PXD005606

PXD005606 is an original dataset announced via ProteomeXchange.

Title	ELM-seq
Description	Quantitative analysis of the sequence determinants of transcription and translation regulation is of special relevance for systems and synthetic biology applications. Here, we developed a novel generic approach for the fast and efficient analysis of these determinants in vivo. ELM-seq (expression level monitoring by DNA methylation) uses Dam coupled to high-throughput sequencing) as a reporter that can be detected by DNA-seq. We used the genome-reduced bacterium Mycoplasma pneumoniae to show that it is a quantitative reporter. We showed that the methylase activity correlates with protein expression, does not affect cell viability, and has a large dynamic range (~10,000-fold). We applied ELM-seq to randomized libraries of promoters or 5’ untranslated regions. We found that transcription is greatly influenced by the bases around the +1 of the transcript and the Pribnow box, and we also identified several epistatic interactions (including the +1 and the “extended Pribnow”). Regarding translation initiation, we confirmed that the Shine-Dalgarno motif is not relevant, but instead, that RNA secondary structure is the main governing factor. With this in hand, we developed a predictor to help tailor gene expression in M. pneumoniae. The simple ELM-seq methodology will allow identifying and optimizing key sequence determinants for promoter strength and translation. The ELM-seq methodology allows both researchers and companies to identify and optimize in an easy and comprehensive manner, key sequence determinants for promoter strength and translation.
HostingRepository	PRIDE
AnnounceDate	2017-08-29
AnnouncementXML	Submission_2017-09-12_02:13:18.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eva Yus
SpeciesList	scientific name: Mycoplasma pneumoniae (strain ATCC 29342 / M129); NCBI TaxID: 272634;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-20 05:37:25	ID requested
1	2017-08-29 00:00:36	announced
⏵ 2	2017-09-12 02:13:19	announced	Updated publication reference for PubMed record(s): 28848232.

Yus E, Yang JS, Sogues A, Serrano L, A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants. Nat Commun, 8(1):368(2017) [pubmed]

curator keyword: Biological

submitter keyword: Screening, transcription, translation, reporter

Eva Yus
contact affiliation	Centre for Genomic Regulation
contact email	eva.yus@crg.eu
lab head
Eva Yus
contact affiliation	Centre for Genomic Regulation
contact email	eva.yus@crg.eu
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/2017/08/PXD005606

PRIDE project URI

• PRIDE
  1. PXD005606
     1. Label: PRIDE project
     2. Name: ELM-seq