Regulation Of Copy Number Research Articles

Dissecting RNA-protein interactions: RNA-RNA recognition by Rop

The ColE1 plasmid of E. coli encodes a small RNA-binding protein, Rop, which is involved in the regulation of plasmid copy number. Rop, a 4-helix bundle protein, facilitates sense-antisense RNA pairing by binding to the transiently formed hairpin pairs of RNA I and the complementary RNA II. We have identified the residues of Rop that are involved in RNA recognition. The residues form a narrow stripe down one face of the bundle and are symmetrically arranged, with recognition centered about two phenylalanine residues. Our results suggest that these phenylalanine residues interact with the loop region of the hairpin pair, with additional interactions between eight polar residues and the phosphate backbone. By modifying the identity of residue 14, we have created a variant of Rop that displays altered RNA binding specificity. The results of our studies allow us to present a detailed picture of RNA-protein recognition in a novel model system.

The Host Range of RK2 Minimal Replicon Copy-Up Mutants Is Limited by Species-Specific Differences in the Maximum Tolerable Copy Number

The minimal replicon of the broad-host-range plasmid RK2 consists of a gene, trfA ( trans-acting replication), encoding a protein required for initiation of plasmid replication. The TrfA protein binds to iterons in the cis -acting origin of vegetative replication ( oriV), but the exact mechanism by which TrfA-mediated replication initiation takes place is not known. We report here the isolation and characterization of five mini RK2 trfA mutant plasmids with an elevated plasmid copy number, four in Pseudomonas aeruginosa and one in Azotobacter vinelandii. The mutations are localized between or downstream of previously reported Escherichia coli copy-up mutations in trfA, and one of the mutations has been described earlier as an independent copy-up isolate in E. coli. The five mutant plasmids were all moderately copy up in both E. coli and their host of origin, in spite of the use of isolation procedures which were expected to select efficiently in favor of plasmid mutants specifying high copy numbers. In contrast, previously described high copy-up mutants isolated in E. coli could not be established in P. aeruginosa and A. vinelandii. These high copy-up mutants were shown to induce cell killing in E. coli under conditions where the plasmid copy number was increased as a physiological response to reduced growth rate. We propose that the reason for this killing effect is that the copy number under these conditions exceeds an upper tolerance level specific for E. coli. By assuming that the corresponding tolerance level is lower in P. aeruginosa and A. vinelandii than in E. coli, and that the mechanism of copy number regulation is similar, the model can explain the phenotypes of all tested copy up mutants in these two hosts. Analogous studies were also performed in Salmonella typhimurium and Acetobacter xylinum. The data obtained in these studies indicate that the above model is probably generally true for gram-negative bacteria, and the results also indicate that the maximum tolerable copy number is surprisingly low in some hosts.

The pAMβ1 CopF repressor regulates plasmid copy number by controlling transcription of the repE gene

pAM beta 1 is a low-copy-number, promiscuous plasmid from Gram-positive bacteria that replicates by a unidirectional theta-type mode. Its replication is initiated by an original mechanism, involving the positive rate-limiting RepE protein. Here we show that the pAM beta 1-encoded CopF protein is involved in negative regulation of the plasmid copy number. CopF represses approximately 10-fold the transcription initiated at the promoter of the repE gene and binds to a 31 bp segment which is located immediately upstream of the -35 box of the repE promoter. We propose that CopF inhibits initiation of transcription at the repE promoter by binding to its operator.

