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On an algorithmic definition for the components of the minimal cell.

ABSTRACT: 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.

SUBMITTER: Martinez O

PROVIDER: S-EPMC5983409 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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On an algorithmic definition for the components of the minimal cell.

Martínez Octavio O Reyes-Valdés M Humberto MH

PloS one 20180601 6

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 represent ...[more]

PMID: 29856803

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Project description:PurposeIn adolescents, the definition and clinical implications of metabolically healthy overweight (MHO) status have not been established. This study aimed to investigate the prevalence of MHO according to its most widespread definition, which is based on metabolic syndrome (MS), and to explore further metabolic indicators such as Homeostatic Model Assessment of Insulin Resistance, total cholesterol, low-density lipoprotein cholesterol, alanine aminotransferase, and C-reactive protein levels, together with metabolic health predictors in a sample of adolescents attending a pediatric obesity clinic.MethodsData from 487 adolescents categorized as overweight (52.6% females, 88.1% white), with a mean body mass index (BMI) z-score of 2.74 (±1.07 standard deviation [SD]), and a mean age of 14.4 years (±2.2 SD) were cross-sectionally analyzed. From this original sample, a subsample of 176 adolescents underwent a second assessment at 12 (±6 SD) months for longitudinal analysis.ResultsFrom the 487 adolescents originally analyzed, 200 (41.1%) were categorized as MHO, but only 93 (19.1%) had none of the metabolic indicators considered in this study. According to longitudinal analysis, 30 of the 68 adolescents (44%) categorized as MHO at baseline became non-MHO over time. BMI z-score was the best predictor of metabolic health both in cross-sectional and longitudinal analyses. Increased BMI z-score reduced the odds of being categorized as MHO (odds ratio [OR], 0.6; 95% confidence interval [CI], 0.4-0.9; P=.008) and increased the odds of having hypertension (OR 2.1, 95% CI: 1.4-3.3, P=0.001), insulin resistance (OR, 2.4; 95% CI, 1.4-4.1, P=0.001), or a proinflammatory state (OR, 1.2; 95% CI, 1.1-1.3, P=0.002).ConclusionDiagnosis of MHO should not be exclusively based on MS parameters, and other metabolic indicators should be considered. Adolescents categorized as overweight should participate in weight-management lifestyle interventions regardless of their metabolic health phenotype.

Project description:The stable inheritance of the broad-host-range plasmid RK2 is due at least in part to functions within a region located at coordinates 32.8 to 35.9 kb, termed the RK2 par locus. This locus encodes four previously identified genes in two operons (parCBA and parD; M. Gerlitz, O. Hrabak, and H. Schwab, J. Bacteriol. 172:6194-6203, 1990, and R. C. Roberts, R. Burioni, and D. R. Helinski, J. Bacteriol. 172:6204-6216, 1990). The parCBA operon is functional in resolving plasmid multimers to monomers. Analysis of the plasmid stabilization capacity of deletions within this region, however, indicates that this multimer resolution operon is required for stabilization only in certain Escherichia coli strains and under specific growth conditions. The deletion analysis further allowed a redefinition of the minimal functional region as 790 bp in length, consisting of the parD gene (243 bp) and its promoter as well as sequences downstream of parD. This minimal region stabilizes an RK2-derived minireplicon in several different gram-negative bacteria and, at least in E. coli, in a vector-independent manner. By insertional mutagenesis, both the parD gene and downstream (3') regions were found to be required for plasmid stabilization. The downstream DNA sequence contained an open reading frame which was subsequently shown by transcriptional and translational fusions to encode a protein with a predicted size of 11,698 Da, designated ParE. Since the parDE operon requires the presence of the parCBA operon for efficient stabilization under certain growth conditions, the potential role of multimer resolution in plasmid stabilization was tested by substituting the ColE1 cer site for the parCBA operon. While the cer site did function to resolve plasmid multimers, it was not sufficient to restore stabilization activity to the parDE operon under growth conditions that require the parCBA operon for plasmid stability. This suggests that plasmid stabilization by the RK2 par locus relies on a complex mechanism, representing a multifaceted stabilization system of which multimer resolution is a conditionally dispensable component, and that the function(s) encoded by the parDE operon is essential.

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On an algorithmic definition for the components of the minimal cell.

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On an algorithmic definition for the components of the minimal cell.

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