PXD064015

PXD064015 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-16 08:29:55	ID requested
⏵ 1	2026-01-02 13:41:01	announced

10.1128/AEM.01942-25;

submitter keyword: acid tolerance, ENIGMA, bacteria, Castellaniella

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

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PRIDE project URI

• PRIDE
  1. PXD064015
     1. Label: PRIDE project
     2. Name: Metabolic adaptations to acidic conditions in Castellaniella isolate: contrasting effects of glutamate and branched-chain amino acids