Amino Acid Restriction Research Articles (Page 1)

A retrograde, non-canonical integrated stress response cascade maintains synaptic strength under amino acid deprivation.

Sulfur amino acids, metabolic health and beyond: Recent advances, translational implications, and future research considerations.

Caloric restriction is well-established as a robust intervention that may extend lifespan and improve metabolic health across species with effects that are increasingly attributed to both host metabolic remodeling and alterations in the gut microbiota. Recent studies suggest that restricting specific dietary components can replicate these benefits. While methionine and branched-chain amino acid restriction improve metabolism and modulate the gut microbiome, the effects of other nutrients remain unclear. Here, we explore the effects of methionine, tryptophan and niacin deprivation on host intestinal gene expression and gut microbiota using female murine models. Through transcriptomic analysis of the intestinal tissue, we found that transient dietary restriction of methionine, tryptophan, and niacin induced significant changes in intestinal gene expression, particularly in genes involved in oxidative phosphorylation and ATP production. Single-cell analysis revealed that dietary restriction of those nutrients led to an increase in intestinal immune cell populations. Gut microbiota profiling also revealed that transient deprivation of those nutrients resulted in changes in microbial composition, with an increased relative abundance of Lactobacillus species observed in some cases. Our findings highlight the potential of targeted nutrient restriction as a strategy to reprogram host-microbiome interactions.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-18046-2.

The COVID-19 pandemic worsened global food insecurity and malnutrition. Protein restriction increases the risk of poor COVID-19 outcomes and cardiovascular disease. Post-COVID-19 syndrome remains a public health concern, although its underlying mechanisms are not yet fully understood. Extracellular vesicles (EVs), released by most cell types in response to infections, have been implicated in endothelial dysfunction during the post-COVID phase. We hypothesized that EV contribute to endothelial cell (EC) dysfunction in long-term COVID-19, particularly in the setting of protein malnutrition. Circulating EVs were isolated from patients at 1 and 6 months (mo) after hospital discharge due to severe COVID-19. Endothelial relaxation was assessed in mouse aortas after a 3-mo normoprotein or low-protein diet (LP). LP feeding reduced endothelium-dependent relaxation to acetylcholine, but EVs from post-COVID patients (1 and 6 mo) restored endothelium-dependent relaxation. This EV effect was abolished by catalase, but not by l-NAME (a nitric oxide synthase inhibitor) or indomethacin (a cyclooxygenase inhibitor). Aortas from LP mice incubated with post-COVID EVs exhibited reduced catalase expression and increased 4-hydroxynonenal (4-HNE) adducts. In vitro amino acid restriction increased EC death (Hoechst/Pi), and reduced nitric oxide (Diaminofluorescein-FM diacetato) and H2O2 (Amplex red) levels. Incubation with post-COVID EVs for 24 h increased H2O2 only in amino acid-restricted EC. EVs had no significant effect on acetylcholine-induced relaxation in normoprotein-fed mice or on EC parameters in vitro under control conditions. These findings suggest that EVs from patients 1 and 6 mo after severe COVID-19 impact aortic endothelial function by increasing H2O2 contribution under conditions of malnutrition.NEW & NOTEWORTHY Our study demonstrated that circulating extracellular vesicles (EVs) from patients 1 and 6 mo after severe COVID-19 altered endothelial function under protein restriction but not in healthy vessels. Post-COVID EVs enhanced the contribution of H2O2 to endothelium-dependent relaxation, associated with reduced catalase and increased 4-HNE-modified protein expression. These findings identified EVs from long COVID patients as potential mediators of endothelial dysfunction particularly under malnutrition-related conditions.

Mitochondrial dysfunction reveals H2S-mediated synaptic sulfhydration as a potential mechanism for autism-associated social defects.

