Translational bypassing joins the information found within two disparate
open reading frames into a single polypeptide chain. The underlying mechanism
centers on the decoding properties of ...peptidyl-transfer RNA (tRNA) and involves
three stages: take-off, scanning, and landing. In take-off, the
peptidyl-tRNA/messenger RNA (mRNA) complex in the P site of the ribosome
dissociates, and the mRNA begins to move through the ribosome. In scanning, the
peptidyl-tRNA probes the mRNA sliding through the decoding center. In landing,
the peptidyl-tRNA re-pairs with a codon with which it can form a stable
interaction. Although few examples of genes are known that rely on
translational bypassing to couple open reading frames, ribosomes appear to have
an innate capacity for bypassing. This suggests that the strategy of
translational bypassing may be more common than presently appreciated. The best
characterized example of this phenomenon is T4 gene
60
, in which a
complex set of signals stimulates bypassing of 50 nucleotides between the two
open reading frames. In this review, we focus on the bypassing mechanism of
gene
60
in terms of take-off, scanning, and landing.
Programmed −1 ribosomal frameshifting, involving tRNA re‐pairing from an AAG codon to an AAA codon, has been reported to occur at the sequences CGA AAG and CAA AAG. In this study, using the recoding ...region of insertion sequence IS3, we have investigated the influence on frameshifting in Escherichia coli of the first codon of this type of motif by changing it to all other NNA codons. Two classes of NNA codons were distinguished, depending on whether they favor or limit frameshifting. Their degree of shiftiness is correlated with wobble propensity, and base 34 modification, of their decoding tRNAs. A more flexible anticodon loop very likely makes the tRNAs with extended wobble more prone to liberate the third codon base, A, for re‐pairing of tRNALys in the −1 frame.
The picornaviruses' genome consists of a positive-sense ssRNA. Like many picornaviruses, cardioviruses synthesize two distinct polyprotein precursors from adjacent but non-overlapping genome ...segments. Both the L-1ABCD-2A and the 2BC-3ABCD polyproteins are proteolytically processed to yield mature capsid and non-structural proteins, respectively. An unusual translational event, known as 'StopGo' or 'Stop-Carry on', is responsible for the release of the L-1ABCD-2A polyprotein from the ribosome and synthesis of the N-terminal amino acid of the 2BC-3ABCD polyprotein. A common feature of these viruses is the presence of a highly conserved signature sequence for StopGo: -D(V/I)ExNPG(↓)P-, where -D(V/I)ExNPG are the last 7 aa of 2A, and the last P- is the first amino acid of 2B. Here, we report that, in contrast to encephalomyocarditis virus and foot-and-mouth disease virus, a functional StopGo does not appear to be essential for Theiler's murine encephalomyelitis virus viability when tested in vitro and in vivo.
A second mammalian ornithine decarboxylase antizyme was discovered. The deduced protein sequence of the human antizyme2 is 54% identical and 67% similar to human antizyme1 but 99.5% identical to ...mouse antizyme2. Polyamine-regulated programmed ribosomal frameshifting is used in decoding antizyme2 mRNA as it is for antizyme1 mRNA. The mRNA signals for the programmed frameshifting are similar in the mRNAs for the two antizymes. However, in the stimulatory pseudoknot 3′ of the shift site, while the sequences of the stems are highly conserved, the sequences of the loops are divergent. Functional distinctions between antizymes seem likely, but no distinction in the tissue distribution of human antizyme1 and 2 mRNAs was distinguished, though antizyme2 mRNA is 16-fold less abundant than its antizyme1 counterpart. In addition to the previously characterized human antizyme1 mRNA, a second antizyme1 mRNA with an additional 160 nucleotides at its 3′ end was identified, and it has a tissue distribution different from that of the shorter antizyme1 mRNA.
The τ and γ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. γ is two-thirds the size of τ and shares virtually all its amino acid ...sequence with τ . E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between τ and γ . Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller γ protein. In E. coli, ≈ 50% of initiating ribosomes translate the dnaX mRNA conventionally to give τ , but the other 50% shift into the -1 reading frame at a specific site (A AAA AAG) in the mRNA to produce γ . In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or +/- multiples of three As) yields τ . The rest of the population of mRNAs (containing nine +/- nonmultiples of three As) puts ribosomes into the alternative reading frames to produce the γ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.
