Profiling of the Cellular Proteome and Phosphoproteome of Klebsiella pneumoniae under Iron Limited and Iron Replete Conditions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 240
ORGANISM(S): Escherichia Coli
SUBMITTER: 
Jennifer Geddes-McAlister
LAB HEAD: Jennifer Geddes-McAlister
PROVIDER: PXD040658 | Pride | 2023-03-09
REPOSITORIES: Pride
Similar Datasets
Project description:Klebsiella pneumoniae is a bacterial pathogen that causes nosocomial infection in humans and is acquiring antibiotic resistance at an alarming rate. This study investigates the effect of zinc limitation on the phosphoproteome of K. pneumoniae using quantitative mass spectrometry to provide insight into the cell signaling methods used to respond to nutrient limited conditions like those experienced when colonizing a host.
2023-03-23 | PXD041015 | Pride
Project description:Nutrient adaptation is key in limiting environments for the promotion of microbial growth and survival. In microbial systems, iron is an essential component for many cellular processes and bioavailability varies greatly among different conditions. In the bacterium, Klebsiella pneumoniae, the impact of iron limitation is known to alter transcriptional expression of iron-acquisition pathways and influences the secretion of iron-binding siderophores; however, a comprehensive view of iron limitation at the protein-level remains to be defined. Here, we apply a mass spectrometry-based quantitative proteomics strategy to profile the global impact of iron limitation on the cellular proteome and extracellular environment (secretome) of K. pneumoniae. Our data defines the impact of iron on proteins involved in transcriptional regulation and emphasizes the modulation of a vast array of proteins associated with iron acquisition, transport, and binding. We also identify proteins in the extracellular environment associated with conventional and nonconventional modes of secretion, as well as vesicle release. In particular, we demonstrate a new role for Lon protease in promoting iron homeostasis outside of the cell. Our characterization of Lon protease in K. pneumoniae validates roles in bacterial growth, cell division, iron utilization, and virulence. Moreover, our results uncover novel degradation candidates of Lon protease. Overall, we provide evidence of novel connections between Lon and iron in a bacterial system and define a unique role for Lon protease in the extracellular environment during nutrient limitation.
2020-03-09 | PXD015623 | Pride
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation. Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur, iron or potassium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.
2016-07-21 | E-GEOD-77602 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae (S. pneumoniae) is a major human pathogen causing morbidity and mortality worldwide. Efficiently acquiring iron from the environment is critical for S. pneumoniae to sustain growth and cause infection. There are only three known iron-uptake systems in Streptococcal species responsible for iron acquisition from the host, including ABC transporters PiaABC, PiuABC and PitABC. Besides, no other iron-transporting system has been suggested. In this work, we employed our newly established translating mRNA analysis integrated with proteomics to evaluate the possible existence of novel iron transporters in the bacterium. We simultaneously deleted the iron-binding protein genes of the three iron-uptake systems to construct a piaA/piuA/pitA triple mutant (Tri-Mut) of S. pneumoniae D39, in which genes and proteins related to iron transport should be regulated in response to the deletion. With ribosome associated mRNA sequencing-based translatomics focusing on translating mRNA and iTRAQ quantitative proteomics based on the covalent labeling of peptides with tags of varying mass, we indeed observed a large number of genes and proteins representing various coordinated biological pathways with significantly altered expression levels in the Tri-Mut mutant. Highlighted in this observation is the identification of several new potential iron-uptake ABC transporters for Streptococcal iron metabolism. In particular, putative protein SPD_1609 in operon 804 was verified to be a novel iron-binding protein with similar function to PitA in S. pneumoniae. These data derived from the integrative translatomics and proteomics analyses provided rich information and insightful clues for further investigations on iron-transporting mechanism in bacteria and the interplay between Streptococcal iron availability and the biological metabolic pathways.
2018-10-26 | PXD003313 | Pride
Project description:Obesity is an independent risk factor for colorectal cancer (CRC) although the underlying mechanisms have not been elucidated. Dietary nutrients play a key role in both the prevention and promotion of CRC. While iron is an essential nutrient, excess iron is associated with carcinogenesis. Unlike the systemic compartment, the intestinal lumen lacks an efficient system to regulate iron. In conditions when dietary iron malabsorption and intestinal inflammation co-exist, greater luminal iron is associated with increased intestinal inflammation and a shift in the gut microbiota to more pro-inflammatory strains. However, treatments designed to reduce luminal, including diet restriction and chelation, are associated with lower intestinal inflammation and the colonization of protective gut microbes. Obesity is associated with inflammation-induced, hepcidin-mediated, iron metabolism dysfunction characterized by iron deficiency and dietary iron malabsorption. Obesity is also linked to intestinal inflammation. Currently, there is a fundamental gap in understanding how altered iron metabolism impacts CRC risk in obesity.