ABSTRACTDecidualization is a critical process for successful pregnancy. It is characterised by the transformation of endometrial stromal cells into decidual cells that support embryo implantation and placental development. Maternal amino acid deficiency is linked to impaired decidualization, which can lead to pregnancy complications such as miscarriage, preeclampsia and fetal growth restriction. Halofuginone (HF), a synthetic alkaloid, induces nutritional stress by triggering the amino acid starvation response. This study investigated the effects of HF‐induced nutritional stress and amino acid supplementation on decidualization of human endometrial stromal cells (HESCs). Exposure of HESCs to decidualization agents caused distinct morphological changes and expression of insulin‐like growth factor binding protein‐1 (IGFBP‐1), indicative of successful decidualization. Treatment of HESCs with HF or leucine‐deprived media inhibited the expression of key decidualization markers. Interestingly, supplementation with proline, but not leucine, rescued the inhibitory effects of HF on decidualization of HESCs. HF inhibited the expression of genes encoding growth factors crucial for decidualization, highlighting their sensitivity to amino acid availability, and disrupted transforming growth factor β‐SMAD signalling, which was restored by proline supplementation. These findings highlight the essential role of amino acids, particularly proline, for proper decidualization and suggest potential therapeutic strategies for improved reproductive health.

Maple Syrup Urine Disease (MSUD) and Type 1 Diabetes Mellitus (T1DM) are two distinct metabolic disorders with unique dietary management requirements. While MSUD necessitates strict restriction of branched-chain amino acids (BCAAs), T1DM requires precise carbohydrate counting to maintain optimal glycemic control. We report two cases of patients diagnosed with both MSUD and T1DM, highlighting the challenges and strategies in dietary management. Case 1, a 5-year-old girl, was diagnosed with T1DM after presenting with hyperglycemia and metabolic acidosis, despite previously stable MSUD management. The dietary regimen was modified to include a leucine-free amino acid formula and controlled carbohydrate intake to stabilize both leucine and glucose levels. Case 2, an 11-year-old boy with the diagnosis of MSUD, presented with hyperglycemia during a routine follow-up. Dietary management involved increasing the leucine-free formula while reducing carbohydrate intake to maintain metabolic control. Both cases emphasize the importance of individualized dietary plans, integrating BCAA restriction and carbohydrate regulation to prevent metabolic crises and achieve optimal glycemic control. These cases also underscore the need for a multidisciplinary approach involving pediatric endocrinologists, metabolic specialists, and dietitians to navigate the complexities of dual metabolic disorders effectively. Further studies are warranted to explore long-term outcomes and potential therapeutic targets in patients with concurrent MSUD and T1DM.

Docosahexaenoic acid prevents peroxisomal and mitochondrial protein loss in a murine hepatic organoid model of severe malnutrition.

Nutrient sensing and signalling of specific amino acids: Insights from Drosophila study.

Dietary protein is a critical regulator of metabolic health and aging in diverse species. Recent discoveries have determined that many benefits of a low protein diet are the result of reduced consumption of the three branched-chain amino acids (BCAAs), leucine, isoleucine, and valine. Intriguingly, each BCAA has distinct physiological and molecular effects, with restriction of isoleucine alone being sufficient to improve metabolic health and extend the lifespan of mice. While restriction of protein or all three BCAAs improves cognition in mouse models of Alzheimer’s disease (AD), the impact of restricting each individual BCAA on the progression and development of AD is unknown. Here, we investigate the effect of restricting each individual BCAA on metabolic health, AD pathology, molecular signaling, and cognition in the 3xTg mouse model. We find that restriction of isoleucine and valine, but not leucine, promotes metabolic health. Restriction of each BCAA had distinct effects on AD pathology and molecular signaling, with transcriptomic analysis of the brain revealing both distinct and shared, and highly sex-specific, molecular impacts of restricting each BCAA. Restricting any of the three BCAAs improved short-term memory in males, with isoleucine restriction having the strongest effect, while restricting valine had the greatest cognitive benefits in females. We identify a set of significantly altered pathways strongly associated with reduced AD pathology and improved cognitive performance in males. Our findings suggest that restricting any of the BCAAs, particularly isoleucine or valine, may form the basis of a novel sex-specific approach to prevent or delay the progression of AD.

