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Small opening frame encoded peptides

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https://www.readbyqxmd.com/read/29909570/functions-and-impact-of-tal-like-genes-in-animals-with-regard-to-applied-aspects
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28759257/in-search-of-lost-small-peptides
#16
REVIEW
Serge Plaza, Gerben Menschaert, François Payre
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules...
October 6, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28759167/small-but-mighty-functional-peptides-encoded-by-small-orfs-in-plants
#17
REVIEW
Polly Yingshan Hsu, Philip N Benfey
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics...
May 2018: Proteomics
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#18
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28589727/identification-of-microprotein-protein-interactions-via-apex-tagging
#19
COMPARATIVE STUDY
Qian Chu, Annie Rathore, Jolene K Diedrich, Cynthia J Donaldson, John R Yates, Alan Saghatelian
Microproteins are peptides and small proteins encoded by small open reading frames (smORFs). Newer technologies have led to the recent discovery of hundreds to thousands of new microproteins. The biological functions of a few microproteins have been elucidated, and these microproteins have fundamental roles in biology ranging from limb development to muscle function, highlighting the value of characterizing these molecules. The identification of microprotein-protein interactions (MPIs) has proven to be a successful approach to the functional characterization of these genes; however, traditional immunoprecipitation methods result in the enrichment of nonspecific interactions for microproteins...
July 5, 2017: Biochemistry
https://www.readbyqxmd.com/read/28577391/shrimp-tab1-interacts-with-tak1-and-p38-and-activates-the-host-innate-immune-response-to-bacterial-infection
#20
Sheng Wang, Mengqiao Li, Bin Yin, Haoyang Li, Bang Xiao, Kai Lǚ, Zhijian Huang, Sedong Li, Jianguo He, Chaozheng Li
Mammalian TAB1 has been previously identified as transforming growth factor-β (TGF-β)-activated kinase 1 (TAK1) binding protein, which functions as the activator of TAK1 and p38. This report, for the first time, identified and characterized the homolog of TAB1 in shrimp, to be specific, the homolog gene from Litopenaeus vannamei, containing a 1560-bp open reading frame (ORF) that encoded a putative protein of 519 amino acids with the conserved PP2Cc (Serine/threonine phosphatases, family 2C, catalytic) domain in N-terminal and a TAK1 binding motif in C-terminus, has been cloned and named LvTAB1...
August 2017: Molecular Immunology
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