PXD004565-5

PXD004565 is an original dataset announced via ProteomeXchange.

Title	Mini-Bacillus - Large-scale reduction of the Bacillus subtilis genome: Consequences for the transcriptional network, resource allocation, and metabolism
Description	In this study, we have applied the top-down approach to reduce the genome of B. subtilis in order to obtain minimal strains with robust growth on complex medium at 37°C. For this purpose, we have evaluated the function of each gene of the B. subtilis genome and identified essential, important and dispensable genomic regions. Using an efficient markerless and scarless deletion method and a system allowing induction of genetic competence in the complete cell population, we have constructed two genome-reduced strains lacking about 36% of dispensable genetic information. Multi-omics analyses with the genome-reduced strains revealed substantial changes in the transcriptome, the proteome and in the metabolome. The massive reorganization of metabolism in the two genome-reduced strains can be explained by the underlying genotypes that were determined by genome re-sequencing. Moreover, the transcriptome and proteome analyses uncovered novel dispensable genomic regions that can be removed to further streamline the B. subtilis genome. In conclusion, both minimal strains show interesting metabolic features and they serve as excellent starting points to generate an ultimate reduced-genome B. subtilis cell containing only genes required for robust growth on complex medium.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:31:12.364.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Praveen Sappa
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-13 00:18:22	ID requested
1	2016-12-07 05:12:18	announced
2	2017-01-02 09:25:10	announced	Updated publication reference for PubMed record(s): 27965289.
3	2017-10-24 05:51:52	announced	Updated project metadata.
4	2017-10-24 06:13:09	announced	Updated project metadata.
⏵ 5	2024-10-22 04:31:20	announced	2024-10-22: Updated project metadata.

Reu, ß DR, Altenbuchner J, M, ä, der U, Rath H, Ischebeck T, Sappa PK, Th, ü, rmer A, Gu, é, rin C, Nicolas P, Steil L, Zhu B, Feussner I, Klumpp S, Daniel R, Commichau FM, V, ö, lker U, St, ü, lke J, Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism. Genome Res, 27(2):289-299(2017) [pubmed]

curator keyword: Biological

submitter keyword: DIA,Bacillus subtilis, LC-MS/MS

Uwe Völker
contact affiliation	Professor Dr. Uwe Völker, Head of the department of Functional Genomics, Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Greifswald, Germany.
contact email	voelker@uni-greifswald.de
lab head
Praveen Sappa
contact affiliation	Universitätsmedizin Greifswald
contact email	praveen.kumar@uni-greifswald.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/2016/12/PXD004565

PRIDE project URI

• PRIDE
  1. PXD004565
     1. Label: PRIDE project
     2. Name: Mini-Bacillus - Large-scale reduction of the Bacillus subtilis genome: Consequences for the transcriptional network, resource allocation, and metabolism