Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response - PubMed (original) (raw)

Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response

Emma Watson et al. Cell. 2013.

Erratum in

Abstract

Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens to delineate a network of 184 genes that affect the C. elegans dietary response to Comamonas DA1877 bacteria. We find that perturbation of a mitochondrial network composed of enzymes involved in amino acid metabolism and the TCA cycle affects the dietary response. In humans, mutations in the corresponding genes cause inborn diseases of amino acid metabolism, most of which are treated by dietary intervention. We identify several transcription factors (TFs) that mediate the changes in gene expression upon metabolic network perturbations. Altogether, our findings unveil a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus.

Copyright © 2013 Elsevier Inc. All rights reserved.

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Figures

Figure 1

Figure 1. Forward Genetic Screen For Dietary Sensor Regulators

(A) Flow chart of EMS mutagenesis screen. (B) Examples of GFP expression in wild type animals and two mutant strains. (C) Cartoon illustrating amino acid changes in four proteins identified in the forward genetic screen. BD – biotin binding domain; B12B – vitamin B12 binding domain. (D) Endogenous acdh-1 and acdh-2 levels in mutants as measured by nCounter assays and normalized to ama-1. (E) Mutants exhibit different responses to starvation. See also Table S1 and Table S2.

Figure 2

Figure 2. Reverse Genetic Screen For Dietary sensor Regulators

(A) RNAi knockdown works efficiently in the presence of Comamonas DA1877. Pacdh-1::GFP animals were fed E. coli HT115 producing either dsRNA directed against mccc-1 (which was found in the forward genetic screen) or no dsRNA (vector control) in the presence and absence of Comamonas DA1877. (B) Flow chart of genome-scale RNAi screen. (C) qRT-PCR of endogenous acdh-1 mRNA in wild type animals subjected to RNAi of 11 genes found in the RNAi screen. Values were normalized to expression in a vector only control (which was set to equal 0) and plotted as log2 fold change. Yellow bars indicate genes whose knockdown caused increased GFP expression and blue bars indicate genes whose knockdown caused decreased GFP expression. Error bars indicated the standard error in three technical repeats. (D) Validation of RNAi results using mutant animals. Bright field and fluorescent images of Pacdh-1::GFP animals with wild type or mutant backgrounds, fed either E. coli OP50 or Comamonas DA1877. Yellow indicates increases in GFP expression and blue indicates decreased GFP expression compared to wild type Pacdh-1:GFP dietary sensor animals. Exposure times that are different from Pacdh-1:GFP dietary sensor animals fed E. coli OP50 are indicated in the top-right corner of the respective panel. (E) qRT-PCR of endogenous acdh-1 mRNA in Δ_sams-5_ and Δ_hlh-11_ mutant compared to wild type animals fed E. coli OP50, E. coli HT115, or Comamonas DA1877. Changes in acdh-1 expression were plotted as log2 fold change compared to acdh-1 levels in wild type animals fed E. coli OP50, which was set to equal 0. Error bars indicated the standard error in three technical repeats. See also Figures S3 and S4, Table S2, Table S3 and Table S5.

Figure 3

Figure 3. Dietary Repressors are Enriched in Four Metabolic Pathways

Cartoon of a metabolic map showing C. elegans BCAA breakdown, methionine metabolism, glycine cleavage system and TCA cycle. Rectangles indicate genes; circles are metabolites. See also Figures S1 and S5.

Figure 4

Figure 4. Metabolic Feedback and Transcriptional Compensation

(A) Increased acdh-1 promoter activity in Δ_acdh-1_ mutants identifies feedback control. (B) qRT-PCR of seven genes (rows) in different strains (columns). (C) Overlap in gene expression changes between two metabolic gene mutants. (D) Overlap between genes that change in expression in the two metabolic gene mutants and those that change in response to a Comamonas DA1877 diet. (E) Opposite changes in gene expression in response to a Comamonas DA1877 diet versus metabolic network perturbations. See also Figure S2 and Table S4.

Figure 5

Figure 5. Orthologs of Dietary Sensor Repressors Confer Human Inborn Metabolic Disorders Relating to Amino Acid Metabolism

Network connecting dietary sensor repressors, C. elegans phenotypes, human orthologs, human inborn metabolic diseases and dietary treatments. Orange nodes – C. elegans phenotypes; colored squares – C. elegans genes found in the screen; diamonds – human orthologs/homologs; gray circles – human diseases; hexagons – nutrients. Red edges indicate dietary avoidance; green edges indicate dietary supplementation.

Figure 6

Figure 6. Mediators of the Response to Metabolic Network Perturbation

(A) Summary of RNAi knockdown analysis in different mutant strains. INS – insulin signaling pathway components. The colors indicate visually examined changes in GFP expression in Pacdh-1::GFP dietary sensor animals. (B) DIC and fluorescent images of indicated strains (columns) exposed to different RNAi knockdowns (rows). Yellow arrowheads indicate an increase in GFP expression in the head hypodermis in acdh-1 RNAi knockdown animals.

Figure 7

Figure 7

Model Reflecting Feedback Communication Between Mitochondrial Metabolic Networks and Nuclear Gene Regulatory Networks

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