ORCID ID

0000-0002-9338-2049

Publication Date

2021-07-06

Document Type

Doctoral Dissertation

Academic Program

Interdisciplinary Graduate Program

Department

Basic and Biomedical Sciences

First Thesis Advisor

Marian Walhout

Keywords

Dissertations, UMMS, Caenorhabditis elegans, Metabolism, Vitamin B12, Gene Regulatory Networks, Homeostasis, S-Adenosylmethionine, One-carbon Metabolism, Methionine, Metabolic Networks, Nuclear Hormone Receptors

Abstract

Cells must regulate their metabolism in order to grow, adapt to changes in nutrient availability and maintain homeostasis. Flux, or the turnover of metabolites, through the metabolic network can be regulated at the allosteric and transcriptional levels. While study of allosteric regulation is limited to biochemical examination of individual proteins, transcriptional control of metabolism can be explored at a systems level. We endeavored to elucidate transcriptional mechanisms of metabolic flux regulation in the model organism Caenorhabditis elegans (C. elegans). We also worked to create a visual tool to explore metabolic pathways that will support future efforts in the research of metabolic gene regulation. C. elegans is a small, free-living nematode that feeds on bacteria and experiences a high level of diversity in nutrient level and composition. Previously, we identified a mechanism by which the essential cofactor, vitamin B12, regulates the expression of genes involved in the degradation of propionate, referred to as B12‑mechanism‑I. This mechanism functions to prevent the toxic accumulation of propionate and requires the TFs NHR-10 and NHR-68. Using genetic screens as well as transcriptomic and metabolomic approaches, we discover a second mechanism by which vitamin B12 regulates metabolic gene expression: B12-mechanism-II. Unlike B12-mechanism-I, B12-mechanism-II is independent of propionate, requires the transcription factor NHR-114 and functions to maintain the metabolic activity of the Methionine/S-adenosylmethionine cycle in a tightly regulated regime. We also present WormPaths, an online resource that allows visualization of C. elegans metabolic pathways and enables metabolic pathway enrichment of user-uploaded transcriptomic data.

DOI

10.13028/fj3q-rx20

Rights and Permissions

Licensed under a Creative Commons license

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License

Supplementary_File_3_1.xlsx (12 kB)
Supplementary file 3.1. mRNA fold change and p adjusted values of genes involved in the propionate shunt, Met/SAM cycle and phospholipid metabolism in the following conditions. Wild type on vitamin B12 vs. wild type on untreated; wild type on vitamin B12 and propionate vs. wild type on vitamin B12; ∆nhr-10 untreated vs. wild type untreated; ∆nhr-10 on vitamin B12 vs. ∆nhr-10 untreated; ∆nhr-68 untreated vs. wild type untreated; ∆nhr-68 on vitamin B12 vs. ∆nhr-68 untreated. This table is a subset of data published in Bulcha et al., 2019 (GSE123507).

Supplementary_File_3_2.xlsx (1867 kB)
Supplementary file 3.2. Genes with an mRNA fold change greater or equal to 1.5 and a p adjusted value less than 0.01 in Met/SAM cycle mutants vs.the parental strain Pacdh1::GFP;∆nhr-10.Genes that change in all four mutant strains are shown in tab 1, while all genes regardless of p adjusted value are shown in tab 2.

Supplementary_File_3_3.xlsx (2362 kB)
Supplementary file 3.3. mRNA fold change and p adjusted values of all detected genes in the following conditions.Pacdh-1::GFP on nhr-114 RNAi vs. vector; Pacdh-1::GFP;∆metr-1 on vector vs. Pacdh-1::GFP on vector; Pacdh-1::GFP;∆metr-1 on nhr-114 RNAi vs. Pacdh-1::GFP on vector; Pacdh-1::GFP;∆metr-1 on nhr-114 RNAi vs. Pacdh1::GFP;∆metr-1 on vector; Pacdh-1::GFP;∆nhr-10;metr-1(ww52) on vector vs. Pacdh-1::GFP on vector; Pacdh-1::GFP;∆nhr-10;metr-1(ww52) on nhr-114 RNAi vs. Pacdh-1::GFP on vector; Pacdh-1::GFP;∆nhr-10;metr-1(ww52) on nhr-114 RNAi vs. Pacdh-1::GFP;∆nhr-10;metr-1(ww52) on vector.

Supplementary_File_3_4.xlsx (1047 kB)
Supplementary file 3.4. mRNA fold change and p adjusted values of all detected genes in the following conditions. Pacdh-1::GFP on methionine vs. Pacdh-1::GFP untreated; Pacdh1::GFP;∆nhr-114 untreated vs. Pacdh-1::GFP untreated; Pacdh-1::GFP;∆nhr-114 on methionine vs. Pacdh-1::GFP on methionine; Pacdh-1::GFP;∆nhr-114 on methionine vs. Pacdh-1::GFP;∆nhr-114 untreated.

Supplementary_File_4_1.xlsx (23 kB)
Supplementary file 4.1. Gene sets per each pathway by level by gene name

Supplementary_File_4_2.xlsx (25 kB)
Supplementary file 4.2. Gene sets per each pathway by level by WormBase ID

Supplementary_File_4_3.xlsx (65 kB)
Supplementary file 4.3. All pathway associations listed by gene.

Share

COinS