0.0 et al. 2023 (PRJNA858256)

General Details

Title Revealing the small proteome of Haloferax volcanii by ribosome profiling and small-protein optimised mass spectrometry
Organism
Number of Samples 5
Release Date 2022/07/13 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP386192
ENA SRP386192
GEO GSE208086
BioProject PRJNA858256

Publication

Title
Authors Hadjeras L, Bartel J, Maier LK, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A
Journal microLife
Publication Date 2023
Abstract In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii . We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea. © The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.
PMC PMC10117724
PMID 37223747
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR20138953 PRJNA858256 Haloferax volcanii NA_archaea Ribo-Seq 0.0
SRR20138952 PRJNA858256 Haloferax volcanii NA_archaea Ribo-Seq 0.0
SRR20138951 PRJNA858256 Haloferax volcanii NA_archaea Ribo-Seq 0.0
SRR20138950 PRJNA858256 Haloferax volcanii NA_archaea RNA-Seq 0.0
SRR20138949 PRJNA858256 Haloferax volcanii NA_archaea RNA-Seq 0.0
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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