1. Evolutionary Biology
  2. Genetics and Genomics
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Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism

  1. Stefan Zdraljevic
  2. Bennett William Fox
  3. Christine Strand
  4. Oishika Panda
  5. Francisco J Tenjo
  6. Shannon C Brady
  7. Tim A Crombie
  8. John G Doench
  9. Frank C Schroeder
  10. Erik C Andersen  Is a corresponding author
  1. Northwestern University, United States
  2. Cornell University, United States
  3. Broad Institute of MIT and Harvard, United States
  4. The Buck Institute for Research on Aging, United States
Cite this article as: eLife 2019;8:e40260 doi: 10.7554/eLife.40260
7 figures, 1 table, 1 data set and 3 additional files

Figures

Figure 1 with 11 supplements
A large-effect QTL on the center of chromosome II explains differences in arsenic trioxide response between N2 and CB4856.

(A) Linkage mapping plots for the first principal component trait in the presence of 1000 µM arsenic trioxide is shown. The significance values (logarithm of odds, LOD, ratio) for 1454 markers between the N2 and CB4856 strains are on the y-axis, and the genomic position (Mb) separated by chromosome is plotted on the x-axis. The associated 1.5 LOD-drop confidence intervals are represented by blue boxes. The phenotypic variance explained by each QTL is shown above the peak QTL marker, which is marked by red triangles. (B) The correlation between brood size (blue; r2 = 0.38, p-value=1.65E-27) or animal length (pink; r2 = 0.74, p-value=3.16E-74) with the first principal component trait. Each dot represents an individual RIAIL’s phenotype, with the animal length and brood size phenotype values on the x-axis and the first principal component phenotype on the y-axis. (C) Tukey box plots of near-isogenic line (NIL) phenotype values for the first principal component trait in the presence of 1000 µM arsenic trioxide is shown. NIL genotypes are indicated below the plot as genomic ranges. The N2 trait is significantly different than the CB4856 and NIL traits (Tukey HSD p-value<1E-5).

https://doi.org/10.7554/eLife.40260.002
Figure 1—source data 1

Arsenic dose-response loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

PCA was performed all arsenic concentrations together in order to look at the relative PC value for each concentration.

https://doi.org/10.7554/eLife.40260.025
Figure 1—source data 2

RIAIL phenotype data used for linkage mapping.

(Used to generate Figure 1B and Figure 1—figure supplement 4).

https://doi.org/10.7554/eLife.40260.026
Figure 1—source data 3

Results from linkage mapping experiment.

https://doi.org/10.7554/eLife.40260.027
Figure 1—source data 4

Phenotypes of NILs and CRISPR allele replacement strains in the presence of 1000 µM arsenic trioxide after correcting for strain differences in control conditions.

https://doi.org/10.7554/eLife.40260.028
Figure 1—source data 5

NIL genotypes generated from whole-genome sequencing.

https://doi.org/10.7554/eLife.40260.029
Figure 1—figure supplement 1
Arsenic trioxide dose response of four diverged C. elegans strains.

Arsenic trioxide concentration in µM is plotted on the x-axis and the (A) normalized brood size, (B) mean progeny length, (C) mean normalized optical density, (D) mean normalized yellow fluorescence, or (E) the first principal component are plotted on the y-axes. For panels A-D, the y-axis values represent individual phenotypic measurements subtracted from the mean value in 0 µM arsenic trioxide. At least 15 replicates for each strain and condition are represented by Tukey box plots. Box plots are colored by strain (CB4856:blue, DL238:teal, JU775:pink, and N2:orange).

https://doi.org/10.7554/eLife.40260.003
Figure 1—figure supplement 1—source data 1

Arsenic dose-response trait data for four strains in 0, 250, 500, 1000, or 2000 µM arsenic, labeled as water, arsenic1, arsenic2, arsenic3, arsenic4 in the Condition column.

https://doi.org/10.7554/eLife.40260.004
Figure 1—figure supplement 1—source data 2

Arsenic dose-response principal component (PC) eigenvectors for the PCs that explain up to 90% of the total variance in the data set.

PCA was performed all arsenic concentrations together in order to look at the relative PC value for each concentration. Condition names correspond to those in Supplementary file 1. (Used to generate Figure 1—figure supplement 1C).

https://doi.org/10.7554/eLife.40260.005
Figure 1—figure supplement 1—source data 3

Arsenic dose-response trait correlations where each row corresponds to the Pearson correlation coefficient for two traits.

Condition names correspond to those in Supplementary file 1. (Used to generate Figure 1—figure supplement 1A-D).

https://doi.org/10.7554/eLife.40260.006
Figure 1—figure supplement 2
Trait correlations and principal component loadings of arsenic trioxide dose response.

