Proteomics

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Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative endosymbiont C4PR_LIV


ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Sodalis Glossinidius

SUBMITTER: Philip Brownridge  

LAB HEAD: Robert Beynon

PROVIDER: PXD007068 | Pride | 2020-05-26

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
091014_FT1and2.raw Raw
091014_FT3andwash.raw Raw
100_061014.raw Raw
151014_Fraction_100_2hour.raw Raw
151014_Fraction_15_2hour.raw Raw
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Publications

Large-scale and significant expression from pseudogenes in <i>Sodalis glossinidius</i> - a facultative bacterial endosymbiont.

Goodhead Ian I   Blow Frances F   Brownridge Philip P   Hughes Margaret M   Kenny John J   Krishna Ritesh R   McLean Lynn L   Pongchaikul Pisut P   Beynon Rob R   Darby Alistair C AC  

Microbial genomics 20200101 1


The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont <i>Sodalis glossinidius</i> contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis  ...[more]

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