Which Type of Mutation Always Produces a Stop Codon

Which Type of Mutation Always Produces a Stop Codon

Terminate Codon

The amber terminate codon (UAG) is e’er inserted at the N-terminus subsequently a brusk-HA ORF, which prevents the expression of the untagged poly peptide in the uninduced condition.


Methods in Cell Biological science

Expression of Viral Genomes

, in

Matthews’ Establish Virology (Fourth Edition), 2002


Stop codon context

Stop codons
take different efficiencies of termination (UAA>UAG>UGA) and the first, and peradventure the 2d, nucleotide three’ of the end codon acts as an important efficiency determinant (

et al., 1995
). It tin can be seen from
Table 7.5
that either amber (UAG) or opal (UGA) cease codons are read through; at that place are no examples of read through of the natural ochre (UAA) stop codon. However, when the suppressible UAG codon of TMV is replaced by a UAA codon the virus can still replicate and produce mature virions (Ishikawa
et al., 1986
). Unlike with retroviruses, there appears to exist no structural requirements for stop codon suppression in plant systems. The context of the TMV amber stop codon at the end of the 126-kDa ORF has been studied in item past insertion into constructs containing the GUS or other genes which enable read through to be quantitated in protoplasts (Valle
et al., 1992
). This experimental approach has defined the sequence (C/A)(A/C)A.UAG.CAR.YYA (R = purine, Y = pyrimidine) equally the optimal consensus context (Skuzeski
et al., 1991
et al., 1993
). Efficiently recognized stop codons normally take a purine immediately downstream and avoid having a C rest (Fütterer and Hohn, 1996).

Still, an analysis of
Table seven.5
shows that the read-through stop codons identified for plant viruses do not necessarily conform to these contexts determined from
in vitro
systems. As the sequence context differs from that described above, the read through of UAG.G in many of the
and the
suggests that a unlike mechanism might be involved. It is possible that in that location may be a requirement for additional cis-acting sequences such equally a conserved CCCCA motif or repeated CCXXXX motifs beginning 12 to 21 bases downstream of many of these read-through
sites (encounter
Fütterer and Hohn, 1996;
et al., 1997a)
. It may be that other long-distance interactions are involved in the deviations from the experimentally determined optimal contexts for TMV.

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Genome Limerick, Organisation, and Expression

, in

Establish Virology (Fifth Edition), 2014


Terminate Codon Context

Stop codons
take different efficiencies of termination (UAA>UAG>UGA) and in the start, and perchance the 2d, nucleotide 3′ of the finish codon

acts as an important efficiency determinant (Stansfield et al., 1995). It can be seen from
Table 6.8
that either bister (UAG) or opal (UGA) stop codons are read through; in that location are no examples of readthrough of the natural ochre (UAA) finish codon. Withal, when the suppressible UAG codon of TMV is replaced by a UAA codon, the virus tin still replicate and produce mature virions (Ishikawa et al., 1986). Unlike retroviruses, there appear to be no structural requirements for cease codon suppression in plant systems.

Diverse motifs have been recognized to stimulate readthrough (Beier and Grimm, 2001; Harrell et al., 2002). Type I (more often than not UAG CAA UYA) is found in tobamovirus replicase and benyvirus and pomovirus CP extension; Blazon 2 [generally UGA CGG or UGA CUA together with a 3′ structure (Firth et al., 2011)] is found in tobravirus, pecluvirus, furovirus, and pomovirus replicase and furovirus CP extension; and Blazon Iii (generally UAG G together with a compact pseudoknot) is found possibly in luteoviruses and tombusviruses.
Firth et al. (2011)
note that there are some exceptions to these motifs (e.g., enamovirus UGA G) and that there may exist modulation of readthrough by 5′ sequences; this may reverberate the level of readthrough required past different viruses.

The context of the TMV amber stop codon at the stop of the 126-kDa ORF has been studied in item by insertion into constructs containing the GUS or other genes which enable readthrough to exist quantitated in protoplasts (Valle et al., 1992). This experimental approach has defined the sequence (C/A)(A/C)A.UAG.CAR.YYA (R=purine, Y=pyrimidine) equally the optimal consensus context (Skuzeski et al., 1991; Hamamoto et al., 1993; Harrell et al., 2002). Efficiently recognized finish codons normally have a purine immediately downstream and avert having a C residue (Fütterer and Hohn, 1996).

