The Small Open Reading Frame‐Encoded Peptides: Advances in Methodologies and Functional Studies

ChemBioChem ◽  
2021 ◽  
Author(s):  
Lei Chen ◽  
Ying Yang ◽  
Yuanliang Zhang ◽  
Kecheng Li ◽  
Hongmin Cai ◽  
...  
Keyword(s):  
Open Reading Frame ◽  
Reading Frame ◽  
Functional Studies ◽  
Small Open Reading Frame

scholarly journals Regulation of the nfsA Gene in Escherichia coli by SoxS

2002 ◽  
Vol 184 (1) ◽  
pp. 51-58 ◽  
Author(s):  
E. Suzanne Paterson ◽  
Sherri E. Boucher ◽  
I. B. Lambert
Keyword(s):  
Escherichia Coli ◽  
Promoter Sequence ◽  
Open Reading Frame ◽  
Base Sequence ◽  
Start Site ◽  
Transcription Start ◽  
Band Shift ◽  
Reading Frame ◽  
Shift Analysis ◽  
Small Open Reading Frame

ABSTRACT In Escherichia coli, the response to oxidative stress due to elevated levels of superoxide is mediated, in part, by the soxRS regulon. One member of the soxRS regulon, nfsA, encodes the major oxygen-insensitive nitroreductase in Escherichia coli which catalyzes the reduction of nitroaromatic and nitroheterocyclic compounds by NADPH. In this study we investigate the regulation of nfsA in response to the superoxide generating compound paraquat. The transcription start site (TSS) of nfsA was located upstream of the ybjC gene, a small open reading frame of unknown function located directly upstream of nfsA, suggesting that these two genes form an operon. The activity of the promoter associated with this TSS was confirmed with lacZ fusions and was shown to be inducible by paraquat. Footprinting and band shift analysis showed that purified His-tagged SoxS protein binds to a 20-base sequence 10 bases upstream of the −35 promoter sequence in the forward orientation, suggesting that the ybjC-nfsA promoter is a class I SoxS-dependent promoter.

scholarly journals Expression and strain variation of the novel “small open reading frame” (smorf) multigene family in Babesia bovis

2012 ◽  
Vol 42 (2) ◽  
pp. 131-138 ◽  
Author(s):  
Lucas M. Ferreri ◽  
Kelly A. Brayton ◽  
Kerry S. Sondgeroth ◽  
Audrey O.T. Lau ◽  
Carlos E. Suarez ◽  
...  
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
Babesia Bovis ◽  
The Novel ◽  
Strain Variation ◽  
Reading Frame ◽  
Small Open Reading Frame

scholarly journals Bioinformatics Analysis Identifies a Small ORF in the Genome of Fish Nidoviruses of Genus Oncotshavirus Predicted to Encode a Novel Integral Protein

2021 ◽  
Vol 12 (4) ◽  
pp. 753-764
Author(s):  
Frederick Kibenge ◽  
Ashley McKibbon ◽  
Molly Kibenge ◽  
Yingwei Wang
Keyword(s):  
Bioinformatics Analysis ◽  
Signal Sequence ◽  
Open Reading Frame ◽  
Type I ◽  
Structural Protein ◽  
Genome Sequence Analysis ◽  
Reading Frame ◽  
The Third ◽  
E Protein ◽  
Small Open Reading Frame

Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein is strikingly similar to the coronavirus E protein in structure. This is the first report to identify a putative E protein ORF in the genome of members of the Oncotshavirus genus (subfamily Piscavirinae, family Tobaniviridae, order Nidovirales) and, if expressed would be the third family (after Coronaviridae and Arteriviridae) within the order to have the E protein as a major structural protein.

scholarly journals Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

2016 ◽  
Vol 88 (7) ◽  
pp. 3967-3975 ◽  
Author(s):  
Jiao Ma ◽  
Jolene K. Diedrich ◽  
Irwin Jungreis ◽  
Cynthia Donaldson ◽  
Joan Vaughan ◽  
...  
Keyword(s):  
Open Reading Frame ◽  
Reading Frame ◽  
Small Open Reading Frame

scholarly journals FAMOSS, a conserved 41-aa peptide involved in plant tip growth regulation

