bims-micpro 2020-09-06 papers

Issue of 2020‒09‒06
seven papers selected by
Thomas Martinez
Salk Institute for Biological Studies

Diabetologia. 2020 Sep 03.

Adiponectin treatment improves insulin resistance in mice by regulating the expression of the mitochondrial-derived peptide MOTS-c and its response to exercise via APPL1-SIRT1-PGC-1α.

Qi Guo, Bo Chang, Qiong-Li Yu, Si-Tong Xu, Xue-Jie Yi, Shi-Cheng Cao.

AIMS/HYPOTHESIS: Adiponectin stimulates mitochondrial biogenesis through peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α), a major regulator of mitochondrial biogenesis. MOTS-c (mitochondrial open reading frame of the 12S rRNA) is a biologically active mitochondrial-derived peptide encoded by mitochondrial DNA. It influences the mechanisms of obesity and diabetes. We hypothesised that the adiponectin pathway may regulate the production and/or secretion of MOTS-c in skeletal muscle. We aimed to determine whether exercise and adiponectin affect MOTS-c to improve insulin resistance in mice.METHODS: To investigate this hypothesis, we used wild-type C57BL/6 mice subjected to high-fat diet, an exercise regimen, and i.p. injection of recombinant mouse adiponectin (Acrp30) or MOTS-c, and adiponectin knockout (Adipoq-/-) mice (C57BL/6 background) subjected to i.p. injection of Acrp30. C2C12 myotubes were also treated with sirtuin 1 (SIRT1) inhibitor, PGC-1α inhibitor, SIRT1 activator, plasmid-expressed active APPL1 (adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper), pcDNA-SIRT1, or siRNA against APPL1, SIRT1 or PGC-1α.
RESULTS: In Adipoq-/- mice, MOTS-c levels in the plasma and skeletal muscle were downregulated. In C2C12 myotubes, adiponectin increased the mRNA expression of MOTS-c. APPL1 protein level following adiponectin treatment positively correlated with MOTS-c protein and mRNA levels in C2C12 myotubes. SIRT1 overexpression increased the adiponectin-induced mRNA and protein expression of MOTS-c, SIRT1 and PGC-1α. Pharmacologic and genetic inhibition of PGC-1α suppressed the increases in MOTS-c mRNA and protein levels induced by SIRT1 overexpression. In mice, plasma and skeletal muscle MOTS-c levels were significantly downregulated following high-fat-diet. Exercise and i.p. Acrp30 or MOTS-c increased MOTS-c levels and adiponectin mRNA and protein expression in the plasma and skeletal muscle.
CONCLUSIONS/INTERPRETATION: Our findings showed that the APPL1-SIRT1-PGC-1α pathway regulates the production and/or secretion of skeletal muscle MOTS-c by mediating adiponectin signalling. Our study provides an insight into the cellular and molecular pathways underlying the pathogenesis of diabetes and shows that MOTS-c is a potential novel therapeutic target in the treatment of diabetes. Graphical abstract.

Keywords: Adiponectin; Diabetes; Exercise-mediated signalling; MOTS-c; Mitochondrial biogenesis; Skeletal muscle

DOI: https://doi.org/10.1007/s00125-020-05269-3

Physiol Genomics. 2020 Aug 31.

An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla.

Cameron T Flower, Lihe Chen, Hyun Jun Jung, Viswanathan Raghuram, Mark A Knepper, Chin-Rang Yang.

Long noncoding RNAs (lncRNAs) are intracellular transcripts longer than 200 nucleotides and lack the capacity to encode protein. A subclass of lncRNA known as long intergenic noncoding RNAs (lincRNAs) are transcribed from genomic regions that share no overlap with annotated protein-coding genes. Increasing evidence has shown that some annotated lincRNA transcripts do in fact contain open reading frames (ORFs) encoding functional short peptides in the cell. Few robust methods for lincRNA-encoded peptide identification have been reported, and the tissue-specific expression of these peptides has been largely unexplored. Here we propose an integrative workflow for lincRNA-encoded peptide discovery and tested it on the mouse kidney inner medulla (IM). In brief, low molecular weight protein fractions were enriched from homogenate of IM and trypsinized into shorter peptides, which were characterized using high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). The challenge is to curate a hypothetical lincRNA-encoded peptide database for peptide-spectrum matching following LC-MS/MS. We performed RNA-Seq on IM, computationally filtered out reads overlapping with annotated protein-coding genes, and re-mapped the remaining reads to a database of mouse noncoding transcripts. The mapped transcripts are likely to be lincRNAs, and further searched for ORFs using an existing rule-based algorithm for peptide-spectrum matching. Peptides identified by LC-MS/MS were further evaluated using several quality control criteria and bioinformatics methods. We discovered three novel lincRNA-peptides, which are conserved in mouse, rat, and human. The workflow can be adapted for discovery of small protein-coding genes in any species or tissue where noncoding transcriptome information is available.

