PXD007068

PXD007068 is an original dataset announced via ProteomeXchange.

Title	Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative endosymbiont C4PR_LIV
Description	The majority of bacterial genomes have high coding efficiencies, but there are an few genomes of the intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple omic strategies: combining single molecule DNA-sequencing and annotation; stranded RNA-sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Core-genome analysis of six Illumina sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions, and demonstrate that pseudogenes are more complex than a simple degrading DNA sequence. For this reason, we show that combining genomics, transcriptomics and proteomics represents an important resource for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.
HostingRepository	PRIDE
AnnounceDate	2020-05-26
AnnouncementXML	Submission_2020-05-26_11:14:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Philip Brownridge
SpeciesList	scientific name: Sodalis glossinidius; NCBI TaxID: 63612;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-17 08:57:57	ID requested
⏵ 1	2020-05-26 11:14:03	announced

Goodhead I, Blow F, Brownridge P, Hughes M, Kenny J, Krishna R, McLean L, Pongchaikul P, Beynon R, Darby AC, - a facultative bacterial endosymbiont. Microb Genom, 6(1):(2020) [pubmed]

curator keyword: Biological

submitter keyword: proteogenomics, genomics, transcriptomics, proteomics

Robert Beynon
contact affiliation	Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool,L69 7ZB
contact email	rbeynon@liverpool.ac.uk
lab head
Philip Brownridge
contact affiliation	University of Liverpool
contact email	philipjb@liv.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007068
     1. Label: PRIDE project
     2. Name: Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative endosymbiont C4PR_LIV