bims-micpro 2022-02-27 papers

Issue of 2022‒02‒27
four papers selected by
Thomas Farid Martínez
University of California, Irvine

J Proteome Res. 2022 Feb 24.

Identification of Microproteins in Hep3B Cells at Different Cell Cycle Stages.

Microproteins are generated from small open reading frames and turn out to play various vital biological functions. As an essential biological event of eukaryotic cells, the cell cycle is involved in cell replication and division. For such a highly regulated event, microproteins associated with cell cycle regulation remained unclarified. Utilizing a combination of bottom-up and top-down proteomics, we analyzed microproteins at specific cell cycle stages of Hep3B cells. A total of 657 microproteins were identified under three cell cycle stages, including 151 in the G0/G1 stage, 163 in the S stage, and 132 in the G2/M stage. The annotation of these microproteins showed their cell cycle-specific functions, such as translation, nuclear assembly, chromatin organization, and the G2/M transition of the mitotic cell cycle. Meanwhile, more than 50% of identified microproteins were ncRNA-encoded. These nonannotated novel microproteins contain several function domains, such as the nucleoside diphosphate kinase domain, the high mobility group domain, and the DNA-binding domain. This suggested the potential functions of these novel microproteins in specific cell cycle stages. This study presented a large-scale profile of microproteins at different cell cycle stages from Hep3B and may provide new perspectives on the regulation mechanism of the cell cycle. Liquid chromatography-mass spectrometry data were deposited to ProteomeXchange using the identifier PXD030286.

Keywords: DNA-binding domain; Hep3B; cell cycle; microprotein; ncRNA

DOI: https://doi.org/10.1021/acs.jproteome.1c00926

Bioinformatics. 2022 Feb 21. pii: btac115. [Epub ahead of print]

µProteInS - a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs.

Eduardo Vieira de Souza, Pedro Ferrari Dalberto, Vinicius Pellisoli Machado, Adriana Canedo Miranda, Alan Saghatelian, Pablo Machado, Luiz Augusto Basso, Cristiano Valim Bizarro.

SUMMARY: Genome annotation pipelines traditionally exclude Open Reading Frames shorter than 100 codons to avoid false identifications. However, studies have been showing that these may encode functional microproteins with meaningful biological roles. We developed µProteInS, a proteogenomics pipeline that combines genomics, transcriptomics, and proteomics to identify novel microproteins in bacteria. Our pipeline employs a model to filter out low confidence spectra, to avoid the need for manually inspecting Mass Spectrometry data. It also overcomes the shortcomings of traditional approaches that usually exclude overlapping genes, leaderless transcripts, and non-conserved sequences, characteristics that are common among smORFs and hamper their identification.AVAILABILITY AND IMPLEMENTATION: µProteInS is implemented in Python 3.8 within an Ubuntu 20.04 environment. It is an open-source software distributed under the GNU General Public License v3, available as a command-line tool. It can be downloaded at https://github.com/Eduardo-vsouza/uproteins and either installed from source or executed as a Docker image.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac115

Genome Res. 2022 Feb 22.

Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation.

Qianru Li, Haiwang Yang, Emily K Stroup, Hongbin Wang, Zhe Ji.

We describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified procedure to selectively capture ribosome footprints based on optimized RNase digestion. It simultaneously maps cytosolic and mitochondrial translation with single-nucleotide resolution. We applied it to reveal selective functions of the elongation factor TUFM in mitochondrial translation, as well as synchronized repression of cytosolic translation after TUFM perturbation. We show the assay is applicable to small amounts of primary tissue samples with low protein synthesis rates, including snap-frozen tissues and immune cells from an individual's blood draw. We showed its feasibility to characterize the personalized immuno-translatome. Our analyses revealed that thousands of genes show lower translation efficiency in monocytes compared with lymphocytes, and identified thousands of translated noncanonical open reading frames (ORFs). Altogether, our RNase footprinting approach opens an avenue to assay transcriptome-wide translation using low-input samples from a wide range of physiological conditions.

DOI: https://doi.org/10.1101/gr.276139.121

Front Endocrinol (Lausanne). 2021 ;12 808120

Mitochondrial-Derived Peptides in Diabetes and Its Complications.

Ying Wu, Liankun Sun, Zhoudao Zhuang, Xiaoqing Hu, Delu Dong.

The changes of mitochondrial function are closely related to diabetes and its complications. Here we describe the effects of mitochondrial-derived peptides (MDPs), short peptides formed by transcription and translation of the open reading frame site in human mitochondrial DNA (mtDNA), on diabetes and its complications. We mainly focus on MDPs that have been discovered so far, such as Humanin (HN), mitochondrial open reading frame of the 12S rRNA-c (MOTS-c) and Small humanin-like peptides (SHLP 1-6), and elucidated the role of MDPs in diabetes and its major complications stroke and myocardial infarction by improving insulin resistance, inhibiting inflammatory response and anti-apoptosis. It provides more possibilities for the clinical application of mitochondrial derived peptides.

Keywords: MOTS-c; SHLPs(1-6); diabetes; humanin; mitochondrial-derived peptides (MDPs); myocardial infarction; stroke

DOI: https://doi.org/10.3389/fendo.2021.808120