Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profile of C. elegans fed E. coli (OP50) and B. subtilis (PY79)

ABSTRACT: We used RNA-seq to assay gene expression changes over time in response to OP50 and PY79 To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans. Whole-worm mRNA was sequenced from E. coli- and B.subtilis-fed worms. For each condidtion, one replicate was sequenced at Day 4 and Day 13

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Stuart Kim

PROVIDER: E-GEOD-79415 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In the past decade, the paradigm which claimed that invertebrate immune systems lack specificity has been reconsidered. Accumulating evidence supports that invertebrate immune systems are able to mount specific responses to the pathogen species-, and even to the pathogen strain-level. However, the underlying molecular mechanisms behind invertebrate immune specificity remain mostly unknown. Studying the molecular basis of invertebrate immune specificity in a genetically tractable model, such as the nematode Caenorhabditis elegans, has the potential to reveal insights into the immune systems of other metazoans, including humans. We chose to study the mechanisms of specific immune responses of the worm to two different pathogenic strains of the Gram-positive bacterium Bacillus thuringiensis (MYBY18247 and MYBT18679), because there is phenotypic evidence of specific genotype-genotype interactions between this host-pathogen pair. We did an initial RNA-Seq experiment upon pathogen exposure and found that 9% of the differentially expressed genes change their expression in different ways when comparing the two pathogen strains. Through promoter region motif enrichment analysis, we found the GATA transcription factor ELT-2 is responsible for the pathogen strain-specific transcriptomic response. Upon elt-2 knockdown worms exposed to MYBT18679 display lower survival rate coupled with higher intestinal damage than non-infected controls. Additionally, by performing further genetic analysis using gene knockdown and knockout, we found that the p38 MAPK pathway acts likely in parallel to elt-2 and the transcription factor skn-1 cooperates with elt-2 to promote resistance to MYBT18679. On the other hand, elt-2 knockdown leads to a substantially higher survival rate, together with lower intestinal tissue damage compared to control worms, upon exposure to MYBT18247, another pathogenic Bacillus thuringiensis strain. The MYBT18247 pathogen load of elt-2(RNAi) worms compared to control worms remained unchanged, suggesting the elt-2 negatively regulates tolerance towards MYBT18247. We found that tolerance to MYBT18247 was positively regulated by the transcription factors: FOXO daf-16, bZip zip-2, nhr-99 and nhr-193. To identify elt-2 negatively-regulated downstream targets that could promote tolerance to MYBT18247, we performed a second RNA-Seq experiment, this time including elt-2(RNAi) worms exposed to both pathogenic strains. We found four genes negatively regulated by elt-2: cdr-2, poml-3, dhs-30 and tre-3, with putative function in detoxification and lipid metabolism, which can mediate tolerance to MYBT18247. We conclude that ELT-2 coordinates strain-specific immune responses in this invertebrate host and promotes resistance upon exposure to MYBT18679, while it negatively regulates tolerance to MYBT18247. The response is likely to be specific to the crystal pore-forming toxins produced by this pathogen.

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Transcriptional profile of C. elegans fed E. coli (OP50) and B. subtilis (PY79)

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