PXD046861-1

PXD046861 is an original dataset announced via ProteomeXchange.

Title	A cell-free strategy for profiling intracellular antibiotic sensitivity and resistance – characterising the proteomes of K. pneumoniae ATCC 13882, ST258-T1b and NJST258-1 and E. coli K-12 MG1655.
Description	Antimicrobial resistance (AMR) is a pandemic spread across multiple infectious disease microbes. To provide a new tool to study AMR, here we develop a Klebsiella pneumoniae cell-free gene expression (CFE) system. To characterise the system, we use proteomics to compare this to a Escherichia coli MG1655 CFE model, to identify relative differences and unique proteins. Then we use this native CFE system to profile antimicrobial activity in comparison to whole cell inhibition, to reveal host differences in IC50/MIC50 values. Finally, we use the CFE tool to study AMR variants, at a proof-of-concept level. As an exemplar, we show that RpoB H526L confers a 58-fold increase in CFE resistance to rifampicin – a common genotype frequently observed in rifampicin-resistant Mycobacterium tuberculosis clinical isolates. In summary, we provide a cell-free synthetic biology strategy for the profiling of antibiotic sensitivity and resistance from K. pneumoniae. While initial processing requires Biosafety Level 2, the final extracts are non-living and suitable for long-term storage, and potentially transfer to a Biosafety Level 1 lab. This bioassay has potential uses for early-stage host-specific antimicrobial development and the testing of AMR variants for structure-activity relationship studies. The data reposited is label-free high-resolution LC-MS proteomics data performed to characterise the proteins in cell-free extract of K. pneumoniae ATCC 13882 and compare to that of E. coli MG1655 to identify common and unique proteins. We also characterised the proteins of K. pneumoniae clinically resistant isolates ST258-T1b and NJST258-1, and compared them to K. pneumoniae ATCC 13882 laboratory strain.
HostingRepository	PRIDE
AnnounceDate	2023-11-29
AnnouncementXML	Submission_2023-11-29_05:53:42.841.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046861
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	KAMESHWARI CHENGAN
SpeciesList	scientific name: Klebsiella pneumoniae subsp. pneumoniae HS11286; NCBI TaxID: 1125630; scientific name: Klebsiella pneumoniae subsp. pneumoniae ST258; NCBI TaxID: 1460422; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Klebsiella pneumoniae 30660/NJST258_1; NCBI TaxID: 1420012;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS; MALDI Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-11 05:11:59	ID requested
⏵ 1	2023-11-29 05:53:43	announced
2	2024-10-22 06:16:33	announced	2024-10-22: Updated project metadata.

10.6019/PXD046861;

submitter keyword: synthetic biology, cell-free protein synthesis, Klebsiella pneumoniae,Antimicrobial resistance, cell-free gene expression

Dr Simon Moore
contact affiliation	School of Biological and Behavioural Sciences Queen Mary University of London
contact email	simon.moore@qmul.ac.uk
lab head
KAMESHWARI CHENGAN
contact affiliation	University of Kent
contact email	kc596@kent.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046861
     1. Label: PRIDE project
     2. Name: A cell-free strategy for profiling intracellular antibiotic sensitivity and resistance – characterising the proteomes of K. pneumoniae ATCC 13882, ST258-T1b and NJST258-1 and E. coli K-12 MG1655.