However, an analysis of
Table vi.eight
shows that the readthrough stop codons identified for plant viruses do non necessarily conform to these contexts determined from
in vitro
systems. Equally the sequence context differs from that described higher up, the readthrough of UAG.K in many of the
and the
advise that a different mechanism might be involved. It is possible that there may be a requirement for boosted
cis-interim sequences such as a conserved CCCCA motif or repeated CCXXXX motifs beginning from 12 to 21 bases downstream of many of these readthrough sites (Fütterer and Hohn, 1996; Miller et al., 1997). It may be that other long-distance interactions are involved in the deviations from the experimentally determined optimal contexts for TMV.

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Mutations and Repair

David P.
, …
Michelle R.
, in

Molecular Biological science (Tertiary Edition), 2019

stop codons
were originally identified past mutations in bacteriophage T4. The first i identified was UAG, the amber codon, which received its proper noun in a curiously convoluted manner. The laboratory of Seymour Benzer at Caltech was looking for a mutation that would let a certain kind of bacteriophage mutant to grow. Benzer said that whoever identified the mutation would have it named after him. The mutation was eventually isolated by a pupil named Harris Bernstein. Since “Bernstein” is High german for “amber” UAG was named the amber codon. The second stop codon to exist found (UAA) was called “ochre” to keep the color theme. The third end codon (UGA) is less common and so the utilise of “opal” or less often “umber” is less frequent and non fully settled.

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Principles and Practice of Molecular Therapies

Louise R.
Jerry R.
, in

Neuromuscular Disorders of Infancy, Babyhood, and Adolescence (Second Edition), 2015

Aminoglycoside Therapy

End codons
account for approximately 13% to xv% of DMD mutations.


Effective treatment of this group has potential impact equivalent to exon skipping. Encouraging results were originally obtained in
mice where the aminoglycoside, gentamicin, successfully increased dystrophin expression to about 20%.

Gentamicin-treated mice showed improved histology and protection against contraction-induced injury. Plasma CK levels were also reduced by 70%. Molecular studies of mutation suppression in the
mouse served as a stimulus to attempt a similar approach using gentamicin in DMD patients. The initial clinical trial reported in four DMD patients carrying premature termination codons in the
gene reported no improvement in clinical measures or dystrophin expression. Of interest, serum CK dropped significantly.

A subsequent gentamicin trial reported more than favorable results in a pocket-sized cohort of four subjects.

When gentamicin was given over 2 cycles, each for 6 days with a seven-week hiatus between dosing, muscle biopsy revealed increased dystrophin expression in 3 out of four patients. Serum CK decreased from day two to 24-hour interval vi of the treatment simply afterward came back to the initial levels. No clinically meaningful outcomes were obtained in any of these patients.

A third clinical trial conducted past our group at the Nationwide Children’due south Hospital consisted of a ii-phase protocol.

An initial short-term gentamicin, 14-day dosing study was carried out in 10 DMD boys with proven stop codon mutations. A biological consequence was established with a l% reduction of CK past day 14. The results were cease codon-dependent since serum CK did non change in a control group with frameshift mutations. Having demonstrated a biological effect in the short-term trial, a half-dozen-calendar month written report was designed with weekly or twice-weekly gentamicin administration. Enrollment was dependent on normal hearing and kidney function, and negative testing for the known A1555G mitochondrial Dna mutation in the 12S rRNA gene predisposing to aminoglycoside-induced hearing loss.

Renal function was monitored using cystatin C to avoid fake negative findings related to decreased serum creatinine and creatinine clearance levels in the DMD population.

16 subjects with documented terminate codon mutations received weekly (N=12) or twice weekly (North=4) gentamicin. No patient demonstrated a reject in renal or hearing function except one patient given a miscalculated dose (125% of recommended) for the kickoff four administrations, resulting in a transient loftier-frequency hearing loss that returned to normal inside 3 months. Attributable to the small sample size, weekly and biweekly treated patients were analyzed as 1 grouping. Twelve subjects agreed to pretreatment and posttreatment muscle biopsies. In 3 of nine subjects, dystrophin poly peptide increased to 13.0–15% of wild-type levels (Figure 51.5). In add-on to dystrophin expression in muscle tissue, serum CK was mildly reduced afterwards 6 months of gentamicin handling (9851±2109
U/Fifty to 5316±850
U/L, p=0.04). Additional clinical issue measures were variable. The average muscle score (AMS), which was expected to decline past 0.2 units over 6 months

showed trivial or no modify (pretreatment AMS 5.37±0.39 compared with posttreatment AMS five.35±0.38). Still, no functional outcomes were improved, such as the time to walk 30 feet, climb four standard steps, or stand from a supine position on the flooring.

