rps18, the trnG-UCC intron, trnH-GUG-psbA, accD-psaI, and petA-psbJ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Hamamelidaceae↗