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 Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

scholarly journals Human Cytomegalovirus Open Reading Frame TRL11/IRL11 Encodes an Immunoglobulin G Fc-Binding Protein

2001 ◽  
Vol 75 (22) ◽  
pp. 11218-11221 ◽  
Author(s):  
Brendan N. Lilley ◽  
Hidde L. Ploegh ◽  
Rebecca S. Tirabassi
Keyword(s):  
Human Cytomegalovirus ◽  
Immunoglobulin G ◽  
Binding Protein ◽  
Fc Receptors ◽  
Binding Activity ◽  
Open Reading Frame ◽  
Membrane Glycoprotein ◽  
Type I ◽  
Reading Frame

ABSTRACT Several herpesviruses encode Fc receptors that may play a role in preventing antibody-mediated clearance of the virus in vivo. Human cytomegalovirus (HCMV) induces an Fc-binding activity in cells upon infection, but the gene that encodes this Fc-binding protein has not been identified. Here, we demonstrate that the HCMV AD169 open reading frame TRL11 and its identical copy, IRL11, encode a type I membrane glycoprotein that possesses IgG Fc-binding capabilities.

Cloning of a gar (Lepisosteus osseus) GH cDNA: trends in actinopterygian GH structure

1996 ◽  
Vol 16 (1) ◽  
pp. 73-80 ◽  
Author(s):  
D A Rubin ◽  
J H Youson ◽  
L E Marra ◽  
R M Dores
Keyword(s):  
Cdna Library ◽  
Untranslated Region ◽  
Signal Sequence ◽  
Leader Sequence ◽  
Open Reading Frame ◽  
Russian Sturgeon ◽  
Reading Frame ◽  
Terminal Codon

ABSTRACT A cDNA containing the sequence of GH was cloned and sequenced from a pituitary cDNA library for the holostean fish Lepisosteus osseus (common name: gar). The gar GH cDNA contained an open reading frame of 633 nucleotides and a 3′ untranslated region (including the terminal codon TAG) of 1058 nucleotides. The overall length of the gar GH cDNA including leader sequence, signal sequence, hormone sequence and 3′ untranslated region was 1713 nucleotides. Thus, the gar GH cDNA is the largest vertebrate GH cDNA yet cloned. A comparison of GH sequences from ancient (holostean fishes — gar and bowfin; one chondrostean fish — the Russian sturgeon) and more modern (27 species of teleosts) members of class Actinopterygii indicate that members of this class have maintained many of the invariant residues deemed necessary for GH folding motifs (intramolecular relationships) observed in mammals.

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 Enhancement of Secretion and Extracellular Stability of Staphylokinase in Bacillus subtilis bywprA Gene Disruption

2000 ◽  
Vol 66 (2) ◽  
pp. 476-480 ◽  
Author(s):  
Sang Jun Lee ◽  
Dong Min Kim ◽  
Kwang Hee Bae ◽  
Si Myung Byun ◽  
Jae Hoon Chung
Keyword(s):  
Bacillus Subtilis ◽  
Gene Disruption ◽  
Therapeutic Potential ◽  
Signal Sequence ◽  
Open Reading Frame ◽  
Expression Plasmid ◽  
Reading Frame ◽  
Extracellular Milieu ◽  
Foreign Proteins

ABSTRACT Staphylokinase (SAK), a polypeptide secreted byStaphylococcus aureus, is a plasminogen activator with a therapeutic potential in thrombosis diseases. A Bacillus subtilis strain which is multiply deficient in exoproteases was transformed by an expression plasmid carrying a promoter and a signal sequence of subtilisin fused in frame with the sak open reading frame. However, the amount of SAK secretion was marginal (45 mg/liter). In contrast, disruption of the wprA gene, which encodes a subtilisin-type protease, strongly promoted the production of SAK in the stationary phase (181 mg/liter). In addition, the extracellular stability of mature SAK was dramatically enhanced. These data indicate a significant role of the wprA gene product in degrading foreign proteins, both during secretion and in the extracellular milieu.

scholarly journals Characterization of the Collagen-Binding S-Layer Protein CbsA of Lactobacillus crispatus

