PXD018858

PXD018858 is an original dataset announced via ProteomeXchange.

Title	Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits
Description	Synthetic biology has focused on engineering genetic modules that operate orthogonally from the host cells. A synthetic circuit, however, can be designed to reprogram the host proteome, which in turn enhances the function of the synthetic circuit. Here, we apply this holistic synthetic biology concept by exploiting the crosstalk between metabolic networks in cells, leading to a protein environment more favorable for protein synthesis. Specifically, we show that a local module expressing translation machinery can reprogram the bacterial proteome, changing the expression levels of more than 780 proteins. The integration of the proteins synthesized by the local modules and the reprogramed proteome generate a cell-free system that can synthesize a diverse set of proteins in different reaction formats, with up to 5-fold higher expression level than classical cell-free systems. Our work demonstrates a holistic approach that integrates synthetic and systems biology concepts. This approach has the potential to achieve outcomes not possible by only local, orthogonal circuits.
HostingRepository	PRIDE
AnnounceDate	2020-05-14
AnnouncementXML	Submission_2020-07-01_22:41:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Conary Meyer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-28 08:22:58	ID requested
1	2020-05-14 03:49:31	announced
⏵ 2	2020-07-01 22:41:58	announced	2020-07-02: Updated publication reference for PubMed record(s): 32561745.

Contreras-Llano LE, Meyer C, Liu Y, Sarker M, Lim S, Longo ML, Tan C, Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits. Nat Commun, 11(1):3138(2020) [pubmed]

submitter keyword: Orthogonality, Synthetic biology, Proteome, Cell-free protein synthesis

Cheemeng Tan
contact affiliation	University of California, Davis Department of Biomedical Engineering
contact email	cmtan@ucdavis.edu
lab head
Conary Meyer
contact affiliation	University of California, Davis
contact email	conmeyer@ucdavis.edu
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/2020/05/PXD018858

PRIDE project URI

• PRIDE
  1. PXD018858
     1. Label: PRIDE project
     2. Name: Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits