PXD064015 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Metabolic adaptations to acidic conditions in Castellaniella isolate: contrasting effects of glutamate and branched-chain amino acids |
| Description | Acidification of groundwater co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in-situ removal of nitrate in groundwater. However, co-existing stressors—like low pH—reduce the efficacy of these biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0 while completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, likely through its decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. Additionally, branched chain amino acid (BCAA) appears to be detrimental to cell growth at lower pHs. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed—concurrent to nitrate removal—during a biostimulation effort to reduce groundwater nitrate concentrations at MT123’s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-01-02 |
| AnnouncementXML | Submission_2026-01-02_13:41:01.095.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Christopher Petzold |
| SpeciesList | scientific name: Castellaniella sp.; NCBI TaxID: NEWT:1955812; |
| ModificationList | monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-05-16 08:29:55 | ID requested | |
| ⏵ 1 | 2026-01-02 13:41:01 | announced | |
Publication List
Keyword List
| submitter keyword: acid tolerance, ENIGMA, bacteria, Castellaniella |
Contact List
| Christopher Petzold |
|---|
| contact affiliation | Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 |
| contact email | cjpetzold@lbl.gov |
| lab head | |
| Christopher Petzold |
|---|
| contact affiliation | Lawrence Berkeley National Laboratory |
| contact email | cjpetzold@lbl.gov |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD064015
- Label: PRIDE project
- Name: Metabolic adaptations to acidic conditions in Castellaniella isolate: contrasting effects of glutamate and branched-chain amino acids