A new gene of bacteriophage P4 that controls DNA replication

Bacteriophage P4 replication may result in either a lytic cycle or plasmid maintenance, depending on the presence or absence, respectively, of helper phase P2 genome. Bacteriophage P4 DNA replication depends on the product of gene alpha, which has origin recognition, primase, and helicase activities. An open reading frame with the coding capacity for a protein of 106 amino acids (orf106) is located upstream of the alpha gene. Genes orf106 and alpha are transcriptionally coregulated. Three amber mutations and an internal deletion (del51) were introduced into orf106. All of the amber mutations exhibited a polar effect on transcription of the downstream alpha gene. The P4 del51 mutant was slightly defective in lytic growth and could not be propagated in the plasmid state. In this latter condition, P4 DNA overreplication was observed. Overexpression of Orf106 severely inhibited P4 DNA replication, preventing P4 lytic growth and plasmid maintenance. The inhibitory effect of Orf106 on P4 replication was not observed when both orf106 and alpha were overexpressed. We suggest that orf106 is involved in P4 replication and that a balanced expression of orf106 relative to alpha may be necessary for proper P4 DNA replication. In particular, orf106 appears to be essential for the control of P4 genome replication in the plasmid state. We propose that orf106 be named cnr, for copy number regulation.

The bovine papillomavirus E2 protein modulates the assembly of but is not stably maintained in a replication-competent multimeric E1-replication origin complex.

Initiation of bovine papillomavirus (BPV) DNA synthesis in vivo and in vitro depends on the interaction of the viral initiator protein E1 with the replication origin (ori+ DNA). The viral E2 protein assists this interaction, resulting in a cooperative assembly of both proteins on the replication origin. Using gel mobility-shift experiments, we demonstrate that in the presence of both E1 and E2 proteins two classes of ori+ DNA complexes were formed: complex 1 (c1) and complex 2 (c2). Formation of c1 depended on both the E1 and E2 proteins and both proteins were contained within c1. The generation of c2 was dependent on the E1 protein and could be enhanced by E2, but the E2 protein was not detected within c2. At high E2/E1 ratios, c1 was the dominant complex formed. Under these conditions, E1-dependent BPV DNA synthesis in vitro was inhibited. At low E2/E1 ratios, the stimulation of c2 was correlated with the stimulation of BPV DNA replication by E2 in vitro. These data suggest that E2 assists E1 in the formation of an intermediate c1 complex, which is replication inactive. The c1 complex is converted in turn to the replication-active c2 complex, which contains E1 but lacks E2. We propose that the ratios of c1 and c2 formed in response to the levels of E1 and E2 protein determine the potential for BPV DNA synthesis in vitro and in vivo and may contribute to copy number regulation of BPV plasmids within the cell.

Two alternative structures can be formed by IHF protein binding to the plasmid R6K gamma origin.

Escherichia coli integration host factor (IHF) contributes to the regulation of R6K plasmid copy number by counteracting the inhibitory activity of the plasmid-encoded replication protein pi. Two IHF-binding sites (ihf1 and ihf2) flank seven iterons in the origin which bind pi protein. As previously shown by electron microscopy, IHF can compact a large segment of the R6K gamma origin DNA, encompassing site ihf1, an AT-rich domain containing ihf1, and some of the seven iterons located downstream of ihf1. We termed this phenomenon IHF-mediated DNA folding. This folding requires a high IHF concentration, and the region of the origin (replication enhancer) located to the left of the AT-rich domain. However, site ihf2 is not necessary in forming the folded structure. As reported here, IHF binding to ihf2 can be detected in gel mobility shift assays only if the leftmost enhancer region is absent. Sites ihf1 and ihf2 each contain two consensus IHF sequences. Site-directed mutagenesis was performed to determine which sequences are recognized by IHF protein and which sites are involved in forming the various gamma origin-IHF complexes. Finally, we define the boundaries of protection from DNaseI digestion when IHF is bound to ihf2. We propose a model in which IHF protein bound to ihf1, in the absence of the enhancer region, facilitates IHF binding to ihf2.

Population genetics of transposable DNA elements. A Drosophila point of view.