Figure 51.v.
Dystrophin expression following gentamicin treatment. Pre- and post-gentamicin treatment musculus biopsies demonstrating dystrophin expression by immunofluorescence (IF) using DYS ii Novacastra and Western blot (WB). (A,
B) Pre- and post-handling IF muscle biopsy sections (patient half-dozen) stained with DYS2 antibiotic; side by side WB shows full-length dystrophin at 427
kDa. Gentamicin–induced dystrophin expression to 15.44%. (C,
D) Pre- and post-treatment muscle biopsy (patient 10) IF sections stained with DYS2 antibody; adjacent WB shows total-length dystrophin at 427
kDa. Gentamicin-induced dystrophin increased to xiii.0%. (E,
F) Pre- and post-treatment muscle biopsy sections from patient v without response to gentamicin showing negligible increase after treatment by IF and WB. Scale bar=100

Reprinted from Malik et al., 2010.


Overall, the clinical trial validates that mutation suppression or readthrough tin can potentially exist translated to patients but would require more frequent or higher dosing to produce clinically meaningful results.

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Laboratory Methods in Cell Biology

Edward A.
, in

Methods in Cell Biology, 2013


Step two—Incorporation of PrK in T4Lysozyme at Specific Position Using In Vivo Amber Suppression

stop codon
TAG is introduced at a specific residue position into the plasmid DNA sequence through site-directed mutagenesis. Cotransforming this vector with pEvol PylRS, a plasmid harboring PylRS under a stiff arabinose inducible promoter, prepares the host to incorporate PrK, which is supplied to the growth media thirty min before consecration of expression with arabinose. Refer to

Fig. 4
for the flowchart of step 2.

Effigy 4.
Flowchart for Step 2.

Duration 4 days (including cloning.)


Step 2A—Generating Amber Mutant

2A.1 Perform site-directed mutagenesis to innovate the
stop codon, TAG, for labeling by mutating the desired residual. We similar to follow the mutagenesis protocol described in

Zheng et al. (2004), but kits are bachelor from various companies. In this protocol, we mutated residuum 38 of T4L Lysozyme157Cys to create the plasmid pBAD-T4Lysozyme157Cys38TAG.
2A.2 Transform
Due east. coli
Top10 cells with pEvol PylRS and pBAD-T4Lysozyme157Cys38TAG and plate cells on LB agar plate with ampicillin (antibody resistance marking on expression plasmid for poly peptide) and chloramphenicol (antibiotic resistance marker on pEvol plasmid). Refer to
Fig. five. Incubate plate at 37 °C for overnight.

Pace 2B—Expression of T4Lysozyme157Cys38TAG

2B.1 Inoculate 5 mL of LB medium containing l μg/mL ampicillin and 33 μg/mL chloramphenicol with a unmarried colony from the plate. Permit it grow at 37 °C for overnight.
Tip To backup the clone for time to come expressions set up a glycerol stock (33% glycerol with 66% of overnight civilization) and store at −fourscore °C.
2B.2 Inoculate two ii L culture flasks, each with 500 mL TB media containing fifty μg/mL ampicillin and 33 μg/mL chloramphenicol, with 500 μL of overnight civilization. Abound them at 37 °C until OD600
value reaches 0.2–0.4. Add sterile PrK solution to the growing cultures to a concluding concentration of 1 mM in one of the ii flasks. The civilisation without PrK will serve as a negative control for Amber suppression.
Tip PrK is a stable chemical compound and tin be added right from first into the culture. However, improver of UAA at to the lowest degree 30 min before induction is recommended, which is sufficient time to prime the synthetase to charge tRNAPyl
with PrK.
2B.three Wait until OD600
reaches 0.v–0.half dozen and then add arabinose to a final concentration of 0.02% in both flasks and let them grow for 12–14 h at 30 °C.
2B.4 Harvest the cells past centrifugation at 5000 rpm for 20 min. Discard the supernatant. The pellet can be stored at −80 °C for subsequently processing.

