Fitness effects of altering gene expression noise in <i>Saccharomyces cerevisiae</i>

Gene expression noise is an evolvable property of biological systems that describes differences in expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the TDH3 gene in Saccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise

Role of Pleiotropy in the Evolution of a Cryptic Developmental Variation in Caenorhabditis elegans

Using vulval phenotypes in Caenorhabditis elegans, the authors show that cryptic genetic variation can evolve through selection for pleiotropic effects that alter fitness, and identify a cryptic variant that has conferred enhanced fitness on domesticated worms under laboratory conditions

Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae.

International audienceUNLABELLED: ABSTRACT: BACKGROUND: The nematode Caenorhabditis elegans is a major model organism in laboratory biology. Very little is known, however, about its ecology, including where it proliferates. In the past, C. elegans was mainly isolated from human-made compost heaps, where it was overwhelmingly found in the non-feeding dauer diapause stage. RESULTS: C. elegans and C. briggsae were found in large, proliferating populations in rotting plant material (fruits and stems) in several locations in mainland France. Both species were found to co-occur in samples isolated from a given plant species. Population counts spanned a range from one to more than 10,000 Caenorhabditis individuals on a single fruit or stem. Some populations with an intermediate census size (10 to 1,000) contained no dauer larvae at all, whereas larger populations always included some larvae in the pre-dauer or dauer stages. We report on associated micro-organisms, including pathogens. We systematically sampled a spatio-temporally structured set of rotting apples in an apple orchard in Orsay over four years. C. elegans and C. briggsae were abundantly found every year, but their temporal distributions did not coincide. C. briggsae was found alone in summer, whereas both species co-occurred in early fall and C. elegans was found alone in late fall. Competition experiments in the laboratory at different temperatures show that C. briggsae out-competes C. elegans at high temperatures, whereas C. elegans out-competes C. briggsae at lower temperatures. CONCLUSIONS: C. elegans and C. briggsae proliferate in the same rotting vegetal substrates. In contrast to previous surveys of populations in compost heaps, we found fully proliferating populations with no dauer larvae. The temporal sharing of the habitat by the two species coincides with their temperature preference in the laboratory, with C. briggsae populations growing faster than C. elegans at higher temperatures, and vice at lower temperatures

A polymorphism in the <i>nath-10</i> gene explains the largest effect QTL.

<p>(A) Fine-mapping of the QTL to a 183 kb region (gray rectangle). Chromosome I genotypes of five near-isogenic lines (NILs) at SNP markers (triangles) are represented. Orange triangles, N2 alleles; blue, AB1. Their vulval index at 25.5°C is indicated below. Genetic distances are represented to scale along full black lines, but not outside. The vulval index is significantly lower in JU1613 compared to the other NILs (Mann-Whitney-Wilcoxon rank sum tests, <i>p</i><10⁻⁴, <i>n</i> = 30–42). (B) RNAi against <i>nath-10</i>. The significance of pairwise Mann-Whitney-Wilcoxon rank sum tests comparing the <i>nath-10</i> RNAi versus control bacteria is represented above each pair of bars (<i>n</i> = 51–64). Combined <i>p</i> values of replicates using Fisher's method is indicated above. (C) Overexpression of N2 and AB1 <i>nath-10</i> alleles. Worms that spontaneously lost the transgene (gray) were compared to sibling worms that retained it (red). Black bars represent non-injected strains. Two replicates were scored per injected strain and allele (<i>n</i> = 36–45). Pairwise comparisons using Mann-Whitney-Wilcoxon rank sum tests were only significant in one case. However, combining the results using Fisher's method (top) showed a significant effect of each allele when injected into JU605, but not into JU1620. (D) Introgression of the <i>nath-10</i> allele from LSJ1 into N2. The vulval index of JU606, JU1610, and JU2000 was compared to N2 in two replicate experiments using Mann-Whitney-Wilcoxon rank sum tests. (B–D) Vulval phenotypes were scored in animals grown at 25.5°C. ns, non-significant, * 0.01<<i>p</i><0.05, *** <i>p</i><0.001. Strain genotypes are schematized below the graphs, with orange for N2 and blue for AB1 background. Orange and blue horizontal lines on chromosome I represent <i>nath-10</i> alleles and the red line on chromosome II <i>let-23(sy1)</i>. Only one chromosome copy is shown (the strains are rendered homozygous through selfing).</p

Cryptic variation in <i>C. elegans</i> vulval cell fate patterning.

