Succinate Dehydrogenase Is a Direct Target of Sirtuin 3 Deacetylase Activity

BACKGROUND: Sirtuins (SIRT1-7) are a family of NAD-dependent deacetylases and/or ADP-ribosyltransferases that are involved in metabolism, stress responses and longevity. SIRT3 is localized to mitochondria, where it deacetylates and activates a number of enzymes involved in fuel oxidation and energy production. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we performed a proteomic screen to identify SIRT3 interacting proteins and identified several subunits of complex II and V of the electron transport chain. Two subunits of complex II (also known as succinate dehydrogenase, or SDH), SDHA and SDHB, interacted specifically with SIRT3. Using mass spectrometry, we identified 13 acetylation sites on SDHA, including six novel acetylated residues. SDHA is hyperacetylated in SIRT3 KO mice and SIRT3 directly deacetylates SDHA in a NAD-dependent manner. Finally, we found that SIRT3 regulates SDH activity both in cells and in murine brown adipose tissue. CONCLUSIONS/SIGNIFICANCE: Our study identifies SDHA as a binding partner and substrate for SIRT3 deacetylase activity. SIRT3 loss results in decreased SDH enzyme activity, suggesting that SIRT3 may be an important physiological regulator of SDH activity

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe

We apply mass spectrometry-based ReDi proteomics to quantify the Clostridium phytofermentans proteome during fermentation of cellulosic substrates. ReDi proteomics gives accurate, low-cost quantification of an extra and intracellular microbial proteome. When combined with physiological measurements, these methods form a general systems biology strategy to evaluate the efficiency of cellulosic bioconversion and to identify enzyme targets to engineer for improving this process.C. phytofermentans expressed more than 100 carbohydrate-active enzymes, of which distinct subsets were upregulated on cellulose and hemicellulose. Numerous extracellular enzymes cleave insoluble plant polysaccharides into oligosaccharides, which are transported into the cell to be further degraded by intracellular carbohydratases. Sugars are catabolized by EMP glycolysis incorporating alternative glycolytic enzymes to maximize the ATP yield of anaerobic metabolism.During cellulosic fermentation, cells adhered to the substrate and altered metabolic processes such as upregulation of tryptophan and nicotinamide synthesis proteins and repression of proteins for fatty acid metabolism and cell motility. These diverse metabolic changes highlight how a systems approach can identify novel ways to optimize cellulosic fermentation

Polymer crystallinity and crystallization kinetics via benchtop 1 H NMR relaxometry: Revisited method, data analysis, and experiments on common polymers

Semi-crystalline polymers play an enormously important role in materials science, engineering, and nature. Two-thirds of all synthetic polymers have the ability to crystallize which allows for the extensive use of these materials in a variety of applications as molded parts, films, or fibers. Here, we present a study on the applicability of benchtop 1H NMR relaxometry to obtain information on the bulk crystallinity and crystallization kinetics of the most relevant synthetic semi-crystalline polymers. In the first part, we investigated the temperature-dependent relaxation behavior and identified T=Tg+100 K as the minimum relative temperature difference with respect to Tg for which the mobility contrast between crystalline and amorphous protons is sufficient for an unambiguous determination of polymer crystallinity. The obtained bulk crystallinities from 1 H NMR were compared to results from DSC and XRD, and all three methods showed relatively good agreement for all polymers. In the second part, we focused on the determination of the crystallization kinetics, i.e., monitoring of isothermal crystallization, which required a robust design of the pulse sequence, precise temperature calibration, and careful data analysis. We found the combination of a magic sandwich echo (MSE) with a short acquisition time followed by a CarrPurcell-Meiboom-Gill (CPMG) echo train with short pulse timings to be the most suitable for monitoring crystallization. This study demonstrates the application of benchtop 1H NMR relaxometry to investigate the bulk crystallinity and crystallization kinetics of polymers, which can lead to its optimal use as an in situ technique in research, quality control, and processing labs

Polymer crystallinity and crystallization kinetics via benchtop 1 H NMR relaxometry: Revisited method, data analysis, and experiments on common polymers

