PXD018912

PXD018912 is an original dataset announced via ProteomeXchange.

Title	Growth Phase-Specific Variations of the Proteome and Acetylome of the Organohalide-Respiring Dehalococcoides mccartyi Strain CBDB1
Description	The strictly anaerobic bacterium Dehalococcoides mccartyi is obligatory dependent on organohalide respiration for energy conservation and growth. Due to its capability to reductively dehalogenate a multitude of toxic halogenated electron acceptors, it plays an important role in the attenuation of these compounds at respective contaminated sites. Here, D. mccartyi strain CBDB1, specialized on the dehalogenation of chloroaromatic compounds, was grown in a two-liquid phase system with 1,2,3-trichlorobenzene as electron acceptor, acetate plus CO2 as carbon source and hydrogen as electron donor. The proteome and Nε-lysine acetylome were analyzed in the lag, exponential and stationary phases. The high and almost invariable abundance of the membrane-localized organohalide respiration complex consisting of the reductive dehalogenases CbrA and CbdbA80, the uptake hydrogenase HupLS and the organohalide respiration molybdoenzyme OmeAB was shown throughout growth and also after a prolonged stationary phase. Quantification of transcripts of reductive dehalogenase genes revealed their major synthesis starting in the lag phase, which might be a prerequisite for balanced growth in the exponential phase. The analyses of the coverage of functional pathways as well as indicator analysis revealed the growth-phase specificity of the proteome, with regulatory proteins identified as important indicators for the stationary phase. The number of acetylated proteins increased from the lag to the stationary phase. We detected pronounced acetylation of key proteins of the acetate metabolism, i.e. the synthesis of acetyl-CoA and its processing via gluconeogenesis and the incomplete Wood-Ljungdahl pathway, as well as of proteins central for the biosynthesis of amino acids, co-factors and terpenoids. In addition, the partial acetylation of the reductive dehalogenases as well as of TatA, a component of the twin-arginine translocation machinery, suggests that acetylation might be directly involved in the maintenance of the organohalide respiration capacity of D. mccartyi over periods without access to halogenated electron acceptors.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:18:55.837.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dominique Türkowsky
SpeciesList	scientific name: Dehalococcoides mccartyi (strain CBDB1); NCBI TaxID: 255470; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-29 15:07:21	ID requested
1	2021-02-15 03:17:47	announced
2	2021-03-03 22:48:29	announced	2021-03-04: Updated publication reference for DOI(s): 10.3390/microorganisms9020365.
3	2021-03-03 22:53:51	announced	2021-03-04: Updated project metadata.
4	2021-03-17 05:12:05	announced	2021-03-04: Updated project metadata. 2021-03-17: Updated publication reference for PubMed record(s): 33673241. 2021-03-17: Updated publication reference for DOI(s): 10.3390/microorganisms9020365.
⏵ 5	2024-10-22 05:18:56	announced	2024-10-22: Updated project metadata.

10.3390/microorganisms9020365;

Greiner-Haas F, Bergen MV, Sawers G, Lechner U, T, ü, rkowsky D, Strain CBDB1. Microorganisms, 9(2):(2021) [pubmed]

submitter keyword: Dehalococcoides mccartyi, growth phase, reductive dehalogenation, Tat transport, chlorobenzene, low biomass, acetate metabolism, anaerobic respiration, acetylome, transcription analysis, Nε-lysine acetylation, organohalide respiration, dehalogenase, proteome

Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ Department of Molekular Systems Biology Permoserstr. 15, 04318 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Dominique Türkowsky
contact affiliation	Helmholtz Centre for Environmental Research - UFZ
contact email	dominique.tuerkowsky@ufz.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/2021/02/PXD018912

PRIDE project URI

• PRIDE
  1. PXD018912
     1. Label: PRIDE project
     2. Name: Growth Phase-Specific Variations of the Proteome and Acetylome of the Organohalide-Respiring Dehalococcoides mccartyi Strain CBDB1