[The 2001 Nobel Prize in Physiology or Medicine].
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Animals↗
Biomedical subjects
E Boye
Publications and source records attributed to E Boye.
Regulation of chromosomal replication by DnaA protein availability in Escherichia coli: effects of the datA region.
Initiation of chromosomal replication in Escherichia coli is dependent on availability of the initiator protein DnaA. We have introduced into E. coli cells plasmids carrying the chromosomal locus datA, which has a high affinity for DnaA. To be able to monitor oriC initiation as a function of datA copy number, we introduced a minichromosome which only replicates from oriC, using a host cell which replicates its chromosome independently of oriC. Our data show that a moderate increase in datA copy number is accompanied by increased DnaA protein synthesis that allows oriC initiation to occur normally, as measured by minichromosome copy number. As datA gene dosage is increased dnaA expression cannot be further derepressed, and the minichromosome copy number is dramatically reduced. Under these conditions the minichromosome was maintained by integration into the chromosome. These findings suggest that the datA locus plays a significant role in regulating oriC initiation, by its capacity to bind DnaA. They also suggest that auto regulation of the dnaA gene is of minor importance in regulation of chromosome initiation.
Bacterial Proteins↗
Defective initiation in an Escherichia coli dnaA(Cs,Sx) mutant.
Mutations in the Escherichia coli gene for initiation of DNA replication, dnaA, which suppress the polymerization defect and growth inhibition caused by temperature-sensitive (Ts) mutations in the polymerization gene, dnaX, are called Cs,Sx. We show here that these mutations, on their own, also cause defects in initiation, including inhibition of initiation at both low (20 degrees C) and high (44 degrees C) temperatures and asynchronous initiation at both the permissive (34 degrees C) and suppression (39 degrees C) temperatures. These findings suggests a relationship between partially defective initiation and suppression of the polymerization defect, both of which occur at 39 degrees C.
Bacterial Proteins↗
The sequence requirements for a functional Escherichia coli replication origin are different for the chromosome and a minichromosome.
We have developed a simple three-step method for transferring oriC mutations from plasmids to the Escherichia coli chromosome. Ten oriC mutations were used to replace the wild-type chromosomal origin of a recBCsbcB host by recombination. The mutations were subsequently transferred to a wild-type host by transduction. oriC mutants with a mutated DnaA box R1 were not obtained, suggesting that R1 is essential for chromosomal origin function. The other mutant strains showed the same growth rates, DNA contents and cell mass as wild-type cells. Mutations in the left half of oriC, in DnaA boxes M, R2 or R3 or in the Fis or IHF binding sites caused moderate asynchrony of the initiation of chromosome replication, as measured by flow cytometry. In mutants with a scrambled DnaA box R4 or with a modified distance between DnaA boxes R3 and R4, initiations were severely asynchronous. Except for oriC14 and oriC21, mutated oriCs could not, or could only poorly, support minichromosome replication, whereas most of them supported chromosome replication, showing that the classical definition of a minimal oriC is not valid for chromosome replication. We present evidence that the functionality of certain mutated oriCs is far better on the chromosome than on a minichromosome.
Blotting, Southern↗
Clonality and altered behavior of endothelial cells from hemangiomas.
Hemangioma, the most common tumor of infancy, is a benign vascular neoplasm of unknown etiology. We show, for the first time to our knowledge, that endothelial cells from proliferating hemangioma are clonal, and we demonstrate that these hemangioma-derived cells differ from normal endothelial cells in their rates of proliferation and migration in vitro. Furthermore, migration of hemangioma endothelial cells is stimulated by the angiogenesis inhibitor endostatin, unlike the inhibition seen with normal endothelial cells. We conclude that hemangiomas constitute clonal expansions of endothelial cells. This is consistent with the possibility that these tumors are caused by somatic mutations in one or more genes regulating endothelial cell proliferation.
Alleles↗
The Escherichia coli SeqA protein destabilizes mutant DnaA204 protein.
