25 research outputs found

    Relationship between specific protein synthesis rate, ribosomal density and control coefficients.

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    <p>(A) The value of the specific synthesis rate estimated for all the genes is indicated in function of the ribosomal density (obtained through the experiment). (B) The control coefficients of each translation step are shown according to ribosomal density of each gene. Initiation control coefficient , elongation control coefficient and termination control coefficient are shown. The numbers in parenthesis at the top of the figure indicate the number of genes in each group.</p

    Functional enrichment analysis for genes grouped by similar translational control.

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    <p>Only the most enriched terms are shown, while the significantly enriched terms (p-value<0.05) are highlighted in bold. The binning is the same as on <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003240#pcbi-1003240-g003" target="_blank">Figure 3</a>. For each group, the ranges of ribosomal densities, specific synthesis rate, absolute synthesis rate and control coefficients are also shown. tells for example that 788 genes were present in the given cluster while 1108 genes are present in total in the data; on the other hand indicates for example that 64 genes of the given category were found in the cluster while 73 genes in total are present in the given category.</p><p>AMI: amino acid biosynthesis, CEL: cellular process, COF: biosynthesis of cofactors, NRJ: energy metabolism, OTH: other categories, PUR: purine, pyrimidine, nucleoside and nucleotide metabolism, REG: regulatory functions, TRD: translation, TSP: transport and binding proteins, UNK: unknown function.</p

    <i>L. lactis</i> under stress.

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    <p>This is the same as <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003240#pcbi-1003240-g004" target="_blank">Figure 4</a>, but for cells grown under stress condition. The ordering of categories is the same as for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003240#pcbi-1003240-g004" target="_blank">Figure 4</a>; categories whose synthesis rate changed significantly between the conditions are marked in bold, with a “+” to indicate an increase and a “−” for a decrease.</p

    Normalized absolute protein synthesis rate by functional categories (shown as boxplots).

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    <p>The number of genes observed in each functional category is between brackets. Medians are symbolized by circle with a point in the middle. The boxes describe the quartiles of the data, while the lines extend to the extreme data points (not including the outliers which are shown as little open rounds). Interval endpoints are defined as the centers of the triangular markers. When the intervals of two groups do not overlap, then their medians can be assumed to be different with 95% confidence. The categories are ordered according to their median value, and the “category ALL” corresponding to all genes together is highlighted to indicate which categories perform better or worse than the cell average. AMI: amino acid biosynthesis, CEL: cellular process, COF: biosynthesis of cofactors, ENV: cell envelope, FAT: fatty acid and phospholipid metabolism, INT: central intermediary metabolism, NRJ: energy metabolism, OTH: other categories, PUR: purine, pyrimidine, nucleoside and nucleotide metabolism, REG: regulatory functions, REP: replication, TRD: translation, TRS: transcription, TSP: transport and binding proteins, UNK: unknown function.</p

    Polysome sizes of genes from experimentally verified operon <i>citCDEFXG</i>.

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    <p>One color was associated to each gene part of this operon (gene is absent of the figure when its experimental polysome size was missing). For each operonic gene, its mRNA proportions (from three repetitions) were plotted according to polysome size. Results from other operons are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003240#pcbi.1003240.s005" target="_blank">Figure S5</a>. The gene names and lengths (in number of codons) are indicated in the first fraction. The number above each polysome size is the p-value of the ANOVA test to check at a given polysome size if the mRNA proportion of the group of operonic gene is significantly different than the mRNA proportion of the rest of the genes in this fraction. For example in this figure, gene citC has a length of 347 codons, and about 10% of its mRNA copies are in fraction B, 17% in fraction C, … and 15% of its copies have a polysome size around 14; moreover, an ANOVA test shows with a p-value of 0.0001 that, in fraction of polysome size 14, the average mRNA proportion from the cit operon's genes is significantly different to the average mRNA proportion from the other gene species in this fraction (and similarly for the other elution fractions), hinting that the genes from cit operon are not distributed among fractions in the same way as the rest of the genes.</p

    Scheme of translation process.

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    <p><i>R<sub>f</sub></i> is the number of free ribosomes, <i>k<sub>I</sub> k<sub>E</sub> k<sub>T</sub></i> are rate constants of translation steps, <i>L</i> is the number of codons covered by one ribosome and <i>n<sup>k</sup></i> is the number of codons of the gene coding sequence.</p

    Main mechanisms controlling mRNA concentrations.

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    <p><i>vs.</i> indicates the growth conditions considered for the calculation of the regulation coefficients. Chemostat and batch indicate that RNA half-lives were determined in continuous or discontinuous cultures, respectively. In chemostat cultures, cells were at a steady state, with growth limited by the isoleucine concentrations. In batch cultures, isoleucine in the medium was progressively consumed (until starvation was reached) and the cells were in a dynamic process of adaptation.</p

    mRNA half-life distribution.

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    <p>A. For transcripts for which stability values at each growth rate were available. B. For the 486 transcripts with half-lives values available for all three growth rates. The darker the histogram, the higher is the growth rate: black for µ = 0.80 h<sup>−1</sup>, dark gray for µ = 0.51 h<sup>−1</sup> and light gray for µ = 0.11 h<sup>−1</sup>. Half-lives are in reported in minutes. The lines are the rolling averages and thus represent the overall tendency of the data.</p

    Cellular processes influencing mRNA concentration.

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    <p>Transcription, mRNA decay and dilution due to growth are involved. Dilution and degradation rates can be modeled as µ*[mRNA] and k*[mRNA], respectively, where µ is the growth rate and k the degradation rate constant.</p
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