(A) The trait Pearson’s correlation coefficient of the assay- and control-regressed measured traits from the dose response experiment with 1000 µM arsenic trioxide is shown. (B) The contribution of each measured trait to the principal components that explain 90% of the total variance is shown. For each plot, the tile color corresponds to the value, where yellow colors represent higher values.

https://doi.org/10.7554/eLife.40260.007
Figure 1—figure supplement 2—source data 1

Arsenic dose-response loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

Condition names correspond to those in Supplementary file 1. (Used to generate Figure 1—figure supplement 2B).

https://doi.org/10.7554/eLife.40260.008
Figure 1—figure supplement 3
Effect size and broad-sense heritability estimates for the arsenic trioxide dose response.

Each panel corresponds to a concentration of arsenic trioxide concentration, which is indicated above the plot panel. The x-axis represents the partial omega squared (ωp2) effect-size estimate, and the y-axis represent the broad-sense heritability estimate (H2). Each dot represents a different BIOSORT-measured or principal component trait.

https://doi.org/10.7554/eLife.40260.009
Figure 1—figure supplement 3—source data 1

Broad-sense heritability estimates from arsenic dose response data.

Estimates were calculated using the lmer function of the lme4 R package by fitting the mixed effect model equation lmer(value ~ (1|strain)), where value is the trait value and strain is the strain name. (Used to generate Figure 1—figure supplement 3).

https://doi.org/10.7554/eLife.40260.010
Figure 1—figure supplement 3—source data 2

Arsenic dose-response estimates of effect sizes estimated by fitting the linear model: trait value ~strain.

(Used to generate Figure 1—figure supplement 3).

https://doi.org/10.7554/eLife.40260.011
Figure 1—figure supplement 4
RIAIL phenotypes from the linkage mapping experiment.

Tukey box plots of the first principal component are shown: (A), assay- and control-regressed mean animal length (B), brood sizes (C), optical density (D), and mean normalized yellow fluorescence (E) of the N2 and CB4856 RIAIL panel after exposure to arsenic trioxide. Each dot corresponds to the phenotype for a single RIAIL. The RIAILs are separated by the N2 (orange) or CB4856 (blue) genotype at each QTL detected by linkage mapping.

https://doi.org/10.7554/eLife.40260.012
Figure 1—figure supplement 5
Linkage mapping results for brood size, animal length, and the first principal component.

Linkage mapping plots for regressed brood size (orange), mean normalized yellow fluorescence (pink), mean animal length (blue) and mean normalized optical density (red) in the presence of 1000 µM arsenic trioxide are shown. The significance values (logarithm of odds (LOD) ratio) for 1454 markers between the N2 and CB4856 strains are on the y-axis, and the genomic position (Mb) separated by chromosome is plotted on the x-axis. The associated 1.5 LOD-drop confidence intervals are represented by colored boxes below significant QTL.

https://doi.org/10.7554/eLife.40260.013
Figure 1—figure supplement 6
Genomic-heritability estimates of linkage mapping traits.

The genomic broad (H2)- and narrow (h2)-sense heritability estimates calculated using the expectation (E(A)) of the realized relatedness matrix or the realized relatedness matrix (A) are shown. Each dot represents a measured or principal component trait. Dots are colored black if that trait mapped to the center of chromosome II and red if no QTL was detected on the center of chromosome II.

https://doi.org/10.7554/eLife.40260.014
Figure 1—figure supplement 6—source data 1

Genomic heritability estimates from RIAIL phenotype data.

(Used to generate Figure 1—figure supplement 6).

https://doi.org/10.7554/eLife.40260.015
Figure 1—figure supplement 7
Linkage mapping QTL summary.

All QTL identified by linkage mapping are shown. Traits are labeled on the y-axis and the genomic position in Mb is plotted on the x-axis. Only PCs that explain greater than 90% of the variance are shown. Triangles represent the peak QTL position and bars represent the associated 1.5-LOD drop QTL confidence interval. Triangles and bars are colored based on the LOD score, where red colors correspond to higher LOD values.

https://doi.org/10.7554/eLife.40260.016
Figure 1—figure supplement 8
NIL recapitulation of chromosome II QTL.

Tukey box plots of near-isogenic line (NIL) phenotype values for, from top to bottom: the brood size, mean animal length, mean normalized optical density, and mean normalized yellow fluorescence traits in the presence of 1000 µM arsenic trioxide are shown. NIL genotypes are indicated below the plot as genomic ranges. The N2 phenotypes are significantly different from all other strains (Brood size: Tukey HSD p-value=2E-7; Animal Length: Tukey HSD p-value<1E-7; Optical Density: Tukey HSD p-value<1E-7; Fluorescence: Tukey HSD p-value<1E-7).

https://doi.org/10.7554/eLife.40260.017
Figure 1—figure supplement 9
Trait correlations and principal component loadings of NIL and allele-replacement recapitulation experiment.

