Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AP-MS analysis of sirtuin-4 interactions in human fibroblasts

ABSTRACT: Sirtuins (SIRTs) form a critical family of nicotinamide adenine dinucleotide (NAD)-dependent enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, SIRTs4-7 have little to no deacetylase activity, and a robust catalytic activity for mitochondrial SIRT4 has remained elusive. Moreover, in vitro characterization of SIRT4 has been hampered by difficulty in maintaining soluble and active recombinant protein. Therefore, to investigate potential cellular substrates of SIRT4, we used proteomics to define its mitochondrial protein interactions in human fibroblasts.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Dr Ileana Cristea

PROVIDER: MSV000079557 | MassIVE | Fri Mar 04 17:36:00 GMT 2016

SECONDARY ACCESSION(S): PXD001447

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity.

Mathias Rommel A RA Greco Todd M TM Oberstein Adam A Budayeva Hanna G HG Chakrabarti Rumela R Rowland Elizabeth A EA Kang Yibin Y Shenk Thomas T Cristea Ileana M IM

Cell 20141201 7

Sirtuins (SIRTs) are critical enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, mitochondrial SIRT4 and SIRT5 have little to no deacetylase activity, and a robust catalytic activity for SIRT4 has been elusive. Here, we establish SIRT4 as a cellular lipoamidase that regulates the pyruvate dehydrogenase complex (PDH). Importantly, SIRT4 catalytic efficiency for lipoyl- and biotinyl-lysine modifications is superior to its deacetylation activity. PD ...[more]

PMID: 25525879

Similar Datasets

AP-MS analysis of sirtuin-4 interactions in human fibroblasts

Project description:Sirtuins (SIRTs) form a critical family of nicotinamide adenine dinucleotide (NAD)-dependent enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, SIRTs4-7 have little to no deacetylase activity, and a robust catalytic activity for mitochondrial SIRT4 has remained elusive. Moreover, in vitro characterization of SIRT4 has been hampered by difficulty in maintaining soluble and active recombinant protein. Therefore, to investigate potential cellular substrates of SIRT4, we used proteomics to define its mitochondrial protein interactions in human fibroblasts.

2015-01-05 | PXD001447 | Pride

Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction by inhibiting sirtuin mediated deacetylation

Project description:Perturbed metabolism of ammonia, an endogenous cytotoxic molecule, causes mitochondrial dysfunction with decreased nicotinamide adenine dinucleotide (NAD+) in skeletal muscle. Consistent with our previous report of enrichment of NAD metabolism and sirtuin pathways during hyperammonemia, NAD+-dependent Sirtuin3 (Sirt3) expression and deacetylase activity weredecreased with increased muscle protein acetylation in murine and human skeletal muscle/myotubes. Acetylomics and cell fractions showed hyperammonemia-induced hyperacetylation of critical mitochondrial and signaling molecules. Overexpression of mitochondrial targeted Lactobacillus brevis NADH oxidase (MitoLbNOX) reversed ammonia-induced oxidative dysfunction, electron transport chain (ETC) supercomplex disassembly, lower ATP content, NAD+, and redox ratio (NAD+/NADH). Protein hyperacetylation, post-mitotic senescence and lower mitochondrial sirtuin (Sirt3) expressionduring hyperammonemia were also reversed by MitoLbNOX. Sirt3 overexpression alone did not reverse ammonia-induced redox or mitochondrial dysfunction but reversed hyperacetylation and senescence. These data show that targeting redox ratio, rather than Sirt3, more consistently restores mitochondrial homeostasis and protein acetylation during hyperammonemia.

2023-10-24 | PXD033430 | Pride

Nicotinamide riboside supplementation confers modest effects on skeletal muscle metabolism without mitochondrial and acetyl-proteome remodelingNicotinamide riboside supplementation confers modest effects on skeletal muscle metabolism without mitochondrial and acetyl-proteome remodeling

Project description:Nicotinamide riboside supplements (NRS) have been touted as a nutraceutical that promotes cardiometabolic and musculoskeletal health by enhancing nicotinamide adenine dinucleotide (NAD+) biosynthesis, mitochondrial function and/or the activities of NAD-dependent sirtuin deacetylase enzymes. This investigation examined the impact of NRS on whole body energy homeostasis, skeletal muscle mitochondrial function, and corresponding shifts in the acetyl-lysine proteome, in the context of diet-induced obesity using C57BL/6NJ mice. The study also included a genetically-modified mouse model that imposes greater demand on sirtuin flux and associated NAD+ consumption, specifically within muscle tissues. In general, whole body glucose control was modestly improved by NRS when administered at the midpoint of a chronic high fat diet, but not when given as a preventative therapy upon initiation of the diet. Contrary to anticipated outcomes, the study produced little evidence that NRS increases tissue NAD+ levels, augments mitochondrial function and/or mitigates diet-induced hyperacetylation of the skeletal muscle proteome.

