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Keywords Small opening frame encoded pe...

Small opening frame encoded peptides

https://read.qxmd.com/read/37712700/multi-integrated-approach-for-unraveling-small-open-reading-frames-potentially-associated-with-secondary-metabolism-in-streptomyces
#21
JOURNAL ARTICLE
Si-Min Fan, Ze-Qi Li, Shi-Zhe Zhang, Liang-Yu Chen, Xi-Ying Wei, Jian Liang, Xin-Qing Zhao, Chun Su
Small open reading frames (smORFs) are widely distributed in various living organisms. However, their functions remain largely unexplored. In addition, annotation and detection of smORFs are limited using existing methods and hindered by their specific properties. In this study, we systematically investigated smORFs and smORF-encoded peptides (SEPs) in Streptomyces , which are well-known bacterial producers of diverse bioactive secondary metabolites. We established a peptidogenomic workflow based on multi-integrated comprehensive database search and database-independent de novo sequencing to identify smORFs in Streptomyces xinghaiensis NRRL B-24674T (S187)...
September 15, 2023: MSystems
https://read.qxmd.com/read/37693399/human-gut-metagenomic-mining-reveals-an-untapped-source-of-peptide-antibiotics
#22
Marcelo D T Torres, Erin Brooks, Angela Cesaro, Hila Sberro, Cosmos Nicolaou, Ami S Bhatt, Cesar de la Fuente-Nunez
Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro , with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them s mORF-encoded peptides (SEPs)...
September 3, 2023: bioRxiv
https://read.qxmd.com/read/37643974/clinical-prospects-and-research-strategies-of-long-non-coding-rna-encoding-micropeptides
#23
REVIEW
Xinyi Wang, Zhen Zhang, Chengyu Shi, Ying Wang, Tianhua Zhou, Aifu Lin
Long non-coding RNAs (lncRNAs) which are usually thought to have no protein coding ability, are widely involved in cell proliferation, signal transduction and other biological activities. However, recent studies have suggested that short open reading frames (sORFs) of some lncRNAs can encode small functional peptides (micropeptides). These micropeptides appear to play important roles in calcium homeostasis, embryonic development and tumorigenesis, suggesting their potential as therapeutic targets and diagnostic biomarkers...
August 25, 2023: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://read.qxmd.com/read/37562954/research-strategies-and-clinical-prospects-of-long-non-coding-rna-encoding-micropeptides
#24
JOURNAL ARTICLE
Xinyi Wang, Zhen Zhang, Chengyu Shi, Ying Wang, Tianhua Zhou, Aifu Lin
Long non-coding RNAs (lncRNAs) are widely involved in cell proliferation, signal transduction and other biological activities, which are usually thought to have no protein coding ability. However, recent studies have suggested that the short open reading frames (sORFs) of some lncRNAs can encode functional small peptides (micropeptides). These micropeptides play important roles in calcium homeostasis, embryonic development and tumorigenesis, suggesting they may be used as potential therapeutic targets and diagnostic biomarkers...
August 9, 2023: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://read.qxmd.com/read/37517040/lncrna-encoded-peptides-unveiling-their-significance-in-cardiovascular-physiology-and-pathology-current-research-insights
#25
JOURNAL ARTICLE
Li Zhang, Mi Tang, Haoyang Diao, Liling Xiong, Xiao Yang, Shasha Xing
Long non-coding RNAs (lncRNAs), which are RNA transcripts exceeding 200 nucleotides, were believed to lack any protein-coding capacity. But advancements in -omics technology have revealed that some lncRNAs have small open reading frames (sORFs) that can be translated by ribosomes to encode peptides, some of which have important biological functions. These encoded peptides subserve important biological functions by interacting with their targets to modulate transcriptional or signaling axes, thereby enhancing or suppressing CVD occurrence and progression...
July 30, 2023: Cardiovascular Research
https://read.qxmd.com/read/37464885/smampstk-a-toolkit-to-unravel-the-smorfome-encoding-amps-of-plant-species
#26
JOURNAL ARTICLE
Mohini Jaiswal, Shailesh Kumar
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms...
July 18, 2023: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/37445739/small-open-reading-frame-encoded-micro-peptides-an-emerging-protein-world
#27
REVIEW
Xiaoping Dong, Kun Zhang, Chengfeng Xun, Tianqi Chu, Songping Liang, Yong Zeng, Zhonghua Liu
Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, and peptidome has facilitated the prediction and identification of many new SEPs. These SEPs were revealed to be involved in a wide range of basic biological processes, such as gene expression regulation, embryonic development, cellular metabolism, inflammation, and even carcinogenesis...