A 50-nucleotide coding gap divides bacteriophage T4 gene
60 into two open reading frames. In response to
cis-acting stimulatory signals encrypted in the mRNA, the anticodon of the ribosome-bound ...peptidyl tRNA dissociates from a GGA codon at the end of the first open reading frame and pairs with a GGA codon 47 nucleotides downstream just before the second open reading frame. Mutations affecting ribosomal protein L9 or tRNA
2
Gly, the tRNA that decodes GGA, alter the efficiency of bypassing. To understand the mechanism of ribosome slippage, this work analyzes the influence of these bypassing signals and mutant translational components on −1 frameshifting at
G GGA and hopping over a stop codon immediately flanked by two GGA glycine codons (stop-hopping). Mutant variants of tRNA
2
Gly that impair bypassing mediate stop-hopping with unexpected landing specificities, suggesting that these variants are defective in ribosomal P-site codon-anticodon pairing. In a direct competition between −1 frameshifting and stop-hopping, the absence of L9 promotes stop-hopping at the expense of −1 frameshifting without substantially impairing the ability of mutant tRNA
2
Gly variants to re-pair with the mRNA by sub-optimal pairing. These observations suggest that L9 defects may stimulate ribosome slippage by enhancing mRNA movement through the ribosome rather than by inducing an extended pause in translation or by destabilizing P-site pairing.
Two of the bypassing signals, a
cis-acting nascent peptide encoded by the first open reading frame and a stemloop signal located in the 5′ portion of the coding gap, stimulate peptidyl-tRNA slippage independently of the rest of the gene
60 context. Evidence is presented suggesting that the nascent peptide signal may stimulate bypassing by destabilizing P-site pairing.
Where alarm signals function to warn others of the presence of threat, variation is likely to exist in the reliability of alarm signalers. Some signalers, with too low a threshold of excitation, will ...issue false alarms and should be ignored if potential alarm recipients are to maximize energy gains. We exposed juvenile Richardson's ground squirrels to reliable signalers, whose alarm calls were paired with the presentation of a predator model, and unreliable signalers, whose alarm calls were played when no potential predator was present. Call recipients discriminated among individual alarm callers, and reduced responsiveness to callers that had been unreliable. Thus, like primates, squirrels are capable of forming a concept of reliability by associating an individual's identity with that individual's past performance.
Antisense oligonucleotides are used for therapeutic applications and in functional genomic studies. In practice, however, many of the oligonucleotides complementary to an mRNA have little or no ...antisense activity. Theoretical strategies to improve the ‘hit rate’ in antisense screens will reduce the cost of discovery and may lead to identification of antisense oligonucleotides with increased potency. Statistical analysis performed on data collected from more than 1000 experiments with phosphorothioate‐modified oligonucleotides revealed that the oligo‐probes, which form stable duplexes with RNA (ΔGo37 ≤ –30 kcal/mol) and have small self‐interaction potential, are more frequently efficient than molecules that form less stable oligonucleotide–RNA hybrids or more stable self‐structures. To achieve optimal statistical preference, the values for self‐interaction should be (ΔGo37) ≥ –8 kcal/mol for inter‐oligonucleotide pairing and (ΔGo37) ≥ –1.1 kcal/mol for intra‐molecular pairing. Selection of oligonucleotides with these thermodynamic values in the analyzed experiments would have increased the ‘hit rate’ by as much as 6‐fold.
RECODE 2003 Baranov, Pavel V.; Gurvich, Olga L.; Hammer, Andrew W. ...
Nucleic acids research,
01/2003, Letnik:
31, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the ...genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information. The Database is freely available at http://recode.genetics.utah.edu/.
Milagrito, a detector sensitive to very high energy gamma rays, monitored the northern sky from 1997 February through 1998 May. With a large field of view and a high duty cycle, this instrument was ...well suited to perform a search for TeV gamma-ray bursts (GRBs). We report on a search made for TeV counterparts to GRBs observed by BATSE. BATSE detected 54 GRBs within the field of view of Milagrito during this period. An excess of events coincident in time and space with one of these bursts, GRB 970417a, was observed by Milagrito. The excess has a chance probability of 2.8x10-5 of being a fluctuation of the background. The probability for observing an excess at least this large from any of the 54 bursts is 1.5x10-3. No significant correlations were detected from the other bursts.
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