(A) The Pearson’s correlation coefficients of the assay- and control-regressed measured traits are shown. (B) The contribution of each measured trait to the principal components that explain 90% of the total variance in the NIL and allele replacement-recapitulation experiment, which was performed at 1000 µM, is shown. For each plot, the tile color represents the value, where yellow colors represent higher values.

https://doi.org/10.7554/eLife.40260.018
Figure 1—figure supplement 9—source data 1

NIL and CRISPR allele replacement trait correlations.

(Used to generate Figure 1—figure supplement 9A).

https://doi.org/10.7554/eLife.40260.019
Figure 1—figure supplement 9—source data 2

NIL and CRISPR allele replacement trait loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

(Used to generate Figure 1—figure supplement 9B).

https://doi.org/10.7554/eLife.40260.020
Figure 1—figure supplement 10
Brood size and animal length are correlated with the first principal component for the NIL recapitulation experiment.

The correlation between brood size (blue) or animal length (pink) (A), mean normalized optical density (B) or mean normalized yellow fluorescence (C) traits with the first principal component (PC1) trait for the NIL recapitulation experiment are shown. Each dot represents an individual NIL or parental strain replicate phenotype with the animal length and brood size phenotype values on the x-axis and the first principal component (PC1) phenotype on the y-axis.

https://doi.org/10.7554/eLife.40260.021
Figure 1—figure supplement 11
Trait correlations and principal component loadings of linkage mapping experiment.

(A) The trait Pearson’s correlation coefficient of the assay- and control-regressed measured traits is shown. (B) The contribution of each measured trait to the principal components that explain 90% of the total variance in the linkage mapping experiment, which was performed at 1000 µM, is shown. For each plot, the tile color represents the value, where yellow colors represent higher values.

https://doi.org/10.7554/eLife.40260.022
Figure 1—figure supplement 11—source data 1

RIAIL trait correlations where each row corresponds to the Pearson correlation coefficient for two traits.

https://doi.org/10.7554/eLife.40260.023
Figure 1—figure supplement 11—source data 2

RIAIL loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

https://doi.org/10.7554/eLife.40260.024
Figure 2 with 6 supplements
Variation in C. elegans wild isolates responses to arsenic trioxide maps to the center of chromosome II.

(A) A manhattan plot for the first principal component in the presence of 1000 µM arsenic trioxide is shown. Each dot represents an SNV that is present in at least 5% of the assayed wild population. The genomic position in Mb, separated by chromosome, is plotted on the x-axis and the -log10(p) for each SNV is plotted on the y-axis. SNVs are colored red if they pass the genome-wide Bonferroni-corrected significance (BF) threshold, which is denoted by the gray horizontal line. SNVs are colored pink if they pass the genome-wide eigen-decomposition significance (ED) threshold, which is denoted by the dotted gray horizontal line. The genomic region of interests surrounding the QTL that pass the BF and ED thresholds are represented by cyan and pink rectangles, respectively. (B) Tukey box plots of phenotypes used for association mapping in (A) are shown. Each dot corresponds to the phenotype of an individual strain, which is plotted on the y-axis. Strains are grouped by their genotype at the peak QTL position (red SNV from panel A, ChrII:7,931,252), where REF corresponds to the allele from the reference N2 strain. The N2 (orange) and CB4856 (blue) strains are highlighted. (C) Fine mapping of the chromosome II region of interest (cyan region from panel A, 7.60–8.21 Mb) is shown. Each dot represents an SNV present in the CB4856 strain. The association between the SNV and first principal component is shown on the y-axis and the genomic position of the SNV is shown on the x-axis. Dots are colored by their SnpEff predicted effect.

https://doi.org/10.7554/eLife.40260.030
Figure 2—source data 1

Fine-mapping results for PC1.

(Used to generate Figure 2C and Figure 2—figure supplement 2).

https://doi.org/10.7554/eLife.40260.040
Figure 2—source data 2

All wild-isolate traits used for genome-wide association mapping.

https://doi.org/10.7554/eLife.40260.041
Figure 2—source data 3

Genotype matrix used for genome-wide mapping.

https://doi.org/10.7554/eLife.40260.044
Figure 2—source data 4

GWA mapping results for PC1.

(Used to generate Figure 2A–B).

https://doi.org/10.7554/eLife.40260.045
Figure 2—figure supplement 1
GWA mapping QTL summary.

