Single-cell model of prokaryotic cell cycle

Abner, Kristo; Aaviksaar, Tõnis; Adamberg, Kaarel; Vilu, Raivo

doi:10.1016/j.jtbi.2013.09.035

Cited by 19 publications

(19 citation statements)

References 45 publications

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“…3D). The concurrent nature of the prokaryotic chromosome cycle, in which all chromosomal events roll in a single succession once the replication is initiated, is likely why the prokaryotic cell cycle requires no CDK-like engine and is simply driven by replication initiation (148). In contrast to the eukaryotic chromosomes, prokaryotic chromosomes stay maximally compacted for most of the cell cycle (Fig.…”

Section: The Two Chromosome Cyclesmentioning

confidence: 99%

“…However, the key to the real reason may be the fact that, even with several replicons in the cell, there is always only one replicon driven by the oriC/DnaA pair. The unique oriC/DnaA pair per cell may be behind the preference for a single chromosome in bacteria, for example, due to the fact that it is initiation at oriC by DnaA that is believed to pace the bacterial cell cycle (148). According to this logic, since other replicons in the same cell are driven by their oriP/Rep pairs, they should not influence the cell cycle.…”

Section: Why Do Prokaryotes Prefer a Single Master Chromosome?mentioning

confidence: 99%

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The Precarious Prokaryotic Chromosome

Kuzminov

2014

J Bacteriol

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Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other "precarious" features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.

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Section: The Two Chromosome Cyclesmentioning

confidence: 99%

Section: Why Do Prokaryotes Prefer a Single Master Chromosome?mentioning

confidence: 99%

The Precarious Prokaryotic Chromosome

Kuzminov

2014

J Bacteriol

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“…Koch [17] provided a review (as of 1993) explaining what led biologists to choose one growth rate over the other. Abner et al [1] compared and contrasted the two growth rates in the context of the Cooper-Helmstetter (CH) theory for prokaryotic cell cycles.…”

Section: Introductionmentioning

confidence: 99%

On a Cell Division Equation With a Linear Growth Rate

Brunt¹,

Almalki²,

Lynch³

et al. 2018

ANZIAM J.

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We consider an initial–boundary value problem that involves a partial differential equation with a functional term. The problem is motivated by a cell division model for size structured cell cohorts in which growth and division occur. Although much is known about the large time asymptotic behaviour of solutions to these problems for constant growth rates, general solution techniques are rare. We analyse the case where the growth rate is linear and the division rate is a monomial, and we develop a method to determine the general solution for a general class of initial data. The large time dynamics of solutions for this case are significantly different from the constant growth rate case. We show that solutions approach a time-dependent attracting solution that is periodic in the time variable.

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“…Classification of cell elements into these separately defined categories 6 has been carried out within all domains of life, ranging from prokaryotes such as E. 7 coli [4], to humans [5], and there is a database exclusively devoted to essential genes [6], 8 which current version includes also noncoding genomic elements [7]. 9 Even when the determination of essential cell components has been biased toward 10 genetic elements [8], the recognition of the fact that the concurrent presence of 11 non-genomic elements is indispensable for cell survival resulted in the concept of 12 'minimal cell', which began with the pioneering efforts to construct artificial cells in the 13 1960s [9], and advanced to form the field of synthetic biology [10]. On the other hand, Help to study interactomes has come from graph theory [48], which allows a formal 144 treatment of the implicit relations between structures and grants the construction and 145 visualization of biological networks [49,50] (see also [51] and references thereafter).…”

Section: Introductionmentioning

confidence: 99%

“…The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed. 14 the determination of the smallest set of components that can sustain life has obvious 15 importance for a solid foundation of biology, and will help in the understanding of 16 critical cellular processes [7,11,12].…”

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confidence: 99%

On an algorithmic definition for the components of the minimal cell

Vega

Reyes-Valdés

2018

Preprint

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Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the 'minimal cell' and the corresponding 'minimal genome', we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed. 14 the determination of the smallest set of components that can sustain life has obvious 15 importance for a solid foundation of biology, and will help in the understanding of 16 critical cellular processes [7,11,12]. 17 PLOS1/33It is important to underline that the definition of 'essential cell components', 18 genomic or otherwise, depends to some extent on particular environmental 19 conditions [13], e.g., in a bacteria with a mutation affecting the synthesis of an amino 20 acid 'x ', such amino acid will be classified as 'essential' only when it is absent form the 21 culture media. However, if we take a functional view, it appears impossible to avoid the 22 fact that, for example, an element to synthesize RNA from a DNA template (an RNA 23 polymerase) is essential for all free-living cells. 24Experimental approaches 25 Experimental approaches to determine minimal gene sets began, before the genomic era, 26 65 method could be claimed to be a 'completely artificial life form' -even if the design of 66 genomes and other cell elements was guided by templates from living organisms. In [27] 67 the authors underline the fact that alien prokaryotic genomes fail to give 'instructions' 68 PLOS 2/33 to a eukaryotic cell, even when the alien genome is faithfully replicated. 69So far, genome synthesis and transplantation in prokaryotes as well as design and 70 construction of chromosomes in eukaryotes, have shown that it is possible to substitute 71 native DNA by artificial sequences, designed using as template the original genome. 72Currently, these wet-lab models allow the segregation of essential versus 'unnecessary' 73 or dispensable genome elements, and are leading to a deeper understanding of the 74 function of each element in the cell. 75An application of the knowledge about essential cell components is the construction 76 of synthetic cells. This approach expli...

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Single-cell model of prokaryotic cell cycle

Cited by 19 publications

References 45 publications

The Precarious Prokaryotic Chromosome

The Precarious Prokaryotic Chromosome

On a Cell Division Equation With a Linear Growth Rate

On an algorithmic definition for the components of the minimal cell

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