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PXD045039-1

PXD045039 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleExploring the hidden world of Methanosarcina mazei: Unravelling the secrets of its small proteome and its nitrogen-dependent regulation
DescriptionThe mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1, is crucial for climate and environmental research due to its ability to produce methane from H2 plus CO2, acetate, and methylamines. Here, we established the first Ribo-seq protocol for M. mazei strain Gö1 under two growth conditions (nitrogen sufficiency (+N) versus nitrogen limitation (-N)). Translation of 93 previously annotated and 311 novel small open reading frames (sORFs), coding for proteins ≤ 70 amino acids in length was predicted with high confidence based on Ribo-seq data. Epitope tagging followed by immunoblotting analysis confirmed the translation of 12 out of 15 selected novel sORFs, the remaining three were validated by LC-MS-MS analysis. In total, LC-MS-MS analysis validated translation for 60 annotated sORFs and 26 novel sORFs. A comprehensive differential expression analysis revealed that 29 of 311 novel sORFs were differentially regulated in response to nitrogen availability at the transcriptional and 49 at the translational level. Several reported sRNAs are now emerging as dual-functional sRNAs, including sRNA154, the central regulatory sRNA in regulation of nitrogen metabolism. Numerous of the novel sORFs identified in this study are conserved in Methanosarcina species, some of which showed a phenotype when overproduced, pinpointing important physiological functions. Overall, the comprehensive analysis opens a new avenue to start elucidating the function(s) of small proteins in M. mazei.
HostingRepositoryPRIDE
AnnounceDate2024-09-13
AnnouncementXMLSubmission_2024-09-13_07:25:41.411.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAndreas Tholey
SpeciesList scientific name: Methanosarcina mazei Go1; NCBI TaxID: 192952;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos; Q Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-09-01 09:00:01ID requested
12024-09-13 07:25:41announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Archaea
Methanoarchaea
Ribosome profiling
Ribo-seq
small proteome
sORF
nitrogen
dual function sRNA
Contact List
Andreas Tholey
contact affiliationInstitut für Experimentelle Medizin Christian-Albrechts-Universität zu Kiel Niemannsweg 11 24105 Kiel, Germany
contact emailA.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliationSystematic Proteome Research & Bioanalytics, University of Kiel
contact emaila.tholey@iem.uni-kiel.de
dataset submitter
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