ABSTRACT The human gut microbiome impacts host health through metabolite production, notably short-chain fatty acids (SCFAs) derived from digestion-resistant carbohydrates (DRCs). While DRC supplementation offers a means to modulate the microbiome therapeutically, its effectiveness is often limited by the microbial community’s complexity and individual variability in microbiome functionality. We utilized genome-scale metabolic models (GEMs) from the AGORA collection to provide a system-level overview of the metabolic capabilities of human gut microbes in terms of carbohydrate trophic networks and propose improved therapeutic interventions, based on microbial community design. Our study inferred the capability of AGORA strains to consume carbohydrates of varying structural complexities – including DRCs – and to produce metabolites amenable to cross-feeding, such as SCFAs. The resulting functional database indicated that DRC-degrading abilities are rare among gut microbes, suggesting that the presence or absence of specific taxa can determine the success of DRC-based interventions. Additionally, we found that metabolite production profiles exceed family-level variation, highlighting the limitations in predicting intervention outcomes based on gut microbial composition assessed at higher taxonomic levels. In response to these findings, we integrate reverse ecology principles, network analysis and GEM community modeling to guide the design of minimal yet resilient microbial communities to better guarantee intervention response (purpose-based communities). As a proof of principle, we predicted a purpose-based community designed to enhance butyrate production when used in conjunction with DRC supplementation that displays resilience under nutritional stress, such as amino acid restriction. We further seeded the identified purpose-based community into modeled human microbiomes previously demonstrated to accurately predict SCFA production profiles. The analysis confirmed that such intervention significantly promotes butyrate production across samples, with those that presented a comparatively lower butyrate production pre-intervention displaying the largest increase in butyrate production after seeding. Our work highlights the potential of combining GEMs with community design to infer effective microbiome interventions, ultimately leading to improved health outcomes.

BackgroundClostridium perfringens is a pathogen that secretes multiple toxins, impacting humans and animals. It can cause intestinal diseases such as necrotic enteritis. Although tannins inhibit C. perfringens proliferation, the precise underlying mechanisms are unclear.ObjectiveThis study integrated transcriptomics and metabolomics to systematically investigate the mechanism by which tannins, specifically pentagalloylglucose (PGG) and tannic acid (TA), inhibit C. perfringens and potential pathways to alleviate infection in vivo.ResultsIon concentration measurements, flow cytometric analysis, and transmission electron microscopy revealed that PGG and TA damaged the cell membrane structure of C. perfringens, triggering cytoplasmic content leakage. Additionally, PGG and TA significantly affected C. perfringens at the transcriptional and metabolic levels. Bioinformatics analysis revealed that PGG and TA induced amino acid restriction, disrupted energy metabolism, and impeded the ability of C. perfringens to sense and respond to the external environment. In an in vitro C. perfringens-infected intestinal cell model, PGG and TA bound α toxin, significantly reduced the mRNA expression of inflammatory factors, and improved intestinal barrier function and cell viability. Compared to PGG, TA exhibited stronger inhibitory activity against C. perfringens and binding to α toxin. In vivo, PGG and TA alleviated C. perfringens-induced weight loss in mice, improved intestinal villi morphology, and reduced intestinal inflammation and tight junction gene dysregulation.ConclusionThese findings indicate that tannins inhibit C. perfringens, improve gut tissue integrity and reduce inflammation, demonstrating their multi-target effects of resisting intestinal diseases caused by harmful bacteria. This offers new insights for plant polyphenol-based strategies against necrotic enteritis.Graphical