<p>(A) Patterning of vulval cell fates in <i>C. elegans</i> through an intercellular signaling network. After induction, each cell divides with a characteristic division pattern. Letters indicate the orientation of the last division as follows: T, transverse (left-right); L, longitudinal (anteroposterior); U, undivided. Cells attached to the cuticle are underlined. (S) corresponds to a fusion with the hypodermal syncytium cell hyp7, which is a non-vulval fate. (B) Variable vulval expressivity of the <i>let-23(sy1)/egfr</i> sensitizing mutation in the N2 genetic background, observed under Nomarski optics at the L4 stage. The number of induced vulval precursor cells is inferred from their progeny number and morphology in the L4 stage. The expressivity of the mutation differs among genetically identical individuals. The gray arrows point to the expected position of the vulva. (C) Schematic representation of cryptic variation. Genetic variation between wild genotypes leads to variation in intermediate developmental processes such as signaling pathway activities, while the final system output (here vulval cell fates) remains invariant. (D) For instance, the level of expression of the Ras pathway reporter <i>egl-17::cfp</i> in P6.p during vulval induction (L3 stage) is about twice lower in the N2 reference strain compared to the AB1 wild isolate <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio.1001230-Milloz1" target="_blank">[10]</a>, yet for both strains the resulting number of induced vulval cells is 3. (E) Cryptic variation is uncovered by sensitizing the system with a mutation. The <i>let-23(sy1)/egfr</i> mutation shifts the system outside the buffered region of genotypic space (neutral space). The initially silent difference between N2 and AB1 is now phenotypically expressed at the level of the final product. (F) Expressivity of vulval defects of <i>let-23(sy1)/egfr</i> as a function of wild genetic background and temperature. In particular, the N2 genetic background leads to a lower vulval induction index compared to the AB1 background when the system is sensitized, which might be explained by the difference of Ras pathway activity observed in (C). A two-way Scheirer-Ray-Hare extension of the Kruskal-Wallis test detected significant effects of <i>strain</i> and <i>temperature</i> on the number of induced vulval cells (<i>strain</i>: <i>F</i> = 15.91, <i>p</i> = 0.0005; <i>temperature</i>: <i>F</i> = 63.69, <i>p</i><0.0001). The genotype-by-environment interaction was not significant in this overall analysis (<i>strain</i>×<i>temperature</i>: <i>F</i> = 1.21, <i>p</i> = 0.3386). All pairwise comparisons were performed using Mann-Whitney-Wilcoxon rank sum tests with Holm-Bonferroni method to correct for multiple comparisons. Two bars are significantly different (<i>p</i><0.05) if they are not labeled with a same letter. Error bars indicate the standard error of the mean (SE) over individuals (<i>n</i> = 30–72).</p

Role of <i>nath-10</i> in germ line sex determination.

<p>(A) Fitness trade-off between minimal generation time and total fertility in <i>C. elegans</i> hermaphrodites. Sperm number is a limiting factor for self-brood size. A variation of self-brood size observed among wild isolates could be explained by a variation in the timing of the sperm/oocyte switch (dotted brown line). The optimal duration of spermatogenesis that maximizes the fitness likely depends on the environmental and genetic context <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio.1001230-Cutter1" target="_blank">[52]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio.1001230-Murray1" target="_blank">[72]</a>. (B) Effect of the <i>nath-10</i> polymorphism on the number of sperm produced per gonad arm at 20°C (<i>n</i> = 39). One gonad arm per animal was scored. We found no significant difference in the number of sperm produced by the anterior and posterior arms (Mann-Whitney-Wilcoxon test, <i>p</i> = 0.5). The number per gonad arm was thus doubled on the <i>y</i>-axis on the right for direct comparison with brood size (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio-1001230-g006" target="_blank">Figure 6B</a>). The phenotypes of the two strains were compared using Mann-Whitney-Wilcoxon test: *** <i>p</i><0.001. (C–D) Gonad arms of adult hermaphrodites fixed 1 d after sexual maturity and stained with DAPI. (C) In wild-type adults, maturing oocytes are located distally to the spermatheca and present a characteristic size and shape. Spermatozoa are located mainly in the spermatheca, but some may be driven into the uterus by newly fertilized eggs. Hyper-condensed sperm nuclei can be easily distinguished using DAPI staining. The uterus contains developing embryos. (D) <i>nath(RNAi)</i> leads to complete sterility and a partially penetrant absence of differentiated oocytes. Sperm-like cells spread throughout the proximal arm of the gonad. The animal also displays a Protruding Vulva phenotype. Bar: 40 µm.</p

Competitive advantage of N2 over an introgressed line carrying the <i>nath-10(haw6805)</i> allele.