2022-02-17 | PXD027904 | Pride

Nanopore RNA-seq of human cell lines treated with or without nicotinamide adenine dinucleotide (NAD+)

Project description:Investigation of transcriptome changes in four human cell lines (BJ, BJ-5ta, U2OS and HeLa) after treatment for 24 hours with nicotinamide adenine dinucleotide (NAD+). Cells were untreated as the control condition. Nanopore sequencing of cDNA was performed after library preparation with the ONT SQK-PCB109 kit.

2023-09-20 | E-MTAB-13187 | biostudies-arrayexpress

GNPS - Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

Project description:Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

2022-02-12 | MSV000088828 | GNPS

Luna2013_CircadianClock_SIRT1

Project description:An in silico model to examine damage-induced circadian phase shifts by investigating a possible mechanism linking circadian rhythms to metabolism. The proposed model involves two DNA damage response proteins, SIRT1 and PARP1, that are each consumers of nicotinamide adenine dinucleotide (NAD), a metabolite involved in oxidation-reduction reactions and in ATP synthesis.

2021-12-31 | MODEL2112310002 | BioModels

Urolithin A and Nicotinamide Riboside differentially regulate innate immune defenses and metabolism.

Project description:During aging, general cellular processes such as autophagic clearance, DNA repair, mitochondrial health, metabolism, nicotinamide adenine dinucleotide (NAD+) levels, and immunological responses become compromised. Urolithin A (UA) and NAD+ supplementation stimulate mitophagy, reduce pathological plaque load, and inflammation while improving learning in models of Alzheimer’s disease (Hou et al 2021; Fang et al 2019). Here we have performed a During aging, general cellular processes such as autophagic clearance, DNA repair, mitochondrial health, metabolism, nicotinamide adenine dinucleotide (NAD+) levels, and immunological responses become compromised. Urolithin A (UA) and NAD+ supplementation stimulate mitophagy, reduce pathological plaque load, and inflammation while improving learning in models of Alzheimer’s disease (Hou et al 2021; Fang et al 2019). Here we have performed a pairwise analysis of UA and nicotinamide riboside (NR) to investigate how these compounds modulate inflammation. The role of microglia in driving neuroinflammation is becoming more recognized in several neurodegenerative diseases, yet the effects of these drugs on microglia cells have not been thoroughly investigated. As both UA and NR are recognized as safe dietary supplements, their function in normal cells is equally important to understand as in a disease state. Here we investigated the effects of UA and NR in the human microglia cell line, HMC3.

2024-12-19 | GSE266162 | GEO

ALDH7A1 inhibits the intracellular transport pathways during hypoxia and starvation to promote cellular energy homeostasis

Project description:Aldehyde dehydrogenase 7A1 (ALDH7A1) is a metabolic enzyme that converts aldehydes to carboxylates. Here, we find that the reductive consequence of this catalytic activity, which generates NADH (nicotinamide adenine dinucleotide, reduced form) from NAD (nicotinamide adenine dinucleotide), underlies how ALDH7A1 coordinates a broad inhibition of the intracellular transport pathways. Studying vesicle formation by the Coat Protein I (COPI) complex, we elucidate that NADH generated by ALDH7A1 targets Brefeldin-A ADP-Ribosylated Substrate (BARS) to inhibit the fission stage. Moreover, defining a physiologic role for the broad transport inhibition exerted by ALDH7A1, we find that it acts to reduce energy consumption during hypoxia and starvation to promote cellular energy homeostasis. These findings uncover a non-canonical function of ALDH7A1, and also an unexpected way that NADH acts in cellular energetics. Moreover, the findings advance the understanding of intracellular transport by elucidating how multiple pathways can be coordinated, as well as defining physiologic circumstances in which this coordination occurs.

2019-09-12 | PXD014645 | Pride

Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization and prediction of chronological age

Project description:The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA synthesis to result in NAD-capped RNAs (NAD-RNA). We investigated the dynamics of NAD-modified epitranscriptome during human normal aging.

2023-12-20 | GSE226636 | GEO

AP-MS analysis of CobB interactions in E. coli

Project description:Sirtuins are an essential family of nicotinamide adenine dinucleotide (NAD)-dependent enzymes, conserved from bacteria to humans. Here we study the bacterial sirtuin CobB in E. coli. To demonstrate its highly conserved enzymatic activities and substrates, we used proteomics to define CobB protein interactions in E. coli.

2017-10-04 | PXD007864 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data