Ribosomal RNA cistrons in Euglena gracilis

Euglena gracilis chloroplasts contain about 12 fg DNA of average density 1.686 g cm^?3 and 1.7 pg RNA. The large (1.1 × 10⁶ mol. wt) and small (0.56 × 10⁶ mol. wt) ribosomal RNA components are coded for by separate cistrons, both of which band at a density of 1.696 g cm^?3 in a CsCl gradient. About 6% of the chloroplast DNA codes for rRNA indicating that there are 240 cistrons for rRNA in each chloroplast or about three to six cistrons per chloroplast genome. Similar studies with rRNA from cytoplasmic ribosomes indicate that the cistrons for cytoplasmic rRNA band at a density of 1.716 g cm^?3, denser than that of the main-band DNA, and that there are 1000 cistrons for cytoplasmic rRNA per cell. Fractionation of E. gracilis DNA on CsCl gradients and subsequent hybridization experiments, as well as melting curves of DNA-RNA hybrids, show that chloroplast rRNA does not anneal specifically with either the cistrons for cytoplasmic rRNA or any DNA in the dark-grown cell, in contrast to those results found in some higher plants.     

Ribosomal RNA cistrons in Allomyces arbuscula

Bulk and nuclear DNA have been fractionated by preparative neutral CsCl equilibrium density gradient centrifugation and each fraction hybridized to labeled rRNA (25 + 18 S). The cistrons coding for rRNA appeared on the light side of the main peak. Hybridization of the nuclear DNA fractionated by preparative Ag+-Cs2SO4 gradients at different pHs showed that the banding profile did not change as compared to the CsCl pattern. In Hg2+-Cs2SO4 gradients, however, the peak of the fRNA-DNA hybrids shifted on the heavier side of the profile. This indicates that the ribosomal RNA cistrons in Allomyces are A-T-rich. Hybridization with homologous rRNA showed that, at saturation, 3.25% of the DNA is complementary to rRNA. With the genome size of 1.7-10(10) daltons, the multiplicity of rRNA cistrons has been found to be close to 270.     

Analysis of the structure of DNA cistrons coding proteins with known sequences]

Proceeding from the amino acid sequence of a number of proteins, with the help of a special computer program we have determined the frequency of pyrimidine isopliths of different length, the degree of clustering and the degree of asymmetry of complementary chains of the corresponding DNA cistrons, as well as the range of variation of these parametres which depends on the code degeneracy. The degree of asymmetry of the chains of DNA cistrons (H/L), calculated for 255 proteins of a known composition, may vary from 0.7 to 1.8. For 90% of these proteins the mean Py/Pu ratio in the coding chain of DNA is above 1. The conclusion has been made that the majority of amino acids contained in the proteins is coded for by purine triplets. It was found that the distribution of pyrimidine isopliths between DNA cistrons coding for different proteins is other than random and has a "DNA-like" character. The degree of clustering of pyrimidines (beta) in cistrons of different proteins may vary from 6.0 to 14.3. The cistrons of some proteins were found to contain long lyrimidine fragments with about 24 residues. A positive correlation (r2 = 0.74) was found to exist between the degree of clustering of pyrimidines and the degree of asymmetry of the chains corresponding to different proteins of DNA cistrons.     

Further mapping of 5S RNA cistrons in Escherichia coli

Summary Fine mapping data for four 5S RNA cistrons in E. coli are presented.     

Use of disomic strains to study the arrangement of ribosomal cistrons in saccharomyces of ribosomal cistrons in Saccharomyces cerevisiae

Summary Disomic strains ofSaccharomyces cerevisiae were studied by DNA-rRNA hybridization to examine the arrangement of rRNA cistrons on yeast chromosomes as well as to identify a disomic strain which was enriched for rRNA cistrons. Four of the five disomic strains tested showed a per cent hybridization lower than wild type. Two of these strains were found to be disomic for more than one chromosome. A slight increase in the per cent hybridization was observed with DNA isolated from one disomic strain. It was concluded that some chromosomes inSaccharomyces cerevisiae had few if any rRNA cistrons suggesting that the rRNA cistrons are non randomly distributed over the genome. From DNA-tRNA hybridization experiments, evidence for the presence of tyrosine tRNA genes on chromosomes VI was obtained.     

Assembly of Bacillus subtilis phage phe29. 2. Mutants in the cistrons coding for the non-structural proteins.