All QTL identified by GWA mapping above the eigen significance threshold are shown. Traits are labeled on the y-axis and the genomic position in Mb is plotted on the x-axis. Only PCs that explain greater than 90% of the variance are shown. Triangles represent the peak QTL position, and bars represent the associated QTL region of interest. Triangles and bars are colored based on the significance value where red colors correspond to higher significance values.

https://doi.org/10.7554/eLife.40260.031
Figure 2—figure supplement 1—source data 1

All QTL identified by GWA mapping (Used to generate Figure 2—figure supplement 1).

https://doi.org/10.7554/eLife.40260.032
Figure 2—figure supplement 2
Fine-mapping of the chromosome II QTL identified by GWA mapping.

Fine mapping of the chromosome II region of interest (cyan region from Figure 1A, 7.71–8.18 Mb) is shown. Each dot represents an SNV present in the phenotyped population. SNVs present in the CB4856 strain are shown in the left panel and SNVs present in other phenotyped strains, but REF in CB4856, are shown in the right panel. The association between the SNV and first principal component (PC1) is shown on the y-axis, and the genomic position of the SNV is shown on the x-axis. Dots are colored by their SnpEff predicted effect.

https://doi.org/10.7554/eLife.40260.033
Figure 2—figure supplement 3
Tajima’s D across the arsenic trioxide QTL confidence interval.

Divergence, as measured by Tajima's D, is shown across the arsenic trioxide QTL confidence interval (II:7,430,000–8,330,000). The whole-genome SNV data set (Cook et al., 2016; Cook et al., 2017) was used for Tajima’s D calculations. Window size for the calculations was 500 SNVs with a 10 SNV sliding window size. The vertical red line marks the position of the dbt-1 locus.

https://doi.org/10.7554/eLife.40260.034
Figure 2—figure supplement 3—source data 1

Isolation locations of strains used in GWA mapping.

(Used to generate Figure 2—figure supplement 3).

https://doi.org/10.7554/eLife.40260.035
Figure 2—figure supplement 4
The worldwide distribution of the DBT-1(C78S) allele.

Cysteine (REF) is shown in orange, and serine (ALT) is shown in blue. Latitude and longitude coordinates of sampling locations were used to plot individual strains on the map.

https://doi.org/10.7554/eLife.40260.036
Figure 2—figure supplement 5
Genomic-heritability estimates of GWA mapping traits.

The genomic broad (H2)- and narrow (h2)-sense heritability estimates calculated using the realized relatedness matrix are shown. Each dot represents a measured or principal component trait. The five traits discussed throughout the manuscript are highlighted (purple: first principal component, pink: mean animal length, blue: brood size, orange; mean normalized optical density, and red: mean normalized yellow fluorescence). The four input traits for PCA in the left panel are mean normalized optical density, brood size, and mean animal length. For the right panel, mean normalized yellow fluorescence was also added.

https://doi.org/10.7554/eLife.40260.037
Figure 2—figure supplement 5—source data 1

Genomic heritability estimates of wild isolate traits.

(Used to generate Figure 2—figure supplement 5).

https://doi.org/10.7554/eLife.40260.038
Figure 2—figure supplement 6
Trait correlations and principal component loadings of GWA mapping experiment.

(A) The Pearson’s correlation coefficients of the assay- and control-regressed for measured traits are shown. (B) The contribution of each measured traits to the principal components that explain 90% of the total variance in the GWA mapping experiment, which was performed at 1000 µM, is shown. For each plot, the tile color represents the value, where yellow colors represent higher values.

https://doi.org/10.7554/eLife.40260.039
Figure 2—figure supplement 6—source data 1

Wild isolate trait loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

(Used to generate Figure 2—figure supplement 6B).

https://doi.org/10.7554/eLife.40260.042
Figure 2—figure supplement 6—source data 2

Wild isolate trait correlations.

(Used to generate Figure 2—figure supplement 6A).

https://doi.org/10.7554/eLife.40260.043
Figure 3 with 2 supplements
The DBT-1(C78S) variant contributes to arsenic trioxide responses.

Tukey box plots of the first principal component generated by PCA on allele-replacement strainphenotypes measured by the COPAS BIOSORT 1000 μM arsenic trioxide exposure are shown (N2,orange; CB4856, blue; allele replacement strains, gray). Labels correspond to the genetic backgroundand the corresponding residue at position 78 of DBT-1 (C for cysteine, S for serine). All pair-wise comparisons are significantly different (Tukey HSD, p-value < 1E-7).

https://doi.org/10.7554/eLife.40260.046
Figure 3—figure supplement 1
The DBT-1 C78S variant underlies arsenic trioxide sensitivity in C. elegans.

