Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy

Trends in Endocrinology and Metabolism

Volumn 25, Issue 10, 2014, Pages 502-508

  Watson, Emma ^a   Walhout, Albertha J M ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Bacteria; C. elegans; Gene expression; Gene regulatory network; Life history traits; Metabolic network; Nuclear hormone receptors; Nutrient response; Transcription

Indexed keywords

HORMONE RECEPTOR; MICRORNA; TRACE ELEMENT; TRANSCRIPTION FACTOR; TRANSCRIPTOME; CAENORHABDITIS ELEGANS PROTEIN;

CAENORHABDITIS ELEGANS; CELL METABOLISM; DIETARY INTAKE; FATTY ACID METABOLISM; FEEDBACK SYSTEM; GENE FUNCTION; GENE REGULATORY NETWORK; GENETIC REGULATION; HUMAN; METABOLIC REGULATION; METABOLOME; METABOLOMICS; MODEL; NONHUMAN; PHENOTYPE; REVIEW; SPHINGOLIPID METABOLISM; TRANSCRIPTION INITIATION; TRANSCRIPTOMICS; XENOBIOTIC METABOLISM; ANIMAL; CELLS; DIET; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CELLS; DIET; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS;

EID: 84908099415     PISSN: 10432760     EISSN: 18793061     Source Type: Journal    
DOI: 10.1016/j.tem.2014.03.004     Document Type: Review

References (69)

