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Small opening frame encoded peptides

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https://www.readbyqxmd.com/read/30321192/large-scale-docking-predicts-that-sorf-encoded-peptides-may-function-through-protein-peptide-interactions-in-arabidopsis-thaliana
#1
Rashmi R Hazarika, Nikolina Sostaric, Yifeng Sun, Vera van Noort
Several recent studies indicate that small Open Reading Frames (sORFs) embedded within multiple eukaryotic non-coding RNAs can be translated into bioactive peptides of up to 100 amino acids in size. However, the functional roles of the 607 Stress Induced Peptides (SIPs) previously identified from 189 Transcriptionally Active Regions (TARs) in Arabidopsis thaliana remain unclear. To provide a starting point for functional annotation of these plant-derived peptides, we performed a large-scale prediction of peptide binding sites on protein surfaces using coarse-grained peptide docking...
2018: PloS One
https://www.readbyqxmd.com/read/30317668/prokaryotic-sphinx-1-8-rep-protein-is-tissue-specific-and-expressed-in-human-germline-cells
#2
Laura Manuelidis
Small circular DNAs of 1.8 and 2.4 kb were initially discovered in highly infectious Creutzfeldt-Jakob Disease (CJD) and scrapie particles from mammalian brain and cultured cells. Surprisingly, these protected cytoplasmic "SPHINX" DNAs contained replication (REP) initiation sequences resembling those of Acinetobacter phage viruses. An antibody was generated against a REP peptide encoded by the SPHINX 1.8 open reading frame (ORF) that was not present in mammals. It bound to a 41kd "spx1" protein on Western blots...
October 14, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/30218823/molecular-characterization-and-expression-of-tlr7-and-tlr8-in-barbel-chub-squaliobarbus-curriculus-responses-to-stimulation-of-grass-carp-reovirus-and-lipopolysaccharide
#3
Shengzhen Jin, Xin Zhao, Hongquan Wang, Jianming Su, Jing'an Wang, Chunhua Ding, Yaoguo Li, Tiaoyi Xiao
The barbel chub (Squaliobarbus curriculus) is a kind of small size commercial fish species that is widely spread in Asia and has shown significant resistance to disease. In this study, the full-length cDNA sequences of Toll-like receptor (TLR) 7 and 8 from S. curriculus, designated as ScTLR7 and ScTLR8, were cloned, and their differences in the structure and the responses to the grass carp (GCRV) infection and lipopolysaccharide stimulation were investigated. The full-length 3715 base pair (bp) cDNA of ScTLR7 contained a complete open reading frame of 3162 bp and encoded a putative polypeptide of 1053 amino acid residues...
September 12, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/30215512/mief1-microprotein-regulates-mitochondrial-translation
#4
Annie Rathore, Qian Chu, Dan Tan, Thomas F Martinez, Cynthia J Donaldson, Jolene K Diedrich, John R Yates, Alan Saghatelian
Recent technological advances led to the discovery of hundreds to thousands of peptides and small proteins (microproteins) encoded by small open reading frames (smORFs). Characterization of new microproteins demonstrates their role in fundamental biological processes and highlights the value in discovering and characterizing more microproteins. The elucidation of microprotein-protein interactions (MPIs) is useful for determining the biochemical and cellular roles of microproteins. In this study, we characterize the protein interaction partners of mitochondrial elongation factor 1 microprotein (MIEF1-MP) using a proximity labeling strategy that relies on APEX2...
September 25, 2018: Biochemistry
https://www.readbyqxmd.com/read/30172902/identification-of-novel-open-reading-frames-in-the-intergenic-regions-of-mycobacterium-leprae-genome-and-detection-of-transcript-by-qrt-pcr
#5
Mukul Sharma, Madhusmita Das, D Diana, Anna Wedderburn, Roy Anindya
Mycobacterium leprae is an unculturable obligate pathogen and causative agent for debilitating human disease leprosy. Due to reductive genome evolution M leprae genome harbours large number of pseudogenes and small number of genes (∼1600 genes and ∼1300 pseudogenes). How M leprae remained a successful human parasite with small set of genes remains poorly understood and provided us the impetus to investigate the intergenic regions of M leprae genome for the presence of possible open reading frames (ORFs)...