From top to bottom: Tukey box plots of residual mean animal length, brood size, mean normalized yellow fluorescence, and mean normalized optical density after exposure to 1000 µM arsenic trioxide are shown (N2, orange; CB4856, blue; allele replacement strains, gray). Labels correspond to the genetic background and the corresponding residue at position 78 of DBT-1 (C for cysteine, S for serine). Every pairwise strain comparison was significant (Brood size: Tukey’s HSD p-value<1.55E-5; Animal length: p-value<2E-73; Fluorescence: p-value<1E-7; Optical Density: p-value<1E-7).

https://doi.org/10.7554/eLife.40260.047
Figure 3—figure supplement 2
Brood size and animal length are correlated with the first principal component for the allele- replacement recapitulation experiment.

The correlations between brood size (blue) or animal length (pink) with the first principal component trait for the allele- replacement recapitulation experiment are shown. Each dot represents an individual allele-replacement or parental strain replicate phenotype, with the animal length and brood size phenotype values on the x-axis and the first principal component (PC1) phenotype on the y-axis.

https://doi.org/10.7554/eLife.40260.048
Figure 4 with 9 supplements
Differential production of mmBCFA underlies DBT-1(C78)-mediated sensitivity to arsenic trioxide.

(A) A simplified model of BCAA catabolism in C. elegans. The BCKDH complex, which consists of DBT-1, catalyzes the irreversible oxidative decarboxylation of branched-chain ketoacids. The products of thesebreakdown can then serve as building blocks for the mmBCFA that are required for developmental progression. (B) The difference in the C15ISO/C15SC (left panel) or C17ISO/C17SC (right panel) ratios between 100 μM arsenic trioxide and control conditions is plotted on the y-axis for three independent replicates of the CB4856 and CB4856 allele replacement strains and six independent replicates of the N2and N2 allele replacement strains. The difference between the C15 ratio for the CB4856-CB4856 allele replacement comparison is significant (Tukey HSD p-value = 0.0427733), but the difference between the C17 ratios for these two strains is not (Tukey HSD p-value = 0.164721). The difference between the C15and C17 ratios for the N2-N2 allele replacement comparisons are both significant (C15: Tukey HSD p-value = 0.0358; C17: Tukey HSD p-value = 0.003747). (C) Tukey box plots median animal length after arsenic trioxide or arsenic trioxide and 0.64 μM C15ISO exposure are shown (N2, orange; CB4856, blue; allele replacement strains, gray). Labels correspond to the genetic background and the corresponding residue at position 78 of DBT-1 (C for cysteine, S for serine). Every pair-wise strain comparison is significant except for the N2 DBT-1(S78) - CB4856 comparisons (Tukey’s HSD p-value < 1.43E-6).

https://doi.org/10.7554/eLife.40260.049
Figure 4—source data 1

Metabolite measurements for the CB4856 and CB4856 allele replacement strains (Used for Figure 4B and Figure 4—figure supplement 13).

https://doi.org/10.7554/eLife.40260.062
Figure 4—source data 2

Processed metabolite measurements for the CB4856 and CB4856 allele replacement strains (Used for Figure 4B and Figure 4—figure supplement 13).

https://doi.org/10.7554/eLife.40260.063
Figure 4—source data 3

Metabolite measurements for the N2 and N2 allele replacement strains (Used for Figure 4B and Figure 4—figure supplement 13).

https://doi.org/10.7554/eLife.40260.064
Figure 4—source data 4

Processed phenotype data for the C15ISO rescue experiment (Used to generate Figure 4C).

https://doi.org/10.7554/eLife.40260.065
Figure 4—figure supplement 1
Raw abundance of C17ISO for CB4856 and CB4856 allele replacement.

The raw abundance of C17ISO is plotted on the y-axis for three independent replicates of the CB4856 and CB4856 allele replacement strains exposed to control (teal) or 100 µM arsenic trioxide (pink) conditions. The difference between CB4856 replacement mock and arsenic conditions was significant (Tukey HSD p-value=0.029), but the difference between CB4856 mock and arsenic conditions was not significant (Tukey HSD p-value=0.10).

https://doi.org/10.7554/eLife.40260.050
Figure 4—figure supplement 2
Straight-chain fatty acids are not affected by arsenic trioxide.

The difference in raw C15SC (left panel) or C17SC (right panel) abundances between 100 µM arsenic trioxide and control conditions is plotted on the y-axis for three independent replicates of the CB4856 and CB4856 allele replacement strains and six independent replicates of the N2 and N2 allele replacement strains. We found no significant differences when comparing the abundances between parental and allele-replacement strains.

https://doi.org/10.7554/eLife.40260.051
Figure 4—figure supplement 2—source data 1

C15ISO rescue trait loadings of principal components (PCs) for the PCs that explain up to 90% of the total variance in the trait data.

(Used to generate Figure 4—figure supplement 2B).

https://doi.org/10.7554/eLife.40260.052
Figure 4—figure supplement 3
C15ISO and C17ISO to strait-chain ratios in control conditions.