In wild-type Escherichia coli cells, initiation of DNA replication is tightly coupled to cell growth. In slowly growing dnaA204 (Ts) mutant cells, the cell mass at initiation and its variability is increased two- to threefold relative to wild type. Here, we show that the DnaA protein concentration was two- to threefold lower in the dnaA204 mutant compared with the wild-type strain. The reason for the DnaA protein deficiency was found to be a rapid degradation of the mutant protein. Absence of SeqA protein stabilized the DnaA204 protein, increased the DnaA protein concentration and normalized the initiation mass in the dnaA204 mutant cells. During rapid growth, the dnaA204 mutant displayed cell cycle parameters similar to wild-type cells as well as a normal DnaA protein concentration, even though the DnaA204 protein was highly unstable. Apparently, the increased DnaA protein synthesis compensated for the protein degradation under these growth conditions, in which the doubling time was of the same order of magnitude as the half-life of the protein. Our results suggest that the DnaA204 protein has essentially wild-type activity at permissive temperature but, as a result of instability, the protein is present at lower concentration under certain growth conditions. The basis for the stabilization in the absence of SeqA is not known. We suggest that the formation of stable DnaA-DNA complexes is enhanced in the absence of SeqA, thereby protecting the DnaA protein from degradation.
Bacterial Outer Membrane Proteins↗
Limiting DNA replication to once and only once.
In Escherichia coli cells, the origin of chromosomal replication is temporarily inactivated after initiation has occurred. Origin sequestration is the first line of defence against over-initiation, providing a time window during which the initiation potential can be reduced by: (i) titration of DnaA proteins to newly replicated chromosomal elements; (ii) regulation of the activity of the DnaA initiator protein; and (iii) sequestration of the dnaA gene promoter. This review represents the first attempt to consider together older and more recent data on such inactivation mechanisms in order to analyze their contributions to the overall tight replication control observed in vivo. All cells have developed mechanisms for origin inactivation, but those of other bacteria and eukaryotic cells are clearly distinct from those of E. coli. Possible differences and similarities are discussed.
Bacterial Proteins↗
Somatic mosaicism associated with a mild Alport syndrome phenotype.
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Adult↗
A fission yeast general translation factor reveals links between protein synthesis and cell cycle controls.
In two independent screens we isolated fission yeast mutations with phenotypes suggesting defects in B-cyclin function or expression. These mutations define a single gene which we call ded1. We show that ded1 encodes a general translation factor that is related in sequence and function to RNA helicases required for translation in other species. Levels of the B-cyclins Cig2 and Cdc13 are dramatically reduced upon inactivation of Ded1, and this reduction is independent of degradation by the anaphase promoting complex. When a ded1 mutant is grown under semi-restrictive conditions, the translation of Cig2 (and to a lesser extent Cdc13), is impaired relative to other proteins. We show that B-cyclin translation is specifically inhibited upon nitrogen starvation of wild-type cells, when B-cyclin/Cdc2 inactivation is a prerequisite for G(1) arrest and subsequent mating. Our data suggest that translational inhibition of B-cyclin expression represents a third mechanism, in addition to cyclin degradation and Rum1 inhibition, that contributes to Cdc2 inactivation as cells exit from the mitotic cell cycle and prepare for meiosis.
Cell Cycle↗
The gene for 2-phosphoglycolate phosphatase (gph) in Escherichia coli is located in the same operon as dam and at least five other diverse genes.
Downstream of the dam gene in the Escherichia coli genome the following three genes are located: first rpe, then a gene encoding a 27 kDa protein and finally trpS. Here we present evidence that the 27 kDa protein has 2-phosphoglycolate phosphatase activity, and we name the gene gph. Phosphoglycolate phosphatase is needed in autotrophic organisms performing the Calvin-Benson-Bassham (CBB) reductive pentose-phosphate cycle. E. coli is not capable of autotrophic growth and probably utilizes Gph activity for other function(s) than in the CBB cycle. We found no physiological effect of deleting gph and its function in E. coli remains unclear. The use of fusion plasmids, where lacZ was inserted into gph and trpS, and deletion derivatives of these fusion plasmids, showed that rpe, gph and trpS are all members of the dam-containing operon. A novel promoter was identified in the distal part of the dam gene. The operon, which contains aroK, aroB, urf74.3, dam, rpe, gph, and trpS, can be termed a superoperon, since it consists of (at least) seven apparently unrelated genes which are under complex regulatory control.
