bims-micpro 2024-04-28 papers

Issue of 2024‒04‒28
four papers selected by
Thomas Farid Martínez, University of California, Irvine

bioRxiv. 2024 Apr 15. pii: 2024.04.12.589296. [Epub ahead of print]

Biophysical characterization of high-confidence, small human proteins.

A M Whited, Irwin Jungreis, Jeffre Allen, Christina Cleveland, Jonathan M Mudge, Manolis Kellis, John Rinn, Loren E Hough.

Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.

DOI: https://doi.org/10.1101/2024.04.12.589296

Plants (Basel). 2024 Apr 18. pii: 1137. [Epub ahead of print]13(8):

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs.

T N Erokhina, D Y Ryazantsev, S K Zavriev, S Y Morozov.

Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.

Keywords: biotechnology; functions of miPEPs; lncRNA; miPEP; micropeptide; plants; primary microRNA; transcription

DOI: https://doi.org/10.3390/plants13081137

Noncoding RNA. 2024 Apr 09. pii: 20. [Epub ahead of print]10(2):

FuncPEP v2.0: An Updated Database of Functional Short Peptides Translated from Non-Coding RNAs.

Swati Mohapatra, Anik Banerjee, Paola Rausseo, Mihnea P Dragomir, Ganiraju C Manyam, Bradley M Broom, George A Calin.

Over the past decade, there have been reports of short novel functional peptides (less than 100 aa in length) translated from so-called non-coding RNAs (ncRNAs) that have been characterized using mass spectrometry (MS) and large-scale proteomics studies. Therefore, understanding the bivalent functions of some ncRNAs as transcripts that encode both functional RNAs and short peptides, which we named ncPEPs, will deepen our understanding of biology and disease. In 2020, we published the first database of functional peptides translated from non-coding RNAs-FuncPEP. Herein, we have performed an update including the newly published ncPEPs from the last 3 years along with the categorization of host ncRNAs. FuncPEP v2.0 contains 152 functional ncPEPs, out of which 40 are novel entries. A PubMed search from August 2020 to July 2023 incorporating specific keywords was performed and screened for publications reporting validated functional peptides derived from ncRNAs. We did not observe a significant increase in newly discovered functional ncPEPs, but a steady increase. The novel identified ncPEPs included in the database were characterized by a wide array of molecular and physiological parameters (i.e., types of host ncRNA, species distribution, chromosomal density, distribution of ncRNA length, identification methods, molecular weight, and functional distribution across humans and other species). We consider that, despite the fact that MS can now easily identify ncPEPs, there still are important limitations in proving their functionality.

Keywords: immunity; micro-peptides; ncRNA-encoded peptides; non-coding RNAs

DOI: https://doi.org/10.3390/ncrna10020020

Int J Mol Sci. 2024 Apr 16. pii: 4381. [Epub ahead of print]25(8):

A Multi-Faceted Analysis Showing CRNDE Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis.

Anna Balcerak, Laura Aleksandra Szafron, Tymon Rubel, Bianka Swiderska, Arkadiusz M Bonna, Magdalena Konarzewska, Ireneusz Sołtyszewski, Jolanta Kupryjanczyk, Lukasz Michal Szafron.

CRNDE is considered an oncogene expressed as long non-coding RNA. Our previous paper is the only one reporting CRNDE as a micropeptide-coding gene. The amino acid sequence of this micropeptide (CRNDEP) has recently been confirmed by other researchers. This study aimed at providing a mass spectrometry (MS)-based validation of the CRNDEP sequence and an investigation of how the differential expression of CRNDE(P) influences the metabolism and chemoresistance of ovarian cancer (OvCa) cells. We also assessed cellular localization changes of CRNDEP, looked for its protein partners, and bioinformatically evaluated its RNA-binding capacities. Herein, we detected most of the CRNDEP sequence by MS. Moreover, our results corroborated the oncogenic role of CRNDE, portraying it as the gene impacting carcinogenesis at the stages of DNA transcription and replication, affecting the RNA metabolism, and stimulating the cell cycle progression and proliferation, with CRNDEP being detected in the centrosomes of dividing cells. We also showed that CRNDEP is located in nucleoli and revealed interactions of this micropeptide with p54, an RNA helicase. Additionally, we proved that high CRNDE(P) expression increases the resistance of OvCa cells to treatment with microtubule-targeted cytostatics. Furthermore, altered CRNDE(P) expression affected the activity of the microtubular cytoskeleton and the formation of focal adhesion plaques. Finally, according to our in silico analyses, CRNDEP is likely capable of RNA binding. All these results contribute to a better understanding of the CRNDE(P) role in OvCa biology, which may potentially improve the screening, diagnosis, and treatment of this disease.

Keywords: CRNDE; RNA-Seq; SEP; adhesion; affinity chromatography; centrosome; cytoskeleton; lncRNA; mass spectrometry; micropeptide; microtubule; nucleolus; ovarian cancer

DOI: https://doi.org/10.3390/ijms25084381