The C15ISO/C15SC (left panel) or C17ISO/C17SC (right panel) ratios in control conditions are plotted on the y-axis for three independent replicates of the CB4856 and CB4856 allele replacement strains and six independent replicates of the N2 and N2 allele replacement strains. The C15 and C17 ratios for the CB4856-CB4856 allele replacement comparison were significant (C15: Tukey HSD p-value=0.0168749; C17: Tukey HSD p-value=0.0342525). The difference between the C17 ratio for the N2-N2 allele replacement comparison was significant (Tukey HSD p-value=0.0044667), but the difference in the C15 ratio was not significant (Tukey HSD p-value=0.1239674).

https://doi.org/10.7554/eLife.40260.053
Figure 4—figure supplement 4
Strains with the DBT-1(C78) allele produce more branched chain fatty acids in the L1 larval stage in control conditions.

Branched chain (left panel) and straight chain (right panel) fatty acid measurements in L1 animals arerepresented on the y-axis. We found significant differences in abundances when comparing all parentaland allele-replacement strains for C15ISO and C17ISO chain fatty acids (CB4856-C15ISO DBT-1(C78):Tukey HSD p-value = 0.0036201, n=3; N2-C15ISO DBT-1(C78): Tukey HSD p-value = 0.0265059, n=6;CB4856-C17ISO DBT-1(C78): Tukey HSD p-value = 0.0086572, n=3; N2-C17ISO DBT-1(C78): TukeyHSD p-value = 0.0022501, n=6). Conversely, we observed no significant differences in straight chain fattyproduction except for C17n production in the CB4856 background (CB4856-C15n DBT-1(C78): TukeyHSD p-value = 0.0787388, n=3; N2-C15n DBT-1(C78): Tukey HSD p-value = 0.5817993, n=6; CB4856-C17n DBT-1(C78): Tukey HSD p-value = 0.0086572, n=3; N2-C17n DBT-1(C78): Tukey HSD p-value =0.35827, n=6).

https://doi.org/10.7554/eLife.40260.054
Figure 4—figure supplement 4—source data 1

Metabolite measurements for N2, CB4856, and both allele-replacement strains at the L4 larval stage.

(Used to generate Figure 4—figure supplement 4).

https://doi.org/10.7554/eLife.40260.055
Figure 4—figure supplement 5
Young adult C15ISO and C17ISO to strait-chain ratios in control conditions.

The C15ISO/C18SC (top panel) or C17ISO/C18SC(bottom panel) ratios of young adult animals in control conditions are plotted on the y-axis for six independent replicates for all strains. We found no significant differences when comparing the abundances between parental and allele-replacement strains.

https://doi.org/10.7554/eLife.40260.056
Figure 4—figure supplement 5—source data 1

Trait correlations for the for the C15ISO rescue experiment (Used to generate Figure 4—figure supplement 5).

https://doi.org/10.7554/eLife.40260.057
Figure 4—figure supplement 6
Complete results from C15iso rescue experiment.Tukey box plots for the PC1 trait after 0.64 µM C15ISO, arsenic trioxide, or arsenic trioxide and 0.64 µM C15ISO exposure are shown (N2, orange; CB4856, blue; allele replacement strains, gray).

Labels correspond to the genetic background and the corresponding residue at position 78 of DBT-1 (C for cysteine, S for serine). Every pairwise strain comparison was significant except for the N2 DBT-1(S78) - CB4856 comparisons (Tukey’s HSD p-value<1.43E-6).

https://doi.org/10.7554/eLife.40260.058
Figure 4—figure supplement 7
BIOSORT-quantified traits for C15ISO rescue experiment Tukey box plots for the mean normalized optical density.

(A), mean animal length (B), brood size (C), and mean normalized yellow fluorescence (D) traits after 0.64 µM C15ISO, arsenic trioxide, or arsenic trioxide and 0.64 µM C15ISO exposure are shown (N2, orange; CB4856, blue; allele replacement strains, gray). Labels correspond to the genetic background and the corresponding residue at position 78 of DBT-1 (C for cysteine, S for serine). For all traits, except brood size, the comparison between arsenic and arsenic with C15ISO for strains with the DBT-1(C78) allele was significant (Tukey’s HSD p-value<2E-3).

https://doi.org/10.7554/eLife.40260.059
Figure 4—figure supplement 8
Trait correlations and principal component loadings of C15ISO rescue experiment.

(A) The Pearson’s correlation coefficients of the assay- and control-regressed measured traits are shown. (B) The contribution of each measured trait to the principal components that explain 90% of the total variance in the GWA mapping experiment, which was performed at 1000 µM, is shown. For each plot, the tile colors represent the value, where yellow colors represent higher values.

https://doi.org/10.7554/eLife.40260.060
Figure 4—figure supplement 9
Brood size and animal length are correlated with the first principal component for the C15ISO rescue experiment.