2021 ◽  
Author(s):  
Anna Mamaeva ◽  
Andrey Kniazev ◽  
Ilia Sedlov ◽  
Nina Golub ◽  
Daria Kharlampieva ◽  
...  
Keyword(s):  
Growth Regulation ◽  
Opposite Effect ◽  
Transmembrane Domain ◽  
Functional Characterization ◽  
Small Gtpase ◽  
Reading Frame ◽  
Functional Studies ◽  
Non Coding Rnas ◽  
Small Open Reading Frame

Recent evidence shows that small open reading frame (smORF; <100 codons)-encoded peptides (SEPs) containing transmembrane domains are preadapted to be progenitors of novel functional genes. A dozen of such SEPs translated from long non-coding RNAs (lncRNAs) are already functionally characterised in animals. However, functional plant lncRNA-smORF-coded peptides are not yet described. Here, we report detailed functional characterization of a 41-aa peptide encoded by lncRNA-smORFs in the moss Physcomitrium patens, which was named "FAst-growing MOSS" (FAMOSS). We found that the FAMOSS interacts with the Rab-type small GTPase proteins and its overexpression leads to faster moss growth rate and more intensive vesicular transport in apical cells, while its knockout results in the opposite effect. The FAMOSS contains a predicted transmembrane domain and possible orthologs from streptophyta algae to flowering plants have a very conserved structure. Thus, the FAMOSS peptide is a previously unknown conserved player of Rab-mediated processes in plants. Our findings are in line with functional studies of transmembrane SEPs in animals and prove the principles of SEPs evolution. This study provides new insights into functions of plant lncRNA-smORFs.

scholarly journals The rIIA gene of bacteriophage T4. I. Its DNA sequence and discovery of a new open reading frame between genes 60 and rIIA.

Genetics ◽  
1990 ◽  
Vol 125 (2) ◽  
pp. 237-248
Author(s):  
P Daegelen ◽  
E Brody
Keyword(s):  
Dna Sequence ◽  
Bacteriophage T4 ◽  
Regulation Of Gene Expression ◽  
High Sensitivity ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Molecular Weights ◽  
Control Regulation ◽  
Small Open Reading Frame ◽  
Repeated Motif

Abstract We have determined the DNA sequence of the rIIA gene and have discovered a small open reading frame, rIIA.1, between genes 60 and rIIA. The predicted molecular weights of these proteins are 82,840 for rIIA and 8,124 for rIIA.1. The rIIA protein has a repeated motif which suggests that the gene has evolved by duplication. It also has a motif which suggests that it belongs to a group of ompR-like proteins that control regulation of gene expression in response to changes in the external environment. We have sequenced three different missense mutants whose mutations lie in the Ala segment of the rIIA genetic map. All three changes are found within the first 35 bp of the rIIA coding sequence. The region of control of protein synthesis is identical in the rIIA gene and in gene 44 of T4. We relate this finding to the high sensitivity of both RNAs to translational repression by the T4 regA gene product.

TheSCH9 protein kinase mRNA contains a long 5′ leader with a small open reading frame

Yeast ◽  
1993 ◽  
Vol 9 (1) ◽  
pp. 21-32 ◽  
Author(s):  
Francesco Di Blasi ◽  
Elena Carra ◽  
Emmanuele De Vendittis ◽  
Pietro Masturzo ◽  
Emanuele Burderi ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Small Open Reading Frame

scholarly journals Small open reading frames and cellular stress responses

2019 ◽  
Vol 15 (2) ◽  
pp. 108-116 ◽  
Author(s):  
Alexandra Khitun ◽  
Travis J. Ness ◽  
Sarah A. Slavoff
Keyword(s):  
Stress Responses ◽  
Cellular Stress ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Cellular Stress Responses ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Increasing evidence suggests that some small open reading frame-encoded polypeptides (SEPs) function in prokaryotic and eukaryotic cellular stress responses.

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