Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

Nakic, Zrinka Raguz; Seisenbacher, Gerhard; Posas, Francesc; Sauer, Uwe

doi:10.1186/s12918-016-0350-8

Cited by 16 publications

(12 citation statements)

References 65 publications

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“…Although some recent work elucidated the genetic underpinning of these metabolic changes ( Gaude and Frezza, 2016 , Hu et al, 2013 ), whether cancer metabolism is tuned via post-translational changes is still largely unknown. In yeast, several studies have shown that signalling has a broad importance in regulating the activity of metabolic enzymes involved in central carbon metabolism and other peripheral pathways ( Gonçalves et al, 2017 , Oliveira et al, 2015 , Raguz Nakic et al, 2016 ). By contrast, regulatory phosphorylation of metabolic enzymes in human cells remains largely uncharacterised.…”

Section: Introductionmentioning

confidence: 99%

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Gonçalvès

Sciacovelli

Costa

et al. 2018

Metabolic Engineering

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Deregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (FH) deficient cells and developed a computational modelling approach to identify putative regulatory phosphorylation-sites of metabolic enzymes. We identified previously reported functionally relevant phosphosites and potentially novel regulatory residues in enzymes of the central carbon metabolism. In particular, we showed that pyruvate dehydrogenase (PDHA1) enzymatic activity is inhibited by increased phosphorylation in FH-deficient cells, restricting carbon entry from glucose to the tricarboxylic acid cycle. Moreover, we confirmed PDHA1 phosphorylation in human FH-deficient tumours. Our work provides a novel approach to investigate how post-translational modifications of enzymes regulate metabolism and could have important implications for understanding the metabolic transformation of FH-deficient cancers with potential clinical applications.

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Section: Introductionmentioning

confidence: 99%

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Gonçalvès

Sciacovelli

Costa

et al. 2018

Metabolic Engineering

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“…However, functionality of the vast majority of phosphorylation sites remains unclear. Untargeted metabolomics was used to overcome some of these challenges to unveil the biological roles of functional phosphosites to regulate metabolic pathways and potentially cellular function …”

Section: Understand Biological Impact Of Metabolomicsmentioning

confidence: 99%

Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseases

Liang

Lee

2018

Mass Spectrometry Reviews

291

169

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In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks. Second, partial, incomplete metabolomes persist due to factors such as limitations in mass spectrometry data acquisition speeds, wide-range of metabolites concentrations, and cellular/tissue/temporal-specific expression changes that confound our understanding of metabolite perturbations. Third, to contextualize metabolites in pathways and biology is difficult because many metabolites partake in multiple pathways, have yet to be described species specificity, or possess unannotated or more-complex functions that are not easily characterized through metabolomics analyses. From a translational perspective, information related to novel metabolite biomarkers, metabolic pathways, and drug targets might be sparser than they should be. Thankfully, significant progress has been made and novel solutions are emerging, achieved through sustained academic and industrial community efforts in terms of hardware, computational, and experimental approaches. Given the rapidly growing utility of metabolomics, this review will offer new perspectives, increase awareness of the major challenges in LC-MS metabolomics that will significantly benefit the metabolomics community and also the broader the biomedical community metabolomics aspire to serve.

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“…Already, mutation studies of important p-sites in combination with proteomics and flux analysis or untargeted metabolomics show the way forward [44–46]. Considering the large number of p-sites estimated in this analysis, it is likely that such a daunting challenge will need to be addressed by a fusion of bioinformatics filtering analyses together with highly automated HTP omics and experimental processes that assess the phenotype of mutants [47,48].…”

Section: Discussionmentioning

confidence: 99%

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

et al. 2017

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BackgroundPhosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast).ResultsIn all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable.ConclusionsMost of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70 % to 95 % of total phosphoproteins, but only 40 % to 60 % of total p-sites.

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Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

Cited by 16 publications

References 65 publications

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseases

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

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