Adaption of the proteome and phosphoproteome of Xanthomonas campestris pv. campestris B100 to the different growth phases during the growth under batch culture conditions

Musa YR. Adaption of the proteome and phosphoproteome of Xanthomonas campestris pv. campestris B100 to the different growth phases during the growth under batch culture conditions. Bielefeld; 2012

Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach

Musa YR, Baesell K, Schatschneider S, Vorhölter F-J, Becher D, Niehaus K. Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach. Journal of Biotechnology. 2013;167(2):111-122.Xanthomonas campestris pv. campestris (Xcc) synthesizes huge amounts of the exopolysaccharide xanthan and is a plant pathogen affecting Brassicaceae, among them the model plant Arabidopsis thaliana. Xanthan is produced as a thickening agent at industrial scale by fermentation of Xcc. In an approach based on 2D gel electrophoresis, protein samples from different growth phases were characterized to initialize analysis of the Xanthomonas phosphoproteome. The 2D gels were stained with Pro-Q Diamond phosphoprotein stain to identify putatively phosphorylated proteins. Spots of putatively phosphorylated proteins were excised from the gel and analyzed by mass spectrometry. Three proteins were confirmed to be phosphorylated, the phosphoglucomutase/phosphomannomutase XanA that is important for xanthan and lipopolysaccharide biosynthesis, the phosphoenolpyruvate synthase PspA that is involved in gluconeogenesis, and an anti-sigma factor antagonist RsbR that was so far uncharacterized in xanthomonads. The growth phase in which the samples were collected had an influence on protein phosphorylation in Xcc, particular distinct in case of RsbR, which was phosphorylated during the transition from the late exponential growth phase to the stationary phase. (C) 2013 Elsevier B.V. All rights reserved

Complete loss of H3K9 methylation dissolves mouse heterochromatin organization

Histone H3K9 methylation (H3K9me) states define repressed chromatin in eukaryotic cells. Here the authors reveal complete loss of all H3K9me in mammalian cells through successive deletion of H3K9 methyltransferase genes that results in the dissolution of heterochromatin and the derepression of nearly all repeat families

Comprehensive Proteomic Investigation of <i>Ebf1</i> Heterozygosity in Pro‑B Lymphocytes Utilizing Data Independent Acquisition

Early B cell factor 1 (EBF1) is one of the key transcription factors required for orchestrating B-cell lineage development. Although studies have shown that <i>Ebf1</i> haploinsufficiency is involved in the development of leukemia, no study has been conducted that characterizes the global effect of <i>Ebf1</i> heterozygosity on the proteome of pro-B lymphocytes. Here, we employ both data independent acquisition (DIA) and shotgun data dependent acquisition (DDA) workflows for profiling proteins that are differently expressed between <i>Ebf1</i>^<i>+/+</i> and <i>Ebf1</i>^<i>+/-</i> cells. Both DDA and DIA were able to reveal the downregulation of the EBF1 transcription factor in <i>Ebf1</i>^<i>+/-</i> pro-B lymphocytes. Further examination of differentially expressed proteins by DIA revealed that, similar to EBF1, the expression of other B-cell lineage regulators, such as TCF3 and Pax5, is also downregulated in <i>Ebf1</i> heterozygous cells. Functional DIA analysis of differentially expressed proteins showed that EBF1 heterozygosity resulted in the deregulation of at least eight transcription factors involved in lymphopoiesis and the deregulation of key proteins playing crucial roles in survival, development, and differentiation of pro-B lymphocytes

Polyamine metabolism is a central determinant of helper T cell lineage fidelity

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

An LKB1-mitochondria axis controls T(H)17 effector function

CD4(+) T cell differentiation requires metabolic reprogramming to fulfil the bioenergetic demands of proliferation and effector function, and enforce specific transcriptional programmes(1-3). Mitochondrial membrane dynamics sustains mitochondrial processes(4), including respiration and tricarboxylic acid (TCA) cycle metabolism(5), but whether mitochondrial membrane remodelling orchestrates CD4(+) T cell differentiation remains unclear. Here we show that unlike other CD4(+) T cell subsets, T helper 17 (T(H)17) cells have fused mitochondria with tight cristae. T cell-specific deletion of optic atrophy 1 (OPA1), which regulates inner mitochondrial membrane fusion and cristae morphology(6), revealed that T(H)17 cells require OPA1 for its control of the TCA cycle, rather than respiration. OPA1 deletion amplifies glutamine oxidation, leading to impaired NADH/NAD(+) balance and accumulation of TCA cycle metabolites and 2-hydroxyglutarate-a metabolite that influences the epigenetic landscape(5,7). Our multi-omics approach revealed that the serine/threonine kinase liver-associated kinase B1 (LKB1) couples mitochondrial function to cytokine expression in T(H)17 cells by regulating TCA cycle metabolism and transcriptional remodelling. Mitochondrial membrane disruption activates LKB1, which restrains IL-17 expression. LKB1 deletion restores IL-17 expression in T(H)17 cells with disrupted mitochondrial membranes, rectifying aberrant TCA cycle glutamine flux, balancing NADH/NAD(+) and preventing 2-hydroxyglutarate production from the promiscuous activity of the serine biosynthesis enzyme phosphoglycerate dehydrogenase (PHGDH). These findings identify OPA1 as a major determinant of T(H)17 cell function, and uncover LKB1 as a sensor linking mitochondrial cues to effector programmes in T(H)17 cells