PXD007892

PXD007892 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	A systematic and scalable approach for dissecting the molecular 2 mechanisms of transcriptional regulation in bacteria
Description	Gene regulation is one of the most ubiquitous processes in biology. And yet, while the catalogue of 15 bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in 16 these genomes are regulated. Characterizing the molecular mechanisms by which regulatory sequences 17 operate still requires focused efforts using low-throughput methods. Here we show how a combination of 18 massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used 19 to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both 20 well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all 21 cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including 22 previously unannotated ones, we can further extract quantitative biophysical models describing 23 input-output relationships. This method opens up the possibility of exhaustively dissecting the 24 mechanisms of promoter function in E. coli and a wide range of other bacteria.
HostingRepository	jPOST
AnnounceDate	2018-04-13
AnnouncementXML	Submission_2022-09-18_02:32:19.738.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michael Sweredoski
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	S-carboxamidomethyl-L-cysteine; Label:13C(6)15N(2); alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	LTQ Orbitrap Elite

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-02 11:56:14	ID requested
1	2018-04-13 15:10:30	announced
2	2018-05-11 08:54:56	announced	Updated PubMed.
3	2018-09-19 00:38:52	announced	Updated CV, FTP location and Modification list.
4	2021-02-04 17:31:17	announced	2021-02-04: Updated FTP location.
⏵ 5	2022-09-18 02:32:20	announced	2022-09-18: Updated FTP location.

Publication List

Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115(21):E4796-E4805(2018) [pubmed]

Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115(21):E4796-E4805(2018) [pubmed]

Keyword List

submitter keyword: e coli, SILAC, DNA affinity, transcription factors

submitter keyword: e coli, SILAC, DNA affinity, transcription factors

Contact List

Rob Phillips
lab head
Michael Sweredoski
contact affiliation	California Institute of Technology
dataset submitter

Full Dataset Link List

jPOST dataset URI
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.jpostdb.org/JPST000330/

jPOST dataset URI

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.jpostdb.org/JPST000330/