Clone banks of the mung bean, pea and spinach chloroplast genomes

All but one of the PstI restriction fragments from mung bean, pea, and spinach chloroplast DNAs have been stably cloned into pBR322. Large fragments (15-54 kb) were cloned at low efficiencies which decreased with increasing fragment length. However, plasmids containing fragments above 25-30 kb were too unstable to be useful. In particular, pBR322 derivatives containing the largest mung bean and spinach fragments (34 kb and 54 kb, respectively) are extremely unstable and rapidly delete parts of the plasmid sequence. The PstI fragments of mung bean chloroplast DNA which cover the 34-kb PstI fragment have been cloned into pACYC177. After a search of several thousand recombinants we were unable to recover a clone containing a 12.2-kb pea chloroplast PstI fragment and suggest that some property of its sequence may be inimical to the cloning process. The identity of the cloned fragments to native chloroplast DNA restriction fragments is demonstrated by restriction analysis and the ability to construct detailed restriction maps of the mung bean and pea chloroplast genomes.     

Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost

We examined the arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber are essentially colinear. They share with the corn chloroplast genome a large inversion of approximately 50 kb relative to the genomes of three legumes--mung bean, pea and broad bean. There is one additional rearrangement, a second, smaller inversion within the 50 kb inversion, which is specific to the corn genome. These two changes are the only detectable rearrangements that have occurred during the evolution of the species examined (corn, spinach, petunia, cucumber and mung bean) whose chloroplast genomes contain a large inverted repeat sequence of 22-25 kb. In contrast, we find extensive sequence rearrangements in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus there is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it. We discuss several explanations for this correlation, including the possibility that the inverted repeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.     

Inheritance of a recessive transgene-associated character controlling albinism in transgenic bean (Phaseolus vulgaris L.)

We identified a transgenic line exhibiting albinism during our work to introduce genes through genetic engineering in dry bean (Phaseolus vulgaris). The transgenic mother plant (R0) presented a normal phenotype and generated albino and normal green plants in the first generation (R1). The segregation ratio of the albino character in the R1 and R2 generations fitted the expected ratio for a character controlled by a single recessive gene linked to a foreign gus gene, suggesting that albinism could be a consequence of insertional mutation caused by introduction of the exogenous gene. Analysis by electron microscope revealed that the albino cells possessed no chloroplasts and a greater number of mitochondria when compared to normal green plants. This transgenic bean line may be used in understanding the genetic control of chloroplast genesis, for acquiring additional knowledge of genomic structure or in physiological studies. This is the first described transgene-associated mutant bean plant.     

Arrangement of the ribosomal RNA genes in chloroplast DNA of Leguminosae

Summary The circular chloroplast DNA from three species of plants in the taxonomic family Leguminosae were examined using electron microscopic techniques and restriction endonuclease digestion. Chloroplast DNAs from chickpea (Cicer arietinum), mung bean (Vigna radiata), and soy bean (Glycine max) were found to range in size from 119–151 kilobase pairs by contour length measurements. Sizes of the chloroplast DNAs have been further confirmed using different restriction endonucleases. Two of the chloroplast DNAs examined, soy bean and mung bean, contain a region approximately 15.9–18% of their monomer length that is repeated in reverse polarity. This repeated region separates a small unique region that ranges in size from 18.75–20.4 kilobase pairs and a large unique region that ranges in size from 73.4–85 kbp. This feature was not found in the chloroplast DNA of chickpea. R-loop hybridizations performed using chloroplast ribosomal RNAs demonstrate that the two ribosomal gene sets of the mung been and soy bean are arranged in inverted orientation within this repeated region. In contrast, the chickpea chloroplast DNA posesses a single ribosomal RNA gene set in the circular molecule. In all three chloroplast DNAs examined, the genes encoding the chloroplast 23S and 16S ribosomal RNA genes are separated by a spacer region which ranges in size from 2.2 to 2.48 kbp.     

Cytochrome oxidase subunit III gene in Neurospora crassa mitochondria. Location and sequence

We have located and sequenced the gene for cytochrome oxidase subunit III (CoIII) in Neurospora crassa mitochondria. The CoIII gene is located downstream from the small rRNA gene within a cluster of tRNA genes and is coded by the same strand as the tRNA and the rRNA genes. Like the tRNA and the rRNA genes, the CoIII gene is also flanked by the GC-rich palindromic DNA sequences which are highly conserved in N. crassa mitochondria. The CoIII coding sequence predicts a protein 269 amino acids long including 8 tryptophan residues. All 8 tryptophan residues are coded for by UGA. This supports our previous conclusion based on the anticodon sequence of N. crassa mitochondrial tryptophan tRNA and provides evidence for the notion that use of UGA as a codon for tryptophan rather than chain termination may be a feature common to most mitochondrial protein synthesis systems. The close correspondence between the amino acid composition of N. crassa CoIII and that of the protein predicted by the CoIII gene sequence suggests that unlike in mammalian mitochondria, AUA is a codon for isoleucine and not for methionine in N. crassa mitochondria. The N. crassa CoIII sequence shows strong homologies to the corresponding yeast and human proteins (53 and 47%, respectively). The overall hydrophobic character of the protein is consistent with suggestions that most of CoIII is embedded in the mitochondrial inner membrane.     

