PXD061547

PXD061547 is an original dataset announced via ProteomeXchange.

Title	An Isoprenol Biosensor for Combinatorial High Throughput Strain Engineering in Pseudomonas putida
Description	Our group has evaluated the productivity of the alcohol isoprenol (3-methyl-3-buten-1-ol), platform commodity chemical with attractive properties specifically as a diesel fuel blendstock and precursor for the bio-jetfuel DMCO, across a number of microbial hosts. While there are strengths and drawbacks to producing isoprenol in any one microbe, Pseudomonas putida KT2440 has a naturally versatile catabolic profile competent of consuming isoprenol. The pathway for this catabolism was revealed using functional genomics data (RB-TnSeq - Thompson et al) and we speculated that this data could also provide a path to developing an isoprenol biosensor. Refactoring knowledge of the isoprenol catabolism signaling system could provide a readout for intracellular isoprenol, in turn enabling an alternative approach to strain engineering that did not rely on a mechanistic understanding of how a heterologous pathway modulates native metabolism. We define a biosensor as the system where a ligand is recognized by a transcriptional activator, which in turn binds to a cognate DNA sequence driving transcription of a downstream reporter gene. The resulting gene expression linearly increases in response to the initial ligand concentration. There are undoubtedly other biosensor modalities (such as directly converting the ligand into a colored molecule) but the advantage of a biosensor that activates a genetic circuit is that the response can also be integrated back into cellular physiology for high throughput selection with growth based assay. For example, strains can be devised where cell growth is concomitant with the increased production of the ligand. Prokaryotic systems are also advantaged over eukaryotes for biosensor development as the determinants of ribosome translation efficiency are dictated by simple RBS sequences adjacent to the start codon as opposed to complex transcriptional regulators, enabling fine protein level expression tuning while maintaining inducibility.
HostingRepository	PRIDE
AnnounceDate	2025-09-12
AnnouncementXML	Submission_2025-09-12_14:51:19.134.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-06 13:31:28	ID requested
⏵ 1	2025-09-12 14:51:19	announced

Dataset with its publication pending

submitter keyword: Biomanufacturing, Biosensors, Strain engineering, High-throughput, JBEI,Biofuels, Isoprenol, P. putida

Christopher J. Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061547
     1. Label: PRIDE project
     2. Name: An Isoprenol Biosensor for Combinatorial High Throughput Strain Engineering in Pseudomonas putida