This paper is an attempt to bring together the various, dispersed data published in the literature on insertion polymorphism of transposable elements from various kinds of populations (natural populations, laboratory strains, isofemale and inbred lines). Although the results deal mainly with Drosophila, data on other organisms have been incorporated when necessary to illustrate the discussion. The data pertinent to the regions of insertion, the rates of transposition and excision, the copy number regulation, and the degree of heterozygosity were analysed in order to be confronted with the speculations made with various theoretical models of population biology of transposable elements. The parameters of these models are very sensitive to the values of the transposable element characteristics estimated on populations, and according to the difficulties of these estimations (population not at equilibrium, particular mutations used to estimate the transposition and excision rates, trouble with the in situ technique used to localize the insertions, undesired mobilization of TEs in crosses, spontaneous genome resetting, environmental effects, etc.) it cannot be decided accurately which model better accounts for the population dynamics of these TEs. Tendencies, however, emerge in Drosophila: the copia element shows evidence for deficiency of insertions on the X chromosomes, a result consistent with selection against mutational effects of copia insertions; the P element repartition does not significantly deviate from the neutral assumption, in spite of a systematic copy number of insertions higher on the X than on the autosomes. Data on other elements support either the neutral model of TE containment, neither of the two models, or both. Prudence in conclusion should then be de rigueur when dealing with such kind of data. Finally the potential roles of TEs in population adaptation and evolution are discussed.

PSAR1, a natural plasmid from Streptomyces arenae, shows rapid increase and decrease of copy numbers on changes of growth media

A natural plasmid, pSAR1, was isolated from the antibiotic producer Streptomyces arenae TU469. Its size is estimated to approx. 80 kbp by restriction analysis. pSAR1 occurs in two copy-number states differing by a factor of at least 10, depending on culture conditions. The high copy-number state is strongly correlated with the production of the antibiotic pentalenolactone. The decrease of copy numbers after change of culture conditions is completed within 1 h. These unusually rapid kinetics and the occurrence of degradational intermediates suggest the participation of specific catalytic mechanisms in copy number regulation.

PSAR1, a natural plasmid fromStreptomyces arenae, shows rapid increase and decrease of copy numbers on changes of growth media

A natural plasmid, pSAR1, was isolated from the antibiotic producer Streptomyces arenae TÜ469. Its size is estimated to approx. 80 kbp by restriction analysis. pSAR1 occurs in two copy-number states differing by a factor of at least 10, depending on culture conditions. The hifh copy-number state is strongly correlated with the production of the antibiotic pentalenolactone. The decrease of copy numbers after change of culture conditions is completed within 1 h. These unusually rapid kinetics and the occurrence of degradational intermediates suggest the participation of specific catalytic mechanisms in copy number regulation.

Localization of P elements, copy number regulation, and cytotype determination inDrosophila melanogaster

Seventeen highly-inbred lines of Drosophila melanogaster extracted from an M' strain (in the P/M system of hybrid dysgenesis) were studied for their cytotype and the number and chromosomal location of complete and defective P elements. While most lines were of M cytotype, three presented a P cytotype (the condition that represses P-element activity) and one was intermediate between M and P. All lines were found to possess KP elements and only eight to bear full-sized P elements. Only the lines with full-sized P elements showed detectable changes in their P-insertion pattern over generations; their rates of gain and of loss of P-element sites were equal to 0.12 and 0.09 per genome, per generation, respectively. There was no correlation between these two rates within lines, suggesting independent transpositions and excisions in the inbred genomes. The results of both Southern blot analysis and in situ hybridization of probes made from left and right sides of the P element strongly suggested the presence of a putative complete P element in region 1A of the X chromosome in the three lines with a P cytotype; the absence of P copy in this 1A region in lines with an M cytotype, favours the hypothesis that the P element inserted in 1A could play a major role in the P-cytotype determination. Insertion of a defective 2 kb P element was also observed in region 93F in 9 of the 13 M lines. The regulation of the P-element copy number in our lines appeared not to be associated with the ratio of full-length and defective P elements.

