Endonuclease recognition sites mapped on Zea mays chloroplast DNA

A detailed restriction endonuclease site map of theZea mays plastid genome

Fragments produced by partial digestion of plastid DNA fromZea mays withEco RI were cloned in Charon 4A. A circular, fine structure physical map of the plastid DNA was then constructed from restriction endonucleaseSal I,Pst I,Eco RI, andBam HI recognition site maps of cloned overlapping segments of the plastid genome. These fragments were assigned molecular weights by reference to size markers from both pBR322 and lambda phage DNA. Because of the detail and extent of the derived map, it has been possible to construct a coordinate system which has a unique zero point and within which all the restriction fragments and previously described structural features can be mapped. A computer program was constructed which will display in a circular fashion any of the above features using an X-Y plotter.

Transfer RNA genes ofZea mays chloroplast DNA

A minimum of 37 genes corresponding to tRNAs for 17 different amino acids have been localized on the restriction endonuclease cleavage site map of theZea mays chloroplast DNA molecule. Of these, 14 genes corresponding to tRNAs for 11 amino acids are located in the larger of the two single-copy regions which separate the two inverted copies of the repeat region. One tRNA gene is in the smaller single-copy region. Each copy of the large repeated sequence contains, in addition to the ribosomal RNA genes, 11 tRNA genes corresponding to tRNAs for 8 amino acids. The genes for tRNA2 (Ile) and tRNA(Ala) map in the ribosomal spacer sequence separating the 16S and 23S ribosomal RNA genes. The three isoaccepting species for the tRNAs(Leu) and the three for tRNAs(Ser), as well as the two isoaccepting species for tRNA(Asn), tRNA(Gly), tRNAs(Ile), tRNAs(Met), tRNAs(Thr), are shown to be encoded at different loci.Two independent methods have been used for the localization of tRNA genes on the physical map of the maize chloroplast DNA molecule: (a) cloned chloroplast DNA fragments were hybridized with radioactively-labelled total 4S RNAs, the hybridized RNAs were then eluted, and identified by two-dimensional polyacrylamide gel electrophoresis, and (b) individual tRNAs were(32)P-labelledin vitro and hybridized to DNA fragments generated by digestion of maize chloroplast DNA with various restriction endonucleases.

Plastid gene expression in a yellow-green leaf mutant of Petunia hybrida

We have analyzed the morphology and gene expression in plastids of a yellow-green leaf mutant of Petunia hybrida (E 5059). Under normal light intensities (20,000 lx), yellow-green leaves develop with a typical proplastid morphology (few membranes, incomplete stacking). When such plants are grown under low light intensities (3,000 lx), the newly formed leaves are green. The plastids in these green leaves have a wild-type like chloroplast morphology (thylakoids and grana structure). Pre-existing green leaves remain green in 20,000 lx, indicating that chlorophyll is not degraded. An analysis of polypeptides synthesized in isolated plastids from the yellow-green and green leaves of this mutant plant shows several differences. In the yellow-green leaf plastids only a very small amount of the large subunit of ribulose-1,5-bisphosphate carboxylase (RuBPCase) is present, while in green plastids this polypeptide is present in much higher amounts. Hybridization experiments indicated that in plastids from the yellow-green leaves the mRNA coding for the large subunit polypeptide is present in much lower amounts than in plastids from the 3,000 lx green leaves of this mutant or in chloroplasts from wild type plants. These results indicate regulation at the mRNA level. Furthermore, in yellow-green leaf plastids eleven polypeptides are present with high molecular wieght (higher than 67,000 d). Five of them are synthesized by the yellow-green leaf plastid itself. Such high molecular weight polypeptides are also synthesized by proplastids isolated from white petunia cell suspension cultures, but are not synthesized by 3,000 lx green leaf plastids, or by isolated normal leaf chloroplasts. These results indicate that the synthesis of these polypeptides is specific for the proplastid stage of chloroplast biogenesis.