Keywords: RNA-Seq; lincRNA; noncoding RNA; protein mass spectrometry; proteogenomics

DOI: https://doi.org/10.1152/physiolgenomics.00048.2020

Int J Mol Sci. 2020 Aug 28. pii: E6238. [Epub ahead of print]21(17):

uORFs: Important Cis-Regulatory Elements in Plants.

Ting Zhang, Anqi Wu, Yaping Yue, Yu Zhao.

Gene expression is regulated at many levels, including mRNA transcription, translation, and post-translational modification. Compared with transcriptional regulation, mRNA translational control is a more critical step in gene expression and allows for more rapid changes of encoded protein concentrations in cells. Translation is highly regulated by complex interactions between cis-acting elements and trans-acting factors. Initiation is not only the first phase of translation, but also the core of translational regulation, because it limits the rate of protein synthesis. As potent cis-regulatory elements in eukaryotic mRNAs, upstream open reading frames (uORFs) generally inhibit the translation initiation of downstream major ORFs (mORFs) through ribosome stalling. During the past few years, with the development of RNA-seq and ribosome profiling, functional uORFs have been identified and characterized in many organisms. Here, we review uORF identification, uORF classification, and uORF-mediated translation initiation. More importantly, we summarize the translational regulation of uORFs in plant metabolic pathways, morphogenesis, disease resistance, and nutrient absorption, which open up an avenue for precisely modulating the plant growth and development, as well as environmental adaption. Additionally, we also discuss prospective applications of uORFs in plant breeding.

Keywords: disease resistance; metabolic pathways; morphogenesis; nutrient absorption; plant breeding; translational regulation; uORFs

DOI: https://doi.org/10.3390/ijms21176238

Annu Rev Genet. 2020 Sep 01.

Conserved Upstream Open Reading Frame Nascent Peptides that Control Translation.

Thomas E Dever, Ivaylo P Ivanov, Matthew S Sachs.

Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants. Expected final online publication date for the Annual Review of Genetics, Volume 54 is November 23, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-genet-112618-043822

IEEE/ACM Trans Comput Biol Bioinform. 2020 Sep 04. PP

Predicting Coding Potential of RNA Sequences by Solving Local Data Imbalance.

Xian-Gan Chen, Shuai Liu, Wen Zhang.

Non-coding RNAs (ncRNAs) play an important role in various biological processes and are associated with diseases. Distinguishing between coding RNAs and ncRNAs, also known as predicting coding potential of RNA sequences, is critical for downstream biological function analysis. Many machine learning-based methods have been proposed for predicting coding potential of RNA sequences. Recent studies reveal that most existing methods have poor performance on RNA sequences with short Open Reading Frames (sORF, ORF length<303nt). In this work, we analyze the distribution of ORF length of RNA sequences, and observe that the number of coding RNAs with sORF is inadequate and coding RNAs with sORF are much less than ncRNAs with sORF. Thus, there exists the problem of local data imbalance in RNA sequences with sORF. We propose a coding potential prediction method CPE-SLDI, which uses data oversampling techniques to augment samples for coding RNAs with sORF so as to alleviate local data imbalance. Compared with existing methods, CPE-SLDI produces the better performances, and studies reveal that the data augmentation by various data oversampling techniques can enhance the performance of coding potential prediction, especially for RNA sequences with sORF. The implementation of the proposed method is available at https://github.com/chenxgscuec/CPESLDI.

DOI: https://doi.org/10.1109/TCBB.2020.3021800

Int J Mol Sci. 2020 Sep 01. pii: E6341. [Epub ahead of print]21(17):

Using a Simple Cellular Assay to Map NES Motifs in Cancer-Related Proteins, Gain Insight into CRM1-Mediated NES Export, and Search for NES-Harboring Micropeptides.

Maria Sendino, Miren Josu Omaetxebarria, Gorka Prieto, Jose Antonio Rodriguez.

The nuclear export receptor CRM1 (XPO1) recognizes and binds specific sequence motifs termed nuclear export signals (NESs) in cargo proteins. About 200 NES motifs have been identified, but over a thousand human proteins are potential CRM1 cargos, and most of their NESs remain to be identified. On the other hand, the interaction of NES peptides with the "NES-binding groove" of CRM1 was studied in detail using structural and biochemical analyses, but a better understanding of CRM1 function requires further investigation of how the results from these in vitro studies translate into actual NES export in a cellular context. Here we show that a simple cellular assay, based on a recently described reporter (SRVB/A), can be applied to identify novel potential NESs motifs, and to obtain relevant information on different aspects of CRM1-mediated NES export. Using cellular assays, we first map 19 new sequence motifs with nuclear export activity in 14 cancer-related proteins that are potential CRM1 cargos. Next, we investigate the effect of mutations in individual NES-binding groove residues, providing further insight into CRM1-mediated NES export. Finally, we extend the search for CRM1-dependent NESs to a recently uncovered, but potentially vast, set of small proteins called micropeptides. By doing so, we report the first NES-harboring human micropeptides.

Keywords: CRM1; NES; XPO1; cellular assay; micropeptide; nuclear export; nuclear export signal

DOI: https://doi.org/10.3390/ijms21176341