Semi-crystalline polymers play an enormously important role in materials science, engineering, and nature. Two-thirds of all synthetic polymers have the ability to crystallize which allows for the extensive use of these materials in a variety of applications as molded parts, films, or fibers. Here, we present a study on the applicability of benchtop 1H NMR relaxometry to obtain information on the bulk crystallinity and crystallization kinetics of the most relevant synthetic semi-crystalline polymers. In the first part, we investigated the temperature-dependent relaxation behavior and identified T=Tg+100 K as the minimum relative temperature difference with respect to Tg for which the mobility contrast between crystalline and amorphous protons is sufficient for an unambiguous determination of polymer crystallinity. The obtained bulk crystallinities from 1 H NMR were compared to results from DSC and XRD, and all three methods showed relatively good agreement for all polymers. In the second part, we focused on the determination of the crystallization kinetics, i.e., monitoring of isothermal crystallization, which required a robust design of the pulse sequence, precise temperature calibration, and careful data analysis. We found the combination of a magic sandwich echo (MSE) with a short acquisition time followed by a CarrPurcell-Meiboom-Gill (CPMG) echo train with short pulse timings to be the most suitable for monitoring crystallization. This study demonstrates the application of benchtop 1H NMR relaxometry to investigate the bulk crystallinity and crystallization kinetics of polymers, which can lead to its optimal use as an in situ technique in research, quality control, and processing labs

Bacterial rotary export ATPases are allosterically regulated by the nucleotide second messenger cyclic-di-GMP

The widespread second messenger molecule cyclic di-GMP (cdG) regulates the transition from motile and virulent lifestyles to sessile, biofilm-forming ones in a wide range of bacteria. Many pathogenic and commensal bacterial-host interactions are known to be controlled by cdG signaling. Although the biochemistry of cyclic dinucleotide metabolism is well understood, much remains to be discovered about the downstream signaling pathways that induce bacterial responses upon cdG binding. As part of our ongoing research into the role of cdG signaling in plant-associated Pseudomonas species, we carried out an affinity capture screen for cdG binding proteins in the model organism Pseudomonas fluorescens SBW25. The flagella export AAA+ ATPase FliI was identified as a result of this screen and subsequently shown to bind specifically to the cdG molecule, with a KD in the low micromolar range. The interaction between FliI and cdG appears to be very widespread. In addition to FliI homologs from diverse bacterial species, high affinity binding was also observed for the type III secretion system homolog HrcN and the type VI ATPase ClpB2. The addition of cdG was shown to inhibit FliI and HrcN ATPase activity in vitro. Finally, a combination of site-specific mutagenesis, mass spectrometry, and in silico analysis was used to predict that cdG binds to FliI in a pocket of highly conserved residues at the interface between two FliI subunits. Our results suggest a novel, fundamental role for cdG in controlling the function of multiple important bacterial export pathways, through direct allosteric control of export ATPase proteins

LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation. At the same time, DNA methyltransferases are upregulated, leading to elevation in DNA methylation with particular enrichment at retrotransposon elements associated with their transcriptional silencing. Correspondingly, LKB1 deficiency sensitizes cells and tumours to inhibition of serine biosynthesis and DNA methylation. Thus, we define a hypermetabolic state that incites changes in the epigenetic landscape to support tumorigenic growth of LKB1-mutant cells, while resulting in potential therapeutic vulnerabilities

Lambda and Antilambda polarization from deep inelastic muon scattering

We report results of the first measurements of Lambda and Antilambda polarization produced in deep inelastic polarized muon scattering on the nucleon. The results are consistent with an expected trend towards positive polarization with increasing x_F. The polarizations of Lambda and Antilambda appear to have opposite signs. A large negative polarization for Lambda at low positive x_F is observed and is not explained by existing models.A possible interpretation is presented.Comment: 9 pages, 2 figure

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

Recent advances in high-throughput sequencing present a new opportunity to deeply probe an organism's transcriptome. In this study, we used Illumina-based massively parallel sequencing to gain new insight into the transcriptome (RNA-Seq) of the human malaria parasite, Plasmodium falciparum. Using data collected at seven time points during the intraerythrocytic developmental cycle, we (i) detect novel gene transcripts; (ii) correct hundreds of gene models; (iii) propose alternative splicing events; and (iv) predict 5′ and 3′ untranslated regions. Approximately 70% of the unique sequencing reads map to previously annotated protein-coding genes. The RNA-Seq results greatly improve existing annotation of the P. falciparum genome with over 10% of gene models modified. Our data confirm 75% of predicted splice sites and identify 202 new splice sites, including 84 previously uncharacterized alternative splicing events. We also discovered 107 novel transcripts and expression of 38 pseudogenes, with many demonstrating differential expression across the developmental time series. Our RNA-Seq results correlate well with DNA microarray analysis performed in parallel on the same samples, and provide improved resolution over the microarray-based method. These data reveal new features of the P. falciparum transcriptional landscape and significantly advance our understanding of the parasite's red blood cell-stage transcriptome