PXD011161

PXD011161 is an original dataset announced via ProteomeXchange.

Title	Iron regulation in Clostridioides difficile
Description	The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (760 g/l) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron transporters were found induced by Fur regulation during low iron (11 g/l) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were found significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some initial intermediates (phenylpyruvate, oxo-isocaproate, 3-hydroxy-butanoyl-CoA, crotonyl-CoA) were found accumulated, while some end product like isocaproate and butanoate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were found enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB,) of the F0F1-type was found induced while the formation of a V-type, mostly proton-pumping, ATP-consuming ATPase (atpDBAFCEKI, was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. An intensive remodeling of the cell wall was observed most likely to increase antibiotic resistance. Polyamine biosynthesis (spe) was found induced leading to an accumulation of spermine, spermidine and putrescine. The fur mutant lost most of its flagella. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, significant decrease in metabolic iron utilization and protection during the complex transition.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:14:34.588.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: Clostridioides difficile 050-P50-2011; NCBI TaxID: 997828;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-24 00:41:15	ID requested
1	2019-01-11 00:58:39	announced
⏵ 2	2024-10-22 04:14:38	announced	2024-10-22: Updated project metadata.

10.3389/fmicb.2018.03183;

Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maa, ß S, Rohde M, Eckweiler D, Borrero-de Acu, ñ, a JM, Jahn M, Neumann-Schaal M, Jahn D, . Front Microbiol, 9():3183(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: metabolism,Fur, iron transport. cell wall, iron regulation, polyamine

Dörte Becher
contact affiliation	University of Greifswald Institute for Microbiology Department for Microbial Proteomics
contact email	dbecher@uni-greifswald.de
lab head
Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/01/PXD011161

PRIDE project URI

• PRIDE
  1. PXD011161
     1. Label: PRIDE project
     2. Name: Iron regulation in Clostridioides difficile