Systematic Identification of Microproteins during the Development of <i>Drosophila melanogaster</i>

Wang, Zhiwei; Ni, Peihong; Yan, Jun; Wan, Jian; Wan, Cuihong

doi:10.1021/acs.jproteome.2c00004

Cited by 7 publications

(5 citation statements)

References 50 publications

(88 reference statements)

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“…The history of high‐throughput identification of SEPs in different species by Ribo‐seq [29, 34‐71] and MS‐based proteomics [8, 10‐12, 33, 38‐56], and representative functional SEPs [5, 14, 16, 18‐21, 36, 72‐91]…”

Section: Analysis Strategies and Methodologies Of Sepsmentioning

confidence: 99%

Proteomics‐driven identification of short open reading frame‐encoded peptides

Zhang

Yuan

et al. 2022

Proteomics

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Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of largescale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods.

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Section: Analysis Strategies and Methodologies Of Sepsmentioning

confidence: 99%

Proteomics‐driven identification of short open reading frame‐encoded peptides

Zhang

Yuan

et al. 2022

Proteomics

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“…The majority of the AltProts identified here are short proteins (88.8% of AltProts are less than 150 amino acids) (Supplementary Figure 1B). Comparing the AltProts identified to the ones with MS evidence in OpenProt and a recent article (Wang et al, 2022), only 2 were common to the three datasets, 29 were found in at least two datasets and 374 new AltProts were identified in this study (Supplementary Figure 1C). The low overlap between the datasets might be explained by the different sample types and extraction and fractionation protocols used (Cardon et al, 2020).…”

Section: Genome Wide Identification Of Alternative Proteins In Drosop...mentioning

confidence: 51%

In depth exploration of the alternative proteome of Drosophila melanogaster

Fabre

Choteau

Duboé

et al. 2022

Preprint

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Recent studies have shown that hundreds of small proteins were occulted when protein coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocystronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome wide exploration of the alternative proteome is still limited to a few species. In the present article we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains and short linear motifs were predicted for 235 of the alternative proteins identified and point towards specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed fourteen alternative proteins with developmentally regulated expression patterns and ten induced upon heat shock treatment of embryos, demonstrating stage or stress specific production of alternative proteins.

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“…The majority of the AltProts identified here are short proteins (88.8% of AltProts are less than 150 amino acids) (Supplementary Figure S1B). Comparing the AltProts identified to the ones with MS evidence in OpenProt and a recent article (Wang et al, 2022), only two were common to the three datasets, 29 were found in at least two datasets and 374 new AltProts were identified in this study (Supplementary Figure S1C). The low overlap between the datasets might be explained by the different sample types and extraction and fractionation protocols used (Cardon et al, 2020).…”

Section: Genome-wide Identification Of Alternative Proteins In Drosop...mentioning

confidence: 52%

In Depth Exploration of the Alternative Proteome of Drosophila melanogaster

Fabre

Choteau

Duboé

et al. 2022

Front. Cell Dev. Biol.

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Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.

show abstract

Systematic Identification of Microproteins during the Development of Drosophila melanogaster

Cited by 7 publications

References 50 publications

Proteomics‐driven identification of short open reading frame‐encoded peptides

Proteomics‐driven identification of short open reading frame‐encoded peptides

In depth exploration of the alternative proteome of Drosophila melanogaster

In Depth Exploration of the Alternative Proteome of Drosophila melanogaster

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