Artificial Gene Fusion↗
Regulation of the start of DNA replication in Schizosaccharomyces pombe.
Cells of Schizosaccharomyces pombe were grown in minimal medium with different nitrogen sources under steady-state conditions, with doubling times ranging from 2.5 to 14 hours. Flow cytometry and fluorescence microscopy confirmed earlier findings that at rapid growth rates, the G1 phase was short and cell separation occurred at the end of S phase. For some nitrogen sources, the growth rate was greatly decreased, the G1 phase occupied 30-50% of the cell cycle, and cell separation occurred in early G1. In contrast, other nitrogen sources supported low growth rates without any significant increase in G1 duration. The method described allows manipulation of the length of G1 and the relative cell cycle position of S phase in wild-type cells. Cell mass was measured by flow cytometry as scattered light and as protein-associated fluorescence. The extensions of G1 were not related to cell mass at entry into S phase. Our data do not support the hypothesis that the cells must reach a certain fixed, critical mass before entry into S. We suggest that cell mass at the G1/S transition point is variable and determined by a set of molecular parameters. In the present experiments, these parameters were influenced by the different nitrogen sources in a way that was independent of the actual growth rate.
Biomass↗
Impaired growth of an Escherichia coli rpe mutant lacking ribulose-5-phosphate epimerase activity.
We present evidence that ribulose-5-phosphate epimerase, a central metabolic enzyme acting in the non-oxidative branch of the pentose-phosphate pathway, is encoded by a gene in the dam containing operon of Escherichia coli. Enzymatic assays confirm that this gene encodes ribulose-5-phosphate epimerase activity. Disruption of the gene (rpe) causes loss of enzymatic activity and renders the rpe mutant unable to utilize single pentose sugars, indicating that rpe supplies the only ribulose-5-phosphate epimerase activity in E. coli. Growth of the rpe mutant is impaired in complex LB medium and severely impaired in minimal medium containing glycolytic carbon sources or gluconate. Enrichment with casamino acids abolishes or strongly relieves growth suppression in minimal medium. Aspartate counteracts the impaired growth in glycolytic carbon sources but not in gluconate. We suggest that the absence of the Rpe enzyme causes changes in the pentose-phosphate levels which alter the regulation of (a) metabolic enzyme(s) and thereby cause growth suppression and that the severity of growth suppression is related to the internal concentration of pentose-phosphates. Target enzymes for negative regulation may be located in the early parts of the Embden-Meyerhof-Parnas pathway and of the Entner-Doudoroff pathway and/or of carbohydrate transport systems feeding sugars into these sections of central metabolic pathways.
Aspartic Acid↗
Effects of purified SeqA protein on oriC-dependent DNA replication in vitro.
In vivo studies suggest that the Escherichia coli SeqA protein modulates replication initiation in two ways: by delaying initiation and by sequestering newly replicated origins from undergoing re-replication. As a first approach towards understanding the biochemical bases for these effects, we have examined the effects of purified SeqA protein on replication reactions performed in vitro on an oriC plasmid. Our results demonstrate that SeqA directly affects the biochemical events occurring at oriC. First, SeqA inhibits formation of the pre-priming complex. Secondly, SeqA can inhibit replication from an established pre-priming complex, without disrupting the complex. Thirdly, SeqA alters the dependence of the replication system on DnaA protein concentration, stimulating replication at low concentrations of DnaA. Our data suggest that SeqA participates in the assembly of initiation-competent complexes at oriC and, at a later stage, influences the behaviour of these complexes.
Bacterial Outer Membrane Proteins↗
Flow cytometry of bacterial cells: comparison between different flow cytometers and different DNA stains.
