Preprocessing of liquid chromatography-mass spectrometry (LC-MS) raw data facilitates downstream statistical and biological data analyses. In the case of targeted LC-MS data, consistent recognition ...of chromatographic peaks is a main challenge, in particular, for low abundant signals. Fully automatic preprocessing is faster than manual peak review and does not depend on the individual operator. Here, we present the R package automRm for fully automatic preprocessing of LC-MS data recorded in MRM mode. Using machine learning (ML) for detection of chromatographic peaks and quality control of reported results enables the automatic recognition of complex patterns in raw data. In addition, this approach renders automRm generally applicable to a wide range of analytical methods including hydrophilic interaction liquid chromatography (HILIC), which is known for sample-to-sample variations in peak shape and retention time. We demonstrate the impact of the choice of training data set, of the applied ML algorithm, and of individual peak characteristics on automRm’s ability to correctly report chromatographic peaks. Next, we show that automRm can replicate results obtained by manual peak review on published data. Moreover, automRm outperforms alternative software solutions regarding the variation in peak integration among replicate measurements and the number of correctly reported peaks when applied to a HILIC-MS data set. The R package is freely available from gitlab (https://gitlab.gwdg.de/joerg.buescher/automrm).
Polyamine synthesis represents one of the most profound metabolic changes during T cell activation, but the biological implications of this are scarcely known. Here, we show that polyamine metabolism ...is a fundamental process governing the ability of CD4+ helper T cells (TH) to polarize into different functional fates. Deficiency in ornithine decarboxylase, a crucial enzyme for polyamine synthesis, results in a severe failure of CD4+ T cells to adopt correct subset specification, underscored by ectopic expression of multiple cytokines and lineage-defining transcription factors across TH cell subsets. Polyamines control TH differentiation by providing substrates for deoxyhypusine synthase, which synthesizes the amino acid hypusine, and mice in which T cells are deficient for hypusine develop severe intestinal inflammatory disease. Polyamine-hypusine deficiency caused widespread epigenetic remodeling driven by alterations in histone acetylation and a re-wired tricarboxylic acid (TCA) cycle. Thus, polyamine metabolism is critical for maintaining the epigenome to focus TH cell subset fidelity.
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•Polyamines govern the ability of CD4+ T cells to differentiate into distinct subsets•Through the synthesis of hypusine, polyamines direct the T cell epigenome•Loss of polyamines or hypusine perturbs the TCA cycle and histone acetylation•HAT deletion restores TH differentiation in polyamine-deficient cells
The ability of CD4+ T helper cells to develop into specified functional subsets depends upon polyamine-driven metabolic and epigenetic regulation.
The adoption of Warburg metabolism is critical for the activation of macrophages in response to lipopolysaccharide. Macrophages stimulated with lipopolysaccharide increase their expression of ...nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in NAD
salvage, and loss of NAMPT activity alters their inflammatory potential. However, the events that lead to the cells' becoming dependent on NAD
salvage remain poorly defined. We found that depletion of NAD
and increased expression of NAMPT occurred rapidly after inflammatory activation and coincided with DNA damage caused by reactive oxygen species (ROS). ROS produced by complex III of the mitochondrial electron-transport chain were required for macrophage activation. DNA damage was associated with activation of poly(ADP-ribose) polymerase, which led to consumption of NAD
. In this setting, increased NAMPT expression allowed the maintenance of NAD
pools sufficient for glyceraldehyde-3-phosphate dehydrogenase activity and Warburg metabolism. Our findings provide an integrated explanation for the dependence of inflammatory macrophages on the NAD
salvage pathway.
ABSTRACT
This review article provides an updated critical literature review on the production and applications of Polyglutamic Acid (PGA). α-PGA is synthesized chemically, whereas γ-PGA can be ...produced by a number of microbial species, most prominently various Bacilli. Great insight into the microbial formation of γ-PGA has been gained thanks to the development of molecular biological techniques. Moreover, there is a great variety of applications for both isoforms of PGA, many of which have not been discovered until recently. These applications include: wastewater treatment, food products, drug delivery, medical adhesives, vaccines, PGA nanoparticles for on-site drug release in cancer chemotherapy, and tissue engineering.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Microglial function declines during aging. The interaction of microglia with the gut microbiota has been well characterized during development and adulthood but not in aging. Here, we compared ...microglial transcriptomes from young-adult and aged mice housed under germ-free and specific pathogen-free conditions and found that the microbiota influenced aging associated-changes in microglial gene expression. The absence of gut microbiota diminished oxidative stress and ameliorated mitochondrial dysfunction in microglia from the brains of aged mice. Unbiased metabolomic analyses of serum and brain tissue revealed the accumulation of N
-carboxymethyllysine (CML) in the microglia of the aging brain. CML mediated a burst of reactive oxygen species and impeded mitochondrial activity and ATP reservoirs in microglia. We validated the age-dependent rise in CML levels in the sera and brains of humans. Finally, a microbiota-dependent increase in intestinal permeability in aged mice mediated the elevated levels of CML. This study adds insight into how specific features of microglia from aged mice are regulated by the gut microbiota.