Amino acid restriction in obesity management: Inducing energy discharge

Introduction and Objective: Dietary sulfur amino acid (SAA) restriction (SAAR) mitigates obesity and impaired glucose control in humans and rodents. The improved glucose homeostasis by SAAR is associated with hepatic and systemic adaptations. This study tested if adaptations in the liver de novo serine synthesis pathway are required for SAAR to improve glucose control Methods: Mice with a liver-specific knockout (KO) of the serine synthetic enzyme, phosphoserine aminotransferase 1 (PSAT1), and wild type (WT) littermates were fed a high-fat, SAA-sufficient (CTRL) or SAAR diet for 6 weeks. Glucose and insulin tolerance tests evaluated glucose homeostasis. Isotope tracing untargeted metabolomics was completed by combining an intravenous infusion of [U-13C]glucose in the conscious, unrestrained mouse with LC-MS/MS untargeted metabolomics to define the in vivo fate of glucose within the liver. Body composition, metabolite concentrations, and molecular regulators of glucose metabolism were measured to interpret glucose phenotypes Results: SAAR lowered body weight and adiposity similarly in both genotypes. SAAR increased liver PSAT1 protein ~60-fold in WT mice. The increased PSAT1 was accompanied by higher liver serine and glycine (~1.5-2-fold) in WT-SAAR compared to WT-CTRL mice. The rise in liver serine and glycine was mitigated in KO-SAAR mice. On a CTRL diet, KO mice had impaired insulin tolerance compared to WT mice. Glucose tolerance was comparable between WT-CTRL and KO-CTRL mice. SAAR improved glucose tolerance and insulin tolerance in both genotypes. However, the increase in glucose tolerance was blunted in KO-SAAR compared to WT-SAAR mice. Furthermore, WT-SAAR mice showed elevated liver 13C-serine labeling following [U-13C]glucose infusion compared to KO-SAAR mice. Conclusion: SAAR promotes glucose partitioning to serine within the liver, linked to improved glucose tolerance. These results suggest heightened liver serine synthesis is required for glucoregulatory adaptations to SAAR Disclosure A.F. Ortega: None. C. Vang: None. R.E. Pfeiffer: None. C.C. Hughey: None. Funding National Institutes of Health (DK136772)

BackgroundCells adapt to nutrient fluctuations through both signaling and epigenetic mechanisms. While amino acid (AA) deprivation is known to suppress protein synthesis via mTORC1 inactivation, the epigenetic pathways that support cellular adaptation and recovery remain poorly understood. We investigated how chromatin and transcriptional changes contribute to maintaining translational capacity during AA restriction and priming cells for growth upon AA repletion.MethodsHuman cells were cultured under amino acid-replete or -depleted conditions, and global histone methylation levels were assessed by Western blotting and ChIP-seq. RNA-seq and chromatin-associated RNA-seq (chromRNA-seq) were used to evaluate gene expression and transcriptional output. Ribosome profiling and [35S]-methionine/cysteine or O-propargyl-puromycin (OPP) incorporation assays measured protein synthesis. Functional contributions of SETD8 and MYC were tested through knockdown and overexpression experiments.ResultsAA deprivation induced a selective, genome-wide loss of H4K20me1, particularly from gene bodies, and led to increased MYC expression and binding at promoter regions. These changes were most pronounced at genes encoding ribosomal proteins and translation initiation factors. Although overall protein synthesis declined during AA restriction, these cells showed increased translational capacity evidenced by accumulation of monomeric ribosomes and enhanced translation upon AA repletion. Loss of H4K20me1 was independent of mTORC1 signaling and partly driven by SETD8 protein downregulation. While MYC overexpression alone was insufficient to upregulate translation-related genes, its combination with SETD8 knockdown in nutrient-rich conditions was both necessary and sufficient to induce expression of these genes and enhance protein synthesis.ConclusionsOur findings reveal a chromatin-based mechanism by which cells integrate metabolic status with transcriptional regulation to adapt to amino acid limitation. Loss of H4K20me1 and increased MYC activity act in parallel to prime the translational machinery during AA deprivation, enabling rapid recovery of protein synthesis upon nutrient restoration. This mechanism may help explain how cells maintain competitive growth potential under fluctuating nutrient conditions and has implications for understanding MYC-driven cancer progression.

Around 40% of the US population and 1 in 6 individuals worldwide have obesity, with the incidence surging globally1,2. Various dietary interventions, including carbohydrate, fat and, more recently, amino acid restriction, have been explored to combat this epidemic3-6. Here we investigated the impact of removing individual amino acids on the weight profiles of mice. We show that conditional cysteine restriction resulted in the most substantial weight loss when compared to essential amino acid restriction, amounting to 30% within 1 week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, partly explaining the phenotype7-9. Notably, we observed lower levels of tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective tricarboxylic acid cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen-rich compounds and amino acids. In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism and stress signalling compared with other amino acid restrictions. These findings suggest strategies for addressing a range of metabolic diseases and the growing obesity crisis.

