Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.
Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP) levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.
Department of Biology, Duke University, Durham, North Carolina, United States of America.
Horia
H
Todor
Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
Jessica
J
Gooding
Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
Olga R
OR
Ilkayeva
Department of Biology, Duke University, Durham, North Carolina, United States of America; University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America; Center for Systems Biology, Duke University, Durham, North Carolina, United States of America.
Amy K
AK
Schmid
D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D019848:Gene Expression Regulation, Archaeal; D005943:Gluconeogenesis / Q000235:genetics; D019617:Halobacterium salinarum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D055432:Metabolomics; D009154:Mutation; D010754:Phosphoribosyl Pyrophosphate / Q000378:metabolism; D011687:Purines / Q000096:biosynthesis / Q000378:metabolism; D014158:Transcription, Genetic
D019843:Archaeal Proteins; D011687:Purines; D010754:Phosphoribosyl Pyrophosphate; C030985:purine