Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID

Na, Zhenkun; Dai, Xiaoyun; Zheng, Shu-Jian; Bryant, Carson J; Loh, Ken H.; Su, Haomiao; Luo, Yang; Buhagiar, Amber F.; Cao, Xiongwen; Baserga, Susan J.; Chen, Sidi; Slavoff, Sarah A.

doi:10.1016/j.molcel.2022.06.035

Cited by 25 publications

(20 citation statements)

References 95 publications

(120 reference statements)

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“…Remarkably, some methods yield ribosome protected fragments that are consistent enough to define the reading frame 18 ( Figure 1 B). Complementary detection of short ORF encoded peptide products with targeted proteomics has supported widespread translation of short ORFs on polycistronic mRNAs across many eukaryotic taxa 16 , 17 , 21 , 23 , 24 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ( Figure 1 B). Omics-based approaches have consequently completed the paradigm shift in RNA biology—many eukaryotic mRNAs exhibit multiple, distinct translation events rather than producing a single peptide product.…”

Section: Pioneering the Discovery Of Eukaryotic Microproteinsmentioning

confidence: 99%

“…Further supporting initial functional genetics and bioinformatics, the advent of ribosome profiling 16 , 17 , 18 and targeted proteomic approaches 19 , 20 , 21 , 22 , 23 , 24 , 25 over the last decade has revolutionized our ability to detect short ORF translation. Ribosome profiling, for example, leverages that ribosomes protect short fragments of bound mRNAs which are amenable to isolation and next-generation sequencing.…”

Section: Pioneering the Discovery Of Eukaryotic Microproteinsmentioning

confidence: 99%

“… 4 However, with a few notable exceptions 5 , 6 , 7 , 8 , most functional microproteins have been discovered in the last ten years with the aid of ribosome profiling 16 , 17 and advances in proteomic and biochemical tools. 21 , 24 , 25 , 63 Although microproteins encoded in animal genomes will be the main focus of this review, microproteins also play critical and emerging roles in fungi, 4 , 12 , 64 bacteria 65 , 66 , 67 (reviewed in 68 ), and plants 5 , 69 , 70 (reviewed in 36 , 71 ).…”

Section: Microproteins Are Integral In Diverse Eukaryotic Biology Inc...mentioning

confidence: 99%

“…Furthermore, application of the dead Cas13-based RNA imaging approaches (developed in mammalian cell culture) to the accessible live imaging provided by developing zebrafish would illuminate the spatiotemporal dynamics of microprotein mRNA and/or non-coding RNA in a living organism. 115 Finally, implementing novel microprotein tagging approaches (e.g., MicroID, 24 non-canonical amino acid labeling 63 ) in zebrafish would complement functional studies with CRISPR-Cas13d to better elucidate microprotein functions in their native contexts.…”

Section: Future Perspectives For Crispr-cas13 Microproteins and Non-c...mentioning

confidence: 99%

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Casting CRISPR-Cas13d to fish for microprotein functions in animal development

Treichel¹,

Bazzini²

2022

iScience

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Section: Pioneering the Discovery Of Eukaryotic Microproteinsmentioning

confidence: 99%

Section: Pioneering the Discovery Of Eukaryotic Microproteinsmentioning

confidence: 99%

Section: Microproteins Are Integral In Diverse Eukaryotic Biology Inc...mentioning

confidence: 99%

Section: Future Perspectives For Crispr-cas13 Microproteins and Non-c...mentioning

confidence: 99%

See 2 more Smart Citations

Casting CRISPR-Cas13d to fish for microprotein functions in animal development

Treichel¹,

Bazzini²

2022

iScience

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“…These show a wide variety of molecular functions, such as ligands for cellular receptors, signalling modulators, ionic pump inhibitors and translation regulators (Galindo et al, 2007;Kondo et al, 2010;Magny et al, 2013;Pauli et al, 2014;Rathore et al, 2018). Notably, recent genome-wide functional screens in cultured cells have demonstrated that translated smORFs are indeed required for cell growth and viability (Chen et al, 2020;Prensner et al, 2021;Na et al, 2022). However, the lack of annotation of smORFs in the genome, due to differences in experimental and bioinformatic approaches in these studies, plus the relatively small number of translated smORF being characterised, has prevented a more comprehensive understanding of their physiological, cellular and molecular roles.…”

Section: Introductionmentioning

confidence: 99%

Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila

Pueyo

Salazar²,

Grincho³

et al. 2023

Front. Cell Dev. Biol.

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Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.

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Biotin‐Based Strategies to Explore the World of Ubiquitin and Ubiquitin‐Like Modifiers

Merino‐Cacho,

Barroso‐Gomila,

Hernández‐Sánchez

et al. 2024

ChemBioChem

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A complex code of cellular signals is mediated by ubiquitin and ubiquitin‐like (Ub/UbL) modifications on substrate proteins. The so‐called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non‐modified cellular substrates, and protease‐mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin‐based tools we have developed for this purpose (for example BioUbLs, UbL‐ID, BioE3), taking advantage of the strong affinity of biotin‐streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass‐spectrometry‐based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL‐ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.

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Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID

Cited by 25 publications

References 95 publications

Casting CRISPR-Cas13d to fish for microprotein functions in animal development

Casting CRISPR-Cas13d to fish for microprotein functions in animal development

Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila

Biotin‐Based Strategies to Explore the World of Ubiquitin and Ubiquitin‐Like Modifiers

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