The DNA content and light scatter from individual Escherichia coli cells were measured in two flow cytometers with different configurations. The DNA content could be measured with similar resolution either in an Argus flow cytometer equipped with a mercury lamp, or in a FACStar flow cytometer with two argon lasers as light sources. In contrast, light scatter measurements appeared to be a good measure of cell mass only in the Argus instrument. Three DNA stains were compared:, DAPI, Hoechst 33258, and mithramycin A together with ethidium bromide. All three stains yielded DNA histograms of similar quality in both flow cytometers. Optimal results required that the stain and cell concentrations were kept similar, that a fixed rate of sample introduction was used, and that a period of equilibration was allowed during running of each sample. The results demonstrate that conventional, laser-based flow cytometers may be used for high-resolution measurements of bacterial DNA content, thereby making flow cytometry available to an increased number of research groups working with prokaryotes.
Cell Separation↗
Are minichromosomes valid model systems for DNA replication control? Lessons learned from Escherichia coli.
Initiation of chromosome replication is a key event in the life cycle of any organism. Little is known, however, about the regulatory mechanisms of this vital process. Conventionally, the initiation mechanism of chromosome replication in microorganisms has been studied using plasmids in which an origin of chromosome replication has been cloned, rather than using the chromosome itself. The reason for this is that even bacterial chromosomes are so large that biochemical and genetic manipulations become difficult and cumbersome. Recently, the combination of flow cytometry and genetic methods, in which modifications of the replication origin are systematically introduced onto the chromosome, has made possible detailed studies of the molecular events involved in the control of replication initiation in Escherichia coli. The results indicate that requirements for initiation at the chromosomal origin, oriC, are drastically different from those for initiation at cloned oriC.
Chromosomes, Bacterial↗
Determination of the genomic structure of the COL4A4 gene and of novel mutations causing autosomal recessive Alport syndrome.
Autosomal recessive Alport syndrome is a progressive hematuric glomerulonephritis characterized by glomerular basement membrane abnormalities and associated with mutations in either the COL4A3 or the COL4A4 gene, which encode the alpha3 and alpha4 type IV collagen chains, respectively. To date, mutation screening in the two genes has been hampered by the lack of genomic structure information. We report here the complete characterization of the 48 exons of the COL4A4 gene, a comprehensive gene screen, and the subsequent detection of 10 novel mutations in eight patients diagnosed with autosomal recessive Alport syndrome. Furthermore, we identified a glycine to alanine substitution in the collagenous domain that is apparently silent in the heterozygous carriers, in 11.5% of all control individuals, and in one control individual homozygous for this glycine substitution. There has been no previous finding of a glycine substitution that is not associated with any obvious phenotype in homozygous individuals.
Alanine↗
Somatic deletion of the 5' ends of both the COL4A5 and COL4A6 genes in a sporadic leiomyoma of the esophagus.
Leiomyomata of the esophagus are sporadic benign tumors of unknown etiology. We studied a collection of nine tumors for the expression of extracellular matrix components and found the same aberrant expression pattern as previously observed in inherited diffuse leiomyomatosis. We demonstrate here the occurrence of a somatic deletion at the COL4A5/COL4A6 locus at Xq22 in a frozen leiomyoma sample. These data confirm the hypothesis that the same underlying etiology is responsible for circumscribed smooth muscle proliferation in sporadic leiomyomata as for diffuse smooth muscle cell proliferation in inherited diffuse leiomyomatosis.
Basement Membrane↗
The absence of effect of gid or mioC transcription on the initiation of chromosomal replication in Escherichia coli.
Despite the widely accepted view that transcription of gid and mioC is required for efficient initiation of cloned oriC, we show that these transcriptions have very little effect on initiation of chromosome replication at wild-type chromosomal oriC. Furthermore, neither gid nor mioC transcription is required in cells deficient in the histone-like proteins Fis or IHF. However, oriC that is sufficiently impaired for initiation by deletion of DnaA box R4 requires transcription of at least one of these genes. We conclude that transcription of mioC and especially gid is needed to activate oriC only under suboptimal conditions. We suggest that either the rifampicin-sensitive step of initiation is some other transcription occurring from promoter(s) within oriC, or the original inference of transcriptional activation derived from the rifampicin experiments is incorrect.
Bacterial Proteins↗