The naturally occurring silent invertase structural gene suc2° contains an amber stop codon that is occasionally read through

1989 ◽  
Vol 216 (2-3) ◽  
pp. 511-516 ◽  
Author(s):  
Daniel Gozalbo ◽  
Stefan Hohmann
Keyword(s):  
Structural Gene ◽  
Stop Codon ◽  
Naturally Occurring ◽  
Amber Stop Codon

scholarly journals Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 546 ◽  
Author(s):  
David Schwark ◽  
Margaret Schmitt ◽  
John Fisk
Keyword(s):  
Stop Codon ◽  
Release Factor ◽  
Codon Reassignment ◽  
Methanocaldococcus Jannaschii ◽  
E Coli ◽  
Amber Stop Codon ◽  
Orthogonal Pair ◽  
Amber Codon ◽  
Quantitative Contribution ◽  
Stop Codon Reassignment

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.

scholarly journals Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

2020 ◽  
Author(s):  
Cristina Andres ◽  
Damir Garcia-Cehic ◽  
Josep Gregori ◽  
Maria Piñana ◽  
Francisco Rodriguez-Frias ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
Stop Codon ◽  
Mutation Rates ◽  
Viral Quasispecies ◽  
Gene Deletions ◽  
Naturally Occurring ◽  
Viral Particles ◽  
Transmission Capability

ABSTRACTThe SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We propose that natural selection has favored a “Don’t burn down the house” strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.

Antimicrobial characterization and safety aspects of the bacteriocinogenicEnterococcus hiraeF420 isolated from Moroccan raw goat milk

2012 ◽  
Vol 58 (5) ◽  
pp. 596-604 ◽  
Author(s):  
F. Achemchem ◽  
R. Cebrián ◽  
J. Abrini ◽  
M. Martínez-Bueno ◽  
E. Valdivia ◽  
...  
Keyword(s):  
Structural Gene ◽  
Food Systems ◽  
Goat Milk ◽  
Mass Spectrometry Analysis ◽  
Decarboxylase Activity ◽  
Strong Activity ◽  
Spectrometry Analysis ◽  
Gram Positive Bacteria ◽  
Naturally Occurring ◽  
Resistance To Heat

The F420 strain, isolated from raw goat milk and identified as Enterococcus hirae , was selected because of its strong activity against Gram-positive bacteria, including Listeria monocytogenes . Interestingly, the F420 strain lacks the virulence genes and decarboxylase activity of histidine, lysine, and ornithine, and it is susceptible to 11 of 14 tested antibiotics, including vancomycin. The antimicrobial compounds produced by E. hirae F420 strain showed high resistance to heat treatment and to acidic and basic pHs. The MALDI-TOF mass spectrometry analysis coupled with the sequence of peptide and structural gene analysis of one of the purified enterocins showed 100% identity with enterocin P (EntP), previously described in E. faecium strains. The structural gene for EntP is located on a plasmid of 65 kb. Other enterocins with molecular mass higher than 7 kDa were also detected. This is the first report of the production of EntP by E. hirae species naturally occurring in foods. The biotechnological characteristics of the F420 strain and its enterocins indicate their potential for application in the control of L. monocytogenes and other undesirable bacteria in food systems.

scholarly journals Identification and characteristics of the structural gene for the Drosophila eye colour mutant sepia, encoding PDA synthase, a member of the Omega class glutathione S-transferases

2006 ◽  
Vol 398 (3) ◽  
pp. 451-460 ◽  
Author(s):  
Jaekwang Kim ◽  
Hyunsuk Suh ◽  
Songhee Kim ◽  
Kiyoung Kim ◽  
Chiyoung Ahn ◽  
...  
Keyword(s):  
Structural Gene ◽  
Stop Codon ◽  
Gel Filtration ◽  
Premature Stop Codon ◽  
Genomic Region ◽  
Gene Encoding ◽  
Colour Mutant ◽  
Eye Colour ◽  
Glutathione S Transferases