The investigator’s objective is to conduct a crossover controlled feeding trial of: 1) a "Typical American" diet with "high" heme/non-heme iron", 2) a "Typical American" diet with "low" iron, and 3) a Mediterranean diet with "high" non heme iron and examine effects on colonic and systemic inflammation and the gut microbiome.
| 2274754 | ecrin-mdr-crc
Project description:Iron is an essential nutrient yet toxic in excess. Our understanding of mammalian mechanisms of dietary iron absorption exceeds our understanding of mechanisms of iron excretion. Here we demonstrate that biliary excretion of excess iron in mice requires the metal transporter SLC39A14 and that excess Fe is excreted into bile as ferritin and heme. The identification of a molecular determinant of iron excretion and the biochemical form of bile iron could lead to development of novel therapeutics for human diseases of iron excess
2021-02-10 | MSV000086836 | MassIVE
Project description:All living cells require a minimal iron threshold to sustain anabolic metabolism. However, the mechanisms by which cells sense iron to regulate anabolic processes are unclear. Here, we report a universal eukaryotic pathway for iron sensing in which molecular iron is required to sustain active histone demethylation and maintain the expression of critical components of the pro-anabolic mTORC1 pathway. Specifically, we identify the iron-binding histone-demethylase KDM3B as an intrinsic iron sensor that regulates mTORC1 activity by demethylating H3K9me2 at enhancers of genes encoding high-affinity leucine transporters and RAPTOR. By directly suppressing leucine availability and RAPTOR levels, iron deficiency (ID) supersedes other nutrient inputs into mTORC1. This process occurs in vivo, and is not an indirect effect by canonical iron-utilizing pathways. Elevated expression of KDM3B targets is associated with reduced survival in a subset of human cancers and ID represses mTORC1 in patient-derived tumor cells and sensitizes cancer cells to chemotherapy. These data demonstrate a novel mechanism of eukaryotic iron sensing through dynamic chromatin remodeling and repression of mTORC1 mediated anabolism. Due to ancestral eukaryotes sharing homologues of KDMs and mTORC1 core components, this pathway likely predated the emergence of the other kingdom-specific nutrient sensors for mTORC1
2023-07-18 | GSE214019 | GEO
Project description:In Neisseria meningitidis iron responsive gene regulation is mediated primarily by the Ferric Uptake Regulator (Fur) protein. When complexed with iron, Fur represses gene expression by preventing transcription initiation. Fur can also indirectly activate gene expression via the repression of regulatory small RNAs (sRNA). One such Fur-and iron-regulated sRNA, NrrF, was previously identified in N. meningitidis and shown to repress expression of the sdhA and sdhC genes encoding subunits of the succinate dehydrogenase complex. In the majority of Gram-negative bacteria sRNA-mediated regulation requires a cofactor RNA-binding protein (Hfq) for proper gene regulation and stabilization. In this study we examined the role of Hfq in NrrF-mediated regulation of the succinate dehydrogenase genes in N. meningitidis and the effect of an hfq- mutation on iron-responsive gene regulation more broadly. We first demonstrated that the stability of Nrrf as well as the regulation of sdhC and sdhA in vivo was unaltered in the hfq- mutant. Secondly, we established that iron responsive gene regulation of the Fur-regulated sodB gene was dependent on Hfq. Finally, we demonstrate that in N. meningitidis Hfq functions to control expression of both ORFs and intergenic regions via iron independent mechanisms. Collectively these studies demonstrate that in N. meningitidis iron and NrrF mediated regulation of sdhC and sdhA can occur independently of Hfq, although Hfq functions more globally to control regulation of other N. meningitidis genes primarily by iron-independent mechanisms. RNA was isolated from wild-type MC58 Neisseria meningitidis, from an hfq- mutant, and from a complemented hfq- mutant under both iron-replete and iron-deplete conditions. Three biological replicates were analyzed for each strain and condition were analyzed.
2010-05-14 | E-GEOD-20294 | biostudies-arrayexpress
Project description:Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses. The global transcriptome responded specifically to sulfur, iron or potassium deprivation.
2016-07-21 | GSE77602 | GEO
Project description:Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.
| EGAS00001006112 | EGA