Metabolic programming a lean phenotype by deregulation of RNA polymerase III

Abstract

As a master negative regulator of RNA polymerase (Pol) III, Maf1 modulates transcription in response to nutrients and stress to balance the production of highly abundant tRNAs, 5S rRNA, and other small noncoding RNAs with cell growth and maintenance. This regulation of Pol III transcription is important for energetic economy as mice lacking Maf1 are lean and resist weight gain on normal and high fat diets. The lean phenotype of Maf1 knockout (KO) mice is attributed in part to metabolic inefficiencies which increase the demand for cellular energy and elevate catabolic processes, including autophagy/lipophagy and lipolysis. A futile RNA cycle involving increased synthesis and turnover of Pol III transcripts has been proposed as an important driver of these changes. Here, using targeted metabolomics, we find changes in the liver of fed and fasted Maf1 KO mice consistent with the function of mammalian Maf1 as a chronic Pol III repressor. Differences in long-chain acylcarnitine levels suggest that energy demand is higher in the fed state of Maf1 KO mice versus the fasted state. Quantitative metabolite profiling supports increased activity in the TCA cycle, the pentose phosphate pathway, and the urea cycle and reveals changes in nucleotide levels and the creatine system. Metabolite profiling also confirms key predictions of the futile RNA cycle hypothesis by identifying changes in many metabolites involved in nucleotide synthesis and turnover. Thus, constitutively high levels of Pol III transcription in Maf1 KO mice reprogram central metabolic pathways and waste metabolic energy through a futile RNA cycle.

MAF1 is a Chronic Repressor of RNA Polymerase III Transcription in the Mouse

“…Thus, the results are consistent with the idea that derepression of pol III transcription during all hours of the day, regardless of the feedingfasting cycle, contributes to energy expenditure, with a larger share of that expenditure coming in the fed state. The wasteful use of this energy, which we previously proposed is driven by a futile RNA cycle 11,12 , also seems to be enhanced in fed versus fasted liver: Higher levels of pol III occupancy in this condition are not accompanied by correspondingly large increases in precursor tRNAs in the liver (although large increases were observed in other tissues). This suggests that, reminiscent of S. cerevisiae where as much as 50% of pre-tRNA is degraded by the exosome before maturation 37 , there is a high turnover of precursor tRNAs in fed Maf1 -/liver.…”

“…Importantly, while a futile RNA cycle may be the main driver of energy expenditure in Maf1 -/mice, other energy costs coming from enhanced cycling of hepatic lipids and increased activity of the urea cycle are likely incurred indirectly and contribute to the overall energy budget 11,12 . Consistent with energy expenditure being higher in Maf1 -/mice at night (i.e. when mice are actively feeding), changes in amino acid and fatty acid metabolism are more pronounced in fed versus fasted animals 12 . Thus, somewhat counterintuitively (since MAF1 function is inhibited by nutrient signaling), futile RNA cycling is likely to be higher in the fed state.…”

“…The greater magnitude of effect of Maf1 -/on pol III occupancy over WT in fed versus fasted liver ( Figure 2B and 2C) correlates with other changes under these conditions. Whole body energy expenditure is higher and metabolic changes in the liver involving amino acids and fatty acids are more prominent in the fed state versus the fasted state 11,12 . Thus, the results are consistent with the idea that derepression of pol III transcription during all hours of the day, regardless of the feedingfasting cycle, contributes to energy expenditure, with a larger share of that expenditure coming in the fed state.…”

“…In the context of a mouse model of increased energy demand, these findings are further supported by increased lipolysis in white adipose tissue (WAT) and increased autophagy/lipophagy in the liver, processes that together provide TCA cycle substrates for enhanced energy metabolism 13 . Metabolomic support for changes in these processes has also be obtained: The levels of many amino acids are increased in liver and skeletal muscle and changes in acyl carnitine levels are consistent with increased oxidation of fatty acids 11,12 . Importantly, while a futile RNA cycle may be the main driver of energy expenditure in Maf1 -/mice, other energy costs coming from enhanced cycling of hepatic lipids and increased activity of the urea cycle are likely incurred indirectly and contribute to the overall energy budget 11,12 . Consistent with energy expenditure being higher in Maf1 -/mice at night (i.e.…”

“…Gene ontology (GO) analysis of the differentially expressed transcripts identified a family of enriched GO bioprocess terms involving various aspects of lipid metabolism, storage and transport that relate to the lean phenotype of Maf1 -/mice including previously reported changes in lipid droplets, liver triglyceride levels, lipolysis and fatty acid metabolism (Table S7) 11,12 . Additionally, consistent with the bias towards gene down-regulation, numerous GO terms involving gene transcription and its negative regulation were recovered (Table S7).…”