The eye colour mutant sepia (se1) is defective in PDA {6-acetyl-2-amino-3,7,8,9-tetrahydro-4H-pyrimido[4,5-b]-[1,4]diazepin-4-one or pyrimidodiazepine} synthase involved in the conversion of 6-PTP (2-amino-4-oxo-6-pyruvoyl-5,6,7,8-tetrahydropteridine; also known as 6-pyruvoyltetrahydropterin) into PDA, a key intermediate in drosopterin biosynthesis. However, the identity of the gene encoding this enzyme, as well as its molecular properties, have not yet been established. Here, we identify and characterize the gene encoding PDA synthase and show that it is the structural gene for sepia. Based on previously reported information [Wiederrecht, Paton and Brown (1984) J. Biol. Chem. 259, 2195–2200; Wiederrecht and Brown (1984) J. Biol. Chem. 259, 14121–14127; Andres (1945) Drosoph. Inf. Serv. 19, 45; Ingham, Pinchin, Howard and Ish-Horowicz (1985) Genetics 111, 463–486; Howard, Ingham and Rushlow (1988) Genes Dev. 2, 1037–1046], we isolated five candidate genes predicted to encode GSTs (glutathione S-transferases) from the presumed sepia locus (region 66D5 on chromosome 3L). All cloned and expressed candidates exhibited relatively high thiol transferase and dehydroascorbate reductase activities and low activity towards 1-chloro-2,4-dinitrobenzene, characteristic of Omega class GSTs, whereas only CG6781 catalysed the synthesis of PDA in vitro. The molecular mass of recombinant CG6781 was estimated to be 28 kDa by SDS/PAGE and 56 kDa by gel filtration, indicating that it is a homodimer under native conditions. Sequencing of the genomic region spanning CG6781 revealed that the se1 allele has a frameshift mutation from ‘AAGAA’ to ‘GTG’ at nt 190–194, and that this generates a premature stop codon. Expression of the CG6781 open reading frame in an se1 background rescued the eye colour defect as well as PDA synthase activity and drosopterins content. The extent of rescue was dependent on the dosage of transgenic CG6781. In conclusion, we have discovered a new catalytic activity for an Omega class GST and that CG6781 is the structural gene for sepia which encodes PDA synthase.

Gene function analysis by amber stop codon suppression: CMBF is a nuclear protein that supports growth and development of Dictyostelium amoebae

2001 ◽  
Vol 305 (4) ◽  
pp. 703-714 ◽  
Author(s):  
Thomas Winckler ◽  
Christine Trautwein ◽  
Christina Tschepke ◽  
Christin Neuhäuser ◽  
Ilse Zündorf ◽  
...  
Keyword(s):  
Gene Function ◽  
Growth And Development ◽  
Nuclear Protein ◽  
Stop Codon ◽  
Function Analysis ◽  
Amber Stop Codon ◽  
Gene Function Analysis

scholarly journals A Concept for Selection of Codon-Suppressor tRNAs Based on Read-Through Ribosome Display in anIn VitroCompartmentalized Cell-Free Translation System

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Atsushi Ogawa ◽  
Masayoshi Hayami ◽  
Shinsuke Sando ◽  
Yasuhiro Aoyama
Keyword(s):  
Stop Codon ◽  
Full Length ◽  
Translation System ◽  
Anticodon Loop ◽  
Ribosome Display ◽  
Amber Stop Codon ◽  
Free Translation ◽  
Translatable Mrna ◽  
Selection Of

Here is presented a concept forin vitroselection of suppressor tRNAs. It uses a pool of dsDNA templates in compartmentalized water-in-oil micelles. The template contains a transcription/translation trigger, an amber stop codon, and another transcription trigger for the anticodon- or anticodon loop-randomized gene for tRNASer. Upon transcription are generated two types of RNAs, a tRNA and a translatable mRNA (mRNA-tRNA). When the tRNA suppresses the stop codon (UAG) of the mRNA, the full-length protein obtained upon translation remains attached to the mRNA (read-through ribosome display) that contains the sequence of the tRNA. In this way, the active suppressor tRNAs can be selected (amplified) and their sequences read out. The enriched anticodon (CUA) was complementary to the UAG stop codon and the enriched anticodon-loop was the same as that in the natural tRNASer.

scholarly journals Laboratory Evolution of Toluene Dioxygenase To Accept 4-Picoline as a Substrate

2001 ◽  
Vol 67 (9) ◽  
pp. 3882-3887 ◽  
Author(s):  
Takeshi Sakamoto ◽  
John M. Joern ◽  
Akira Arisawa ◽  
Frances H. Arnold
Keyword(s):  
Escherichia Coli ◽  
Directed Evolution ◽  
Stop Codon ◽  
Random Mutagenesis ◽  
Product Formation ◽  
Saturation Mutagenesis ◽  
Wild Type ◽  
Laboratory Evolution ◽  
Toluene Dioxygenase ◽  
Naturally Occurring

ABSTRACT We are using directed evolution to extend the range of dioxygenase-catalyzed biotransformations to include substrates that are either poorly accepted or not accepted at all by the naturally occurring enzymes. Here we report on the oxidation of a heterocyclic substrate, 4-picoline, by toluene dioxygenase (TDO) and improvement of the enzyme's activity by laboratory evolution. The biotransformation of 4-picoline proceeds at only ∼4.5% of the rate of the natural reaction on toluene. Random mutagenesis, saturation mutagenesis, and screening directly for product formation using a modified Gibbs assay generated mutant TDO 3-B38, in which the wild-type stop codon was replaced with a codon encoding threonine. Escherichia coli-expressed TDO 3-B38 exhibited 5.6 times higher activity toward 4-picoline and ∼20% more activity towards toluene than wild-type TDO. The product of the biotransformation of 4-picoline is 3-hydroxy-4-picoline; no cis-diols of 4-picoline were observed.

Sign in / Sign up

Export Citation Format

Share Document