Research ArticleGENETICS

Extrinsic noise prevents the independent tuning of gene expression noise and protein mean abundance in bacteria

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Science Advances  07 Oct 2020:
Vol. 6, no. 41, eabc3478
DOI: 10.1126/sciadv.abc3478
  • Fig. 1 Design and characterization of the 40-strain custom-made library.

    (A) Synthetic sequences are made of a combination of eight transcription modules (promoters and eTSS) exhibiting different transcription strengths (yellow intensity) and five translation modules (TIRs) exhibiting different translation efficiencies (blue intensity). Combined modules are cloned upstream of the GFPmut3 coding sequence, resulting in a library of 40 synthetic sequences, which allow a wide range of GFPmut3 expression, that is representative of the natural range of protein expression in B. subtilis (fig. S2). (B and C) Mean protein abundance (B) and protein concentration noise strength (C) of all the strains of the library. To facilitate the interpretation, the protein concentration is expressed in number of proteins in 1 fl, which is the average cell volume. Therefore, the mean concentration corresponds to the mean number of proteins per cell (mean protein abundance). The noise strength is defined as the variance of the single-cell protein concentration divided by the mean. For each strain, at least two replicate experiments were performed. Each dot represents a single experiment. Experiments using the same strains are represented with vertically aligned dots of identical color. (D and E) The strains are ordered in a two-dimensional map according to their transcription (x axis) and translation (y axis) modules. Translation modules (1, fbaAhs; 2, fbaA; 3, fbaAshort; 4, gtlX; and 5, tufA) and transcription modules (1, ykwB; 2, yufK; 3, yqzM; 4, zwf; 5, ykpA; 6, fbaA; 7, rrnJP2; and 8, ylxM) are ordered according to their strength. The color of the pixels represents the log-transformed mean protein abundance (D) and log-transformed noise strength (E). White pixels correspond to the strains that could not be constructed or measured. Crossed-out pixels correspond to strains with an unexpected mean fluorescence, suggesting specific interactions between the transcription and translation modules.

  • Fig. 2 Noise strength of the protein concentration as a function of mean protein abundance when the translation module varies.

    Each subplot corresponds to a group of strains with the same transcription module: (A) fbaA, strains S1 to S3 and S5; (B) rrnJP2, strains S7 to S9; (C) ykpA, strains S11 to S15; (D) ykwB, strains S16 to S20; (E) ylxM, strains S21 to S24; (F) yqzM, strains S26 and S30; (G) yufK, strains S31 to S35; and (H) zwf, strains S36 to S40. In each subplot, the different colors correspond to different translation modules (blue, fbaAhs; cyan, fbaA; green, fbaAshort; magenta, gtlX; and red, tufA). Black lines are linear regressions (parameters are given in table S3). To facilitate the interpretation, the protein concentration is expressed in number of proteins in 1 fl, which is the average cell volume. Therefore, the mean concentration corresponds to the mean number of proteins per cell (mean abundance).

  • Fig. 3 Noise strength of the protein concentration as a function of mean protein abundance when the transcription module varies.

    Each subplot corresponds to a group of strains with the same translation module: (A) fbaA, (B) fbaAhs, (C) fbaAshort, (D) gtlX, and (E) tufA. In each subplot, the different colors correspond to different transcription modules (blue, yufK; cyan, yqzM; green, ykpA; yellow, zwf; magenta, ykwB; orange, fbaA; red, rrnJP2; and brown, ylxM). Black lines are linear regressions (parameters are given in table S4). To facilitate the interpretation, the protein concentration is expressed in number of proteins in 1 fl, which is the average cell volume. Therefore, the mean concentration corresponds to the mean number of proteins per cell (mean abundance).

  • Fig. 4 Noise strength of the protein concentration as a function of mean protein abundance when different control elements vary.

    To facilitate the interpretation, the protein concentration is expressed in number of proteins in 1 fl, which is the average cell volume. Therefore, the mean concentration corresponds to the mean number of proteins per cell (mean abundance). (A) The mean protein abundance is modulated by changing the transcription (red) or the translation (green) module. The green dots correspond to the strains with the ylxM transcription module (and different translation modules, strains S21 to S24), and the red diamonds corresponds to the strains with the fbaAshort translation module (and different transcription modules, strains S03, S08, S13, S18, S23, S33, S38, A1 to A7, and B1 to B7). The superimposed green dot and red diamond correspond to the S23 strain (transcription module, ylxM and translation module, fbaAshort). Straight lines are linear regressions. (B) The mean protein abundance is modulated by changing only the promoter. The red squares correspond to different strains with the same eTSS and translation module (strains S03 and A1 to A7), and the black straight line is a linear regression. (C) The mean protein abundance is modulated by changing either the promoter [red squares, strains S03 and A1 to A7 as in (B)], the eTSS (blue circles, strains S8 and B1 to B7), or both (green diamonds, strains S13, S18, S23, S33, and S38).

  • Fig. 5 Impact of extrinsic noise.

    (A) The noise (squared coefficient of variation: CV2, y) of the protein concentration as a function of the mean protein abundance (x) for all the strains. Each blue circle corresponds to a single experiment with a single strain. The red line corresponds to a fit y = C/x for all the experiments for which x < 50 (left part of the graph). (B) The total noise (blue), extrinsic noise (green), and intrinsic noise (red; y) as a function of the mean (x), for the two-colored strains (same eTSS and translation module and different promoters). The red line is a fit y = k1/x + k2, as in (4). (C) The total (blue dots), extrinsic (green dots), and intrinsic (red dots) noise strength as a function of the mean, for the two-colored strains. Straight lines are linear regressions. To facilitate the interpretation, the protein concentration is expressed in number of proteins in 1 fl, which is the average cell volume. Therefore, the mean concentration corresponds to the mean number of proteins per cell (mean abundance).

  • Fig. 6 Expression strategies for essential and nonessential genes.

    (A to C) Genes are grouped according to the protein abundance, and each group is divided into three subgroups of identical size according to the transcription rate. The subgroups are formed with the third of the genes that have the highest transcription rate, the third that has the lowest transcription rate, and the remaining third. Then, the number of essential genes in each subgroup is computed. Red circles, number of essential genes in the high-transcription subgroup; blue circles, number of essential genes in the low-transcription subgroup. The filled circles indicate significant differences based on Fisher’s exact test (P < 0.05). (A) The analysis is performed on all genes in the genome. (B) The analysis is performed on a subset of genes that are weakly transcribed (less transcribed than yqzM). (C) The analysis is performed on the rest of the genes (i.e., those more transcribed than yqzM). In (A) to (C), the procedure to group the genes of identical protein abundance is not a simple binning and creates groups of genes whose levels of expression are not significantly based on an ANOVA (see Materials and Methods for details). The different groups therefore do not contain the same number of genes, and the number of groups is different in (A) to (C).

Supplementary Materials

  • Supplementary Materials

    Extrinsic noise prevents the independent tuning of gene expression noise and protein mean abundance in bacteria

    A. Deloupy, V. Sauveplane, J. Robert, S. Aymerich, M. Jules, L. Robert

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