2000 ◽  
Vol 182 (22) ◽  
pp. 6440-6450 ◽  
Author(s):  
Jouko Sillanpää ◽  
Beatriz Martínez ◽  
Jenni Antikainen ◽  
Takahiro Toba ◽  
Nisse Kalkkinen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Type I Collagen ◽  
Signal Sequence ◽  
Type I ◽  
Binding Region ◽  
Sequence Comparisons ◽  
Collagen Binding ◽  
Reading Frame ◽  
Lactobacillus Crispatus ◽  
C Terminus

The cbsA gene of Lactobacillus crispatusstrain JCM 5810, encoding a protein that mediates adhesiveness to collagens, was characterized and expressed in Escherichia coli. The cbsA open reading frame encoded a signal sequence of 30 amino acids and a mature polypeptide of 410 amino acids with typical features of a bacterial S-layer protein. ThecbsA gene product was expressed as a His tag fusion protein, purified by affinity chromatography, and shown to bind solubilized as well as immobilized type I and IV collagens. Three otherLactobacillus S-layer proteins, SlpA, CbsB, and SlpnB, bound collagens only weakly, and sequence comparisons of CbsA with these S-layer proteins were used to select sites in cbsAwhere deletions and mutations were introduced. In addition, hybrid S-layer proteins that contained the N or the C terminus from CbsA, SlpA, or SlpnB as well as N- and C-terminally truncated peptides from CbsA were constructed by gene fusion. Analysis of these molecules revealed the major collagen-binding region within the N-terminal 287 residues and a weaker type I collagen-binding region in the C terminus of the CbsA molecule. The mutated or hybrid CbsA molecules and peptides that failed to polymerize into a periodic S-layer did not bind collagens, suggesting that the crystal structure with a regular array is optimal for expression of collagen binding by CbsA. Strain JCM 5810 was found to contain another S-layer gene termed cbsB that was 44% identical in sequence to cbsA. RNA analysis showed that cbsA, but not cbsB, was transcribed under laboratory conditions. S-layer-protein-expressing cells of strain JCM 5810 adhered to collagen-containing regions in the chicken colon, suggesting that CbsA-mediated collagen binding represents a true tissue adherence property of L. crispatus.

scholarly journals The Bovine Herpesvirus Type 1 UL3.5 Open Reading Frame Encodes a Virion Structural Protein

Virology ◽  
1998 ◽  
Vol 240 (1) ◽  
pp. 76-82 ◽  
Author(s):  
Beate Schikora ◽  
Zhiqiang Lu ◽  
Gerald F. Kutish ◽  
Daniel Rock ◽  
Gábor Magyar ◽  
...  
Keyword(s):  
Bovine Herpesvirus ◽  
Open Reading Frame ◽  
Structural Protein ◽  
Reading Frame ◽  
Herpesvirus Type ◽  
Bovine Herpesvirus Type 1

scholarly journals Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins

2021 ◽  
Vol 49 (18) ◽  
pp. 10677-10688
Author(s):  
Feiyue Cheng ◽  
Rui Wang ◽  
Haiying Yu ◽  
Chao Liu ◽  
Jun Yang ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Deep Sequencing ◽  
Small Rnas ◽  
Transfer Rna ◽  
Open Reading Frame ◽  
Type I ◽  
Essential Information ◽  
Reading Frame ◽  
Crea Gene

Abstract Aside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking ‘CRISPR repeats’, which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5′ handle and a 22-nt 3′ handle, respectively, i.e., the conserved elements of a canonical CRISPR RNA, indicating they both retained critical nucleotides for Cas6 processing during divergent degeneration. We also uncovered a minimal CreT toxin that sequesters the rare transfer RNA for isoleucine, tRNAIleCAU, with a six-codon open reading frame containing two consecutive AUA codons. To fully relieve its toxicity, both tRNAIleCAU overexpression and supply of extra agmatine (modifies the wobble base of tRNAIleCAU to decipher AUA codons) are required. By replacing AUA to AGA/AGG codons, we reprogrammed this toxin to sequester rare arginine tRNAs. These data provide essential information on CreTA origin and for future CreTA prediction, and enrich the knowledge of tRNA-sequestering small RNAs that are employed by CRISPR-Cas to get addictive to the host.

Sign in / Sign up

Export Citation Format

Share Document