PXD024231

PXD024231 is an original dataset announced via ProteomeXchange.

Title	A proteomic study of bacterial growth arrest in a synthetic biology application
Description	Scaling up the functioning of synthetic circuits from microplates to bioreactors is far from trivial to achieve. We here test the scalability performance of a previously developed growth switch for increasing product yields in bacteria, based on external control of RNA polymerase expression. We show that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multi-omics quantification of the physiology of the cells shows that apart from acetate production, few metabolic side-effects occur, while a number of specific responses to growth slow-down and growth arrest are launched on the transcriptional level. These responses include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation, and the upregulation of heat shock genes. Interestingly, these transcriptional responses are buffered on the proteomic level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. This transforms the growth-arrested cells in “bags of proteins“ with a functioning metabolism. More generally, the analysis shows that physiological characterization of bacterial cells hosting a synthetic circuit may reveal complex patterns of adaptation on different time-scales, dynamically interacting with the bioreactor environment.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_08:14:45.680.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024231
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yohann Couté
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-18 01:39:09	ID requested
⏵ 1	2021-11-25 08:14:46	announced

Dataset with its publication pending

submitter keyword: Escherichia coli, metabolic engineering, growth switch, nanoLC-MS/MS

Virginie Brun
contact affiliation	EDyP
contact email	virginie.brun@cea.fr
lab head
Yohann Couté
contact affiliation	EDyP
contact email	yohann.coute@cea.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD024231
     1. Label: PRIDE project
     2. Name: A proteomic study of bacterial growth arrest in a synthetic biology application