June 23, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/37347740/peptide-encoded-by-lncrna-bves-as1-promotes-cell-viability-migration-and-invasion-in-colorectal-cancer-cells-via-the-src-mtor-signaling-pathway
#28
JOURNAL ARTICLE
Weiwei Zheng, Yingchang Guo, Guangtan Zhang, Junwei Bai, Yucheng Song, Xiaofei Song, Qinhui Zhu, Xuebin Bao, Gang Wu, Chao Zhang
Long non-coding RNAs (lncRNAs) have been revealed to harbor open reading frames (ORFs) that can be translated into small peptides. The peptides may participate in the pathogenesis of colorectal cancer (CRC). Herein, we investigated the role of a lncRNA BVES-AS1-encoded peptide in colorectal tumorigenesis. Through bioinformatic analysis, lncRNA BVES-AS1 was predicted to have encoding potential and to be associated with poor prognosis of patients with CRC. In CRC cells, BVES-AS1 was validated to encode a 50-aa-length micro-peptide, named BVES-AS1-201-50aa, through a western blotting method...
2023: PloS One
https://read.qxmd.com/read/37285335/a-short-peptide-linc00665_18aa-encoded-by-lncrna-linc00665-suppresses-the-proliferation-and-migration-of-osteosarcoma-cells-through-the-regulation-of-the-creb1-rps6ka3-interaction
#29
JOURNAL ARTICLE
Junwei Pan, Ming Liu, Xiaozong Duan, Dan Wang
Long noncoding RNAs (lncRNAs) encompass short open reading frames (sORFs) that can be translated into small peptides. Here, we investigated the encoding potential of lncRNA LINC00665 in osteosarcoma (OS) cells. Bioinformatic analyses were utilized to predict the lncRNAs with encoding potential in human U2OS cells. Protein expression was assessed by an immunoblotting or immunofluorescence method. Cell viability was assessed by cell counting Kit-8 (CCK-8). Cell proliferation was detected by 5-ethynyl-2'-deoxyuridine (EdU) assay...
2023: PloS One
https://read.qxmd.com/read/37271324/characterization-of-hepcidin-gene-and-protection-of-recombinant-hepcidin-supplemented-in-feed-against-aeromonas-hydrophila-infection-in-yellow-river-carp-cyprinus-carpio-haematopterus
#30
JOURNAL ARTICLE
Dan Qiao, Yan Yan, Chao Pei, Jinghang Zhang, Xianliang Zhao, Xinyu Jiang, Lei Zhu, Jie Zhang, Li Li, Xianghui Kong
Hepcidin is a small peptide of defensins with antibacterial activity, and plays an important role in innate immunity against pathogenic microorganisms, which can also participate in the regulation of iron metabolism. The hepcidin gene in Yellow River carp (Cyprinus carpio haematopterus) (CcHep) was cloned and identified. The total length of CcHep cDNA was 480 bp, containing an open reading frame (ORF) that encoded 91 amino acids (aa), which contained a 24-aa signal peptide, a 42-aa propeptide, and a 25-aa mature peptide...
June 2, 2023: Fish & Shellfish Immunology
https://read.qxmd.com/read/37198654/a-small-protein-coded-within-the-mitochondrial-canonical-gene-nd4-regulates-mitochondrial-bioenergetics
#31
JOURNAL ARTICLE
Laura Kienzle, Stefano Bettinazzi, Thierry Choquette, Marie Brunet, Hajar Hosseini Khorami, Jean-François Jacques, Mathilde Moreau, Xavier Roucou, Christian R Landry, Annie Angers, Sophie Breton
BACKGROUND: Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties...
May 18, 2023: BMC Biology
https://read.qxmd.com/read/37184890/uorf4u-a-tool-for-annotation-of-conserved-upstream-open-reading-frames
#32
JOURNAL ARTICLE
Artyom A Egorov, Gemma C Atkinson
SUMMARY: Upstream open reading frames (uORFs, often encoding so-called leader peptides) can regulate translation and transcription of downstream main ORFs (mORFs) in prokaryotes and eukaryotes. However, annotation of novel functional uORFs is challenging due their short size of usually less than 100 codons. While transcription- and translation-level next generation sequencing (NGS) methods can be used for genome-wide functional uORF identification, this data is not available for the vast majority of species with sequenced genomes...
May 15, 2023: Bioinformatics
https://read.qxmd.com/read/37154857/a-hidden-translatome-in-tumors-the-coding-lncrnas
#33
REVIEW
Jinsong Wang, Wenna Wang, Fei Ma, Haili Qian
Long noncoding RNAs (lncRNAs) have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers. Through the application and development of ribosome analysis and sequencing technologies, advanced studies have discovered the translation of lncRNAs. Although lncRNAs were originally defined as noncoding RNAs, many lncRNAs actually contain small open reading frames that are translated into peptides. This opens a broad area for the functional investigation of lncRNAs...
May 5, 2023: Science China. Life Sciences
https://read.qxmd.com/read/37127568/small-open-reading-frames-a-comparative-genetics-approach-to-validation
#34
JOURNAL ARTICLE
Niyati Jain, Felix Richter, Ivan Adzhubei, Andrew J Sharp, Bruce D Gelb
Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence...
