Hadjeras et al. 2023 (PRJNA851064)

General Details

Title The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti
Organism
Number of Samples 2
Release Date 2022/06/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP382728
ENA SRP382728
GEO
BioProject PRJNA851064

Publication

Title
Authors Hadjeras L,Heiniger B,Maaß S,Scheuer R,Gelhausen R,Azarderakhsh S,Barth-Weber S,Backofen R,Becher D,Ahrens CH,Sharma CM,Evguenieva-Hackenberg E
Journal microLife
Publication Date 2023
Abstract The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions. © The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.
PMC PMC10117765
PMID 37223733
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR19754257 PRJNA851064 Sinorhizobium meliloti Ribo-Seq untreated
SRR19754255 PRJNA851064 Sinorhizobium meliloti Ribo-Seq untreated
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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