Partial penetrance facilitates developmental evolution in bacteria - PubMed (original) (raw)

Partial penetrance facilitates developmental evolution in bacteria

Avigdor Eldar et al. Nature. 2009.

Abstract

Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.

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Figures

Figure 1

Figure 1. Partial penetrance in the developmental process of sporulation

(a) In wild-type sporulation each sporulating cell produces a single spore. (b) Partially penetrant mutants exhibit a mixture of normal sporulation, lethal failures (‘X’) and alternative viable fates (‘?’) due to cellular fluctuations (cloud). (c,d) Schematic illustrations of events (c) and genetic interactions (d) leading to differentiation of the mother cell and forespore compartments (see text).

Figure 2

Figure 2. Time-lapse movies reveal alternative developmental pathways in spoIIRPP signaling mutants

(a-d) Green and red represent fluorescent protein expression from σF and σE-dependent promoters, respectively, overlaid on phase contrast images (gray). Developing forespores appear white at late times. Times indicated in minutes from σF activation. (a) Normal sporulation. (b) Abortively disporic cells. (c) Escaping cells activate σF but continue to elongate without activating σE (Fig. S5). Note that the activated forespore (right) does not develop further. (d) Twin sporulation occurs after escape. Green fluorescence at the initial time-point is a remnant of escape from the previous sporulation attempt. (e) Chromosome over-replication occurs prior to the formation of twin forespores. TetR-GFP-tagged chromosomal loci appear as green “dots”. Membrane staining (red) shows septation events. The rightmost dot is the remnant from a previous escape. (f) Schematic diagram showing the temporal sequence of events leading to observed terminal fates, which are classified by the numbers of chromosomes (x-axis) and compartments (y-axis). * indicates potential for return to vegetative division and/or additional sporulation attempt. Scale bar, 1μm.

Figure 3

Figure 3. Noise and gene expression control cell fate in a hierarchical fashion

(a) Time traces indicating delay (arrow) and reduction (slope of yellow line compared to cyan line) in spoIIR expression rate of a typical spoIIRPP-CY cell. (b) Cumulative histograms of spoIIR expression rate are shown for two sub-populations of a single spoIIRPP strain in the same microcolony (_n_=150 cells). Sporulating cells show a systematically higher level of spoIIR expression. Inset: cell-cell variability in spoIIR expression rate. (c-e) Systematic genetic manipulation of fate penetrance. Error bars (s.e) are based on three replicate experiments. (c) spoIIR expression controls the overall frequency of sporulation (x-axis) but does not systematically affect the ratio of escape cells to abortive disporics (y-axis). Points represent spoIIRPP strains differing in spoIIR expression level and delay (supplementary methods). (d) spoIIE expression level tunes the penetrance ratio of escape to abortively disporic fates (methods, Fig. S12). (e) Deletion of yabA interacts synergistically with spoIIRPP mutants to increase twin penetrance (see also Fig. S11). (f) Fate determination can be controlled hierarchically—different genes affect different decision points.

Figure 4

Figure 4. Evolution of twin sporulation

(a) Fate tree showing relative frequencies of over-replication (second row) and additional septation (third row) inferred from analysis of terminal fates (bottom row) of _n=_285 individual cells. Note that the probability of having three compartments depends on chromosome number (blue percentages). Day to day variation was ≤ 2% across all measurements. (b) Strain backgrounds PY79 (used throughout the paper) and BR151 differ in twin penetrance with the same spoIIRPP mutation (error bars, s.e., based on multiple experiments). yabA mutations reduce this difference. (c-e) Twin sporulation in C. oceanicum resembles that in B. subtilis mutants. (c) Filmstrip shows typical events during C. oceanicum sporulation (times in minutes from first frame). Shown are DNA (green), membrane staining (red), and phase contrast (gray). Yellow arrowheads mark first appearance of asymmetric septa. (d) The distribution of time intervals between two septation events during twin sporulation (_n_=70). (e) The rate of change of DNA staining was quantified in individual cells. Staining increases prior to septation (green area), consistent with chromosome replication, and decreases after septation (red area), consistent with transport of DNA into forespores. Data were averaged over _n_=30 cells due to cell-cell variability (error bars, s.e.m.).

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