May 1, 2023: BMC Genomics
https://read.qxmd.com/read/36968202/-purriato-is-a-conserved-small-open-reading-frame-gene-that-interacts-with-the-casa-pathway-to-regulate-muscle-homeostasis-and-epithelial-tissue-growth-in-drosophila
#35
JOURNAL ARTICLE
Jose I Pueyo, Jorge Salazar, Carolina Grincho, Jimena Berni, Benjamin P Towler, Sarah F Newbury
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes...
2023: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/36924731/identification-of-small-open-reading-frames-in-plant-lncrna-using-class-imbalance-learning
#36
JOURNAL ARTICLE
Siyuan Zhao, Jun Meng, Jael Sanyanda Wekesa, Yushi Luan
Recently, small open reading frames (sORFs) in long noncoding RNA (lncRNA) have been demonstrated to encode small peptides that can help study the mechanisms of growth and development in organisms. Since machine learning-based computational methods are less costly compared with biological experiments, they can be used to identify sORFs and provide a basis for biological experiments. However, few computational methods and data resources have been exploited for identifying sORFs in plant lncRNA. Besides, machine learning models produce underperforming classifiers when faced with a class-imbalance problem...
March 11, 2023: Computers in Biology and Medicine
https://read.qxmd.com/read/36841868/long-non-coding-rna-derived-peptides-are-immunogenic-and-drive-a-potent-anti-tumour-response
#37
JOURNAL ARTICLE
Wojciech Barczak, Simon M Carr, Geng Liu, Shonagh Munro, Annalisa Nicastri, Lian Ni Lee, Claire Hutchings, Nicola Ternette, Paul Klenerman, Alexander Kanapin, Anastasia Samsonova, Nicholas B La Thangue
Protein arginine methyltransferase (PRMT) 5 is over-expressed in a variety of cancers and the master transcription regulator E2F1 is an important methylation target. We have explored the role of PRMT5 and E2F1 in regulating the non-coding genome and report here a striking effect on long non-coding (lnc) RNA gene expression. Moreover, many MHC class I protein-associated peptides were derived from small open reading frames in the lncRNA genes. Pharmacological inhibition of PRMT5 or adjusting E2F1 levels qualitatively altered the repertoire of lncRNA-derived peptide antigens displayed by tumour cells...
February 25, 2023: Nature Communications
https://read.qxmd.com/read/36833212/novel-insights-into-mitochondrial-dna-mitochondrial-microproteins-and-mtdna-variants-modulate-athletic-performance-and-age-related-diseases
#38
REVIEW
Hiroshi Kumagai, Brendan Miller, Su-Jeong Kim, Naphada Leelaprachakul, Naoki Kikuchi, Kelvin Yen, Pinchas Cohen
Sports genetics research began in the late 1990s and over 200 variants have been reported as athletic performance- and sports injuries-related genetic polymorphisms. Genetic polymorphisms in the α-actinin-3 (ACTN3) and angiotensin-converting enzyme (ACE) genes are well-established for athletic performance, while collagen-, inflammation-, and estrogen-related genetic polymorphisms are reported as genetic markers for sports injuries. Although the Human Genome Project was completed in the early 2000s, recent studies have discovered previously unannotated microproteins encoded in small open reading frames...
January 21, 2023: Genes
https://read.qxmd.com/read/36830576/the-essentials-on-microrna-encoded-peptides-from-plants-to-animals
#39
REVIEW
Mélanie Ormancey, Patrice Thuleau, Jean-Philippe Combier, Serge Plaza
Primary transcripts of microRNAs (pri-miRNAs) were initially defined as long non-coding RNAs that host miRNAs further processed by the microRNA processor complex. A few years ago, however, it was discovered in plants that pri-miRNAs actually contain functional open reading frames (sORFs) that translate into small peptides called miPEPs, for microRNA-encoded peptides. Initially detected in Arabidopsis thaliana and Medicago truncatula , recent studies have revealed the presence of miPEPs in other pri-miRNAs as well as in other species ranging from various plant species to animals...
January 19, 2023: Biomolecules
https://read.qxmd.com/read/36824008/mitochondrial-encoded-peptide-mots-c-diabetes-and-aging-related-diseases
#40
REVIEW
Byung Soo Kong, Changhan Lee, Young Min Cho
Mitochondria are complex metabolic organelles with manifold pathophysiological implications in diabetes. Currently published mitochondrial-encoded peptides, which are expressed from the mitochondrial open reading frame of the 12S ribosomal RNA type-c (MOTS-c), 16S rRNA (humanin and short humanin like peptide 1-6 [SHLP1-6]), or small human mitochondrial open reading frame over serine tRNA (SHMOOSE) are associated with regulation of cellular metabolism and insulin action in age-related diseases, such as type 2 diabetes mellitus...
May 2023: Diabetes & Metabolism Journal
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