Doublet frequencies in the DNA of genetic code limit organisms

Summary Unrelated organisms with DNA of extreme G + C content (25% or 70%) are found to share very specific patterns of nearest neighbour base doublet frequency in their DNAs. This is shown to be a result of restrictions on the extremity of amino acid composition in their proteins, combined with a maximisation of the use of one type of base pair in redundant codon positions. Inferences are made about the universal nature of the genetic code and the proportion of DNA used for specifying protein in different species. The composition of coding DNA strands in these organisms is also discussed.     

Doublet frequency analysis of bacterial DNAs

Summary Nearest neighbour base frequency analyses of the DNAs of fifteen bacteria and two blue-green algae are reported. When expressed in terms of deviations from random expectation, the frequencies can be placed in four distinct groups sharing similarities not dependent on the G + C contents of the DNAs. The majority of the groupings found are in agreement with those of conventional taxonomy but several interesting discrepancies are shown to exist, some of which confirm other recent molecular evidence. The frequencies for the algal DNAs closely resemble those of the largest group of bacteria. The results are considered in relation to possible evolutionary pressures on polypeptide-specifying DNA and inferences are made about the relative usage of alternative codons in different species.Member of the scientific staff of the Medical Research Council Virology Unit.     

Doublet frequencies in evolutionary distinct groups.

We analyze the dinucleotide frequencies of occurrence and preferences separately within the vertebrates, nonvertebrates, DNA viruses, mitochondria, RNA viruses, bacteria and phage sequences. Over half a million nucleotides from more than 400 sequences were used in this study. Distinct patterns are observed. Some of the patterns are common to all sequences, some to either eukaryotes or prokaryotes and others to the subgroups within them. Doublets are the most basic ingredient of order in nucleotide sequences. We suggest that their preferences and the arrangement of nucleotides in the DNA in general is determined to a large extent by the conformational and packaging considerations of the double helix. Some principles of DNA conformation are viewed in light of our results.     

Fluorescence cytometry of microtubules and nuclear DNA during cell-cycle and reverse-transformation.

Synchronized CHO-K1 cells and their dibutyryl c-AMP treated counterparts have been characterized by means of static and flow fluorescence cytometry at the level of nuclear DNA and cytoplasmic microtubules. In order to confirm earlier findings on synchronized population, Carnoy fixed and hydrolyzed, several new findings are here reported at the level of single intact cell. The fluorescence intensity of DAPI-stained glutaraldehyde fixed 2C cells correlates well with the average absorbance of the corresponding Feulgen-stained cells, thereby appearing also to be a measure of chromatin condensation during the G1 phase. In the early part of G1, the drastic alteration in anti-beta tubulin immunostaining is shown to parallel microtubule depolymerization induced by calcium or colcemide. The known 1-2 h lengthening of the G1 period after reverse-transformation appears to correlate with a similar delay in the abrupt chromatin decondensation. The above results are discussed in terms of the role of microtubules and nuclear morphometry (and their coupling) in the control of cell cycle progression of transformed vs. fibroblast-like cells.     

Unscheduled DNA synthesis in diploid yeast after X-irradiation in diffent phases of the cell-cycle.

The uptake of radioactive 5'-dTMP into the DNA of diploid yeast cells was measured in the G1 and S-phase of the cell-cycle. In control cells, the uptake is zero in G1 and increases with time in the S-phase. Cells irradiated in early G1 show an uptake (unscheduled DNA synthesis) which is higher than if irradiation is performed later in G1. An analysis which takes into consideration the incomplete synchronization of the cell population shows that, at the end of G1, no uptake would be present in an ideally-synchronous population. At the end of G1 the shoulder in the dose-effect curve for cell survival also disappears. This provides additional evidence that the shoulder in a dose-effect curve might be due to repair reactions in living cells.     

Doublet frequencies and codon weighting in the DNA ofEscherichia coli and its phages

Summary A compilation of nucleic acid sequences fromE.coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations inE.coli also appear to occur in and in the coat protein gene of MS2, whereas T4 and other parts of the MS2 genome show different sequence properties. These and other findings are discussed in relation to the hypothesis that rapidity of translation of mRNAs in theE. coli system is dependent on doublet frequency and codon usage patterns.     

Transfection-mediated cell-cycle signaling: considerations for transient transfection-based cell-cycle studies.

Transient transfection of recombinant genes into cells is a commonly used approach for analyzing cell-cycle- and/or apoptotic-related activities of cell-cycle control proteins. In this approach, information regarding the functional consequence of expressing a recombinant protein transiently is garnered by comparing against results obtained from cells which are transfected with either a control expression plasmid and/or with mutant expression plasmids. In general however, little attention is paid to whether the transfection procedure itself influences these experiments. Using the calcium phosphate transfection method, we show that the introduction of DNA into cells induces signaling of the cell-cycle control machinery. In Hela cells, a transient increase in G0/G1 cells is observed 8 h after transfection. Furthermore, the introduction of DNA into several cell lines induces apoptosis. Transfection-mediated apoptosis can be elicited through a p53-independent mechanism, suggesting the possible extrapolation to many tumor cell lines. Last, we show that due to a likely cell-cycle-specific entry of marker genes into the nucleus, a highly biased cell-cycle distribution is observed in successfully transfected cells at early times following transfection. The importance of these issues in the interpretation as well as the design of transient transfection-based cell-cycle experiments is discussed.     

