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Biotin starvation in yeast - Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p

ABSTRACT: yeast cells were starved for biotin and the proteome and acetylome changes were analyzed by quantitative mass spectrometry

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Diploid Cell

DISEASE(S): Disease Free

SUBMITTER: Michael Lund Nielsen

LAB HEAD: Michael L. Nielsen

PROVIDER: PXD002168 | Pride | 2016-12-13

REPOSITORIES: Pride

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			Action	DRS
	20120814_QE5_LC2_CTM_SA_Yeast_BioAcetyl_SILAC_NormNothing_40.raw	Raw
	20120814_QE5_LC2_CTM_SA_Yeast_BioAcetyl_SILAC_NormNothing_45.raw	Raw
	20120814_QE5_LC2_CTM_SA_Yeast_BioAcetyl_SILAC_NormNothing_50.raw	Raw
	20120814_QE5_LC2_CTM_SA_Yeast_BioAcetyl_SILAC_NormNothing_60.raw	Raw
	20120814_QE5_LC2_CTM_SA_Yeast_BioAcetyl_SILAC_NormNothing_84.raw	Raw

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Publications

Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p.

Madsen Christian T CT Sylvestersen Kathrine B KB Young Clifford C Larsen Sara C SC Poulsen Jon W JW Andersen Marianne A MA Palmqvist Eva A EA Hey-Mogensen Martin M Jensen Per B PB Treebak Jonas T JT Lisby Michael M Nielsen Michael L ML

Nature communications 20150709

The essential vitamin biotin is a covalent and tenaciously attached prosthetic group in several carboxylases that play important roles in the regulation of energy metabolism. Here we describe increased acetyl-CoA levels and mitochondrial hyperacetylation as downstream metabolic effects of biotin deficiency. Upregulated mitochondrial acetylation sites correlate with the cellular deficiency of the Hst4p deacetylase, and a biotin-starvation-induced accumulation of Hst4p in mitochondria supports a r ...[more]

PMID: 26158509

Similar Datasets

Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p.

Project description:The essential vitamin biotin is a covalent and tenaciously attached prosthetic group in several carboxylases that play important roles in the regulation of energy metabolism. Here we describe increased acetyl-CoA levels and mitochondrial hyperacetylation as downstream metabolic effects of biotin deficiency. Upregulated mitochondrial acetylation sites correlate with the cellular deficiency of the Hst4p deacetylase, and a biotin-starvation-induced accumulation of Hst4p in mitochondria supports a role for Hst4p in lowering mitochondrial acetylation. We show that biotin starvation and knockout of Hst4p cause alterations in cellular respiration and an increase in reactive oxygen species (ROS). These results suggest that Hst4p plays a pivotal role in biotin metabolism and cellular energy homeostasis, and supports that Hst4p is a functional yeast homologue of the sirtuin deacetylase SIRT3. With biotin deficiency being involved in various metabolic disorders, this study provides valuable insight into the metabolic effects biotin exerts on eukaryotic cells.

| S-EPMC4510963 | biostudies-literature

SIRT3 Deacetylates TFAM to Promote Mitochondrial Biogenesis

Project description:SIRT3 is a NAD+-dependent mitochondrial protein deacetylase participating in the regulation of central metabolism and mitochondrial proteostasis. SIRT3 is downregulated in clear cell renal cell carcinoma (ccRCC), a main type of renal cancers, but the function of SIRT3 in tumorigenesis and development of ccRCC remains unknown. In this study, we established a SIRT3 overexpressed cell line to explore the changes of proteomics and metabolomics regulated by SIRT3 expression. Both the results of quantitative proteomics, metabolomics and acetylome showed overexpression of SIRT3 increased mitochondrial biogenesis and reversed the mitochondrial dysfunctions in ccRCC. We found SIRT3 could increase the activity of TFAM through modulation of TFAM transcription, degradation and acetylation level. The acetylation of TFAM K154 decreased while TFAM protein expression increased after SIRT3 overexpression. Further study revealed that SIRT3 could bind with TFAM, and decrease the acetylation of TFAM, promoting TFAM activity in mitochondrial biogenesis. Overall, our results present a new mechanism of SIRT3 in regulating mitochondrial functions, and the downregulation of SIRT3 in ccRCC lowers the activity of TFAM, subsequently inhibits the transcription of mitochondrial genes and mitochondrial biogenesis.

