PXD030393-1

PXD030393 is an original dataset announced via ProteomeXchange.

Title	Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense to fermentative and various respiratory metabolisms
Description	Desulfitobacterium hafniense was originally isolated for its ability to use organohalogens as terminal electron acceptors in the process of organohalide respiration (OHR). However, in contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use many possible electron donors and acceptors and to grow fermentatively also. The sequencing of several Desulfitobacterium genomes displaying numerous and apparently redundant members of redox enzyme families has confirmed their large metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. In the present work, we conducted an extended proteomic study by comparing the proteomes of D. hafniense strain DCB-2 cultivated in different combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. The Tandem Mass Tag labelling proteomic approach allowed us to identify almost 60% of the predicted proteome of strain DCB-2 in all six growth conditions and to quantify the relative abundance of 2796 proteins. This dataset was analysed in order to highlight the proteins that were up-regulated in one or a subset of growth conditions to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium – a very widespread practice in the cultivation of strictly anaerobic bacteria – triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favourable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters including four new proteins, the function of which is discussed. Overall, we believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing present and future research questions.
HostingRepository	PRIDE
AnnounceDate	2023-01-18
AnnouncementXML	Submission_2023-01-18_06:53:55.415.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RomainHamelin
SpeciesList	scientific name: Desulfitobacterium hafniense DCB-2; NCBI TaxID: 272564;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-14 08:04:43	ID requested
⏵ 1	2023-01-18 06:53:55	announced

Dataset with its publication pending

submitter keyword: Desulfitobacterium hafniense strain DCB-2

energy metabolism

organohalide respiration

fermentation

quantitative proteomics

Tandem Mass Tag labelling

ChristofHolliger
contact affiliation	Laboratory for Environmental Biotechnology, Ecole polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
contact email	julien.maillard@epfl.ch
lab head
RomainHamelin
contact affiliation	PCF
contact email	romain.hamelin@epfl.ch
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/2023/01/PXD030393

PRIDE project URI

• PRIDE
  1. PXD030393
     1. Label: PRIDE project
     2. Name: Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense to fermentative and various respiratory metabolisms