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 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 Nuclear Accumulation of IE62, the Varicella-Zoster Virus (VZV) Major Transcriptional Regulatory Protein, Is Inhibited by Phosphorylation Mediated by the VZV Open Reading Frame 66 Protein Kinase

2000 ◽  
Vol 74 (5) ◽  
pp. 2265-2277 ◽  
Author(s):  
Paul R. Kinchington ◽  
Karen Fite ◽  
Stephanie E. Turse
Keyword(s):  
Protein Kinase ◽  
Varicella Zoster Virus ◽  
Nuclear Localization ◽  
Kinase Activity ◽  
Open Reading Frame ◽  
Nuclear Accumulation ◽  
Protein Kinase Activity ◽  
Reading Frame ◽  
Varicella Zoster ◽  
In Cells

ABSTRACT IE62, the major transcriptional activator protein encoded by varicella-zoster virus (VZV), locates to the nucleus when expressed in transfected cells. We show here that cytoplasmic forms of IE62 accumulate in transfected and VZV-infected cells as the result of the protein kinase activity associated with VZV open reading frame 66 (ORF66). Expression of the ORF66 protein kinase but not the VZV ORF47 protein kinase impaired the ability of coexpressed IE62 to transactivate promoter-reporter constructs. IE62 that was coexpressed with the ORF66 protein accumulated predominantly in the cytoplasm, whereas the normal nuclear localization of other proteins was not affected by the ORF66 protein. In cells infected with VZV, IE62 accumulated in the cytoplasm at late times of infection, whereas in cells infected with a VZV recombinant unable to express ORF66 protein (ROka66S), IE62 was completely nuclear. Point mutations introduced into the predicted serine/threonine catalytic domain and ATP binding domain of ORF66 abrogated its ability to influence IE62 nuclear localization, indicating that the protein kinase activity was required. The region of IE62 that was targeted by ORF66 was mapped to amino acids 602 to 733. IE62 peptides containing this region were specifically phosphorylated in cells coexpressing the ORF66 protein kinase and in cells infected with wild-type VZV but were not phosphorylated in cells infected with ROka66S. We conclude that the ORF66 protein kinase phosphorylates IE62 to induce its cytoplasmic accumulation, most likely by inhibiting IE62 nuclear import.

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 Alternate splicing in human Na+-MI cotransporter gene yields differentially regulated transport isoforms

1999 ◽  
Vol 276 (6) ◽  
pp. C1325-C1337 ◽  
Author(s):  
Francesca Porcellati ◽  
Yoshiyuki Hosaka ◽  
Tommy Hlaing ◽  
Masaki Togawa ◽  
Dennis D. Larkin ◽  
...  
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Protein Kinase A ◽  
Phosphorylation Site ◽  
Open Reading Frame ◽  
Phosphorylation Sites ◽  
Reading Frame ◽  
Kinase C ◽  
Multiple Protein ◽  
Kinase A

myo-Inositol is a ubiquitous intracellular organic osmolyte and phosphoinositide precursor maintained at millimolar intracellular concentrations through the action of membrane-associated Na+- myo-inositol cotransporters (SMIT). Functional cloning and expression of a canine SMIT cDNA, which conferred SMIT activity in Xenopus oocytes, predicted a 718-amino acid peptide homologous to the Na+-glucose cotransporter with a potential protein kinase A phosphorylation site and multiple protein kinase C phosphorylation sites. A consistent ∼1.0- to 13.5-kb array of transcripts hybridizing with this cDNA are osmotically induced in a variety of mammalian cells and species, yet SMIT activity appears to vary among different tissues and species. An open reading frame on human chromosome 21 (SLC5A3) homologous to that of the canine cDNA (96.5%) is thought to comprise an intronless human SMIT gene. Recently, this laboratory ascribed multiply sized, osmotically induced SMIT transcripts in human retinal pigment epithelial cells to the alternate utilization of several 3′-untranslated SMIT exons. This article describes an alternate splice donor site within the coding region that extends the open reading frame into the otherwise untranslated 3′ exons, potentially generating novel SMIT isoforms. In these isoforms, the last putative transmembrane domain is replaced with intracellular carboxy termini containing a novel potential protein kinase A phosphorylation site and multiple protein kinase C phosphorylation sites, and this could explain the heterogeneity in the regulation and structure of the SMIT.

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.

scholarly journals Phosphorylation of the Varicella-Zoster Virus (VZV) Major Transcriptional Regulatory Protein IE62 by the VZV Open Reading Frame 66 Protein Kinase

2006 ◽  
Vol 80 (4) ◽  
pp. 1710-1723 ◽  
Author(s):  
Amie J. Eisfeld ◽  
Stephanie E. Turse ◽  
Sara A. Jackson ◽  
Edwina C. Lerner ◽  
Paul R. Kinchington
Keyword(s):  
Protein Kinase ◽  
Varicella Zoster Virus ◽  
Nuclear Import ◽  
Regulatory Protein ◽  
Recombinant Baculovirus ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Varicella Zoster ◽  
Transcriptional Regulatory

ABSTRACT IE62, the major transcriptional regulatory protein encoded by varicella-zoster virus (VZV), is nuclear at early times of VZV infection but then becomes predominantly cytoplasmic as a result of expression of the protein kinase encoded by open reading frame 66 (ORF66). Cytoplasmic forms of IE62 are required for its inclusion as an abundant VZV virion tegument protein. Here we show that ORF66 directly phosphorylates IE62 at two residues, with phosphorylation at S686 being sufficient to regulate IE62 nuclear import. Phosphotryptic peptide analyses established an ORF66 kinase-mediated phosphorylation of the complete IE62 protein in transfected and VZV-infected cells. Using truncated and point-mutated IE62 peptides, ORF66-directed phosphorylation was mapped to residues S686 and S722, immediately downstream of the IE62 nuclear localization signal. An IE62 protein with an S686A mutation retained efficient nuclear import activity, even in the presence of functional ORF66 protein kinase, but an IE62 protein containing an S686D alteration was imported into the nucleus inefficiently. In contrast, the nuclear import of IE62 carrying an S722A mutation was still modulated by ORF66 expression, and IE62 with an S722D mutation was imported efficiently into the nucleus. An in vitro phosphorylation assay was developed using bacterially expressed IE62-maltose binding protein fusions as substrates for immunopurified ORF66 protein kinase from recombinant baculovirus-infected insect cells. ORF66 kinase phosphorylated the IE62 peptides, with similar specificities for residues S686 and S722. These results indicate that IE62 nuclear import is modulated as a result of direct phosphorylation of IE62 by ORF66 kinase. This represents an interaction that is, so far, unique among the alphaherpesviruses.

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