2018-08-14 | PXD009110 | Pride

Mitochondria-targeted inhibitors of the human SIRT3 lysine deacetylase.

Project description:Sirtuin 3 (SIRT3) is the major protein lysine deacetylase in the mitochondria. This hydrolase regulates a wide range of metabolically involved enzymes and has been considered as a potential drug target in certain cancers. Investigation of pharmacological intervention has been challenging due to a lack of potent and selective inhibitors of SIRT3. Here, we developed a strategy for selective inhibition of SIRT3 in cells, over its structurally similar isozymes that localize primarily to the nucleus (SIRT1) and the cytosol (SIRT2). This was achieved by directing the inhibitors to the mitochondria through incorporation of mitochondria-targeting peptide sequences into the inhibitor structures. Our inhibitors exhibited excellent mitochondrial localization in HeLa cells as indicated by fluorophore-conjugated versions, and target engagement was demonstrated by a cellular thermal shift assay of SIRT3 using western blotting. The acetylation state of documented SIRT3 target MnSOD was shown to be increased in cells with little effect on known targets of SIRT1 and SIRT2, showing that our lead compound exhibits selectivity for SIRT3 in cells. We expect that the developed inhibitor will now enable a more detailed investigation of SIRT3 as a potential drug target and help shed further light on the diverse biology regulated by this enzyme.

| S-EPMC8341665 | biostudies-literature

Acetylome analysis of Bordetella pertussis reveals possible targets of novel BP0960 gene-encoded lysine deacetylase

Project description:Acetylation on ε-amino groups of lysine residues (N-ε-lysine acetylation) represents an important mechanism of post-translational regulation of protein function. However, its role and extent in the whooping cough agent Bordetella pertussis remain unknown. In this study, we analyzed the acetylomes of two bacterial mutants lacking putative lysine deacetylases encoded by genes BP0960 and BP3063 and compared them with the acetylome of wild-type B. pertussis. The results suggest that acetylation on lysine residues may modulate the activities of proteins involved in bacterial virulence and of multiple histone-like proteins.

2020-07-19 | PXD016384 | Pride

A role for the mitochondrial deacetylase Sirt3 in regulating energy homeostasis.

Project description:Here, we demonstrate a role for the mitochondrial NAD-dependent deacetylase Sirt3 in the maintenance of basal ATP levels and as a regulator of mitochondrial electron transport. We note that Sirt3(-/-) mouse embryonic fibroblasts have a reduction in basal ATP levels. Reconstitution with wild-type but not a deacetylase-deficient form of Sirt3 restored ATP levels in these cells. Furthermore in wild-type mice, the resting level of ATP correlates with organ-specific Sirt3 protein expression. Remarkably, in mice lacking Sirt3, basal levels of ATP in the heart, kidney, and liver were reduced >50%. We further demonstrate that mitochondrial protein acetylation is markedly elevated in Sirt3(-/-) tissues. In addition, in the absence of Sirt3, multiple components of Complex I of the electron transport chain demonstrate increased acetylation. Sirt3 can also physically interact with at least one of the known subunits of Complex I, the 39-kDa protein NDUFA9. Functional studies demonstrate that mitochondria from Sirt3(-/-) animals display a selective inhibition of Complex I activity. Furthermore, incubation of exogenous Sirt3 with mitochondria can augment Complex I activity. These results implicate protein acetylation as an important regulator of Complex I activity and demonstrate that Sirt3 functions in vivo to regulate and maintain basal ATP levels.

| S-EPMC2567183 | biostudies-literature

Pro-Proliferative Function of Mitochondrial Sirtuin Deacetylase SIRT3 in Human Melanoma.