August 30, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29909570/functions-and-impact-of-tal-like-genes-in-animals-with-regard-to-applied-aspects
#6
REVIEW
Min Zhu, Xiaolong Hu, Guangli Cao, Renyu Xue, Chengliang Gong
A large number of DNAs in eukaryote genomes can code for atypical transcripts, and their functions are controversial. It has been reported that the transcripts contain many small open reading frames (sORFs), which were originally considered as non-translatable RNAs. However, increasing evidence has suggested that some of these sORFs can encode for small peptides and some are conserved across large evolutionary distances. It has been reported that the small peptides have functions and may be involved in varieties of cellular processes, playing important roles in development, physiology, and metabolism...
June 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29902560/a-defensin-like-antimicrobial-peptide-from-the-manila-clam-ruditapes-philippinarum-investigation-of-the-antibacterial-activities-and-mode-of-action
#7
Dinglong Yang, Qianqian Zhang, Qing Wang, Lizhu Chen, Yongliang Liu, Ming Cong, Huifeng Wu, Fei Li, Chenglong Ji, Jianmin Zhao
Defensins are small cysteine-rich cationic proteins that are ubiquitously present in both vertebrates and invertebrates and constitute the front line of host innate immunity. In the present study, a defensin-like antimicrobial peptide (designed as RpdefB) was identified and characterized from the manila clam Ruditapes philippinarum. The open reading frame of RpdefB encoded a 70-amino acid polypeptide with a calculated molecular mass of 7.5 kDa and isoelectric point of 8.16. Multiple alignments and phylogenetic analysis strongly suggested that RpdefB was a new member of the defensin family...
September 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29897761/enrichment-based-proteogenomics-identifies-microproteins-missing-proteins-and-novel-smorfs-in-saccharomyces-cerevisiae
#8
Cuitong He, Chenxi Jia, Yao Zhang, Ping Xu
Microproteins are peptides composed of 100 amino acids (AA) or fewer, encoded by small open reading frames (smORFs). It has been demonstrated that microproteins participate in and regulate a wide range of functions in cells. However, the annotation and identification of microproteins is challenging in part owing to their low molecular weight, low abundancy, and hydrophobicity. These factors have led to the unannotation of smORFs in genome processing and have made their identification at the protein level difficult...
July 6, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29812897/cipergenesis-a-mutagenesis-approach-that-produces-small-libraries-of-circularly-permuted-proteins-randomly-opened-at-a-focused-region-testing-on-the-green-fluorescent-protein
#9
Paul Gaytán, Abigail Roldán-Salgado, Jorge A Yáñez, Sandra Morales-Arrieta, Víctor R Juárez-González
Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs...
July 9, 2018: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29721095/encoding-activities-of-non-coding-rnas
#10
REVIEW
Yanan Pang, Chuanbin Mao, Shanrong Liu
The universal expression of various non-coding RNAs (ncRNAs) is now considered the main feature of organisms' genomes. Many regions in the genome are transcribed but not annotated to encode proteins, yet contain small open reading frames (smORFs). A widely accepted opinion is that a vast majority of ncRNAs are not further translated. However, increasing evidence underlines a series of intriguing translational events from the ncRNAs, which were previously considered to lack coding potential. Recent studies also suggest that products derived from such novel translational events display important regulatory functions in many fundamental biological and pathological processes...
2018: Theranostics
https://www.readbyqxmd.com/read/29675032/fspp-a-tool-for-genome-wide-prediction-of-smorf-encoded-peptides-and-their-functions
#11
Hui Li, Li Xiao, Lili Zhang, Jiarui Wu, Bin Wei, Ninghui Sun, Yi Zhao
smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29584760/the-influence-of-transcript-assembly-on-the-proteogenomics-discovery-of-microproteins
#12
Jiao Ma, Alan Saghatelian, Maxim Nikolaievich Shokhirev
Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in detection and discovery of these molecules...
2018: PloS One
https://www.readbyqxmd.com/read/29571919/age-dependent-expression-pattern-in-the-mammalian-brain-of-a-novel-small-peptide-encoded-in-the-22q11-2-deletion-syndrome-region
#13
Sabrina Kragness, Mark A A Harrison, Joby J Westmoreland, Adam Burstain, Laurie R Earls
22q11.2 deletion syndrome (22q11.2DS) carries increased risk for both physical and psychiatric symptoms, including a high risk for schizophrenia. Understanding the genetic elements within the deletion region therefore has the potential to unlock the mysteries of both diseases. While most of the protein-coding genes in this region have been characterized, novel elements, such as non-coding RNAs and small Open Reading Frames (sORFs) remain unstudied. We have identified a novel, highly-conserved mouse sORF in a region of the mouse genome that is orthologous to a portion of the 22q11...