The effect on phage morphogenesis of sus mutations in the cistrons coding for nonstructural proteins has been studied. Mutants in three cistrons analyzed that are involved in phage DNA synthesis, as well as in cistron 16 which codes for a late nonstructural protein, produce prolate capsids which are more rounded at the corners than complete phage heads and have an internal core; they contain the head proteins, the upper collar protein and protein p7, not present in mature phage particles. Mutants in cistron 7 do not produce capsids nor other phage-related structures; this result and the presence of p7 in phage capsids suggest an essential role in capsid assembly for this protein. The protein product of cistron 13 is probably needed for a stable DNA encapsulation since mutants in this cistron produce mainly DNA-free complete phage particles and only about 10% of uninfective DNA-containing complete phage. Cistron 15 codes for a late, partially dispensable, nonstructural protein which is present in the DNA-free capsids produced after infection with the delayed-lysis mutant sus14(1242), used as the wild-type control, or with mutants in cistrons 9, 11,12 and 13. Proteins p15 and p16 are probably involved in the encapsulation of viral DNA in a prohead.     

tra cistrons and proteins encoded by the Escherichia coli antibiotic resistance plasmid R6-5

Summary Hybrid plasmids obtained by cloning individual EcoRI and HindIII fragments of the conjugative plasmid, R6-5, were analyzed for their ability to complement transfer-deficient point mutations of Flac. As a result, the locations of 10 tra cistrons were defined on the physical map of R6-5. Two cistrons, traE and traG, are interrupted by EcoRI restriction sites and one cistron, traC, probably contains a HindIII restriction site. The origin of DNA transfer, oriT, was also localized. Surprisingly the hybrid plasmid carrying oriT is mobilized by the F factor as well as by R6-5. The surface exclusion cistrons, traS and traT, were mapped and their biological expression analyzed. A total of 18 proteins encoded by cistrons within the tra region were detected by SDS polyacrylamide gel electrophoresis of proteins synthesized in minicells; they represent about 53% of the coding capacity of the cloned DNA. R6-5 DNA fragments containing the cistrons traC, traE, and traT directed the synthesis of proteins which comigrated during SDS gel electrophoresis with the F-coded proteins previously characterized as TraCp, TraEp, and TraTp. A further two proteins encoded by R6-5 comigrated with F-encoded (but genetically unidentified) proteins whose cistrons map in the corresponding part of the tra region. In contrast, no R6-5 proteins corresponding to F proteins TraAp, TraDp, TraJp, TraMp, 6a or 6c were detected. These results are discussed in relation to known DNA sequence homologies between the F and R6-5 plasmids. A preliminary physical map of the tra region of R6-5 is presented and compared with that of F.     

Assembly of Bacillus subtilis phage phi29. 1. Mutants in the cistrons coding for the structural proteins.

The effect of mutations in the cistrons coding for the phage structural proteins has been studied by analyzing the phage-related structures accumulated after restrictive infection. Infection with susmutants in cistron 8, lacking both the major head and the fiber protein, does not produce any phage-related structure, suggesting a single route for the assembly of phage phi29; infection with ts mutants in this cistron produces isometric particles. Mutants is cistron 9, coding for the tail protein, TP1, produce DNA-free prolate heads with an internal core; these particles are abortive and contain the head proteins HPO, HP1 and HP3, the upper collar protein NP2 and the nonstructural proteins p7, p15 and p16. Mutants in cistron 10, coding for the upper collar protein, NP2, produce DNA-free isometric heads also with an internal core; they contain the head proteins and the nonstructural protein p7, suggesting that this protein forms the internal core. Mutants in cistrons 11 and 12, coding for the lower collar protein, NP3, and the neck appendages, NP1, respectively, give rise to the formation of DNA-containing normal capsids and DNA-free prolate particles, more rounded at the corners than the normal capsids and with an internal core; the DNA-containing 11-particles are formed by the head proteins and the upper collar protein; the DNA-free 11-particles contain, besides these proteins, the nonstructural protein p7 and a small amount of proteins p15 and 16. The DNA-containing 12-particles have all the normal phage structural proteins except the neck appendages, formed by protein NP1; the DNA-free particles are similar to the DNA-free 11-particles. After restricitive infection mutant sus14(1241) has a delayed lysis phenotype and produces a phage burst higher than normal, after artificial lysis. It produces DNA-containing particles, identical to wild-type phage, which have all the normal phage structural proteins, and DNA-free prolate particles, more rounded at the corners than the final phage particles and with an internal core; the last particles contain the same proteins as the DNA-free 11 or 12-particles. These particles could represent a prohead state, ready for DNA encapsulation. None of the DNA-containing particles have the nonstructural proteins p7, p15 or p16, suggesting that these proteins are released from the proheads upon DNA encapsulation.     