Project description:Melanoma, the most aggressive form of skin cancer, is often fatal if not treated early. Therefore, novel target-based strategies are required to combat this neoplasm. The objective of this study was to determine the role and functional significance of the mitochondrial sirtuin 3 (SIRT3) in melanoma. We found that compared with normal primary and immortalized human melanocytes, SIRT3 is significantly overexpressed in multiple human melanoma cells at mRNA and protein levels. Further, employing human tissue microarray, we found that SIRT3 is significantly upregulated in clinical melanoma tissues, compared with melanocytic nevi tissues. Furthermore, a short hairpin RNA-mediated knockdown of SIRT3 in human melanoma cells resulted in (i) a decrease in cellular proliferation, colony formation, and cellular migration; (ii) induction of senescence as shown by an increase in senescence-associated beta-galactosidase activity and formation of senescence-associated heterochromatin foci as well as an increase in mRNA and protein levels of p16(INK4a) and p21(Waf1); (iii) G1-phase arrest of the cell cycle; and (iv) decreases in mRNA and protein levels of cyclins (D1, E1) and cyclin-dependent kinases (2, 4, and 6). Conversely, forced exogenous overexpression of SIRT3 promoted an increase in proliferative potential of Hs294T melanoma cells and normal immortalized Mel-ST melanocytes. Finally, we found that SIRT3 knockdown significantly inhibited tumorigenesis in a xenograft model in vivo. To our knowledge, this is the first study supporting the pro-proliferative function of SIRT3 in melanoma.

| S-EPMC4808399 | biostudies-literature

mRNA-seq time series of Caenorhabditis elegans L1 starvation

Project description:Whole starved L1 larvae were collected at twelve time points spanning from hatching to death.

2022-10-11 | GSE173656 | GEO

Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.

Project description:Lysine acetylation is a posttranslational modification that is dynamically regulated by the activity of acetyltransferases and deacetylases. The human and mouse genomes encode 18 different lysine deacetylases (KDACs) which are key regulators of many cellular processes. Identifying substrates of KDACs and pinpointing the regulated acetylation sites on target proteins may provide important information about the molecular basis of their functions. Here we apply quantitative proteomics to identify endogenous substrates of the mitochondrial deacetylase Sirtuin 3 (Sirt3) by comparing site-specific acetylation in wild-type murine embryonic fibroblasts to Sirt3 knockout cells. We confirm Sirt3-regulated acetylation of several mitochondrial proteins in human cells by comparing acetylation in U2OS cells overexpressing Sirt3 to U2OS cells in which Sirt3 expression was reduced by shRNA. Our data demonstrate that ablation of Sirt3 significantly increases acetylation at dozens of sites on mitochondrial proteins. Substrates of Sirt3 are implicated in various metabolic pathways, including fatty acid metabolism and the tricarboxylic acid cycle. These results imply broader regulatory roles of Sirt3 in the mitochondria by modulating acetylation on diverse substrates. The experimental strategy described here is generic and can be applied to identify endogenous substrates of other lysine deacetylases.

| S-EPMC3517600 | biostudies-literature

Integrating multi-omics analyses unveil protein features of gestational diabetes mellitus and preeclampsia

Project description:As one of the most common maternal comorbidities, gestational diabetes mellitus (GDM) and preeclampsia (PE) are associated with maternal and infant health. Although the pathogenesis of PE and GDM remains controversial, oxidative stress is thought to be involved in the underlying pathology of GDM and PE. Protein lysine acetylation (Kac) plays an important regulatory role in biological processes. There is little data regarding the association of the maternal acetylome with GDM and PE. This study aimed to assess the multi-omics (proteome and acetylome) potential value in the underlying pathology for GDM and PE by label-free quantification proteomics technology. In our study, we included placental tissue from healthy individuals (n=6), GDM patients (n=6), and PE patients (n=6). We identified 22 overlapping DEPs (differentially expressed proteins) and 192 overlapping DAPs (differentially acetylated proteins) between the GDM and PE groups. Furthermore, 192 overlapping DAPs were mainly enriched in endoplasmic reticulum stress and ferroptosis pathways. Interestingly, endoplasmic reticulum stress, ferroptosis, and oxidative stress are believed to be related to each other. We also identified that acetylation of the HSP90AA1, HSPA8, PDIA3, GPX4, TF, and CP might serve as novel markers and better therapeutic targets in both complications. We thoroughly analyzed the key characteristics of proteome and acetylome in GDM and PE placental tissues, which may be useful for exploring the underlying pathology and discovering new biomarkers and therapeutic targets.

2024-01-25 | PXD032981 | Pride

Arginine starvation response of Mycobacterium tuberculosis H37Rv ΔargB and ΔargF

Project description:Time -course transcriptional profiling of arginine starved Mycobacterium tuberculosis H37Rv ΔargB or ΔargF realtive to day 0 of starvation

2018-08-31 | GSE98821 | GEO

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