The correlations between brood size (blue) or animal length (pink) with the first principal component trait for the C15ISO rescue experiment are shown. Each dot represents an individual allele-replacement or parental strain replicate phenotype, with the animal length and brood size phenotype values on the x-axis and the first principal component phenotype on the y-axis.

https://doi.org/10.7554/eLife.40260.061
Figure 5 with 1 supplement
Protective effect of cysteine residues in human DBT1.

(A) Alignment of C. elegans DBT-1 and H. sapiens DBT1. The residues tested for an arsenic-specific effect are indicated with arrows - W84C (pink), S112C (blue), and R113C (black). The lysine that is post-translationally modified with a lipoid acid is highlighted in red. (B) The percent increase of edited human cells that contain the W84C, S112C, or R113C amino acid change in DBT1 in the presence 5 µM arsenic trioxide relative to control conditions are shown. The number of reads in 5 µM arsenic trioxide for all replicates are significantly different from control conditions (Fisher’s exact test, p-value<0.011).

https://doi.org/10.7554/eLife.40260.066
Figure 5—source data 1

Human cell line read data for CRISPR replacement experiment in 293 T cells.

(Used to generate Figure 5B).

https://doi.org/10.7554/eLife.40260.069
Figure 5—source data 2

Results from Fisher’s exact test of human cell line read data for CRISPR replacement experiment in 293 T cells.

https://doi.org/10.7554/eLife.40260.070
Figure 5—source data 3

Metabolite measurements from human cell line experiments.

https://doi.org/10.7554/eLife.40260.071
Figure 5—figure supplement 1
Three-dimensional homology model of C. elegans DBT-1 A three-dimensional homology model of C. elegans DBT-1 (black) aligned to human pyruvate dehydrogenase lipoyl domain (PDB:1Y8N) is shown.

The C78 residue that conferred resistance to arsenic trioxide is highlighted in orange, and the C65 residue is highlighted in purple. The C. elegans K71 residue is highlighted in red, and the human lipoylated lysine is highlighted in green.

https://doi.org/10.7554/eLife.40260.067
Figure 5—figure supplement 1—source data 1

Tajima’s D of GWA mapping confidence interval.

(Used to generate Figure 5—figure supplement 1).

https://doi.org/10.7554/eLife.40260.068
Author response image 1
GWA mapping QTL summary.

All QTL identified by GWA mapping are shown. Traits are labeled on the y-axis, and the genomic position in Mb is plotted on the x-axis. Triangles represent the peak QTL position, and bars represent the associated QTL region of interest. Triangles and bars are colored based on the significance value, where red colors correspond to higher significance values.

https://doi.org/10.7554/eLife.40260.076
Author response image 2
Linkage mapping QTL summary.

All QTL identified by linkage mapping are shown. Traits are labeled on the y-axis, and the genomic position in Mb is plotted on the x-axis. Triangles represent the peak QTL position, and bars represent the associated 1.5-LOD drop QTL confidence interval. Triangles and bars are colored based on the LOD score, where red colors correspond to higher LOD values.