Studies on energy status and mitochondrial respiration during growth and senescence of mung bean cotyledons

Several characteristics of mitochondrial respiration and energy status have been studied during growth and senescence of mung bean ( Phaseolus radiatus L.) cotyledons. The results showed that mitochondrial oxygen consumption, respiratory control, ADP:O ratios, and energy charge changed in the cotyledons during germination and growth of the seedlings. The respiration rate of intact cotyledons approximately reflected the trend of the oxidative activities of the isolated mitochondria. An increase was observed in both whole cotyledon respiration and mitochondrial oxygen uptake at the onset of senescence of mung bean cotyledons (day 3 after germination), which thereafter declined gradually. The capacity and activity of the alternative pathway increased markedly in mitochondria isolated from senescent cotyledons. After the onset of senescence, the mung bean cotyledon mitochondria exhibited a decrease both in the respiratory control ratios and ADP:O ratios, and the cotyledons exhibited a gradual decline in energy charge. All these results showed an irreversible deterioration of energy conservation in mung bean cotyledons. The role(s) of the alternative pathway in senescent mung bean cotyledons is discussed.     

The chloroplast genomes of azuki bean and its close relatives: a deletion mutation found in weed azuki bean

A physical map of the azuki bean (Vigna angularis cv. Erimo-shozu) chloroplast DNA (cpDNA) was constructed by localising the cleavage sites of PstI, SalI, SmaI, SacI, KpnI, PvuII and XhoI. The resulting map is more similar to the cpDNA-maps of two Vigna species (mung bean, V. radiata, and V. nakashimae) than to common bean (Phaseolus vulgaris) cpDNA map. Azuki bean was originally classified in the genus Phaseolus, and the inclusion of this taxon in the genus Vigna is a recent taxonomic decision. Our result is thus in favour of the taxonomic placement of azuki bean in the same genus as V. nakashimae and mung bean. We also found that a weed-form accession of azuki bean has a 96-bp deletion relative to the cultivar Erimo-shozu. The 96-bp deletion is located between the trnS-UGA and psbC genes in the large single-copy region of the chloroplast genome. This deletion is flanked by imperfect 9-bp direct repeats, suggesting that the deletion was a result of intra-molecular recombination mediated by these direct repeats.     

Adenosine triphosphatase of bean plastids: its properties and site of formation

Extracts of bean (Phaseolus vulgaris L.) etioplasts and chloroplasts contain a dithiothreitol-activated Ca²⁺-dependent adenosine triphosphatase which is inhibited by Dio-9. The chloroplast and etioplast enzymes have identical R_F values upon disc gel electrophoresis. Optimum extraction of the enzyme from either plastid preparation is accomplished with 1 mm ethylenediamine tetraacetic acid. Photophosphorylation capacity can be partially restored to depleted chloroplast preparations by addition of either the chloroplast or etioplast extract. These results suggest that the adenosine triphosphatase from etioplasts and chloroplasts represents a modified coupling factor for photophosphorylation.     

Identification and characterization of receptors for protein import into chloroplasts and mitochondria

An anti-idiotypic antibody approach was used to identify chloroplast and mitochondrial protein component(s) which interact with the corresponding signal sequence. The proteins thus identified can be operationally defined as receptor(s) for import of proteins into chloroplasts and mitochondria. The import receptor(s) was found in "contact sites" between the outer and inner membrane of chloroplast envelope or of mitochondria.     

Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus

Gene transfer events from organelle genomes (mitochondria and chloroplasts in plants) to the nuclear genome are important processes in the evolution of the eukaryotic cell. It is highly likely that the gene transfer event is still an ongoing process in higher plant mitochondria and chloroplasts. The number and order of genes encoded in the chloroplast genome of higher plants are highly conserved. Recently, several exceptional cases of gene loss from the chloroplast genome have been discovered as the number of complete chloroplast genome sequences has increased. The Populus chloroplast genome has lost the rpl32 gene, while the corresponding the chloroplast rpl32 (cp rpl32) gene has been identified in the nuclear genome. Nuclear genes transferred from the chloroplast genome need to gain a sequence that encodes a transit peptide. Here, we revealed that the nuclear cp rpl32 gene has acquired the exon sequence, which is highly homologous to a transit peptide derived from the chloroplast Cu-Zn superoxide dismutase (cp sod-1) gene. The cp rpl32 gene has acquired the sequence that encodes not only for the transit peptide, but also for the conserved N-terminal portion of the mature SOD protein from the cp sod-1 gene, suggesting the occurrence of DNA sequence duplication. Unlike cp SOD-1, cp RPL32 did not show biased localization in the chloroplasts. This difference may be caused by mutations accumulated in the sequence of the SOD domain on the cp rpl32 gene. We provide new insight into the fate of the inherent sequence derived from a transit peptide.     