Chloroplast DNA and cytoplasmic male-sterility

This paper deals with the relationship of chloroplast DNA (ctDNA) and cytoplasmic malesterility (CMS) of maize, wheat and rape. Intramolecular heterogeneity and fragment patterns of DNA digested with restriction endonucleases were compared and analyzed. For this purpose methods of agarose gel electrophoresis and two dimensional gel electrophoresis with denaturating solvent concentration gradients were applied. 1) Heat denaturation of ctDNA from a male sterile line in maize yielded a profile with three melting regions. This base sequence heterogeneity was not observed for the ctDNA of its maintainer. 2) Maize ctDNA was digested with EcoR1 and BamH1 restriction endonucleases, wheat and rape ctDNA with EcoR1 only. No significant differences were observed in the comparison of the fragment patterns from the sterile lines and their maintainers with the exception of the sterile line in rape which lacked one fragment present in its maintainer. 3) Two dimensional electrophoresis using a gradient of denaturing agents revealed several differences in number and relative positions of the separated restriction endonuclease fragments between the sterile lines and their respective maintainers in all three tested crops. This raises the possibility that changes in ctDNA may be involved in CMS.

Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common

A 12-kilobase DNA sequence has been identified in the maize mitochondrial genome which is homologous to part of the inverted repeat of the maize chloroplast genome. In chloroplasts the sequence contains a 16S rRNA gene, and also the coding sequences for tRNAIle and tRNAVal. Mitochondrial DNA from the male-sterile cytoplasms of maize is altered in this region.

The maize chloroplast genes for the beta and epsilon subunits of the photosynthetic coupling factor CF1 are fused

We have cloned and sequenced the maize chloroplast genome fragment Eco RI e which contains the 2.2 kb transcript previously reported (Link, G. and Bogorad, L. (1980) Proc. Nat. Acad. Sci. 77 6821-6825) to lie next to the maize gene for the large subunit of ribulose bisphosphate carboxylase (LS) and to be transcribed divergently. Immunochemical and sequencing data show that the gene codes for the beta subunit of the maize chloroplast coupling factor complex (CF1). The derived amino acid sequence is highly homologous to that of the corresponding E. coli protein (Saraste et al. (1981) Nucleic Acids Res. 9 5287-5296). The last base of the codon for the terminal lysine residue of the beta subunit of CF1 is the first base of the codon for the initiating methionine of an open reading frame whose derived amino acid composition and size closely match that reported for the epsilon subunit (Binder et al. (1978) J. Biol. Chem. 253 3094-3100). The close coupling of the two genes may serve to in sure their stoichiometric production.

Organization of the mitochondrial ribosomal RNA genes of maize

The organisation of the mitochondrial ribosomal RNA genes in maize is described. Each of the rRNAs is encoded by a single gene. The 5S and 18S rRNA genes are close together, and separated from the 26S rRNA gene by 16 kb of DNA. There is no evidence of heterogeneity in this gene arrangement.

The anticodon of the maize chloroplast gene for tRNA Leu UAA is split by a large intron

The maize chloroplast gene encoding tRNA Leu UAA has been sequenced. It contains a 458 base pair intron between the first and second bases of the anticodon. The tRNA is 88 nucleotides long (the 3'-terminal CCA sequence included which, however, is not encoded by the gene) and differs in only four nucleotides (modified nucleotides are not considered) from the corresponding isoacceptor from bean chloroplasts. The unusual position of the intron in this maize chloroplast tRNA gene suggests a splicing model different from that generally accepted for eukaryotic split tRNA genes.

A design for computer nucleic-acid-sequence storage, retrieval, and manipulation

We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base ("the library") and software that manages and provides access to that data base ("the Librarian").

Extranuclear DNA of a Marine Chromophytic Alga : RESTRICTION ENDONUCLEASE ANALYSIS

Two extranuclear DNA species have been isolated from the marine alga Olisthodiscus luteus. Rapid lysis of cells followed by the immediate addition of CsCl to the lysate was critical to the preservation of these satellite DNA species. Restriction endonuclease analysis demonstrates a molecular weight of 99 x 10(6) for chloroplast DNA and 23 x 10(6) for a second satellite species. The origin of the second satellite is not known. However, this smaller satellite DNA which originates from a nonnuclear, DNAse insensitive cellular component, displays no sequence homology with ctDNA by hybridization experiments. Constancy of restriction endonuclease fragment patterns of chloroplast and second satellite species during all phases of the growth cycle, whether cultures were maintained synchronously or asynchronously, was demonstrated.

Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativa

A rapid and simple method for constructing restriction maps of large DNAs (100-200 kb) is presented. The utility of this method is illustrated by mapping the Sal I, Sac I, and Hpa I sites of the 152 kb Atriplex triangularis chloroplast genome, and the Sal I and Pvu II sites of the 155 kb Cucumis sativa chloroplast genome. These two chloroplast DNAs are very similar in organization; both feature the near-universal chloroplast DNA inverted repeat sequence of 22-25 kb. The positions of four different genes have been localized on these chloroplast DNAs. In both genomes the 16S and 23S ribosomal RNAs are encoded by duplicate genes situated at one end of the inverted repeat, while genes for the large subunit of ribulose-1,5-bisphosphate carboxylase and a 32 kilodalton photosystem II polypeptide are separated by 55 kb of DNA within the large single copy region. The physical and genetic organization of these DNAs is compared to that of spinach chloroplast DNA.

Nicotiana chloroplast genome III. Chloroplast DNA evolution

Nicotiana chloroplast genomes exhibit a high degree of diversity and a general similarity as revealed by restriction enzyme analysis. This property can be measured accurately by restriction enzymes which generate over 20 fragments. However, the restriction enzymes which generate a small number (about 10) of fragments are extremely useful not only in constructing the restriction maps but also in establishing the sequence of ct-DNA evolution. By using a single enzyme, Sma I, a elimination and sequential gain of its recognition sites during the course of ct-DNA evolution is clearly demonstrated. Thus, a sequence of ct-DNA evolution for many Nicotiana species is formulated. The observed changes are all clustered in one region to form a "hot spot" in the circular molecule of ct-DNA. The mechanisms involved for such alterations are mostly point mutations but inversion and deficiency are also indicated. Since there is a close correlation between the ct-DNA evolution and speciation in Nicotiana a high degree of cooperation and coordination betwen organellar and nuclear genomes is evident.

Conservation of sequence arrangement among higher plant chloroplast DNAs: molecular cross hybridization among the Solanaceae and between Nicotiana and Spinacia

Isolated, nick-translated Pvu II fragments of Nicotiana tabacum chloroplast DNA produce specific intra- and intergeneric hybridization signals with chloroplast DNA digests from several representatives of the Solanaceae. These data, along with similarities in restriction enzyme patterns, permit construction of physical maps for Nicotiana line 92 (a cytoplasmic substitution line), Atropa belladonna and Petunia parodii. Plastid-DNA map differences among the Solanaceae are shown to result from single base-pair substitutions as well as local deletions or insertions. Several of these differences of Nicotiana tabacum chloroplast DNA fragments to a chloroplast DNA digest of Spinacia oleracea defines a sequential arrangement of fragments for spinach DNA which is very similar to its published physical map. This is achieved although chloroplast-DNA restriction enzyme patterns from the two organisms are grossly dissimilar. Alignment differences which have been revealed involve the edges of the inverted repeat region where certain single copy stretches in tobacco have been duplicated in spinach.

Isolation, characterization and restriction endonuclease mapping of the Petunia hybrida chloroplast DNA

A procedure is developed for the isolation of intact chloroplast DNA (ctDNA) from Petunia hybrida. The molecular weight, calculated from contour length measurements, is 96.0 +/- 4.5 x 10(6) daltons. This value is in good agreement with the value of 101.2 x 10(6) daltons that was estimated from the electrophoretic mobilities of restriction endonuclease fragments of ctDNA. Analysis of petunia ctDNA in neutral CsCl gradients revealed the presence of only one type of DNA at a buoyant density of 1.6987 +/- 0.0005 gcm-3. This corresponds with a GC-content of 39.3 +/- 0.5%. A physical map of petunia ctDNA was constructed by using the restriction endonucleases Sal I, Bgl I, Hpa I and Kpn I. The map indicates that petunia ctDNA contains two copies of a sequence in an inverted orientation. The inverted repeat regions have a minimum length of 10 x 10(6) daltons. Hybridization data indicate that part of the inverted repeat regions contain the genes for chloroplast ribosomal RNAs.

Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes

Examples of both the 410 and 500 bp size classes of repeating units containing wheat 5S rRNA genes have been cloned in plasmid pBR322 and sequenced. The structural genes showed sequence microheterogeneity. Also the gene in the 500 bp repeat which was sequenced had a 15 bp tandem duplication within it and appears to be representative of non-transcribed subfamily of repeating units. The transcription terminators comprise 14-17 A.T bp immediately preceded by a region of weak dyad symmetry. The spacer regions adjacent to the transcription terminators in the two different size repeat units have interspersed oligonucleotides of high and low homology. The central spacer regions of the two size classes have very different sequences. The only repeated sequence in the spacers has undergone extensive divergence. In contrast to most of the spacer, the 70 bp region preceding the genes of each type of repeat show high homology, suggesting that it has functional importance. The transcription start point obeys the pyrimidine-1 purine+1 rule.

Mapping of rRNA genes in an inverted repeat in Nicotiana tabacum chloroplast DNA

Nicotiana tabacum chloroplast DNA contains two copies each of 16S and 23S rRNA genes. These genes are located in an inverted order as determined from restriction fragment mapping and Southern hybridization to restriction fragments. The position of these genes on the N. tabacum chloroplast DNA molecule has been established relative to a complete map of SalI and SMaI restriction enzyme cleavage sites.

A rapid, single leaf assay for detecting the presence of 'S'-male-sterile cytoplasm in maize

A simple, rapid, and reproducible assay is described for determining unambiguously the presence of S-type cytoplasm in male-sterile and male-fertile (restored) maize lines. Because the assay requires only 0.5 g leaf segment per sample, it is a single plant assay and the plant is not destroyed. Plants at any developmental stage can be used. The assay involves a 30 sec homogenization, 20 min centrifugation, one hour lysis, overnight agarose electrophoresis, 30 min gel staining, and photography of the gel to produce a result in much less than 24 hr. Many samples can be assayed simultaneously. The various assay methods available for classifying maize cytoplasms are compared and discussed.

Chloroplast DNA from three archegoniates

1. DNA from female and male Sphaerocarpos donnellii (liverwort) plants exhibits at least two species with buoyant densities of 1.703 (main band) and 1.691 (satellite) g cm(-3) in CsCl equilibrium gradients. At least part, if not all, of the satellite DNA is localized in plastids. It consists of up to 90% of uniformly sized circular molecules of an average circumference of 38.5 μm. Compared to other Chlorophyta, the liverwort's cpDNA is unusually low both in diensity and contour length. - 2. On the hand, cpDNA from the ferns Asplenium nidus and Pteris vittata resembles those of higher plants in buoyant density (1.697 g cm(-3)) and circumference (about 44.8 μm). - 3. Analysis of DNA from the archegoniate chloroplasts with restriction endonucleases indicates chat the cyclic molecules are monomers. - 4. The results show that the circular molecules found in cpDNA of higher plants do not represent the functionally required minimum size of DNA in plastids.

The presence of DNA in ribosome-deficient plastids of heat-bleached rye leaves

In leaves of rye seedlings (Secale cereale L.) grown at 32 degrees C the formation of plastid (70-S) ribosomes is specifically prevented. The resulting plastid-ribosome-deficient leaves can be used as a suitable system to identify chloroplast proteins which are translation products of cytosolic (80-S) ribosomes. The ribosome deficiency in plastids is accompanied by a bleaching of the leaves in light. In experiments aimed at finding the primary heat-sensitive event leading to ribosome deficiency the DNA of rye chloroplasts has been identified. Its properties are similar to those of chloroplast DNAs from other higher plants. The ribosome-deficient plastids isolated from heat-bleached rye leaves contained a DNA species which was indistinguishable from that of chloroplasts with regard to buoyant density in CsCl equilibrium gradients, reassociation properties and fragment patterns obtained upon cleavage by restriction endonucleases. Its quantity was comparable to that of chloroplast DNA of green leaves grown at a permissive temperature (22 degrees C). These results suggest that, unlike the effect in heat-bleached Euglena strains, lack of chloroplast DNA cannot be considered as the reason for the primary effect of high temperature in rye leaves but steps in the biosynthetic pathway of plastid ribosomes themselves must be affected more directly.