Simultaneous regulation of plasmid replication and heterologous gene expression in Escherichia coli

An expression plasmid in which plasmid DNA replication and heterologous gene expression can be simultaneously regulated was constructed to avoid depression prior to induction. This was achieved by placing a pBR322 origin of replication immediately downstream of an anthranilate synthase-human epidermal growth factor fusion gene ( trpE-hEGF), both under the control of the promoter from the tryptophan biosynthetic operon. Regulation of plasmid copy number ensured tight repression of the trp promoter prior to induction. Upon induction, plasmid copy number increased up to six-fold and the fusion protein accumulated to approximately 12% of total cell protein. Induction experiments with a series of plasmid derivatives with sequentially lower copy numbers revealed that accumulation levels of the TrpE-hEGF fusion protein post-induction correlated well with plasmid copy number. Plasmid constructs where the native trp promoter had been replaced by derivatives deleted of the attenuator resulted in high levels of hEGF accumulation in the tryptophan-free medium prior to induction. Nevertheless, up to two-fold increase in TrpE-hEGF accumulation levels were obtained using the constructs lacking the attenuator compared to those bearing the native trp promoter.

Temporal expression of transcription and relative copy number of plasmid pSFB-1 in Scytalidium flavo-brunneum.

Wild-type cultures of Scytalidium flavo-brunneum produce a 15-azasterol antifungal agent and a reddish brown pigment as secondary metabolites. Spontaneous mutants of S. flavo-brunneum that had simultaneously lost the ability to produce the 15-azasterol and the pigment were transformed with plasmid pSFB-1, which was obtained from wild-type S. flavo-brunneum. Each transformant possessed the plasmid and coincidentally reacquired azasterol and pigment production. Regulation of transcription and relative plasmid copy number was determined as a function of the culture cycle of the organism. Twenty-five-fold amplification of the plasmid was observed in the fungus during the stationary phase. RNA transcripts of 0.9, 1.0, 1.5, 2.0, and 2.5 kilobases were expressed from the plasmid by the organism. While differences in the temporal regulation of the transcripts were seen, all except the 1.0-kilobase transcript increased in abundance on entry of the culture into the stationary phase of growth.

Comparison of the regulation of P elements in M and M′ strains ofDrosophila melanogaster

M and M' strains of Drosophila melanogaster in the P-M system of hybrid dysgenesis were compared in two series of tests, with the following results. (1) The singed-weak hypermutability regulation test showed that M' strains had lower P excision rates than M strains, suggesting that P-elements repression must occur in M' strains although it is not detectable by gonadal dysgenesis assays. (2) The evolution of mixed P+M and mixed P+M' populations was compared, using a strong P strain. The P+M cultures invariably evolved in a few generations into strong P cultures, while the P+M' cultures evolved into P-type cultures with reduced P-factor potentials. However, after 30 generations of culture, both these types of mixed cultures had similar P copy numbers, suggesting that regulation of copy number had occurred in them.

Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster.

Multigene families on the Y chromosome face an unusual array of evolutionary forces. Both ribosomal DNA and Stellate, the two families examined here, have multiple copies of similar sequences on the X and Y chromosomes. Although the rate of sequence divergence on the Y chromosome depends on rates of mutation, gene conversion and exchange with the X chromosome, as well as purifying selection, the regulation of gene copy number may also depend on other pleiotropic functions, such as maintenance of chromosome pairing. Gene copy numbers were estimated for a series of 34 Y chromosome replacement lines using densitometric measurements of slot blots of genomic DNA from adult Drosophila melanogaster. Scans of autoradiographs of the same blots probed with the cloned alcohol dehydrogenase gene, a single copy gene, served as internal standards. Copy numbers span a 6-fold range for ribosomal DNA and a 3-fold range for Stellate DNA. Despite this magnitude of variation, there was no association between copy number and segregation variation of the sex chromosomes.