The nucleotide sequences of the initiator transfer RNAs from bean cytoplasm and chloroplasts

The initiator tRNAsMet from the cytoplasm and chloroplasts of Phaseolus vulgaris have been purified and sequenced. The sequence of bean cytoplasmic initiator tRNAiMet is : pA-U-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-C-G-G-A-A-G-C-G-U-m2G-G-U-G-G-G2-C-C-C-A-U-t6A-A-C-C-C-A-C-A-G-m7G-D-m5C-C-C-A-G-G-A-psi-C-G-m1A-A-A-C-C-U-Gm-G-C-U-C-U-G-A-U-A-C-C-AOH. The sequence of bean cytoplasmic tRNAiMet is almost identical to that of wheat germ and shows a high degree of homology with other cytoplasmic initiator tRNAs. The sequence of bean chloroplast initiator tRNAfMet is : pC-G-C-G-G-A-G-U-A-G-A-G-C-A-A-C-U-U-Gm-G-D-A-G-C-U-C-G-C-A-A-G-G-C-U-C-A-U-A-A-C-C-U-U-G-A-A-m7G-acp3U-U-A-C-G-G-G-T-psi-C-A-A-A-U-C-C-C-G-U-C-U-C-C-G-C-A-A- C-C-AOH. Bean chloroplast initiator tRNAfMet sequence shows procaryotic characteristics at the 5' end of the acceptor stem and in the TpsiC loop, but also contains some distinctive features.     

Effect of light on the formation of multiple molecular forms of glutamine synthetase in plants

Summary The presence of multiple molecular forms (MMF) of glutamine synthetase (GS) has been studied in pumpkin plants and in cotyledons of bean plants. Two MMF of GS have been found in pumpkin leaves and in green cotyledons: chloroplast GS and cytosol GS. Cotyledons of etiolated pumpkin seedlings contain only the cytosol GS. Illumination of etiolated pumpkin seedlings with white light results in the appearance, within one minute, of the second molecular form, the chloroplast GS, which appears to be due to activation rather than de novo synthesis of the enzyme. Cotyledons of resting seeds of horse bean, pea, soybean and lupine contain only one form of GS. The second form, chloroplast GS, appears after germination in the light, but only in those cotyledons of soybean and lupine that can become green.     

Subunit studies of coupling factor 1 of bean chloroplasts.

A bean chloroplast coupling factor (CF1) with latent Ca2+-dependent ATPase activity was studied. Immunodiffusion of bean (Phaseolus vulgaris) chloroplast and etioplast coupling factors and spinach coupling factor against antiserum to spinach coupling factor showed partial identity of the bean coupling factor with that of spinach. An immunoelectrophoretic comparison, under dissociating conditions, of bean leaf extracts and spinach extracts containing CF1 subunits (as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis) gave identical results for both extracts. At least six distinct polypeptide species were found. The major species had molecular weights of 42 000, 59 000 and 63 000 daltons. Amino acid analysis of electrophoretically purified bean CF1 gave results similar to those published for spinach CF1.     

Nucleotide sequences of three soybean chloroplast tRNAsLeu and re-examination of bean chloroplast tRNA2Leu sequence.

The nucleotide sequences of soybean chloroplast tRNAsLeu were determined using post-labeling techniques. Comparison of the primary structures of soybean chloroplast tRNAsLeu with their bean, maize and spinach counterparts only show few base differences. Contrary to previously published results (1) a re-examination of bean tRNALeu sequence shows that this tRNA resembles soybean and maize tRNA2Leu in structure.     

Regulatory aspects of chloroplast growth in leaves ofXanthium pensylvanicum and etiolated red kidney bean seedling leaves

Summary The average chloroplast size was studied as a function of leaf growth in leaves of cocklebur (Xanthium, pensylvanicum) and the primary leaves of 9-day old seedlings of red kidney bean (Phaseolus vulgaris).Diameters of chloroplasts were measured in crude tissue homogenates with the aid of a fluorescence microscope. Chlorophyll content of the leaves was determined spectrophotometrically in acetone extracts.For cocklebur, data are presented to show the relationship of average chloroplast diameter to morphological age of leaves (Leaf Plastochron Index) and are discussed in relation to the available leaf growth analyses. In bean, the increase in chloroplast diameter in response to illumination of etiolated leaves of various size was studied as a function of the duration of continuous illumination. The size of the etiolated bean leaves was varied experimentally by exposing the seedlings in darkness to low energy red light. Average diameter of the chloroplasts was found to be related to the size of leaf lamina.In both cocklebur and bean, a definite relationship of chloroplast size to leaf area and morphological age was established. The observed patterns of chloroplast size increase are interpreted to be a reflection of the integration of growth at three levels of organization: the leaf, its cells and the chloroplasts.This study was performed during the tenure of a U. S. Public Health Service postdoctoral fellowship by the senior author and was supported in part by research grant number GM-08145, from the National Institutes of Health, Public Health Service.Predoctoral fellow of the National Science Foundation.     

Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal

Organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. Even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. Gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. Gene loss is an ongoing process in the mitochondria and chloroplasts of higher plants. The gene for ribosomal protein S16 (rps16) is encoded in the chloroplast genome of most higher plants but not in Medicago truncatula and Populus alba. Here, we show that these 2 species have compensated for loss of the rps16 from the chloroplast genome by having a mitochondrial rps16 that can target the chloroplasts as well as mitochondria. Furthermore, in Arabidopsis thaliana, Lycopersicon esculentum, and Oryza sativa, whose chloroplast genomes encode the rps16, we show that the product of the mitochondrial rps16 has dual targeting ability. These results suggest that the dual targeting of RPS16 to the mitochondria and chloroplasts emerged before the divergence of monocots and dicots (140-150 MYA). The gene substitution of the chloroplast rps16 by the nuclear-encoded rps16 in higher plants is the first report about ongoing gene substitution by dual targeting and provides evidence for an intermediate stage in the formation of this heterogeneous organelle.     

Studies on chloroplast division in young leaf tissues of some higher plants

Summary The process of chloroplast division in young leaves of four species (bean, spinach, wheat, and maize) was investigated by light and electron microscopy. Two types of division, i.e., by fission, and by partition were observed.Chloroplast division by fission prevailed in the plant species examined, as shown by the relative abundance of dumbbell-shaped plastids, the characteristic stage in this type of division. Electron dense material, most commonly in the shape of a ring structure in the isthmus of the dividing plastid, was nearly always present in wheat and maize. Similar, but less distinct structures were usually observed in the neck region of constricted bean and spinach chloroplasts.Chloroplast division by partition was found in young leaf tissues of bean and spinach, but was not observed in wheat and maize. The main indication of this type of division is a centripetal invagination of the inner limiting membrane of the plastid envelope which progressively divides the chloroplast stroma into two, nearly equal, parts. Specific membraneous structures resembling myelin figures were usually found close to a dividing chloroplast and may participate in chloroplastokinesis.     

Effect of 4-Amino-3,5,6-trichloropicolinic acid on Protein Synthesis

The effects of 4-amino-3,5,6-trichloropicolinic acid (picloram) on protein synthesis in bean (Phaseolus vulgaris L. cv. ‘Astro’) hypocotyl and hook tissues were studied. Picloram (10^-4M) was shown to have a stimulatory effect on ¹⁴C-1-DL-leucine uptake in hook but not hypocotyl tissues. Maximum leucine incorporation and maximum total protein concentration occurred in hook tissues treated with 10^-4M picloram. Inhibition of protein synthesis with cycloheximide (CH) and erythromycin (ERY) indicates that endogenous and picloram-stimulated protein synthesis is a function of the 80S cytoplasmic ribosomes rather than 70S chloroplast or mitochondria ribosomes.     

Yeast mitochondrial methionine initiator tRNA: characterization and nucleotide sequence.

Two methionine tRNAs from yeast mitochondria have been purified. The mitochondrial initiator tRNA has been identified by formylation using a mitochondrial enzyme extract. E. coli transformylase however, does not formylate the yeast mitochondrial initiator tRNA. The sequence was determined using both 32P-in vivo labeled and 32P-end labeled mt tRNAf(Met). This tRNA, unlike N. crassa mitochondrial tRNAf(Met), has two structural features typical of procaryotic initiator tRNAs: (i) it lacks a Watson-Crick base-pair at the end of the acceptor stem and (ii) has a T-psi-C-A sequence in loop IV. However, both yeast and N. crassa mitochondrial initiator tRNAs have a U11:A24 base-pair in the D-stem unlike procaryotic initiator tRNAs which have A11:U24. Interestingly, both mitochondrial initiator tRNAs, as well as bean chloroplast tRNAf(Met), have only two G:C pairs next to the anticodon loop, unlike any other initiator tRNA whatever its origin. In terms of overall sequence homology, yeast mitochondrial tRNA(Met)f differs from both procaryotic or eucaryotic initiator tRNAs, showing the highest homology with N. crassa mitochondrial initiator tRNA.