bims-micpro 2021-01-24 papers

Issue of 2021‒01‒24
five papers selected by
Thomas Martinez
Salk Institute for Biological Studies

Nat Commun. 2021 01 21. 12(1): 508

Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24.

Xiongwen Cao, Alexandra Khitun, Yang Luo, Zhenkun Na, Thitima Phoodokmai, Khomkrit Sappakhaw, Elizabeth Olatunji, Chayasith Uttamapinant, Sarah A Slavoff.

Thousands of human small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been annotated. Many alt-ORFs are co-encoded with canonical proteins in multicistronic configurations, but few of their functions are known. Here, we report the detection of alt-RPL36, a protein co-encoded with human RPL36. Alt-RPL36 partially localizes to the endoplasmic reticulum, where it interacts with TMEM24, which transports the phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) precursor phosphatidylinositol from the endoplasmic reticulum to the plasma membrane. Knock-out of alt-RPL36 increases plasma membrane PI(4,5)P2 levels, upregulates PI3K-AKT-mTOR signaling, and increases cell size. Alt-RPL36 contains four phosphoserine residues, point mutations of which abolish interaction with TMEM24 and, consequently, alt-RPL36 effects on PI3K signaling and cell size. These results implicate alt-RPL36 as an upstream regulator of PI3K-AKT-mTOR signaling. More broadly, the RPL36 transcript encodes two sequence-independent polypeptides that co-regulate translation via different molecular mechanisms, expanding our knowledge of multicistronic human gene functions.

DOI: https://doi.org/10.1038/s41467-020-20841-6

Proc Natl Acad Sci U S A. 2021 Jan 26. pii: e2021943118. [Epub ahead of print]118(4):

A short ORF-encoded transcriptional regulator.

Minseob Koh, Insha Ahmad, Yeonjin Ko, Yuxiang Zhang, Thomas F Martinez, Jolene K Diedrich, Qian Chu, James J Moresco, Michael A Erb, Alan Saghatelian, Peter G Schultz, Michael J Bollong.

Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.

Keywords: expanded genetic code; photo-crosslinking; short open reading frame-encoded peptide; transcriptional regulation

DOI: https://doi.org/10.1073/pnas.2021943118

Nat Commun. 2021 01 20. 12(1): 470

MOTS-c is an exercise-induced mitochondrial-encoded regulator of age-dependent physical decline and muscle homeostasis.

Joseph C Reynolds, Rochelle W Lai, Jonathan S T Woodhead, James H Joly, Cameron J Mitchell, David Cameron-Smith, Ryan Lu, Pinchas Cohen, Nicholas A Graham, Bérénice A Benayoun, Troy L Merry, Changhan Lee.

Healthy aging can be promoted by enhanced metabolic fitness and physical capacity. Mitochondria are chief metabolic organelles with strong implications in aging that also coordinate broad physiological functions, in part, using peptides that are encoded within their independent genome. However, mitochondrial-encoded factors that actively regulate aging are unknown. Here, we report that mitochondrial-encoded MOTS-c can significantly enhance physical performance in young (2 mo.), middle-age (12 mo.), and old (22 mo.) mice. MOTS-c can regulate (i) nuclear genes, including those related to metabolism and proteostasis, (ii) skeletal muscle metabolism, and (iii) myoblast adaptation to metabolic stress. We provide evidence that late-life (23.5 mo.) initiated intermittent MOTS-c treatment (3x/week) can increase physical capacity and healthspan in mice. In humans, exercise induces endogenous MOTS-c expression in skeletal muscle and in circulation. Our data indicate that aging is regulated by genes encoded in both of our co-evolved mitochondrial and nuclear genomes.

DOI: https://doi.org/10.1038/s41467-020-20790-0

STAR Protoc. 2021 Mar 19. 2(1): 100250

Global mapping of translation initiation sites by TIS profiling in budding yeast.

Ina Hollerer, Emily N Powers, Gloria A Brar.

Translation initiation site (TIS) profiling allows for the genome-wide identification of TISs in vivo by exclusively capturing mRNA fragments within ribosomes that have just completed translation initiation. It leverages translation inhibitors, such as harringtonine and lactimidomycin (LTM), that preferentially capture ribosomes at start codon positions, protecting TIS-derived mRNA fragments from nuclease digestion. Here, we describe a step-by-step protocol for TIS profiling in LTM-treated budding yeast that we developed to identify TISs and open reading frames in vegetative and meiotic cells. For complete details on the use and execution of this protocol, please refer to Eisenberg et al. (2020).

Keywords: Cell biology; Genomics; High-throughput screening; Model organisms; Molecular biology

DOI: https://doi.org/10.1016/j.xpro.2020.100250

Genome Res. 2021 Jan 19.

A platform for curated products from novel open reading frames prompts reinterpretation of disease variants.

Matthew D C Neville, Robin Kohze, Chaitanya Erady, Narendra Meena, Matthew Hayden, David N Cooper, Matthew Mort, Sudhakaran Prabakaran.

Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in diverse regions of the genome, including in long noncoding RNAs, pseudogenes, 3' UTRs, 5' UTRs, and alternative reading frames of canonical protein coding exons. There is therefore a pressing need to evaluate the potential functional importance of these unannotated transcripts and proteins in biological pathways and human disease on a larger scale, rather than one at a time. In this study, we outline the creation of a valuable nORFs data set with experimental evidence of translation for the community, use measures of heritability and selection that reveal signals for functional importance, and show the potential implications for functional interpretation of genetic variants in nORFs. Our results indicate that some variants that were previously classified as being benign or of uncertain significance may have to be reinterpreted.

DOI: https://doi.org/10.1101/gr.263202.120