PXD004646

PXD004646 is an original dataset announced via ProteomeXchange.

Title	E. coli S30 lysate proteome - The E
Description	Protein production using processed cell lysates, defined precursor cocktails and target specific additives has become a core technology in the field of synthetic biology. Due to their open nature, these artificial systems are excellent to produce difficult proteins such as toxins or membrane proteins. However, the composition of cell lysates as the core component of cell-free systems is still widely a black box. Lysates of Escherichia coli are most productive for cell-free expression, yielding several milligrams of protein per milliliter of reaction. Although proteomics studies of several E. coli strains are available, the preparation of cell-free lysates implies specific fractionation resulting into yet unknown final lysate compositions. Therefore, the identification of prevalent and reliable lysate compounds will be an indispensable prerequisite for directed lysate engineering as an emerging strategy for new applications in synthetic biology. In this study, the S30 lysate proteome from E. coli strain A19 has been analyzed for the first time by using a GeLC-MS/MS approach. A total of 821 proteins were identified in processed S30 lysates. We provide detailed lists of detected proteins relevant for transcription/translation, folding, stability and enzymes involved in metabolic processes. In addition, we also performed a quantitative proteome analysis of modified S30 lysates, generated by induction of the SOS response during cultivation. These altered lysates contain 3-10-fold more folding factors and exhibit improved solubility and folding of difficult proteins. Therefore, the manipulation of the S30 lysate proteome by modified cultivation conditions is an effective approach for the generation of customized cell-free systems.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:36:15.710.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Foshag
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue
Instrument	ultraflex

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-25 02:01:59	ID requested
1	2017-09-29 09:36:00	announced
⏵ 2	2024-10-22 04:36:17	announced	2024-10-22: Updated project metadata.

Foshag D, Henrich E, Hiller E, Sch, ä, fer M, Kerger C, Burger-Kentischer A, Diaz-Moreno I, Garc, í, a-Mauri, ñ, o SM, D, ö, tsch V, Rupp S, Bernhard F, The E. coli S30 lysate proteome: A prototype for cell-free protein production. N Biotechnol, 40(Pt B):245-260(2018) [pubmed]

10.1016/j.nbt.2017.09.005;

submitter keyword: qualitative and quantititative proteomics, Heatshock lysate,E. coli A19, S30 lysate

Steffen Rupp
contact affiliation	Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
contact email	steffen.rupp@igb.fraunhofer.de
lab head
Daniel Foshag
contact affiliation	IGVP, University of Stuttgart
contact email	d.foshag@gmail.com
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/2017/09/PXD004646

PRIDE project URI

• PRIDE
  1. PXD004646
     1. Label: PRIDE project
     2. Name: E. coli S30 lysate proteome - The E