Purification and characterization of RepA, a protein involved in the copy number control of plasmid pLS1

The promiscuous streptococcal plasmid pLS1 encodes for the 5.1 kDa RepA protein, involved in the regulation of the plasmid copy number. Synthesis of RepA was observed both in Bacillus subtilis minicells and in an Escherichia coli expression system. From this system, the protein has been purified and it appears to be a dimer of identical subunits. The amino acid sequence of RepA has been determined. RepA shows the alpha helix-turn-alpha helix motif typical of many DNA-binding proteins and it shares homology with a number of repressors, specially with the TrfB repressor encoded by the broad-host-range plasmid RK2. DNase I footprinting revealed that the RepA target is located in the region of the promoter for the repA and repB genes. Trans-complementation analysis showed that in vivo, RepA behaves as a repressor by regulating the plasmid copy number. We propose that the regulatory role of RepA is by limitation of the synthesis of the initiator protein RepB.

Independent regulation of mobile element copy number in Drosophila melanogaster inbred lines

Using data from in situ hybridization of the giant chromosomes from salivary glands, we have studied hobo mobile element copy numbers in 17 genomes of highly inbred lines of Drosophila melanogaster. A high number of insertions in the 3R arm and a high variance in total copy number characterize the hobo element. The genomic control of copy number (a compensatory effect among chromosome arms) detected previously for mdg-1, I and copia but not for P, was not found for hobo either, and there is no relation between the P and hobo copy numbers per line. From the DNA structure and putative mechanisms of transposition of each element, we suggest that the mechanism of transposition, involving either a reverse transcriptase or a transposase, is a good criterion for determining the way the copy number is regulated.

プラスミドpKYMの不和合性とコピー数のRibonucleic Acidによる調節

Plasmid pKYM is a multicopy plasmid isolated from Shigella sonnei. We have determined the region required for the incompatibility which also controls the copy number. It is partially overlapped with the region required for the initiation of replication. There are two promoters in this region. One promoter synthesizes messenger ribonucleic acid (mRNA) of rep protein (PR promoter) and another one transcribes the opposite strand in the same region (PL promoter). These two RNAs seem to interact through the stem-and-loop structure present in this region. The repression of the synthesis of rep protein which is essential for plasmid replication by the interaction of these two RNAs seems to be the main mechanism of the incompatibility and the regulation of copy number.

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system.

In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants-defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements - the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.

The Responding Site of the Rex Locus of Drosophila melanogaster

Rex is a dominant, maternal-effect locus in the heterochromatin of the X chromosome Drosophila melanogaster. It causes an early mitotic exchange-like event between heterochromatic elements of an attached- XY in X/attached-XY embryos of Rex mothers. Evidence is presented here that the site of Rex action is the ribosomal RNA gene cluster (the bb locus) only; no other heterochromatin is affected. The Rex locus may be useful in studying regulation of rRNA-gene copy number, mitotic chromosome behavior and heterochromatic function.

Copy-number dependent transpositions and excisions of the mdg-1 mobile element in inbred lines of Drosophila melanogaster

The chromosomal location of the mobile element mdg-1 was studied in 17 highly-inbred lines of Drosophila melanogaster. Although some lines were stable for their pattern of insertion sites from the 15th to the 27th and 35th brother–sister generations, others showed a high rate of gain of new insertion sites or a high rate of excision (loss of elements). In one line, 8 new insertion sites on the third chromosome were associated with an inversion on this chromosome; there is evidence that the rearrangement occurred premeiotically, thus suggesting a “transposition burst” in this line. There was no correlation between the rate of gain of new insertions and the rate of excision, this latter rate being higher. We have strong evidence that transposition is replicative. Excisions and, to a lesser extent, gains of insertions have been found to be copy-number dependent, suggesting that this is a main mechanism for copy-number regulation. Most inbred lines tended toward an optimal mdg-1 copy number for which they no longer showed transposition or excision (they became stable). These results may explain the instability sometimes reported in inbred lines.