https://doi.org/10.7554/eLife.40260.077

Tables

Key resources table
Reagent type
(species) or
resource
DesignationSource or
reference
IdentifiersAdditional
information
Gene
(Caenorhabditis elegans)
dbt-1NAWormbase:WBGene00014054
Strain, strain
background
(C. elegans)
N2 DBT-1(S78)This paperAndersen_Lab:ECA581dbt-1(ean15[C78S])
Strain, strain
background
(C. elegans)
CB4856 DBT-1(C78)This paperAndersen_Lab:ECA590dbt-1(ean34[S78C])
Strain, strain
background
(C. elegans)
Left NIL; CB4856 > N2 (II:5.75–8.02 Mb)This paperAndersen_Lab:ECA414eanIR188[II:5.75–8.02 Mb,
CB4856 > N2]
Strain, strain
background
(C. elegans)
Right NIL; CB4856 > N2 (II:7.83–9.66 Mb)This paperAndersen_Lab:ECA434eanIR208[II:7.83–9.66 Mb,
CB4856 > N2]
Sequence-based
reagent
NIL Fd primerThis paperAndersen_Lab:oECA609tttcacacaaaccatgcgct
Sequence-based
reagent
NIL Rv primerThis paperAndersen_Lab:oECA610actcgtctgctgggtattct
Sequence-based
reagent
NIL Fd primerThis paperAndersen_
Lab:oECA611
tgtcttcgcacctttactcg
Sequence-based
reagent
NIL Rv primerThis paperAndersen_
Lab:oECA612
cattcaagtcagggcgtatcc
Sequence-based
reagent
Genotype C78S EditThis paperAndersen_Lab:oECA1163GAAGGAATTGCCGAAGTTCAGGTTAAG
Sequence-based
reagent
Genotype C78S EditThis paperAndersen_Lab:oECA1165CCGTCATCTCCACAAAAAGCTTTATCTCTC
Sequence-based
reagent
dbt-1 gRNAThis paperAndersen_
Lab:crECA97
CCATCTCCTGTAGATACGAC
Sequence-based reagentN2 dbt-1 repair oligoThis paperAndersen_
Lab:oECA1542
CTTCCAGGTACGTGAAAGAAGGAGATACGATTTCGCAGTTCGATAAAGTCTGTGAAGTGCAAAGTGATAAAGCAGCAGTAACCATCTCCAGTAGATACGACGGAATTGTCAAAAAATTGTAAGTTTCTTCCTAA
Sequence-based
reagent
CB4856 dbt-1 repair oligoThis paperAndersen_
Lab:oECA1543
TTAGGAAGAAACTTACAATT
TTTTGACAATTCCGTCGTATCTACAGGAGATGGTTACTGCT
GCTTTATCGCTTTGCACTTCACAGACTTTATCGAACTGCGAAATCGTATCTCCTTCTTTCACGTACCTGGAAG
Sequence-based
reagent
dpy-10 repair oligoKim et al., 2014Andersen_Lab:crECA37CACTTGAACTTCAATACGGCAAGATGAGAATGACTGGAAACCGTACCGCATGCGGTGCCTATGGTAGCGGAGCTTCACATGGCTTCAGACCAACAGCCTAT
Sequence-based
reagent
dpy-10 gRNAKim et al., 2014Andersen_Lab:crECA36GCTACCATAGGCACCACGAG
Sequence-based
reagent
Human gRNA S112C and R113CThis paperGuide_1 used in RDA_74TCCATCATAACGACTAGTGA
Sequence-based
reagent
S112C repair templateThis paper1192 DBT1-repair-S112CATAGCATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACAATCACTTGTCGTTATGATGGAGTCATTAAAAAACTCTATT
Sequence-based
reagent
R113C repair templateThis paper1193 DBT1-repair-R113CATAGCATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACAATCACTAGTTGTTATGATGGAGTCATTAAAAAACTCTATT
Sequence-based reagentFwd PCR CThis paper1188 DBT1-PCR-CTtgtggaaaggacgaaacaccgAGAAGGAGATACAGTGTCTCAGT
Sequence-based
reagent
Fwd PCR DThis paper1189 DBT1-PCR-DTtgtggaaaggacgaaacaccgTGTCTCAGTTTGATAGCATCTGTG
Sequence-based
reagent
Human gRNA W84CThis paperGuide_2 used in RDA_75TCTTTTAGGTATGTAAAAGA
Sequence-based
reagent
W84C repair templateThis paper1195 DBT1-repair-W84C-v2GACTGTTTCCATAAAAGTGTCTCATTTCTTTTTCTTTTAGTTATGTGAAGGAAGGAGATACAGTGTCTCAGTTTGATAGCAT
Sequence-based
reagent
Fwd PCR AThis paper1186 DBT1-PCR-ATtgtggaaaggacgaaacaccgGCATGGCATTTACATCCTTAATATGAT
Sequence-based
reagent
Fwd PCR BThis paper1187 DBT1-PCR-BTtgtggaaaggacgaaacaccgCCTTAATATGATCTGTACTTATGACTGTTT
Sequence-based
reagent
Rev PCR 1This paper1190 DBT1-PCR-Rev1TctactattctttcccctgcactgtCTACTAATGGCTTCCCCACAT
Sequence-based
reagent
Rev PCR 2This paper1191 DBT1-PCR-Rev2TctactattctttcccctgcactgtCAATACCTTTTAAAGCTTCCGTTTCTAT
Transfected
construct
(Homo Sapiens)
S112C and R113C Cas9-sgRNA plasmidThis paperp1054
Transfected
construct
(Homo Sapiens)
W84C Cas9-sgRNA plasmidThis paperp1052

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files.

The following previously published data sets were used
  1. 1
    NCBI Sequence Read Archive
    1. DE Cook
    2. EC Andersen
    (2016)
    ID PRJNA318647. CeNDR wild isolate WGS data.

Additional files

Supplementary file 1

Plasmid used for editing human cells with the S112C and R113C edits.

https://doi.org/10.7554/eLife.40260.072
Supplementary file 2

Plasmid used for editing human cells with the W84C edit.

https://doi.org/10.7554/eLife.40260.073
Transparent reporting form
https://doi.org/10.7554/eLife.40260.074

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