Mitochondrial Priming by CD28 Klein Geltink, Ramon I; O'Sullivan, David; Corrado, Mauro ...
Cell,
10/2017, Letnik:
171, Številka:
2
Journal Article
Recenzirano
Odprti dostop
T cell receptor (TCR) signaling without CD28 can elicit primary effector T cells, but memory T cells generated during this process are anergic, failing to respond to secondary antigen exposure. We ...show that, upon T cell activation, CD28 transiently promotes expression of carnitine palmitoyltransferase 1a (Cpt1a), an enzyme that facilitates mitochondrial fatty acid oxidation (FAO), before the first cell division, coinciding with mitochondrial elongation and enhanced spare respiratory capacity (SRC). microRNA-33 (miR33), a target of thioredoxin-interacting protein (TXNIP), attenuates Cpt1a expression in the absence of CD28, resulting in cells that thereafter are metabolically compromised during reactivation or periods of increased bioenergetic demand. Early CD28-dependent mitochondrial engagement is needed for T cells to remodel cristae, develop SRC, and rapidly produce cytokines upon restimulation-cardinal features of protective memory T cells. Our data show that initial CD28 signals during T cell activation prime mitochondria with latent metabolic capacity that is essential for future T cell responses.
How cells adapt metabolism to meet demands is an active area of interest across biology. Among a broad range of functions, the polyamine spermidine is needed to hypusinate the translation factor ...eukaryotic initiation factor 5A (eIF5A). We show here that hypusinated eIF5A (eIF5AH) promotes the efficient expression of a subset of mitochondrial proteins involved in the TCA cycle and oxidative phosphorylation (OXPHOS). Several of these proteins have mitochondrial targeting sequences (MTSs) that in part confer an increased dependency on eIF5AH. In macrophages, metabolic switching between OXPHOS and glycolysis supports divergent functional fates stimulated by activation signals. In these cells, hypusination of eIF5A appears to be dynamically regulated after activation. Using in vivo and in vitro models, we show that acute inhibition of this pathway blunts OXPHOS-dependent alternative activation, while leaving aerobic glycolysis-dependent classical activation intact. These results might have implications for therapeutically controlling macrophage activation by targeting the polyamine-eIF5A-hypusine axis.
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•The polyamine synthesis pathway and hypusinated eIF5A modulate mitochondrial OXPHOS•Hypusinated eIF5A maintains TCA cycle and ETC integrity in macrophages•Some mitochondrial enzymes depend on eIF5AH for efficient expression•Inhibition of hypusinated eIF5A blunts macrophage alternative activation
Puleston et al. show that polyamine biosynthesis modulates mitochondrial metabolism through eIF5A hypusination (eIF5AH). They find that inhibiting the polyamine-eIF5A-hypusine pathway blocks OXPHOS-dependent macrophage alternative activation, while leaving aerobic glycolysis-dependent macrophage classical activation intact. These results might have implications for therapeutically controlling macrophage activation by targeting the polyamine-eIF5A-hypusine axis.
The behaviour of Dictyostelium discoideum depends on nutrients
. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular ...organism
. This biology makes D. discoideum an ideal model for investigating how fundamental metabolism commands cell differentiation and function. Here we show that reactive oxygen species-generated as a consequence of nutrient limitation-lead to the sequestration of cysteine in the antioxidant glutathione. This sequestration limits the use of the sulfur atom of cysteine in processes that contribute to mitochondrial metabolism and cellular proliferation, such as protein translation and the activity of enzymes that contain an iron-sulfur cluster. The regulated sequestration of sulfur maintains D. discoideum in a nonproliferating state that paves the way for multicellular development. This mechanism of signalling through reactive oxygen species highlights oxygen and sulfur as simple signalling molecules that dictate cell fate in an early eukaryote, with implications for responses to nutrient fluctuations in multicellular eukaryotes.
Measuring intracellular metabolism has increasingly led to important insights in biomedical research. (13)C tracer analysis, although less information-rich than quantitative (13)C flux analysis that ...requires computational data integration, has been established as a time-efficient method to unravel relative pathway activities, qualitative changes in pathway contributions, and nutrient contributions. Here, we review selected key issues in interpreting (13)C metabolite labeling patterns, with the goal of drawing accurate conclusions from steady state and dynamic stable isotopic tracer experiments.
Abstract
Immune cells must adapt to different environments during the course of an immune response. Here we study the adaptation of CD8
+
T cells to the intestinal microenvironment and how this ...process shapes the establishment of the CD8
+
T cell pool. CD8
+
T cells progressively remodel their transcriptome and surface phenotype as they enter the gut wall, and downregulate expression of mitochondrial genes. Human and mouse intestinal CD8
+
T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We find that the intestinal microenvironment is rich in prostaglandin E
2
(PGE
2
), which drives mitochondrial depolarization in CD8
+
T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE
2
sensing promotes CD8
+
T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell pool. Thus, a PGE
2
-autophagy-glutathione axis defines the metabolic adaptation of CD8
+
T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
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