PXD019012-1

PXD019012 is an original dataset announced via ProteomeXchange.

Title	Genome-wide effects of the antimicrobial peptide apidaecin on translation termination
Description	Proline-rich antimicrobial peptide apidaecin (Api) inhibits bacterial protein synthesis in a distinctive way. In vitro biochemical and structural studies showed that Api binds in the nascent peptide exit tunnel of the ribosome that has completed translation of the gene and has released the newly-synthesized protein. Once in the tunnel, Api traps the release factors on the post-termination ribosome leading to cessation of translation. The mode of Api action in the bacterial cell, however, had remained unknow. By analyzing distribution of ribosomes on mRNAs in Api-treated cells using Ribo-seq approach we uncovered a range of effects that stem from the unique mechanism of Api action. Exposure of bacterial cells to Api results in arrest of translation at stop codons, likely in a post-release state, due to the immediate Api action, as well as in a pre-release state due to the depletion of available release factors. In addition, arrest of translation at the end of the open reading frame (ORF) leads to a pronounced queuing of the translating ribosomes behind the one arrested at the stop codon. One of the major consequences of the Api action is a dramatically increased stop codon bypass by the ribosomes paused in a pre-release state, leading to accumulation of proteins with C-terminal extensions, as confirmed by whole-cell proteomics analysis. Stop codon bypass, that occurs either in 0-frame, by misincorporation of a near-cognate aminoacyl-tRNA at the stop codon, or via frameshifting allows for a fraction of the translating ribosomes to reach the 3’ ends of mRNA transcripts. The pervasive stalling of pre-release ribosomes at the stop codons and at the RNA transcripts ends triggers activation of the cellular ribosome rescue systems which, likely due to Api action as well, remain ineffective. While major Api effects are directed towards the ribosome at the end of the ORFs, cells exposed to Api show a somewhat increased ribosome occupancy of the start codons. Understanding the unique mode of Api to inhibit translation termination in the cell can help envisioning the development of treatments for genetic diseases and research tools for genome exploration.
HostingRepository	PRIDE
AnnounceDate	2020-10-05
AnnouncementXML	Submission_2020-10-04_23:28:32.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019012
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yu Gao
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-06 05:25:23	ID requested
⏵ 1	2020-10-04 23:28:33	announced

Dataset with its publication pending

submitter keyword: apidaecin, LC-MS, translation termination, e. coli, peptide

Yu Gao
contact affiliation	University of Illinois at Chicago Department of Pharmaceutical Sciences
contact email	yugao@uic.edu
lab head
Yu Gao
contact affiliation	University of Illinois at Chicago
contact email	yugao@uic.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD019012
     1. Label: PRIDE project
     2. Name: Genome-wide effects of the antimicrobial peptide apidaecin on translation termination