Dataset Information

Iron deficiency response of Corynebacterium glutamicum

ABSTRACT: The response to iron limitation of the Gram-positive soil bacterium Corynebacterium glutamicum was analyzed with respect to proteome during growth in glucose minimal medium. C. glutamicum cells were grown at regular (36 µM) and low (1 µM) iron concentrations and harvested in the late exponential growth phase. Between 1056 and 1357 proteins were detected (1% false discovery rate, FDR) in the measurements of three biological replicates including technical replicates each for low and high iron conditions with a proteomic shotgun analysis using nanoLC-MS/MS, covering in total 1555 proteins. By SWATH-MS measurements, relative levels of 1123 proteins could be quantified. Thereof, 66 proteins exhibited at least two-fold altered ratios with a p-value ≤0.05 in iron-deprived cells compared to the cells cultivated with 36 μM iron. 38 proteins showed a ≥2-fold higher level under iron limitation, 16 of which were members of the DtxR regulon. The levels of 28 proteins were at least 2-fold lower under iron limitation, 10 of which were members of the RipA regulon.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Corynebacterium Glutamicum Atcc 13032 Bacteria

SUBMITTER: Tino Polen

LAB HEAD: Tino Polen

PROVIDER: PXD017349 | Pride | 2020-04-15

REPOSITORIES: Pride

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The Iron Deficiency Response of Corynebacterium glutamicum and a Link to Thiamine Biosynthesis.

Küberl Andreas A Mengus-Kaya Aliye A Polen Tino T Bott Michael M

Applied and environmental microbiology 20200505 10

The response to iron limitation of the Gram-positive soil bacterium <i>Corynebacterium glutamicum</i> was analyzed with respect to secreted metabolites, the transcriptome, and the proteome. During growth in glucose minimal medium, iron limitation caused a shift from lactate to pyruvate as the major secreted organic acid complemented by l-alanine and 2-oxoglutarate. Transcriptome and proteome analyses revealed that a pronounced iron starvation response governed by the transcriptional regulators D ...[more]

PMID: 32144105

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Project description:Pupylation is a posttranslational protein modification in bacteria resembling ubiquitination in eukaryotes. The prokaryotic ubiquitin-like protein Pup is covalently attached to other proteins via an isopeptide bond between its carboxyterminal glutamate residue and a lysine residue in the target. In mycobacteria, pupylation was shown to mark proteins for unfolding by the ATPase Mpa and subsequent degradation by the proteasome. However, the occurrence of pupylation in species without a proteasome like Corynebacterium glutamicum suggests that degradation may not be the only fate of pupylated proteins. The Îpup mutant senses a stronger iron limitation than the wild type. Among the 125 genes showing at least 2-fold changes in transcript levels in the Îpup mutant (p-value â¤ 0.05) were 54% of all genes known to be regulated by the master regulator of iron homeostasis DtxR (Brune et al., 2006; Wennerhold and Bott, 2006). Except for ftn, which is activated by DtxR and showed a 2-fold decreased mRNA level, the other DtxR target genes showed increased mRNA levels in the Îpup strain. These included ripA, encoding a transcriptional regulator of iron proteins, which represses a number of prominent iron-containing proteins under iron limitation, such as aconitase or succinate dehydrogenase (Wennerhold et al., 2005). 79% of the known RipA target genes showed decreased mRNA levels in the Îpup strain. DNA microarray analyses were performed to compare the mRNA levels of the C. glutamicum Îpup mutant and its parent wild type under iron-limited conditions. The two strains precultivated in CGXII medium with 4% (w/v) glucose and 1 ÂµM FeSO4 were inoculated into fresh medium to an OD600 of 1, cultured for 2 h, and harvested on ice by centrifugation (5 min at 4,000 g and 4Â°C). Please note that the GPL16989 array design comprises oligos for 4 different bacterial genomes. In the GPR-files in this study, all IDs/Names (oligonucleotides) which are not from the host C. glutamicum were replaced by the text EMPTY since only C. glutamicum expression was analyzed.

Project description:As integral parts of gene regulatory networks, small regulatory RNAs (sRNAs) play important roles in the adaptation of bacteria to environmental conditions. To adapt to iron limitation, many bacteria exploit an "iron-sparing" response mediated by Fur-regulated sRNAs such as RyhB of E. coli, allowing them to reduce the synthesis of iron-utilizing proteins not essential for growth. In this study, we aimed to confirm the regulatory role of the sRNA IsrR (Iron-sparing response Regulator) of S. aureus and to characterize the IsrR targetome in order to better understand the pathogens adaptation to iron-limited conditions often encountered in the host. To identify potential IsrR targets, two different experimental approaches were used. In the first, proteome profiles of S. aureus HG001 were compared to those of an isogenic ΔisrR mutant under iron-limited conditions. In the second approach, the effects of IsrR on the proteome under iron-rich conditions were analyzed using a strain in which IsrR was constitutively expressed from a plasmid. In silico target prediction was performed using the CopraRNA2 tool. Presence of IsrR caused a large number of consistent changes in protein levels both under iron-limited or iron-rich conditions. Among the proteins exhibiting significantly different abundance, 63 were in common between both experiments. Since sRNAs can have direct and indirect effects on global gene expression, the experimental approach was combined with in silico target prediction. In this way, very likely direct IsrR targets were identified, which include catalase (KatA) and three tricarboxylic acid (TCA) cycle enzymes (CitB, SdhA, SucA). Follow-up analyses confirmed that IsrR negatively affects KatA and CitB enzymatic activities. In contrast to most identified IsrR targets, the predicted interaction region of IsrR with the katA mRNA does not overlap the ribosome binding site, suggesting that IsrR cannot only inhibit translation, but also directly affect mRNA stability. A putative IsrR targetome was identified. In agreement with Fur-regulated sRNAs of other organisms, IsrR negatively affects the expression of TCA cycle and heme biosynthesis enzymes.

			Action	DRS
	MV_Export_Ions.txt	Txt
	MV_Export_Peptides.txt	Txt
	MV_Export_Proteins.txt	Txt
	WT1uM_1_3x.group	Other
	WT1uM_1_Swath30_01.wiff	Wiff