Identification and characterization of sORF-encoded polypeptides

Chu, Qian; Ma, Ji; Saghatelian, Alan

doi:10.3109/10409238.2015.1016215

Cited by 61 publications

(52 citation statements)

References 60 publications

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“…For detailed information regarding such a process and the involved procedures, the readers are referred to other recently published in-depth reviews [9,155,156,157]. …”

Section: Strategies and Methodologiesmentioning

confidence: 99%

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Zhu

Hassan

Lepp

et al. 2017

Toxins

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Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.

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“…For detailed information regarding such a process and the involved procedures, the readers are referred to other recently published in-depth reviews [9,155,156,157]. …”

Section: Strategies and Methodologiesmentioning

confidence: 99%

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Zhu

Hassan

Lepp

et al. 2017

Toxins

View full text Add to dashboard Cite

show abstract

“…In general, strictly bioinformatic approaches require a large number of experimentally validated ORFs to serve as a training set to enable subsequent de novo prediction, but there are presently not a sufficient number of identified sORFs for this purpose. Alternatively, ORFs can be identified based on conservation alone, but for that, reliable prediction generally requires sequences that encode peptides that are longer than 100-aa 21–26 . Direct identification of translated peptides in the cell by proteomic methods is also often highly effective, however these methods are well known to be inefficient at detecting proteins of small size 10 , 27 , 28 .…”

Section: Introductionmentioning

confidence: 99%

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in earlyDrosophilaembryos reveals hundreds of conserved translated sORFs

Bai

et al. 2016

DNA Res

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There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.

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“…Recent studies indicate that one mRNA molecule can actually encode several peptides through different strategies including multiple ORFs or non‐AUG codon‐initiated translation, ribosomal frame shifting, stop codon read through, and termination‐dependent reinitiation . Hundreds of putative coding sORFs have been identified by computing, proteomics, and ribosomal profiling, some of which have been confirmed .…”

Section: Discussionmentioning

confidence: 98%

A histone deacetylase 7-derived peptide promotes vascular regeneration via facilitating 14-3-3γ phosphorylation

Yang

Moraga

et al. 2020

Stem Cells

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Histone deacetylase 7 (HDAC7) plays a pivotal role in the maintenance of the endothelium integrity. In this study, we demonstrated that the intron‐containing Hdac7 mRNA existed in the cytosol and that ribosomes bound to a short open reading frame (sORF) within the 5′‐terminal noncoding area of this Hdac7 mRNA in response to vascular endothelial growth factor (VEGF) stimulation in the isolated stem cell antigen‐1 positive (Sca1+) vascular progenitor cells (VPCs). A 7‐amino acid (7A) peptide has been demonstrated to be translated from the sORF in Sca1+‐VPCs in vitro and in vivo. The 7A peptide was shown to receive phosphate group from the activated mitogen‐activated protein kinase MEKK1 and transfer it to 14‐3‐3 gamma protein, forming an MEKK1‐7A‐14‐3‐3γ signal pathway downstream VEGF. The exogenous synthetic 7A peptide could increase Sca1+‐VPCs cell migration, re‐endothelialization in the femoral artery injury, and angiogenesis in hind limb ischemia. A Hd7‐7sFLAG transgenic mice line was generated as the loss‐of‐function model, in which the 7A peptide was replaced by a FLAG‐tagged scrabbled peptide. Loss of the endogenous 7A impaired Sca1+‐VPCs cell migration, re‐endothelialization of the injured femoral artery, and angiogenesis in ischemic tissues, which could be partially rescued by the addition of the exogenous 7A/7Ap peptide. This study provides evidence that sORFs can be alternatively translated and the derived peptides may play an important role in physiological processes including vascular remodeling.

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Identification and characterization of sORF-encoded polypeptides

Cited by 61 publications

References 60 publications

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in earlyDrosophilaembryos reveals hundreds of conserved translated sORFs

A histone deacetylase 7-derived peptide promotes vascular regeneration via facilitating 14-3-3γ phosphorylation

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