bims-micpro 2022-04-10 papers

Issue of 2022‒04‒10
five papers selected by
Thomas Farid Martínez
University of California, Irvine

Nat Chem Biol. 2022 Apr 07.

Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor.

Xiongwen Cao, Alexandra Khitun, Cecelia M Harold, Carson J Bryant, Shu-Jian Zheng, Susan J Baserga, Sarah A Slavoff.

Many unannotated microproteins and alternative proteins (alt-proteins) are coencoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing regulated synthesis could play important cellular roles, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated alt-proteins or N-terminal extensions, one of which is post-transcriptionally upregulated by DNA damage stress. We further defined a nucleolar, cell-cycle-regulated alt-protein that negatively regulates assembly of the pre-60S ribosomal subunit (MINAS-60). Depletion of MINAS-60 increases the amount of cytoplasmic 60S ribosomal subunit, upregulating global protein synthesis and cell proliferation. Mechanistically, MINAS-60 represses the rate of late-stage pre-60S assembly and export to the cytoplasm. Together, these results implicate MINAS-60 as a potential checkpoint inhibitor of pre-60S assembly and demonstrate that chemoproteomics enables hypothesis generation for uncharacterized alt-proteins.

DOI: https://doi.org/10.1038/s41589-022-01003-9

Proteomics. 2022 Apr 06. e2100312

Proteomic-driven identification of short open reading frame-encoded peptides.

Zheng Zhang, Yujie Li, Wenqian Yuan, Zhiwei Wang, Cuihong Wan.

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 large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.

Keywords: LC/MS/MS; method development; peptidomics; sORF-encode peptides; sample preparation; short open reading frame

DOI: https://doi.org/10.1002/pmic.202100312

Front Cardiovasc Med. 2022 ;9 841032

Common and Rare 5'UTR Variants Altering Upstream Open Reading Frames in Cardiovascular Genomics.

Omar Soukarieh, Caroline Meguerditchian, Carole Proust, Dylan Aïssi, Mélanie Eyries, Aurélie Goyenvalle, David-Alexandre Trégouët.

High-throughput sequencing (HTS) technologies are revolutionizing the research and molecular diagnosis landscape by allowing the exploration of millions of nucleotide sequences at an unprecedented scale. These technologies are of particular interest in the identification of genetic variations contributing to the risk of rare (Mendelian) and common (multifactorial) human diseases. So far, they have led to numerous successes in identifying rare disease-causing mutations in coding regions, but few in non-coding regions that include introns, untranslated (UTR), and intergenic regions. One class of neglected non-coding variations is that of 5'UTR variants that alter upstream open reading frames (upORFs) of the coding sequence (CDS) of a natural protein coding transcript. Following a brief summary of the molecular bases of the origin and functions of upORFs, we will first review known 5'UTR variations altering upORFs and causing rare cardiovascular disorders (CVDs). We will then investigate whether upORF-affecting single nucleotide polymorphisms could be good candidates for explaining association signals detected in the context of genome-wide association studies for common complex CVDs.

Keywords: Mendelian disease; genome wide association analysis (GWAS); non-coding mutations; open reading frame (ORF); polymorphism

DOI: https://doi.org/10.3389/fcvm.2022.841032

Trends Mol Med. 2022 Apr 01. pii: S1471-4914(22)00067-3. [Epub ahead of print]

Circular RNA translation: novel protein isoforms and clinical significance.

Shuo-Yang Wen, Javeria Qadir, Burton B Yang.

In recent years, significant attention has focused on circular RNA (circRNA) translation to determine its clinical significance. Cap-independent translation of circRNAs driven by an internal ribosome entry site (IRES) or an N6-methyladenosine (m6A)-containing short sequence is different from the canonical cap-dependent translation of linear mRNAs. New proteins or isoforms possessing novel physiological roles can be generated from translatable circRNAs. The present review describes the elements involved in circRNA translation, and the functions of the translated novel protein isoforms in human diseases. Bifunctional characteristics of translatable circRNAs exerted by the circRNAs and the translated proteins are also discussed. Furthermore, various molecular strategies that could be used as appropriate therapeutic options are proposed.

Keywords: circRNA translation; circular RNA; disease modulation; rolling translation; targeting translation; therapy; translational inhibition

DOI: https://doi.org/10.1016/j.molmed.2022.03.003

Mol Cancer. 2022 Apr 02. 21(1): 93

A novel peptide encoded by N6-methyladenosine modified circMAP3K4 prevents apoptosis in hepatocellular carcinoma.

Jin-Ling Duan, Wei Chen, Juan-Juan Xie, Mao-Lei Zhang, Run-Cong Nie, Hu Liang, Jie Mei, Kai Han, Zhi-Cheng Xiang, Feng-Wei Wang, Kai Teng, Ri-Xin Chen, Min-Hua Deng, Yi-Xin Yin, Nu Zhang, Dan Xie, Mu-Yan Cai.

BACKGROUND: Circular RNAs (circRNAs) regulate various biological activities and have been shown to play crucial roles in hepatocellular carcinoma (HCC) progression. However, only a few coding circRNAs have been identified in cancers, and their roles in HCC remain elusive. This study aimed to identify coding circRNAs and explore their function in HCC.METHODS: CircMAP3K4 was selected from the CIRCpedia database. We performed a series of experiments to determine the characteristics and coding capacity of circMAP3K4. We then used in vivo and in vitro assays to investigate the biological function and mechanism of circMAP3K4 and its protein product, circMAP3K4-455aa, in HCC.
RESULTS: We found circMAP3K4 to be an upregulated circRNA with coding potential in HCC. IGF2BP1 recognized the circMAP3K4 N6-methyladenosine modification and promoted its translation into circMAP3K4-455aa. Functionally, circMAP3K4-455aa prevented cisplatin-induced apoptosis in HCC cells by interacting with AIF, thus protecting AIF from cleavage and decreasing its nuclear distribution. Moreover, circMAP3K4-455aa was degraded through the ubiquitin-proteasome E3 ligase MIB1 pathway. Clinically, a high level of circMAP3K4 is an independent prognostic factor for adverse overall survival and adverse disease-free survival of HCC patients.
CONCLUSIONS: CircMAP3K4 is a highly expressed circRNA in HCC. Driven by m6A modification, circMAP3K4 encoded circMAP3K4-455aa, protected HCC cells from cisplatin exposure, and predicted worse prognosis of HCC patients. Targeting circMAP3K4-455aa may provide a new therapeutic strategy for HCC patients, especially for those with chemoresistance. CircMAP3K4 is a highly expressed circRNA in HCC. Driven by m6A modification, IGF2BP1 facilitates circMAP3K4 peptide translation, then the circMAP3K4 peptide inhibits AIF cleavage and nuclear distribution, preventing HCC cells from cell death under stress and promoting HCC progression.

Keywords: AIF; Hepatocellular carcinoma; MIB1; N6-methyadenosine; Translation; circMAP3K4

DOI: https://doi.org/10.1186/s12943-022-01537-5