June 2018: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/29428488/a-thymosin-repeated-protein1-reduces-white-spot-syndrome-virus-replication-in-red-claw-crayfish-cherax-quadricarinatus
#14
Dong-Li Li, Xue-Jiao Chang, Xiao-Lu Xie, Shu-Cheng Zheng, Qiu-Xia Zhang, Shu-Ao Jia, Ke-Jian Wang, Hai-Peng Liu
The β-thymosins are a group of structurally related, highly conserved intracellular small peptides in vertebrates with various biological functions, including cytoskeletal remodeling, neuronal development, cell migration, cell survival, tissue repair and inhibition of inflammation. In contrast to vertebrates, the function of β-thymosin is not fully understood in crustaceans. Previously, we found that a thymosin-repeated protein1 (CqTRP1) gene was up-regulated after white spot syndrome virus (WSSV) challenge in hematopoietic tissue (Hpt) cells from the red claw crayfish Cherax quadricarinatus...
July 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29306967/identification-of-tarsal-less-peptides-from-the-silkworm-bombyx-mori
#15
Guangli Cao, Yongchang Gong, Xiaolong Hu, Min Zhu, Zi Liang, Lixu Huang, Lei Yu, Jian Xu, Kun Li, Mian Sahib Zar, Renyu Xue, Chengliang Gong
The polycistronic and non-canonical gene tarsal-less (tal, known as pri) was reported to be required for embryonic and imaginal development in Drosophila; however, there are few reports of the tal gene in the silkworm Bombyx mori. Here, we cloned a tal-like (Bmtal) gene, and a sequence analysis showed that the Bmtal cDNA (1661 bp) contains five small open reading frames (smORFs) (A1, A2, A3, A4, and B) that encode short peptides of 11-12 (A1-A4) amino acid residues containing an LDPTG(E)L(Q)(V)Y motif that is conserved in Drosophila Tal, as well as a 32-amino-acid B peptide...
February 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29188713/mining-for-small-translated-orfs
#16
REVIEW
Anastasia Chugunova, Tsimafei Navalayeu, Olga Dontsova, Petr Sergiev
Peptides encoded by short open reading frames (sORFs) are usually defined as peptides ≤100 aa long. Usually sORFs were ignored by automatic genome annotation programs due to the high probability of false discovery. However, improved computational tools along with a high-throughput RIBO-seq approach identified a myriad of translated sORFs. Their importance becomes evident as we are gaining experimental validation of their diverse cellular functions. This Review examines various computational and experimental approaches of sORFs identification as well as provides the summary of our current knowledge of their functional roles in cells...
January 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29138516/the-functions-and-unique-features-of-long-intergenic-non-coding-rna
#17
REVIEW
Julia D Ransohoff, Yuning Wei, Paul A Khavari
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome...
March 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29128637/a-mads-box-transcription-factor-of-kuerlexiangli-pyrus-sinkiangensis-yu-psjointless-gene-functions-in-floral-organ-abscission
#18
Xiaoxiao Qi, Shi Hu, Hongsheng Zhou, Xing Liu, Lifen Wang, Biying Zhao, Xiaosan Huang, Shaoling Zhang
MADS-box proteins have been implicated in many biological processes. However, plant MADS-box proteins functioning in floral organ abscission and the underlying physiological mechanisms remain poorly understood. Here, we report the identification and functional characterization of PsJOINTLESS isolated from 'Kuerlexiangli'. PsJOINTLESS had a complete open reading frame of 672bp, encoding a 224 amino acid peptide, and shared high sequence identities with MADS-box from other plants. PsJOINTLESS was subcellularly targeted to the nucleus, supporting its role as a transcription factor...
February 5, 2018: Gene
https://www.readbyqxmd.com/read/28994791/subcellular-fractionation-for-erk-activation-upon-mitochondrial-derived-peptide-treatment
#19
Su-Jeong Kim, Jialin Xiao, Pinchas Cohen, Kelvin Yen
Mitochondrial-derived peptides (MDPs) are a new class of peptides that are encoded by small open reading frames within other known genes of the mitochondrial genome. MDPs have a wide variety of biological effects such as protecting neurons from apoptosis, improving metabolic markers, and protecting cells from chemotherapy. Humanin was the first MDP to be discovered and is the most studied peptide among the MDP family. The membrane receptors and downstream signaling pathways of humanin have been carefully characterized...
September 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28825667/viral-infection-identifies-micropeptides-differentially-regulated-in-smorf-containing-lncrnas
#20
Brandon S Razooky, Benedikt Obermayer, Joshua Biggs O'May, Alexander Tarakhovsky
Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i...
August 21, 2017: Genes
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