bims-micpro 2021-12-12 papers

Int J Mol Sci. 2021 Dec 04. pii: 13128. [Epub ahead of print]22(23):

Irina Lyapina, Vadim Ivanov, Igor Fesenko.

Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.

Keywords: biologically active peptides; peptidome generation; peptidomes; protein precursors

DOI: https://doi.org/10.3390/ijms222313128

Front Oncol. 2021 ;11 777374

Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer.

Yao Chen, Weili Long, Liqiong Yang, Yueshui Zhao, Xu Wu, Mingxing Li, Fukuan Du, Yu Chen, Zhihui Yang, Qinglian Wen, Tao Yi, Zhangang Xiao, Jing Shen.

Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.

Keywords: ORF; function; gastrointestinal cancer; long non-coding RNA (lncRNA); small peptide

DOI: https://doi.org/10.3389/fonc.2021.777374

Structure. 2021 Nov 27. pii: S0969-2126(21)00415-9. [Epub ahead of print]

A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca2+-ATPase.

U Venkateswara Reddy, Daniel K Weber, Songlin Wang, Erik K Larsen, Tata Gopinath, Alfonso De Simone, Seth Robia, Gianluigi Veglia.

SERCA is a P-type ATPase embedded in the sarcoplasmic reticulum and plays a central role in muscle relaxation. SERCA's function is regulated by single-pass membrane proteins called regulins. Unlike other regulins, dwarf open reading frame (DWORF) expressed in cardiac muscle has a unique activating effect. Here, we determine the structure and topology of DWORF in lipid bilayers using a combination of oriented sample solid-state NMR spectroscopy and replica-averaged orientationally restrained molecular dynamics. We found that DWORF's structural topology consists of a dynamic N-terminal domain, an amphipathic juxtamembrane helix that crosses the lipid groups at an angle of 64°, and a transmembrane C-terminal helix with an angle of 32°. A kink induced by Pro15, unique to DWORF, separates the two helical domains. A single Pro15Ala mutant significantly decreases the kink and eliminates DWORF's activating effect on SERCA. Overall, our findings directly link DWORF's structural topology to its activating effect on SERCA.

Keywords: Ca(2+) transport; Ca(2+) signaling; SERCA activation; membrane protein-protein interactions; membrane proteins; oriented samples; solid-state NMR; structural topology

DOI: https://doi.org/10.1016/j.str.2021.11.003

Plant Methods. 2021 Dec 07. 17(1): 124

RiboPlotR: a visualization tool for periodic Ribo-seq reads.

Hsin-Yen Larry Wu, Polly Yingshan Hsu.

BACKGROUND: Ribo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time. While 3-nt periodicity has been widely used to study novel translation events such as upstream ORFs in 5' untranslated regions and small ORFs in presumed non-coding RNAs, tools that allow the visualization of these events remain underdeveloped.
RESULTS: RiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads in genomic coordinates for all annotated transcript isoforms of a gene. Specifically, for individual isoform models, RiboPlotR plots Ribo-seq data in the context of gene structures, including 5' and 3' untranslated regions and introns, and it presents the reads for all three reading frames in three different colors. The inclusion of gene structures and color-coding the reading frames facilitate observing new translation events and identifying potential regulatory mechanisms.
CONCLUSIONS: RiboPlotR is freely available ( https://github.com/hsinyenwu/RiboPlotR and https://sourceforge.net/projects/riboplotr/ ) and allows the visualization of translated features identified in Ribo-seq data.

Keywords: 3-nucleotide periodicity; Isoform; Ribo-seq; Small ORF; Upstream ORF

DOI: https://doi.org/10.1186/s13007-021-00824-4

Math Biosci. 2021 Dec 06. pii: S0025-5564(21)00160-7. [Epub ahead of print] 108762

Probabilistic models of uORF-mediated ATF4 translation control.

Olivia N J M Marasco, Marc R Roussel, Nehal Thakor.

ATF4 is a key transcription factor that activates transcription of genes needed to respond to cellular stress. Although the mRNA encoding ATF4 is present at constant levels in the cell during the initial response, translation of ATF4 increases under conditions of cellular stress while the global translation rate decreases. We study two models for the control system that regulates the translation of ATF4, both based on the Vattem-Wek hypothesis. This hypothesis is based on a race to reload, following the translation of a small upstream open reading frame (uORF), the ternary complex that brings the initiator tRNA to the ribosome as the 40S subunit scans along the mRNA, encountering first a start codon for an inhibitory uORF whose reading frame overlaps the start of the ATF4 coding sequence. We develop a pair of simple, analytic, probabilistic models, one of which assumes all nucleotide triplets have identical kinetic properties, while the other recognizes the existence of triplets at which the ternary complex loads more efficiently. We also consider two different functions representing the dependence of the rate of initiation at uORF1 on the ternary complex concentration. In keeping with the theme of this Special Issue, we studied the properties of these models in a Maple document, which can easily be modified to consider different parameters, translation rate initiation functions, and so on.

Keywords: ATF4; Computer algebra; Dynamic publication; Probabilistic model; Translation control; Upstream open reading frame

DOI: https://doi.org/10.1016/j.mbs.2021.108762