The tumor microenvironment (TME) influences cancer cell metabolism and survival. However, how immune and stromal cells respond to metabolic stress in vivo, and how nutrient limitations affect therapy, remains poorly understood. Here, we introduce Dual Ribosome Profiling (DualRP) to simultaneously monitor translation and ribosome stalling in multiple tumor cell populations. DualRP reveals that cancer-fibroblast interactions trigger an inflammatory program that reduces amino acid shortages during glucose starvation. In immunocompetent mice, we show that serine and glycine are essential for optimal T cell function and that their deficiency impairs T cell fitness. Importantly, immune checkpoint blockade therapy imposes amino acid restrictions specifically in T cells, demonstrating that therapies create distinct metabolic demands across TME cell types. By mapping codon-resolved ribosome stalling in a cell‑type‑specific manner, DualRP uncovers metabolic crosstalk that shapes translational programs. DualRP thus offers a powerful, innovative approach for dissecting tumor cell metabolic interplay and guiding combined metabolic-immunotherapeutic strategies.

In aging, chronic diseases such as obesity accelerate metabolic dysfunction through chronic inflammation and insulin resistance. This review compared three different dietary strategies to evaluate their mechanisms and benefits for metabolic health and longevity. A comprehensive database search was conducted, selecting studies in animal models and in humans with or without obesity which have been published since 2004. Fasting-mimicking diets reduce IGF-1, promote autophagy, and improve insulin sensitivity, although long-term adherence remains a challenge. Time-restricted feeding synchronizes food intake with circadian rhythms, benefiting inflammation, glycemic control, and body composition. Protein and amino acid restriction, particularly methionine and branched-chain amino acids, modulates mTOR and reduces oxidative stress but requires adjustments in older adults. According to the available evidence, each intervention offers a non-invasive and adaptive approach to mitigating the effects of aging, provided it is applied in a personalized manner with appropriate follow-up.

Inherited metabolic disorders (IMDs) are a group of genetic conditions affecting metabolic pathways. The treatment of some IMDs requires the dietary restriction of specific amino acids. IMDs may also necessitate the supplementation of one or more amino acids due to factors such as reduced dietary intake, impaired synthesis, defective transport or absorption, or increased utilization. This literature review aims to evaluate the most recent evidence regarding amino acid supplementation in IMDs, considering not only the prevention of amino acid deficiency and toxic accumulation but also the competition with other toxic metabolites. A systematic search strategy was developed and applied to PubMed/Medline and Scopus databases to identify relevant studies. Amino acids were categorized into six groups: branched-chain amino acids, aromatic amino acids, sulfur amino acids, urea cycle amino acids, other essential amino acids, and other non-essential amino acids. A total of 24 rare IMDs were evaluated. A final number of 99 selected articles were assessed based on the Oxford Centre for Evidence-Based Medicine 2011 Levels of Evidence. Although this work represents a preliminary non-systematic review, it highlights the need for further studies and data collection. Future research must establish the plasma amino acid levels that indicate the need for supplementation, specify the appropriate dosages (g/day or mg/kg/day), determine the optimal treatment duration, and, crucially, define the target plasma ranges to be maintained for effective management of IMDs.

Dietary protein and essential amino acid (EAA) restriction promote favorable metabolic reprogramming, although the extent to which shared or EAA-specific mechanisms facilitate diet-associated phenotypes remains unclear. Here, we compared the physiological and molecular effects of dietary methionine, leucine, or isoleucine depletion (Met-D, Leu-D, and Ile-D) in C57BL/6J mice. Each diet elicited responses not phenocopied by mTORC1 inhibition, including reduced fat mass and hepatic amino acid catabolism. Ile-D yielded additional distinct responses, highlighted by histone H2A/H4 hypoacetylation and maintained hepatic acetyl-CoA levels despite downregulated FA β-oxidation. Multi-Omics Factor Analysis of 14,139 data points objectively affirmed Ile-D phenotypes are distinct from Met-D or Leu-D and identified several metabolic and chromatin features as primary discriminators. Metabolic and epigenetic responses to Ile-D were recapitulated in vitro , suggesting underlying mechanisms represent fundamental cellular properties. Together, these results demonstrate EAAs can stimulate unique phenotypes and highlight distinct molecular mechanisms by which EAAs may inform metabolic health.