Chromosomal repatterning in crocodiles: C,G and N-banding and the in situ hybridization of 18S and 26S rRNA cistrons

The chromosomes of Crocodylus porosus, C. johnstoni and Caiman crocodilus have been analysed using C, G and N-banding techniques and the in situ hybridization of 18S+26S rRNA cistrons derived from Xenopus. It is clear that in addition to the gross structural changes (robertsonian rearrangements and pericentric inversions) which are known to distinguish these crocodiles, numerous other modes of repatterning have occurred. These involved both the heterochromatic and euchromatic portions of the genome. They appear to be associated with the gross structural changes which have been established, and involve two distinct forms of chromatin transformation.In addition, the in situ hybridization of 18S+26S rRNA cistrons onto these crocodilian chromosomes has localized the site of nucleolus organizer activity to the C-band positive G-band negative secondary constrictions present in all three species. The significance of these results is discussed.     

The ribosomal cistrons of the water mold Achlya bisexualis

Total DNA was extracted from vegatative mycelia of the water mold Achlya bisexualis. Fractionation of the DNA in CsCl gradients resulted in two components: a major component with a buoyant density of 1.697 g cm^?3 and a minor component with a density of 1.685 g cm^?3. The minor component has been identified as mitochondrial DNA based on extractions from isolated mitochondria and Triton X-100 washed nuclei. Detergent washing of the nuclei yielded DNA in which the mitochondrial DNA component was absent, while the isolated mitochondrial preparations contained DNA enriched in the 1.685 g cm^?3 component. Hybridization studies of A. bisexualis DNA to rRNA show that the ribosomal cistrons have a buoyant density coincident with that obtained with the nuclear DNA. In addition, preliminary evidence indicates that the mitochondrial DNA does not hybridize to the cytoplasmic RNA under the conditions used for this study. Ribosomal RNA hybridized to about 0.65% of the total DNA.     

Structural proteins associated with ribosomal cistrons in Xenopus laevis chromosomes

The N banding technique to define the location of nucleolus organiser in mammalian and marsupial chromosomes was applied to the Xenopus laevis chromosomes. Results obtained are: 1. The N bands coincide with the location of all the clustered ribosomal cistrons including the 18S + 28S RNA genes as well as the 5S RNA genes. 2. The N bands are consistently detected in both metabolically active (interphase) and metabolically inactive (metaphase) nuclei. 3. Cytochemical and chemical extraction tests indicate that the N bands show typical biochemical properties requested for non-histone (residual) chromosomal proteins. 4. Proteins associated with the 5S RNA genes differ, in their acid-solubility, from those for the 18S+28S RNA genes. 5. The N banding proteins comprise a small portion of a total nuclear protein. These findings strongly suggest the existence of ribosomal gene-specific non-histone proteins which probably represent the structural chromatin element rather than the primary gene product. The possible role of N banding proteins in eukaryotes is discussed.     

Under-replication of intron+ rDNA cistrons in polyploid nurse cell nuclei of Calliphora erythrocephala

We have examined the possibility that the intron-containing (intron⁺) rDNA cistrons of Dipteran flies are active in the germ-line derived polyploid nurse cell nuclei of the ovarian follicles. Using the organism, Calliphora erythrocephala, we describe here a procedure which yields very pure nurse cell nuclei and compare the intron-free (intron^–) and intron⁺ rDNA cistron contents of nurse cell nuclei prepared by this procedure to those of 2–18 h embryo nuclei and 3 day pupal nuclei. DNA from three preparations of each nuclear type was examined and the intron^– and intron⁺ cistron contents quantitated using a Southern transfer procedure. The number of intron^– and intron⁺ rDNA cistrons per haploid genome in the presumed diploid 2–18 h embryo DNA was first established, and then the intron^– and intron⁺ cistron contents of nurse cell nuclear DNA and 3 day pupal DNA were determined relative to these values.The intron^– cistron content of nurse cell nuclear DNA was indistinguishable from that of embryonic DNA but the intron⁺ cistrons showed an 8-fold under-replication relative to the presumed diploid DNA. A slight under-representation of the intron^– cistrons and 3-fold under-replication of the intron⁺ cistrons were demonstrated for 3 day pupal DNA. These findings strongly suggest that intron⁺ rDNA cistrons are non-functional in nurse cell nuclei and substantiate the generality of this implication for the whole organism during early pupal life.     