Cloning and characterization of ribosomal RNA genes from wheat and barley

Wheat and barley DNA enriched for ribosomal RNA genes was isolated from actinomycin D-CsCl gradients and used to clone the ribosomal repeating units in the plasmid pAC184. All five chimeric plasmids isolated which contained wheat rDNA and eleven of the thirteen which had barley rDNA were stable and included full length ribosomal repeating units. Physical maps of all length variants cloned have been constructed using the restriction endonucleases Eco Rl, Bam Hl, Bgl II, Hind III and Sal I. Length variation in the repeat units was attributed to differences in the spacer regions. Comparison of Hae III and Hpa II digestion of cereal rDNAs and the cloned repeats suggests that most methylated cytosines in natural rDNA are in -CpG-. Incomplete methylation occurs at specific Bam Hl sites in barley DNA. Detectable quantities of ribosomal spacer sequences are not present at any genomic locations other than those of the ribosomal RNA gene repeats.

Directive segregation in the basis of colE1 plasmid incompatibility

Incompatibility between colE1 plasmids in Escherichia coli can be explained by competition for a limited number of replication sites. These sites ensure directive segregation of plasmids to daughter cells on cell division. The number of sites can be more than one only if a linear segregation mechanism is postulated.

The synthesis of chloroplast high-molecular-weight ribosomal ribonucleic acid in spinach

Illuminated suspensions of chloroplasts isolated from young spinach leaves show incorporation of [3H]uridine into several species of RNA. One such RNA species of Mr 2.7 x 10(6) shows sequence homology with both the chloroplast 23-S rRNA (Mr = 1.05 x 10(6)) and 16-S rRNA (Mr = 0.56 x 10(6)), as judged by DNA/RNA competition hybridization. Leaves labelled in vivo with [32P]orthophosphate in the presence of chloramphenicol accumulate labelled RNAs of Mr 1.28 x 10(6), 0.71/0.75 x 10(6) and 0.47 x 10(6). The 1.28 x 10(6)-Mr RNA shows 80.5% sequence homology with the 1.05 x 10(6)-Mr rRNA and the 0.71/0.75 x 10(6)-Mr RNA mixture shows 76% sequence homology with the 0.56 x 10(6)-Mr rRNA. We conclude that the pathway of rRNA maturation in spinach chloroplasts is similar to that of Escherichia coli.

Mapping of the ribosomal RNA genes on spinach chloroplast DNA

Spinach chloroplast ribosomal RNAs have been hybridized to restriction endonuclease fragments of spinach chloroplast DNA. All three RNA species (23S, 16S and 5S) hybridized to a single large fragment when the DNA was digested with either Sall or Pstl. Hybridization of 23S RNA to fragments produced by Smal yielded two radioactive bands which corresponded to the bi-molar 2.5 X 10(6) and 1.15 X 10(6) Mr fragments. 16S RNA also hybridized to two, bi-molar Smal fragments (3.4 X 10(6) and 2.5 X 10(6) Mr) and 5S RNA hybridized to the 1.15 X 10(6) Mr bi-molar Smal fragment. The 23S RNA and 16S RNA cistrons were each also shown to contain a single EcoRI site. From the data it was possible to conclude that the ribosomal RNA genes are located on the inverted repeat region of the spinach chloroplast DNA restriction map [1,2], that the sequence of the cistrons is 16S - 23S - 5S and that the size of the spacer between the 16S and 23S RNA cistrons is approximately 0.90 X 10(6) Mr.

Plant Genetics: Increasing Crop Yield

Cell cultures of crop plants provide new opportunities to recover induced mutations likely to increase crop yield. Approaches include regulating respiration to conserve carbon fixed by photosynthesis, and increasing the nutritive value of seed protein. They depend on devising selecting conditions which only desired mutant cells can survive. Protoplast fusion offers some promise of tapping sources of genetic variation now unavailable because of sterility barriers between species and genera. Difficulties in regenerating cell lines from protoplasts, and plants from cells, still hamper progress but are becoming less severe. Recombinant DNA techniques may allow detection and selection of bacterial cell lines carrying specific DNA sequences. Isolation and amplification of crop plant genes could then lead to ways of transforming plants that will be useful to breeders.

Recombinant plasmid that carries part of the nitrogen fixation (nif) gene cluster of Klebsiella pneumoniae

We have cloned fragments of the Klebsiella pneumoniae genome that carry part of the his operon and part of the nitrogen fixation (nif) gene cluster on the amplifiable plasmid pMB9. One particular plasmid, pCRA37, complements mutations in the hisD, nifB, and nifF loci. The physical map of pCRA37 as determined by restriction enzyme analysis correlates with the genetic map of the his-nif region as determined previously by phage P1-mediated cotransductional analysis.