Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes

@article{Malys2011ShineDalgarnoSO,
  title={Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes},
  author={Naglis Malys},
  journal={Molecular Biology Reports},
  year={2011},
  volume={39},
  pages={33-39}
}
  • N. Malys
  • Published 2011
  • Biology
  • Molecular Biology Reports
Translation initiation is governed by a limited number of mRNA sequence motifs within the translation initiation region (TIR). In bacteria and bacteriophages, one of the most important determinants is a Shine-Dalgarno (SD) sequence that base pairs with the anti-SD sequence GAUCACCUCCUUA localized in the 3′ end of 16S rRNA. This work assesses a diversity of TIR features in phage T4, focusing on the SD sequence, its spacing to the start codon and relationship to gene expression and essentiality… 
Molecular Study of Cellulase Gene Transcription Regulatory Elements via EMS Mutagenesis in a Novelthermophilic Cellulytic Bacillus sp .
TLDR
Sequencing results of cellulase gene transcription regulatory elements postEMS mutagenesis showed a change in the nucleotides sequence, accompanied by a significant increase in cellulase quantitative activity and total cellulase activity.
Identifying Escherichia Coli factors that selectively bind the mRNA of secreted proteins
TLDR
It was found that the least enzyme involved in functions associated with mRNA translation in the case of in E. coli and thus involved in the regulation of mRNA products is 3-isopropylmalate dehydratase enzyme, while the ATP-dependent helicase Lhr also has a role in mRNA contro.
The plasmid vectors, pBS2ndd and pBS3ndd, for versatile cloning with low background in Escherichia coli
TLDR
Two plasmids, pBS2ndd and pBS3ndd, which resistant to ampicillin and kanamycin respectively, were developed in this study as more advantageous cloning vector and were used to clone PCR product samples for DNA sequencing with low-background and versatile cloning strategies.
Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming
TLDR
Integer Programming is used to identify the A-site location as a function of the fragment’s size and its 5′ end reading frame in Ribo-Seq data generated from S. cerevisiae and mouse embryonic stem cells and increases the signal-to-noise ratio of underlying biological signals associated with translation elongation at the codon length scale.
Inferring features from 5'UTR sequences to Translation Initiation Rates in S.cerevisiae
TLDR
Predicting the exact initiation rates originating from stochastic models is not a trivial task and that many features are of no to little importance.
Unsupervised statistical discovery of spaced motifs in prokaryotic genomes
TLDR
The approach to detection of significant motif pairs can complement existing motif-finding techniques in discovery of novel functional sequence motifs in complete genomes.
Gene Expression Engineering
TLDR
This chapter will evaluate methods for controlling gene expression in the context of heterologous genes, endogenous genes, pathway expression and provide insight into new paradigms for flux control through gene expression circuits.
Chapter 2 Gene Expression Engineering
TLDR
This chapter will evaluate methods for controlling gene expression in the context of heterologous genes, endogenous genes, pathway expression and provide insight into new paradigms for flux control through gene expression circuits.
Clinical Pharmacogenetics Implementation Consortium Guideline for the Use of Aminoglycosides Based on MT‐RNR1 Genotype
TLDR
Use of aminoglycosides should be avoided in individuals with an MT‐RNR1 variant associated with an increased risk of am inoglycoside‐induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available.
Characterization and mechanism of the effects of Mg–Fe layered double hydroxide nanoparticles on a marine bacterium: new insights from genomic and transcriptional analyses
TLDR
The mechanism underlying the physiological effects of Mg–Fe layered double hydroxide nanoparticles on the marine bacterial species Arthrobacter oxidans KQ11 was investigated and will aid in achieving improved marine dextranase production, and even improve such activities in other marine microorganisms.
...
...

References

SHOWING 1-10 OF 50 REFERENCES
An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli
The 5' ends of many bacterial transcripts are important in determining mRNA stability. A series of Shine-Dalgarno (SD) sequence changes showed that the complementarity of the SD sequence to the
Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction.
TLDR
It is found that mutations reducing the SD complementarity by one or two nucleotides diminish translational efficiency only if ribosome binding is impaired by the structure of the messenger, and in the absence of an inhibitory structure, these mutations have no effect.
Activation of RegB endoribonuclease by S1 ribosomal protein requires an 11 nt conserved sequence
TLDR
The data support the notion that RegB alone recognizes only the trinucleotide GGA, which it cleaves very inefficiently, and that stimulation of RegB activity by S1 depends on the nucleotide immediately 3′ to -GGA-.
Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs.
TLDR
A systematic study by inserting two series of synthetic RBSs of varying spacing and SD sequence into a plasmid vector containing the chloramphenicol acetyltransferase gene demonstrated an optimal aligned spacing of 5 nt for both series.
Post-transcriptional control of bacteriophage T4 gene 25 expression: mRNA secondary structure that enhances translational initiation.
TLDR
Results show that the existence of a hairpin structure that includes SD1 and SD2 sequences and brings the SD3, the most typical of these Shine-Dalgarno sequences, to a favourable spacing with the initiation codon of gene 25, and conclude that this structure enhances translation initiation.
Translation initiation region sequence preferences in Escherichia coli
TLDR
It is found that during bacterial growth at 37°C, a six-nucleotide SD (AGGAGG) is more efficient than shorter or longer sequences, and the A/U-rich enhancer contributes strongly to the efficiency of initiation, having the greatest stimulatory effect in the exponential growth phase of the bacteria.
Bacteriophage T4 RegB endoribonuclease.
  • M. Uzan
  • Biology
    Methods in enzymology
  • 2001
The sequences and activities of RegB endoribonucleases of T4-related bacteriophages.
TLDR
Functional studies using plasmid-phage systems indicate that RegB nucleases of phages T4, RB69, TuIa and RB49 exhibit different activity towards GGAG and GGAU motifs in the specific locations, and it is expected that the availability of the different phylogenetic variants of RegB may help to localize the amino acid determinants that contribute to the specificity and cleavage efficiency of this processing enzyme.
Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs.
TLDR
It is shown here that RegB is required for the degradation of bulk T4 early mRNA, and that the GGAG-carrying RNAs that are uncut during T4 infection are not substrates, whatever the period of the T4 cycle when the transcripts are made.
...
...