bims-micpro 2022-02-06 papers

Issue of 2022‒02‒06
five papers selected by
Thomas Farid Martínez
University of California, Irvine

Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2120476119. [Epub ahead of print]119(6):

The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice.

Catherine A Makarewich, Amir Z Munir, Svetlana Bezprozvannaya, Aaron M Gibson, Soo Young Kim, Misty S Martin-Sandoval, Thomas P Mathews, Luke I Szweda, Rhonda Bassel-Duby, Eric N Olson.

Emerging evidence indicates that a subset of RNA molecules annotated as noncoding contain short open reading frames that code for small functional proteins called microproteins, which have largely been overlooked due to their small size. To search for cardiac-expressed microproteins, we used a comparative genomics approach and identified mitolamban (Mtlbn) as a highly conserved 47-amino acid transmembrane protein that is abundantly expressed in the heart. Mtlbn localizes specifically to the inner mitochondrial membrane where it interacts with subunits of complex III of the electron transport chain and with mitochondrial respiratory supercomplexes. Genetic deletion of Mtlbn in mice altered complex III assembly dynamics and reduced complex III activity. Unbiased metabolomic analysis of heart tissue from Mtlbn knockout mice further revealed an altered metabolite profile consistent with deficiencies in complex III activity. Cardiac-specific Mtlbn overexpression in transgenic (TG) mice induced cardiomyopathy with histological, biochemical, and ultrastructural pathologic features that contributed to premature death. Metabolomic analysis and biochemical studies indicated that hearts from Mtlbn TG mice exhibited increased oxidative stress and mitochondrial dysfunction. These findings reveal Mtlbn as a cardiac-expressed inner mitochondrial membrane microprotein that contributes to mitochondrial electron transport chain activity through direct association with complex III and the regulation of its assembly and function.

Keywords: cardiac; microprotein; mitochondria; oxidative phosphorylation

DOI: https://doi.org/10.1073/pnas.2120476119

Allergy. 2022 Jan 29.

Translation and emerging functions of non-coding RNAs in inflammation and immunity.

Elena Della Bella, Jana Koch, Katja Baerenfaller.

Regulatory non-coding RNAs (ncRNAs) including small non-coding RNAs (sRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) have gained considerable attention in the last few years. This is mainly due to their condition- and tissue-specific expression and their various modes of action, which suggests them as promising biomarkers and therapeutic targets. One important mechanism of ncRNAs to regulate gene expression is through translation of short open reading frames (sORFs). These sORFs can be located in lncRNAs, in non-translated regions of mRNAs where upstream ORFs (uORFs) represent the majority, or in circRNAs. Regulation of their translation can function as a quick way to adapt protein production to changing cellular or environmental cues, and can either depend solely on the initiation and elongation of translation, or on the roles of the produced functional peptides. Due to the experimental challenges to pinpoint translation events and to detect the produced peptides, translational regulation through regulatory RNAs is not well studied yet. In the case of circRNAs, they have only recently started to be recognized as regulatory molecules instead of mere artifacts of RNA biosynthesis. Of the many roles described for regulatory ncRNAs, we will focus here on their regulation during inflammation and in immunity.

DOI: https://doi.org/10.1111/all.15234

Nat Commun. 2022 Feb 03. 13(1): 668

Cyclin B/CDK1 and Cyclin A/CDK2 phosphorylate DENR to promote mitotic protein translation and faithful cell division.

Katharina Clemm von Hohenberg, Sandra Müller, Sibylle Schleich, Matthias Meister, Jonathan Bohlen, Thomas G Hofmann, Aurelio A Teleman.

DENR and MCTS1 have been identified as oncogenes in several different tumor entities. The heterodimeric DENR·MCTS1 protein complex promotes translation of mRNAs containing upstream Open Reading Frames (uORFs). We show here that DENR is phosphorylated on Serine 73 by Cyclin B/CDK1 and Cyclin A/CDK2 at the onset of mitosis, and then dephosphorylated as cells exit mitosis. Phosphorylation of Ser73 promotes mitotic stability of DENR protein and prevents its cleavage at Asp26. This leads to enhanced translation of mRNAs involved in mitosis. Indeed, we find that roughly 40% of all mRNAs with elevated translation in mitosis are DENR targets. In the absence of DENR or of Ser73 phosphorylation, cells display elevated levels of aberrant mitoses and cell death. This provides a mechanism how the cell cycle regulates translation of a subset of mitotically relevant mRNAs during mitosis.

DOI: https://doi.org/10.1038/s41467-022-28265-0

Alzheimers Dement. 2021 Dec;17 Suppl 3 e050200

Progranulin upstream open reading frames of different 5' leaders affect downstream protein expression.

Alexandros Frydas, Rita Cacace, Julie van der Zee, Christine Van Broeckhoven, Eline Wauters.

BACKGROUND: Heterozygous loss-of-function (LOF) mutations in the progranulin gene (GRN) cause frontotemporal lobar degeneration (FTLD) by a mechanism of haploinsufficiency. Progranulin expression is regulated at multiple levels, including by its 5' untranslated region (UTR). Two different GRN 5' leaders contain upstream open reading frames (uORFs). These non-coding elements could contribute to the regulation of GRN expression by acting as cis repressors of translation.METHOD: Selected from the Flanders-Belgian FTD patient cohort, 302 unrelated patients (mean age at onset 64.9 ± 9.8 years, range 29 to 84 years, 46.3% female) without a GRN LOF mutation. The GRN cohort of LOF mutation carriers comprised members of the GRN founder family (n=83, mean onset age 63.1 ± 7.7 years) and carriers of other LOF mutations (n=53, mean onset age 58.9 ± 7.1 years). Targeted resequencing of uORF regions of GRN transcripts by amplicon target amplification assays (https://www.agilent.com). Luciferase reporter assays and semi-quantitative Real-Time PCR for characterization of GRN uORFs and identified variants. Western blotting for investigation of uORF-mediated translation. Quantification of alternative splicing by analyzing two brain RNA-seq datasets from healthy controls (AMP-AD Knowledge Portal, https://adknowledgeportal.synapse.org/).
RESULT: We identified the presence of an alternative 5' UTR in human brain. Quantification of the alternative splicing in the exon1-intron1 splicing-site suggests low expression for the alternative spliced 5' UTR with notable variability between samples in both datasets. Abolishment of each uORF (n=3) of the alternative 5' UTR increases protein expression, with a mild impact on mRNA levels. The two ATG-initiated uORFs were capable of initiating translation. Targeted resequencing of the uORF regions identified two genetic variants, one in each 5' UTR. Both variants increase downstream protein levels, with the main 5' UTR variant rs76783532 causing a significant 1.5-fold increase in protein expression (p=0.03), with no impact on mRNA levels.
CONCLUSION: The alternatively spliced GRN 5'UTR contains 3 uORFs that can regulate downstream protein expression by acting on the translational level. The variant identified in the main 5'UTR, significantly increases protein expression by altering uORF codon identity. These results promote further experimental work to elucidate the potential mechanistic involvement of GRN uORFs in GRN associated FTLD.

DOI: https://doi.org/10.1002/alz.050200

Front Plant Sci. 2021 ;12 802802

S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response.

Hong Wang, Yunting Zhang, Ayla Norris, Cai-Zhong Jiang.

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

Keywords: amino acid metabolism; biotic and abiotic stress; plant growth and development; sugar metabolism; uORF

DOI: https://doi.org/10.3389/fpls.2021.802802