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Profiling of the Cellular Proteome and Phosphoproteome of Klebsiella pneumoniae under Iron Limited and Iron Replete Conditions

ABSTRACT: Klebsiella pneumoniae was compared across iron limited and iron replete conditions to assess changes within the cellular proteome and phosphoproteome using quantitative mass spectrometry. These comparative proteomic data provide insight into cellular response to nutrient limitation and how nutrient requirements could be exploited to provide potential antimicrobial targets.

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

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			Action	DRS
	MD015E-Fe1-so1124-phospho-Try-Lyc-V1.raw	Raw
	MD015E-Fe1-so1124-phospho-Try-Lyc-V2.raw	Raw
	MD015E-Fe1-so1124-total-Try-Lyc-V1.raw	Raw
	MD015E-Fe2-so1124-phospho-Try-Lyc-V1.raw	Raw
	MD015E-Fe2-so1124-phospho-Try-Lyc-V2.raw	Raw

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Quantitative proteomics of iron limitation in Klebsiella pneumoniae

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

Profiling of the Cellular Proteome and Phosphoproteome of Klebsiella pneumoniae under Zinc Limited and Zinc Replete Conditions

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

Transcription profiling of jejunum from iron-replete or iron-deficient rats

Project description:12-week-old rats, iron-replete or iron-deficient. Three groups of each condition. 230A and 230B chips used with cRNA derived from jejunal scrapes.

2007-11-11 | E-GEOD-2269 | biostudies-arrayexpress

Expression data from roots of Arabidopsis grown under sulfur, iron or potassium limitation

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

Genome wide expression responses of Fusarium oxysporum wt and ΔhapX mutant to iron depleted and iron replete conditions.

Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of ΔhapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals.

2012-07-14 | GSE39325 | GEO

Genome wide expression responses of Fusarium oxysporum wt and M-NM-^ThapX mutant to iron depleted and iron replete conditions.

Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of M-NM-^ThapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals. Iron dependent gene expression in Fusarium oxysporum wt and M-NM-^ThapX mutant was measured 1 hour after shifting the mycelia to minimal medium with or without 50 M-NM-<M Fe2(SO4)3. Three independent experiments were performed.

2012-07-13 | E-GEOD-39325 | biostudies-arrayexpress

Global gene expression in Moraxella catarrhalis ATCC 43617 grown under iron-replete and iron-limiting conditions

Project description:Total RNA samples were isolated from M. catarrhalis grown in BHI (iron-replete condition, designated DF0) and in BHI containing 30 mM Desferal (iron-limiting condition, designated DF30). Total RNA and M. catarrhalis genome-directed primers (GDPs) were used for synthesis of Cy3- or Cy5-labeled cDNA samples. Three independent M. catarrhalis growth experiments and total RNA isolations were used for synthesis of cDNA samples, and a total of six DNA microarray hybridizations were performed in this study. Keywords: Effect of Growth Environment on Global Gene Expression by Moraxella catarrhalis

2007-12-07 | GSE4346 | GEO

Xanthomonas campestris pv. campestris str. 8004 (Xcc 8004; Indian Isolate): Wild type vs xibR mutant, under the both iron-replete and iron-deplete conditions.

Project description:Transcriptional profiling of low-iron stimulon and XibR influenced regulon using wild-type Xcc 8004 and xibR mutant grown under iron-replete and iron-deplete conditions. Trancriptional analysis under iron-deplete condition, mimicking in planta environment, provides greater insights into expression pattern of several virulence-associated functions under low-iron. A genetic screen sggested the involvement of XibR (Xanthomonas iron binding regulator) in iron-uptake and metabolism. Present transcriptional analysis suggested the co-regulation of virulence associated functions including siderophore biosynthesis, motility, chemotaxis and typeIII effectors by a novel transcriptional regulator of NtrC family protein XibR and iron avability.

2016-11-02 | GSE89267 | GEO

Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae

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

Obesity, Iron Regulation and Colorectal Cancer Risk

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.

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