Tissue-specific regulation of cell-cycle responses to DNA damage in Arabidopsis seedlings

DNA damage-induced cell-cycle "checkpoint" responses reduce the mutagenic effects of this damage. However, the maintenance of genomic stability comes at a price: the slowing of growth and a delay in the development of critical tissues. In mammals, every mutated cell has the potential to become cancerous and therefore lethal. In plants, the risk of lethal cancers is essentially nil and the costs of delays in development are very high. Here, we investigate DNA damage checkpoint responses in meristematic (root and shoot tip) versus strictly somatic (stomatal and endoreduplicating) tissues in plants. We find that the ionizing radiation (IR)-induced cell-cycle responses observed in the root and shoot tip meristems do not apply to more differentiated tissues.     

BrdUrd/DNA flow cytometry analysis demonstrates cis-diamminedichloroplatinum (II)-induced multiple cell-cycle modifications on human lung carcinoma cells.

The treatment of cultured human cells by cis-diamminedichloroplatinum (II) (cis-DDP) has been shown to induce complex modifications in the cell cycle. Using dual parameter DNA/BrdUrd flow cytometric analysis, we were able to monitor the cell cycle traverse of a pulse-labeled cohort of cells in an asynchronous culture of the A549 cell line (human lung adenocarcinoma). Two major modifications of the cell cycle following cis-DDP treatment were observed: 1) after 24 h of treatment, the labeling index was significantly increased and was linked with a prolonged S-phase; the S-phase delay occurred rapidly after cis-DDP and was dose dependent but not exposure time dependent; 2) an accumulation of cells at the S/G2 transition with an onset approximately 12 h after cis-DDP contact, which was found to be dependent on both dose and duration of exposure. The cytokinetic results also predict maximal sensitivity to cis-DDP for G1 cells and minimal for G2 cells. In our model the late S/G2 accumulation was always preceded by a slowing down of the S-phase. However, only the former should be the correct indicator of cytotoxicity since it was correlated with cell survival as evidenced by a colony formation assay, under all treatment conditions.     

Stem cell defects in ATM-deficient undifferentiated spermatogonia through DNA damage-induced cell-cycle arrest

Mammalian spermatogenesis is maintained by stem cell capacity within undifferentiated spermatogonial subpopulation. Here, using a combination of surface markers, we describe a purification method for undifferentiated spermatogonia. Flow cytometric analysis revealed that this population is composed of Plzf-positive cells and exhibits quiescence and the side population phenotype, fulfilling general stem cell criteria. We then applied this method to analyze undifferentiated spermatogonia and stem cell activity of Atm(-/-) mice. Atm(-/-) testis shows progressive depletion of undifferentiated spermatogonia accompanied by cell-cycle arrest. In Atm(-/-) undifferentiated spermatogonia, a self-renewal defect was observed in vitro and in vivo. Accumulation of DNA damage and activation of the p19(Arf)-p53-p21(Cip1/Waf1) pathway were observed in Atm(-/-) undifferentiated spermatogonia. Moreover, suppression of p21(Cip1/Waf1) in an Atm(-/-) background restored transplantation ability of undifferentiated spermatogonia, indicating that ATM plays an essential role in maintenance of undifferentiated spermatogonia and their stem cell capacity by suppressing DNA damage-induced cell-cycle arrest.     

Precise discrimination among homologous sequences by DNA probe column chromatography.

Synthesized oligo probes were immobilized to a HPLC gel in high concentrations (30-40 O.D. per gram dry gel), packed in a column (2mm x 10cm) and incorporated into a conventional HPLC system. The system was applied to the discrimination among homologous sequences. Two probes different in sequence and length (16mer and 24mer) were investigated under isothermal and isocratic conditions. For each probe, 4 oligos of similar sequences, one perfectly matched to the probe and others containing one mismatch in the center of the chain, were synthesized. The chromatogram obtained as the results of high performance liquid affinity chromatography (HPLAC) considerably varied with the column temperature and the type of mismatches. The dependency of the deformation of elution profile upon mismatch seemed to reflect the stability of the hybrid composed of samples and immobilized probe.     

A festival of cell-cycle controls.

The second biennial Salk Cell Cycle meeting convened on 22 June 2001 in San Diego, California. Organized by Tony Hunter and Susan Forsburg of the Salk Institute, the five-day conference was highlighted by enlightening science and plenty of San Diego sunshine. Presentations covered a broad range of contemporary cell-cycle topics, ranging from regulation of DNA replication and mitosis to DNA damage recognition and checkpoint control.