PXD059988

PXD059988 is an original dataset announced via ProteomeXchange.

Title	Growth in Low Carbon Conditions Reveals Amino-Acid-Coupled Iron Uptake
Description	Bacteria in nature encounter substrates at widely varying concentrations, yet studies of bacterial physiology have focused more on nutrient type than concentration, partly due to challenges in maintaining low concentrations. We developed a Millifluidic Continuous Culture Device (MCCD) to culture bacteria under precisely controlled nutrient conditions, including very low concentrations, in a manner suitable for proteomic analysis. Using the MCCD, we cultured 35 Escherichia coli with a mixture of amino acids as the sole carbon source at three concentrations supporting growth rates spanning a fivefold range. Surprisingly, at the lowest concentration, cells exhibited proteomic signatures of iron shortage despite constant iron levels across conditions. Uptake of labeled iron-histidine and iron-cysteine complexes demonstrated that amino-acidbound iron is bioavailable to E. coli. These findings reveal a previously unknown mechanism of 40 bacterial iron acquisition that emerged under the flow imposed by the MCCD, which diluted the siderophore pool and reduced their efficacy. This work highlights the importance of studying bacterial physiology under low nutrient concentrations and demonstrates how physical conditions, such as flow, shape microbial nutrient acquisition strategies.
HostingRepository	PRIDE
AnnounceDate	2026-09-09
AnnouncementXML	Submission_2026-09-09_01:59:17.202.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD059988
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew McIlvin
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-20 11:21:13	ID requested
⏵ 1	2026-09-09 01:59:18	announced

Lara-Guti, é, rrez J, Nguyen J, McIlvin MR, Sugiyama I, Landry ZC, Alcolombri U, Pontrelli S, Jim, é, nez-Mart, í, nez J, Sauer U, Hwa T, Keegstra JM, Saito MA, Stocker R, is facilitated by amino acid complexation in a rapid-renewal environment. Proc Natl Acad Sci U S A, 123(7):e2520431123(2026) [pubmed]

10.6019/PXD059988;

10.1073/pnas.2520431123;

submitter keyword: LC-MSMS, E. coli,iron uptake

Mak Saito
contact affiliation	Marine Chemistry and Geochemistry Woods Hole Oceanographic Institute
contact email	msaito@whoi.edu
lab head
Matthew McIlvin
contact affiliation	Woods Hole Oceanographic Inst.
contact email	mmcilvin@whoi.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059988
     1. Label: PRIDE project
     2. Name: Growth in Low Carbon Conditions Reveals Amino-Acid-Coupled Iron Uptake