<p>N2 was competed in alternance of growth and starvation against JU1648 (red curve) and in continuous growth conditions against JU1648 (blue curve), JU2041 (green curve), and JU2047 (purple curve) strains. Cultures were transferred every ≈42 h for continuous growth and every week for the alternance with starvation. All experiments were started with equal numbers of synchronized individuals from each strain in 40 replicates. The frequency of <i>nath-10</i> alleles was assessed at different time points by quantitative pyrosequencing. In all cases, the frequency of the <i>nath-10(haw6805)</i> allele significantly decreased through time (comparisons between transfer 1 and 5 with Mann-Whitney-Wilcoxon rank sum test, <i>p</i> = 0.02249 for N2 versus JU2047 and <i>p</i> = 0.01797 for N2 versus JU2041, see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio.1001230.s012" target="_blank">Table S7</a> for statistical analysis of the N2 versus JU1648 experiments). The competitions of N2 against JU2041 or JU2047 were performed at the same time, but not in parallel to the N2 versus JU1648 experiments. The genotype of JU2041 and JU2047 in the vicinity of <i>nath-10</i> is shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio.1001230.s005" target="_blank">Figure S5A</a>.</p

Non-cryptic effect of the <i>nath-10</i> polymorphism on life history traits.

<p>(A) Minimal generation time at 20°C (<i>n</i> = 19–20). (B) Brood size at 20°C (<i>n</i> = 17–20 parents). (C) Maximal egg laying rate at 20°C (<i>n</i> = 17–20). Each strain carrying <i>nath-10(haw6805)</i> (and no sensitizing mutation) was compared to N2 (Mann-Whitney-Wilcoxon rank sum test). Bars of different shades represent replicates, with the same shade in different panels indicating that the same individuals were scored for different traits. The <i>p</i> values of replicates were combined using Fisher's method and represented above the dotted lines. ns, non-significant; * <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001. Genotypes are schematized below as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio-1001230-g003" target="_blank">Figure 3</a>.</p

Effect of the QTL on expressivity of <i>let-60(n1046)/ras</i>.

<p>The bar shades represent four independent replicates. Mann-Whitney-Wilcoxon rank sum tests followed by Holm-Bonferroni correction for multiple testing were used to test for significant differences of strains carrying the AB1 QTL allele (JU473 or JU1756) with the strain carrying the N2 allele (JU601). ns, non-significant; <b>**</b><i>p</i><0.01, <b>***</b><i>p</i><0.001 (<i>n</i> = 21–46). Stars above dotted lines represent the combination of the <i>p</i> values obtained for the four replicates using Fisher's method. Genotypes are schematized as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001230#pbio-1001230-g003" target="_blank">Figure 3</a>, except that green lines indicate <i>let-60(n1046)</i>.</p

Intraspecific evolution of the intercellular signaling network underlying a robust developmental system

Many biological systems produce an invariant output when faced with stochastic or environmental variation. This robustness of system output to variation affecting the underlying process may allow for “cryptic” genetic evolution within the system without change in output. We studied variation of cell fate patterning of Caenorhabditis elegans vulva precursors, a developmental system that relies on a simple intercellular signaling network and yields an invariant output of cell fates and lineages among C. elegans wild isolates. We first investigated the system’s genetic variation in C. elegans by means of genetic tools and cell ablation to break down its buffering mechanisms. We uncovered distinct architectures of quantitative variation along the Ras signaling cascade, including compensatory variation, and differences in cell sensitivity to induction along the anteroposterior axis. In the unperturbed system, we further found variation between isolates in spatio-temporal dynamics of Ras pathway activity, which can explain the phenotypic differences revealed upon perturbation. Finally, the variation mostly affects the signaling pathways in a tissue-specific manner. We thus demonstrate and characterize microevolution of a developmental signaling network. In addition, our results suggest that the vulva genetic screens would have yielded a different mutation spectrum, especially for Wnt pathway mutations, had they been performed in another C. elegans genetic background