1. Sanderson S., et al. The incidence of inherited metabolic disorders in the West Midlands, UK. Arch. Dis. Child. 2006, 91:896-899.
2. Wild S., et al. Global prevalence of diabetes: estimates for the year 2000 and projections for 2030. Diabetes Care 2004, 27:1047-1053.
3. Pegklidou K., et al. Nutritional overview on the management of type 2 diabetes and the prevention of its complications. Curr. Diabetes Rev. 2010, 6:400-409.
4. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018. The C. elegans Sequencing Consortium.
5. Stein L., et al. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 2001, 29:82-86.
6. Kamath R.S., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237.
7. Rual J.F., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 2004, 14:2162-2168.
8. Deplancke B., et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125:1193-1205.
9. Li S., et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
10. Reece-Hoyes J.S., et al. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol. Cell 2013, 51:116-127.
11. Tikhanovich I., et al. Forkhead box class O transcription factors in liver function and disease. J. Gastroenterol. Hepatol. 2013, 28(Suppl. 1):125-131.
12. Jewell J.L., et al. Amino acid signalling upstream of mTOR. Nat. Rev. Mol. Cell Biol. 2013, 14:133-139.
13. Mark M., et al. A genetic dissection of the retinoid signalling pathway in the mouse. Proc. Nutr. Soc. 1999, 58:609-613.
14. Carlberg C., Campbell M.J. Vitamin D receptor signaling mechanisms: integrated actions of a well-defined transcription factor. Steroids 2013, 78:127-136.
15. Contreras A.V., et al. PPAR-alpha as a key nutritional and environmental sensor for metabolic adaptation. Adv. Nutr. 2013, 4:439-452.
16. Desvergne B., et al. Transcriptional regulation of metabolism. Physiol. Rev. 2006, 86:465-514.
17. Taubert S., et al. Nuclear hormone receptors in nematodes: evolution and function. Mol. Cell. Endocrinol. 2011, 334:49-55.
18. Motola D.L., et al. Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans. Cell 2006, 124:1209-1223.
19. Mahanti P., et al. Comparative metabolomics reveals endogenous ligands of DAF-12, a nuclear hormone receptor, regulating C. elegans development and lifespan. Cell Metab. 2014, 19:73-83.
20. Arda H.E., et al. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol. Syst. Biol. 2010, 6:367.
21. Macneil L.T., Walhout A.J. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011, 21:645-657.
22. Ravasz E., et al. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
23. Babu M.M., et al. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 2004, 14:283-291.
24. Ritter A.D., et al. Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res. 2013, 23:954-965.
25. Felix M.A., Braendle C. The natural history of Caenorhabditis elegans. Curr. Biol. 2010, 20:R965-R969.
26. Shtonda B.B., Avery L. Dietary choice behavior in Caenorhabditis elegans. J. Exp. Biol. 2006, 209:89-102.
27. Avery L., Shtonda B.B. Food transport in the C. elegans pharynx. J. Exp. Biol. 2003, 206:2441-2457.
28. MacNeil L.T., et al. Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell 2013, 153:240-252.
29. Soukas A.A., et al. Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans. Genes Dev. 2009, 23:496-511.
30. Coolon J.D., et al. Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PLoS Genet. 2009, 5:e1000503.
31. Watson E., et al. Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell 2013, 153:253-266.
32. Jones L.M., et al. Adaptive and specialised transcriptional responses to xenobiotic stress in Caenorhabditis elegans are regulated by nuclear hormone receptors. PLoS ONE 2013, 8:e69956.
33. Wang J., et al. RNAi screening implicates a SKN-1-dependent transcriptional response in stress resistance and longevity deriving from translation inhibition. PLoS Genet. 2010, 6:e1001048.
34. O'Rourke E.J., Ruvkun G. MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat. Cell Biol. 2013, 15:668-676.
35. Handschin C., Meyer U.A. Induction of drug metabolism: the role of nuclear receptors. Pharmacol. Rev. 2003, 55:649-673.
36. Virk B., et al. Excessive folate synthesis limits lifespan in the C. elegans: E. coli aging model. BMC Biol. 2012, 10:67.
37. Gusarov I., et al. Bacterial nitric oxide extends the lifespan of C. elegans. Cell 2013, 152:818-830.
38. Watson E., et al. Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. Cell 2014, 156:759-770.
39. Pang S., Curran S.P. Adaptive capacity to bacterial diet modulates aging in C. elegans. Cell Metab. 2014, 19:221-231.
40. Gracida X., Eckmann C.R. Fertility and germline stem cell maintenance under different diets requires nhr-114/HNF4 in C. elegans. Curr. Biol. 2013, 23:607-613.
41. Magner D.B., et al. The NHR-8 nuclear receptor regulates cholesterol and bile acid homeostasis in C. elegans. Cell Metab. 2013, 18:212-224.
42. Kumar M., et al. MicroRNAs: a new ray of hope for diabetes mellitus. Protein Cell 2012, 3:726-738.
43. Vora M., et al. Deletion of microRNA-80 activates dietary restriction to extend C. elegans healthspan and lifespan. PLoS Genet. 2013, 9:e1003737.
44. Pedersen M.E., et al. An epidermal microRNA regulates neuronal migration through control of the cellular glycosylation state. Science 2013, 341:1404-1408.
45. Kemp B.J., et al. miR-786 regulation of a fatty-acid elongase contributes to rhythmic calcium-wave initiation in C. elegans. Curr. Biol. 2012, 22:2213-2220.
46. Ludewig A.H., et al. A novel nuclear receptor/coregulator complex controls C. elegans lipid metabolism, larval development, and aging. Genes Dev. 2004, 18:2120-2133.
47. Hammell C.M., et al. A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:18668-18673.
48. Bethke A., et al. Nuclear hormone receptor regulation of microRNAs controls developmental progression. Science 2009, 324:95-98.
49. Kasuga H., et al. The microRNA miR-235 couples blast-cell quiescence to the nutritional state. Nature 2013, 497:503-506.
50. Castro C., et al. A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks. Mol. Biosyst. 2013, 9:1632-1642.
51. Martin F.P., et al. Metabotyping of Caenorhabditis elegans and their culture media revealed unique metabolic phenotypes associated to amino acid deficiency and insulin-like signaling. J. Proteome Res. 2011, 10:990-1003.
52. Schrier Vergano S., et al. In vivo metabolic flux profiling with stable isotopes discriminates sites and quantifies effects of mitochondrial dysfunction in C. elegans. Mol. Genet. Metab. 2013, 111:331-341.
53. An Y.J., et al. Metabotyping of the C. elegans sir-2.1 mutant using in vivo labeling and (13)C-heteronuclear multidimensional NMR metabolomics. ACS Chem. Biol. 2012, 7:2012-2018.
54. Butler J.A., et al. A metabolic signature for long life in the Caenorhabditis elegans Mit mutants. Aging Cell 2013, 12:130-138.
55. Butler J.A., et al. Long-lived mitochondrial (Mit) mutants of Caenorhabditis elegans utilize a novel metabolism. FASEB J. 2010, 24:4977-4988.
56. Castro C., et al. A metabolomic strategy defines the regulation of lipid content and global metabolism by Delta9 desaturases in Caenorhabditis elegans. BMC Genomics 2012, 13:36.
57. Butler J.A., et al. Profiling the anaerobic response of C. elegans using GC-MS. PLoS ONE 2012, 7:e46140.
58. Reinke S.N., et al. Caenorhabditis elegans diet significantly affects metabolic profile, mitochondrial DNA levels, lifespan and brood size. Mol. Genet. Metab. 2010, 100:274-282.
59. Brooks K.K., et al. The influence of bacterial diet on fat storage in C. elegans. PLoS ONE 2009, 4:e7545.
60. Hochbaum D., et al. DAF-12 regulates a connected network of genes to ensure robust developmental decisions. PLoS Genet. 2011, 7:e1002179.
61. McCormick M., et al. New genes that extend Caenorhabditis elegans' lifespan in response to reproductive signals. Aging Cell 2012, 11:192-202.
62. Van Gilst M.R., et al. Nuclear hormone receptor NHR-49 controls fat consumption and fatty acid composition in C. elegans. PLoS Biol. 2005, 3:e53.
63. Pathare P.P., et al. Coordinate regulation of lipid metabolism by novel nuclear receptor partnerships. PLoS Genet. 2012, 8:e1002645.
64. Brock T.J., et al. Genetic regulation of unsaturated fatty acid composition in C. elegans. PLoS Genet. 2006, 2:e108.
65. Goudeau J., et al. Fatty acid desaturation links germ cell loss to longevity through NHR-80/HNF4 in C. elegans. PLoS Biol. 2011, 9:e1000599.
66. Heestand B.N., et al. Dietary restriction induced longevity is mediated by nuclear receptor NHR-62 in Caenorhabditis elegans. PLoS Genet. 2013, 9:e1003651.
67. Pohludka M., et al. Proteomic analysis uncovers a metabolic phenotype in C. elegans after nhr-40 reduction of function. Biochem. Biophys. Res. Commun. 2008, 374:49-54.
68. Brozova E., et al. NHR-40, a Caenorhabditis elegans supplementary nuclear receptor, regulates embryonic and early larval development. Mech. Dev. 2006, 123:689-701.
69. Liang B., et al. The role of nuclear receptor NHR-64 in fat storage regulation in Caenorhabditis elegans. PLoS ONE 2010, 5:e9869.