Kinetic proteomics identifies targeted changes in liver metabolism and the ribo-interactome by dietary sulfur amino acid restriction

Abstract

Dietary sulfur amino acid restriction (SAAR) protects against diet-induced obesity, extends healthspan, and coincides with an overall reduction in hepatic protein synthesis. To explore the underpinnings of SAAR-induced slowed growth and its impact on liver metabolism and proteostasis, we resolved changes in hepatic mRNA and protein abundances and compared synthesis rates of individual liver proteins. To achieve this, adult male mice were provided deuterium-labeled drinking water while freely consuming either a regular-fat or high-fat diet that was SAA restricted. Livers from these mice and their respective dietary controls were used to conduct transcriptomic, proteomic, and kinetic proteomic analyses. We found that remodeling of the transcriptome by SAAR was largely agnostic to dietary fat content. Shared signatures included activation of the integrated stress response alongside alterations in metabolic processes impacting lipids, fatty acids, and amino acids. Changes to the proteome correlated poorly with the transcriptome, and yet, functional clustering of kinetic proteomic changes in the liver during SAAR revealed that the management of fatty acids and amino acids were altered to support central metabolism and redox balance. Dietary SAAR also strongly influenced the synthesis rates of ribosomal proteins and ribosome-interacting proteins regardless of dietary fat. Taken together, dietary SAAR alters the transcriptome and proteome in the liver to safely manage increased fatty acid flux and energy use and couples this with targeted changes in the ribo-interactome to support proteostasis and slowed growth.

Dietary sulfur amino acid restriction in humans with overweight and obesity: a translational randomized controlled trial

“…Furthermore, GAGE analyses revealed that SAAR was associated with a seemingly paradoxical regulation of GO terms: SAAR was associated with upregulated cytoplasmic translation, but decreased transcription regulation complex, both of which are implicated in protein synthesis. In animals, SAAR slows overall protein synthesis 50 , but a recent publication outlines a complicated and dynamic machinery in which ribosomal proteins may be both upregulated and downregulated, possibly reflecting a shift in metabolic processes during SAAR 51 . However, these processes were studied in animal livers, and does not necessarily reflect processes in human WAT.…”