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MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part4

ABSTRACT: All species continuously evolve small open reading frames (sORFs) that can be templated for protein synthesis and may provide raw material for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionary young and emerged de novo. We additionally discovered 221 yet uncataloged peptides smaller than 16 amino acids, for which we found evidence of translation in human and rodent tissues. To investigate the potential bioactivity of microproteins and peptides translated from young and very small ORFs we established MiPRISMA: a mass spectrometry-based interactome screen with sequence motif resolution. We assessed 266 candidates and implicated several in essential cellular processes including splicing, translational regulation, and endocytosis, a subset of which we validate in cellular assays. MiPRISMA provides a scalable platform to characterize small and evolutionarily young proteins, shedding light on a largely unexplored territory of the putative human proteome.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

SUBMITTER: Marieluise Kirchner

LAB HEAD: Philipp Mertins

PROVIDER: PXD033631 | Pride | 2023-02-17

REPOSITORIES: Pride

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			Action	DRS
	Microprotein_SearchDatabase_20190524.fasta	Fasta
	Phospho__STY_Sites_MPIP.txt	Txt
	Statler_20190401_SN_HS_IP_MP_D1.raw	Raw
	Statler_20190401_SN_HS_IP_MP_D2.raw	Raw
	Statler_20190401_SN_HS_IP_MP_D3.raw	Raw

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MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames

Project description:All species continuously evolve small open reading frames (sORFs) that can be templated for protein synthesis and may provide raw material for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionary young and emerged de novo. We additionally discovered 221 yet uncataloged peptides smaller than 16 amino acids, for which we found evidence of translation in human and rodent tissues. To investigate the potential bioactivity of microproteins and peptides translated from young and very small ORFs we established MiPRISMA: a mass spectrometry-based interactome screen with sequence motif resolution. We assessed 266 candidates and implicated several in essential cellular processes including splicing, translational regulation, and endocytosis, a subset of which we validate in cellular assays. MiPRISMA provides a scalable platform to characterize small and evolutionarily young proteins, shedding light on a largely unexplored territory of the putative human proteome.

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MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part2

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MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part3

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The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:Ribosome profiling was applied for the first time on S. meliloti to generate a translatome map. Our work reveals active translation for several ORFs including small ORFs (sORFs). In addition, our ribosome profiling data led to the discovery of several translated non-annotated sORFs. Translation of these non-annotated sORFs was validated by proteomics and western blotting.

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Expression analysis of Shigella flexneri 2a strain 301

Project description:Investigation of whole genome gene expression to identify overlooked sRNAs and sORFs. Background The completion of numerous genome sequences has introduced an era of whole-genome study. However, many real genes, including small RNAs (sRNAs) and small ORFs (sORFs), are missed in genome annotation. In order to improve genome annotation, we sought to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery or shigellosis. Results Firstly, we identified 64 sRNAs in Shigella which is experimentally validated in other bacteria based on sequence conservation. Secondly, among possible approaches to search for sRNAs, we employed computer-based and tiling array based methods, followed by RT-PCR and northern blots. This allowed us to identify 12 sRNAs in Shigella flexneri strain 301. We also find 29 candidate sORFs. Conclusions This investigation provides an updated and comprehensive annotation of the Shigella genome, increases the expected numbers of sORFs and sRNAs with the corresponding impact on future functional genomics and proteomics studies. Our method can be used for the large scale reannotation of sRNAs and sORFs in any microbe whose genome sequence is available. Study using total RNA recovered from five conditions.

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Expression analysis of Shigella flexneri 2a strain 301

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TINCR lncRNA encodes a ubiquitin-like protein that activates CDC42, promotes epithelial differentiation and suppresses tumor growth

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Project description:The small proteome has already been well explored in eukaryal and bacterial species, but so far, archaeal genomes have not yet been analysed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental information 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. Translation was demonstrated for 67% of the annotated small coding sequences by both methods. Annotation-independent data analysis allowed for the prediction of 47 sites of ribosomal engagement outside known coding regions by Ribo-seq, seven of whom correspond to the eight un-annotated small proteins identified by a similar independent analysis of proteomic data. We also present independent evidence in vivo for the translation of a subset of small proteins (comprising both previously annotated and newly identified), underlining the validity of our identification scheme. Moreover, several of these translated sORFs are conserved in Haloferax and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously expected and that the combined use of mass spectrometry to detect protein presence with Ribo-seq to inform on translation is a powerful tool for the discovery of new small protein-coding genes in diverse organisms. This data-set contains the validation of novel sORFs by synthetic reference peptides and spectral-library searches.

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