Localization of some 5s RNA cistrons on Escherichia coli chromosome

Summary 3 5S RNA cistrons, characterized by specific nucleotides sequences, are shown not to be linked.     

The ribosomal DNA of Calliphora erythrocephala: The cistron classes of total genomic DNA

The composition of the genome set of ribosomal DNA cistrons in Calliphora erythrocephala (a Dipteran fly) has been analyzed. In contrast to previously cloned fragments of the rDNA (see Beckingham & White, 1980), the great majority of the rDNA cistrons do not contain introns in the 28 S β coding region. In the strain of flies studied, however, most cistrons fall into two discrete length classes that are present in approximately equal amounts in the genome. These results from distinct size variants of the non-transcribed spacer in the cistron population.The major genome class of intron-containing (intron⁺) rDNA cistrons was found to constitute approximately 5% of all cistrons and to contain introns of 6·1 × 10³ base-pairs. Interestingly, the intron⁺ cistrons were shown to be clustered within the rDNA and to contain a different population of non-transcribed spacer/external transcribed spacer (NTS + ETS) regions to that seen amongst the intron^? cistrons. The implications of these findings in relation to the mechanisms that maintain homogeneity within tandemly repeated gene sets are discussed.Some evidence for the existence of intron sequence DNA outside the rDNA is presented.     

Distribution of nucleotide differences between two randomly chosen cistrons in a population of variable size

The distribution of the number of nucleotide differences between two randomly chosen cistrons in a finite population is studied here when the population size changes from generation to generation. When genetic variability is measured by heterozygosity (i.e., the probability that two cistrons are different), by the probability that two cistrons differ at two or more nucleotide sites, or by mean number of site differences between cistrons, it is seen that in a population going through a small bottleneck all of these measures decline rapidly but, as soon as population size becomes large, they start to increase owing to new mutations. The amount of reduction in these measures depends not only on the size of bottleneck but also on the rate of population growth. The implications of this study explaining the observed variations in the rates of amino acid substitutions during the evolutionary process are also discussed.     

On the constancy of the evolutionary rate of cistrons

Summary The variations of evolutionary rates in hemoglobins and cytochrome c among various lines of vertebrates are analysed by estimating the variance. The observed variances appear to be larger than expected purely by chance.If the amino acid substitutions in evolution are the result of random fixation of selectively neutral or nearly neutral mutations, the evolutionary rate of cistrons can be represented by the integral of the product of mutation rate and fixation probability in terms of selective values around the neutral point. This integral is called the effective neutral mutation rate.The influence of effective population number and generation time on the effective neutral mutation rate is discussed. It is concluded that the uniformity of the rate of amino acid substitutions over diverse lines is compatible with random fixation of neutral or very slightly deleterious mutations which have some chance of being selected against during the course of substitution. On the other hand, definitely advantageous mutations will introduce significant variation in the substitution rate among lines. Approximately 10% of the amino acid substitutions of average cistrons might be adaptive and create slight but significant variations in evolutionary rate among vertebrate lines, although the uniformity of evolutionary rate is still valid as a first approximation.Contribution No. 813 from the National Institute of Genetics, Mishima, Shizuokaken 411 Japan. Aided in part by a grant-in-aid from the Ministry of Education, Japan.     

Identification of cistrons involved in conjugal transfer of narrow-host-range R plasmid R91-5 of Pseudomonas aeruginosa.

The development of a transductional method for complementation tests between transfer-deficient mutants of the narrow-host-range R plasmic R91-5 of Pseudomonas aeruginosa has allowed the indentification of cistrons involved in the conjugal transfer of this plasmid. Complementation tests performed between transfer-deficient mutants characterized phenotypically with respect to sensitivity to donor-specific phage, ability to inhibit the replication of phage G101, and expression of entry-exclusion has identified a minimum of 10 transfer cistrons. Although most mutagen-induced mutants were relatively heterogeneous and appeared to be affected in a single cistron only, a high proportion of mutants isolated after selection for donor-specific phage resistance had deletions but always included tra Y. Mutants selected directly on the basis of transfer deficiency which also became donor-specific phage resistant fell into all 10 cistrons, suggesting that many R91-5 transfer cistrons are concerned with the synthesis of sex pili and other surface structures necessary for conjugal transfer. Conversely, most retaining donor-specific phage sensitivity belonged to one cistron, whereas transfer-deficient mutants which had also lost the ability to inhibit the replication of phage G101 comprised four cistrons.