An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions

Bremer, H. J.; Churchward, Gordon

doi:10.1016/0022-5193(77)90373-3

Cited by 105 publications

(128 citation statements)

References 11 publications

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“…Primer pairs for oriII, terI and terII gave comparable signals in the measurement of standard DNA, whereas the primer pair for oriI gave a somewhat lower signal. The ratio of origin copies to terminus copies in an exponentially growing population is given by the formula ori=ter52 C t , where C is the time it takes to replicate the chromosome from the origin to the terminus and t is the doubling time of the population (Bremer & Churchward, 1977). C periods were calculated using this formula with the indicated variation according to the standard deviation.…”

Section: Methodsmentioning

confidence: 99%

“…To obtain an independent measure of the duration of the C phase, we performed Q-PCR of the origin and terminus regions ( Table 1). The ratio of origin copies to terminus copies in an exponentially growing population is given by the formula ori=ter~2 C t , where C is the time it takes to replicate the chromosome from the origin to the terminus and t is the doubling time of the population (Bremer & Churchward, 1977). In the following simulations, the C and D values were iterated to find the best theoretical fits to the experimental DNA histograms.…”

Section: Both Chri and Chrii Have Increased Copy Numbers During Rapidmentioning

confidence: 99%

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Replication patterns and organization of replication forks in Vibrio cholerae

2011

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We have investigated the replication patterns of the two chromosomes of the bacterium Vibrio cholerae grown in four different media. By combining flow cytometry and quantitative real-time PCR with computer simulations, we show that in rich media, V. cholerae cells grow with overlapping replication cycles of both the large chromosome (ChrI) and the small chromosome (ChrII). In Luria-Bertani (LB) medium, initiation occurs at four copies of the ChrI origin and two copies of the ChrII origin. Replication of ChrII was found to occur at the end of the ChrI replication period in all four growth conditions. Novel cell-sorting experiments with marker frequency analysis support these conclusions. Incubation with protein synthesis inhibitors indicated that the potential for initiation of replication of ChrII was present at the same time as that of ChrI, but was actively delayed until much of ChrI was replicated. Investigations of the localization of SeqA bound to new DNA at replication forks indicated that the forks were co-localized in pairs when cells grew without overlapping replication cycles and in higher-order structures during more rapid growth. The increased degree of fork organization during rapid growth may be a means by which correct segregation of daughter molecules is facilitated.

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Section: Methodsmentioning

confidence: 99%

Section: Both Chri and Chrii Have Increased Copy Numbers During Rapidmentioning

confidence: 99%

Replication patterns and organization of replication forks in Vibrio cholerae

2011

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“…Chromosomal DNA was prepared, and the origin to terminus ratio (O/T) was determined by marker frequency analysis exactly as described by Atlung & Hansen (1999). When a culture has a doubling time t and a chromosomal replication time C, the stoichiometry between origins, O, and termini, T, is given by the formula O/T=2 C/t (Bremer & Churchward, 1977), from which C is extracted as C=ln(O/T)?t? [ln (2) …”

mentioning

confidence: 99%

“…The number of active replication forks, F c , is given by the formula F c =2(I c 2T c ) (Bremer & Churchward, 1977), where I c is the mean number of origins per cell and T c is the mean number of termini per cell. I c was determined by flow cytometry and T c was determined by I c divided by O/T.…”

mentioning

confidence: 99%

Reduced initiation frequency from oriC restores viability of a temperature-sensitive Escherichia coli replisome mutant

Skovgaard

Løbner-Olesen

2005

Microbiology

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The dnaX gene of Escherichia coli encodes t and c clamp loader subunits of the replisome. Cells carrying the temperature-sensitive dnaX2016 mutation were induced for the SOS response at non-permissive temperature. The SOS induction most likely resulted from extensive replication fork collapse that exceeded the cells' capacity for restart. Seven mutations in the dnaA gene that partly suppressed the dnaX2016 temperature sensitivity were isolated and characterized. Each of the mutations caused a single amino acid change in domains III and IV of the DnaA protein, where nucleotide binding and DNA binding, respectively, reside. The diversity of dnaA(Sx) mutants obtained indicated that a direct interaction between the DnaA protein and t or c is unlikely and that the mechanism behind suppression is related to DnaA function. All dnaA(Sx) mutant cells were compromised for initiation of DNA replication, and contained fewer active replication forks than their wild-type counterparts. Conceivably, this led to a reduced number of replication fork collapses within each dnaX2016 dnaA(Sx) cell and prevented the SOS response. Lowered availability of wild-type DnaA protein also led to partial suppression of the dnaX2016 mutation, confirming that the dnaA(Sx) mode of suppression is indirect and results from a reduced initiation frequency at oriC.

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“…It is well established that bacterial replication initiates at origin of replication (ori) bidirectionally, hence the regions already replicated will have two copies of ori in contrast to unreplicated regions. The same concept was earlier applied only on yeast cells with coordinated stage of replication [63]; however it stands true for all the cells at any stage of replication as well [64,65]. Using genome data from multiple bacteria, it was found that the region in the proximity of ori is present in high copy number in actively growing bacteria as compared to the DNA segment present towards the terminus [63] (Fig.…”

Section: Using (Meta)genomics Data In Deciphering Growth Dynamics Of mentioning

confidence: 92%

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

Sharma

Lal

2016

Indian J Microbiol

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Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering ''who is out there?'' based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable. In this review we have underlined the appeal of metagenomic-derived genomes in providing insights into the evolutionary patterns, growth dynamics, genome/gene-specific sweeps, and durability of environmental pressures. We have demonstrated the use of culturebased genomics and environmental shotgun metagenome data together to elucidate environment specific genome modulations via metagenomic recruitments in terms of gene loss/gain, accessory and core-genome extent. We further illustrated the benefit of (meta)genomics in the understanding of infectious diseases by deducing the relationship between human microbiota and clinical microbiology. This review summarizes the technological advances in the (meta)genomic strategies using the genome and metagenome datasets together to increase the resolution of microbial population studies.

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An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions

Cited by 105 publications

References 11 publications

Replication patterns and organization of replication forks in Vibrio cholerae

Replication patterns and organization of replication forks in Vibrio cholerae

Reduced initiation frequency from oriC restores viability of a temperature-sensitive Escherichia coli replisome mutant

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

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