bims-micpro 2022-05-29 papers

Issue of 2022‒05‒29
four papers selected by
Thomas Farid Martínez
University of California, Irvine

J Biol Chem. 2022 May 20. pii: S0021-9258(22)00500-2. [Epub ahead of print] 102060

Inhibitory and Stimulatory Micropeptides Preferentially Bind to Different Conformations of the Cardiac Calcium Pump.

Sean R Cleary, Xuan Fang, Ellen E Cho, Marsha P Pribadi, Jaroslava Seflova, Jordan R Beach, Peter M Kekenes-Huskey, Seth L Robia.

The ATP-dependent ion pump SERCA sequesters Ca2+ in the endoplasmic reticulum to establish a reservoir for cell signaling. Because of its central importance in physiology, the activity of this transporter is tightly controlled via direct interactions with tissue-specific regulatory micropeptides that tune SERCA function to match changing physiological conditions. In the heart, the micropeptide phospholamban (PLB) inhibits SERCA, while dwarf open reading frame (DWORF) stimulates SERCA. These competing interactions determine cardiac performance by modulating the amplitude of Ca2+ signals that drive the contraction/relaxation cycle. We hypothesized the functions of these peptides may relate to their reciprocal preferences for SERCA binding; SERCA binds PLB more avidly at low cytoplasmic [Ca2+] but binds DWORF better when [Ca2+] is high. In the present study, we demonstrated this opposing Ca2+ sensitivity is due to preferential binding of DWORF and PLB to different intermediate states that SERCA samples during the Ca2+ transport cycle. We show PLB binds best to the SERCA E1-ATP state, which prevails at low [Ca2+]. In contrast, DWORF binds most avidly to E1P and E2P states that are more populated when Ca2+ is elevated. Moreover, FRET microscopy revealed dynamic shifts in SERCA-micropeptide binding equilibria during cellular Ca2+ elevations. In a computational model of these regulatory interactions under different heart rates, we found DWORF exaggerates changes in PLB-SERCA binding during the cardiac cycle. These results suggest a mechanistic basis for inhibitory versus stimulatory micropeptide function, as well as a new role for DWORF as a modulator of dynamic oscillations of PLB-SERCA regulatory interactions.

Keywords: Bowditch effect; Post-Albers cycle; SERCA2a; binding kinetics; calcium signaling; calcium transient; calcium transporter; cardiac calcium handling; conformational selection; dissociation constant (KD); dwarf open reading frame (DWORF); fluorescence microscopy; fluorescence resonance energy transfer (FRET); force-frequency relationship; membrane protein regulatory complex; membrane protein-protein interactions; micropeptides; phospholamban; physiological model; sarco(endo)plasmic reticulum; transport ATPase

DOI: https://doi.org/10.1016/j.jbc.2022.102060

Genome Res. 2022 May 24. pii: gr.275831.121. [Epub ahead of print]

TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation.

Wenli Xu, Chang Liu, Bing Deng, Penghui Lin, Zhenghua Sun, Anrui Liu, Jiajia Xuan, Yuying Li, Keren Zhou, Xiaoqin Zhang, Qiaojuan Huang, Hui Zhou, Qingyu He, Bin Li, Lianghu Qu, Jianhua Yang.

Polypeptides encoded by long non-coding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate in the TP53 pathway and play a significant biological role is still unclear. Here, we discover that TP53-regulated lncRNAs encode peptides, two of which are functional in various human cell lines. Using ribosome profiling and RNA-seq approaches in HepG2 cells, we systematically identified more than 300 novel TP53-regulated lncRNAs and further confirmed that fifteen of these TP53-regulated lncRNAs encode peptides. Furthermore, several peptides were validated by multiple mass spectrometry measures. Ten of the novel translational lncRNAs were directly inducible by TP53 in response to DNA damage. Notably, we showed that the TP53-inducible peptides TP53LC02 and TP53LC04, but not their lncRNAs, could suppress cell proliferation. TP53LC04 peptide also had a function associated with cell proliferation by regulating the cell cycle in response to DNA damage. This study demonstrates that TP53-inducible lncRNAs encode new functional peptides, leading to the enlargement of the components of TP53 tumor suppressor network and providing novel potential targets for cancer therapy.

DOI: https://doi.org/10.1101/gr.275831.121

FEBS J. 2022 May 23.

Mitochondrion-located peptides and their pleiotropic physiological functions.

Xintong Zheng, Mengqing Xiang.

With the development of advanced technologies, many small open reading frames (sORFs) have been found to be translated into micropeptides. Interestingly, a considerable proportion of micropeptides are located in mitochondria, which are designated here as mitochondrion-located peptides (MLPs). These MLPs often contain a transmembrane domain and show a high degree of conservation across species. They usually act as co-factors of large proteins and play regulatory roles in mitochondria such as electron transport in the respiratory chain, reactive oxygen species (ROS) production, metabolic homeostasis, and so on. Deficiency of MLPs disturbs diverse physiological processes including immunity, differentiation and metabolism both in vivo and in vitro. These findings reveal crucial functions for MLPs and provide fresh insights into diverse mitochondrion-associated biological processes and diseases.

Keywords: Mitochondrion-located peptides (MLPs); lncRNA; micropeptides; mitochondria; sORF-encoded peptides (SEPs); single transmembrane domain (STMD); small open reading frames (sORFs)

DOI: https://doi.org/10.1111/febs.16532

Int J Mol Sci. 2022 May 20. pii: 5764. [Epub ahead of print]23(10):

Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila.

Christine Dozier, Audrey Montigny, Mireia Viladrich, Raphael Culerrier, Jean-Philippe Combier, Arnaud Besson, Serge Plaza.

MicroRNAs (miRNAs) are small regulatory non-coding RNAs, resulting from the cleavage of long primary transcripts (pri-miRNAs) in the nucleus by the Microprocessor complex generating precursors (pre-miRNAs) that are then exported to the cytoplasm and processed into mature miRNAs. Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). However, several lnc pri-miRNAs contain translatable small open reading frames (smORFs). If smORFs present within lncRNAs can encode functional small peptides, they can also constitute cis-regulatory elements involved in lncRNA decay. Here, we investigated the possible involvement of smORFs in the regulation of lnc pri-miRNAs in Human and Drosophila, focusing on pri-miRNAs previously shown to contain translatable smORFs. We show that smORFs regulate the expression levels of human pri-miR-155 and pri-miR-497, and Drosophila pri-miR-8 and pri-miR-14, and also affect the expression and activity of their associated miRNAs. This smORF-dependent regulation is independent of the nucleotidic and amino acidic sequences of the smORFs and is sensitive to the ribosome-stalling drug cycloheximide, suggesting the involvement of translational events. This study identifies smORFs as new cis-acting elements involved in the regulation of pri-miRNAs and miRNAs expression, in both Human and Drosophila melanogaster.

Keywords: miRNA; pri-miRNA; smORFs

DOI: https://doi.org/10.3390/ijms23105764