Footstep 2C—Purification of T4Lysozyme157cys38TAG

2C.one Suspend the pellet in 3 volumes of lysis buffer and sonicate to lyse cells.
2C.2 Centrifuge the lysate at 18,000 rpm, 4 °C for i h. Wash 1 mL of Ni-NTA bead volume with lysis buffer and incubate the supernatant for two h at 4 °C on the chaplet.
2C.3 Allow the lysate to pass through and collect Ni-NTA chaplet. Wash beads with 20 bed volumes of lysis buffer followed by ten bed volumes of wash buffer. Elute the protein with iii bed volumes of elution buffer.
2C.4 Analyze the eluate samples of the positive and negative control on SDS Page. After Coomassie staining, the negative sample will show no band at the corresponding height for the protein as compared to the positive sample. This will ostend the successful and selective incorporation of PrK in T4Lysozyme. Refer to
Fig. v.
Tip In the absence of UAA, loose binding of natural amino acids in the AA-binding pocket of PylRS tin can cause Amber suppression, which can account for ascertainment of a less-intense band also at the expected size for the negative command, which is frequently not a concern. If there is an every bit stiff band for the negative control, this might indicate that either site-directed mutagenesis to TAG codon or that Amber suppression was not successful. If protein expression for the positive sample is not satisfactory, expression tin can be tried at different conditions including host strain, temperature, and expression time, also equally increasing concentrations of PrK. Besides, testing culling mutagenesis sites can alleviate the trouble.
2C.5 Concentrate the eluate for the positive sample in a centrifugal filter and substitution the buffer to MonoS buffer A. Precipitate will appear; discard information technology as it contains impurities that are insoluble at pH half-dozen.3 (Steps 2C.5–2C.7 are specific for T4Lysozyme and other proteins might require other purification conditions).
2C.half-dozen Load ane mL of the sample onto a MonoS column using FPLC purification organization. Apply the gradient of 100% MonoS buffer A to 100% MonoS buffer B over 30 min. This purification is based on cation exchange purification. T4Lysozyme elutes at approximately 60% table salt slope.
2C.7 Clarify eluate fractions on SDS PAGE and puddle the fractions containing pure poly peptide. Concentrate the fractions and determine the protein concentration on a UV/VIS spectrophotometer.

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RNA and the Cellular Biochemistry Revisited

Robert E.
, in

RNA Methodologies (Fourth Edition), 2010

Trailer sequence

Beyond the
terminate codon
lies another not-translated area known as the trailer sequence or simply the iii′ UTR. This sequence usually ranges from l–150 nucleotides long, although trailer sequences as long as thousand bases have been reported. Further, unlike mRNA molecules encoding the same polypeptide may differ simply with respect to the length of their 3′ trailer region, of which dihydrofolate reductase mRNA is ane instance (

Will and Dolnick, 1989;
et al., 2006
). Although no part has yet been ascribed to the trailer region, it is believed to influence the stability of the molecule in the cytoplasm due to
cis-interim elements which bind various proteins and that may also influence mRNA localization. It is worth noting that virtually trailer regions manifest a highly conserved AAUAAA sequence within thirty nucleotides of the location where the synthesis of the poly(A) tail volition begin (Proudfoot and Brownlee, 1976). Newer prove suggests that microRNA (miRNA) molecules may target the trailer sequence and, in and then doing, influence gene expression (Lai, 2002).

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Fidelity and Quality Control in Factor Expression

Marina V.
, in

Advances in Poly peptide Chemistry and Structural Biology, 2012


Fidelity of Peptide Release

The intrinsic fidelity of stop-codon recognition past RF1 and RF2 is quite loftier: the catalytic proficiency of the factors (expressed in terms of
Grand) is decreased by three to half dozen orders of magnitude by unmarried base exchanges (Freistroffer et al., 2000). Assuming similar concentrations of RFs and individual aa-tRNAs (Bremer and Dennis, 1987), this predicts a frequency of sense-codon misreading of <

and in most cases shut to 10

. This high allegiance of terminate-codon recognition is achieved without proofreading, presumably in a unmarried selection footstep, and is due to the specific structural lucifer between the recognition motifs of RF1/2 and their cognate
stop codons

Weixlbaumer et al., 2008; Korostelev et al., 2010). For both RFs, the
values contribute shut to three orders of magnitude to the accurateness with relatively small variations between different codons, providing a dominant contribution to the discrimination against near-cognate codons (Freistroffer et al., 2000): in other words, RFs simply do not bind to the sense codons. This is possible because the hydrolysis reaction that leads to peptide release is much slower than the preceding recognition reactions (Freistroffer et al., 2000; Youngman et al., 2007; Kuhlenkoetter et al., 2011), and hence the intrinsic thermodynamic differences between cognate and near-cognate complexes tin exist used in full. Notwithstanding, the
values on near-cognate codons vary significantly as well, accounting for a twofold to more than than yard-fold reduction in the rate of hydrolysis (Freistroffer et al., 2000), suggesting that the construction of the RF1/RF2 complexes on stop codons and sense codons are different. In fact, biochemical studies indicated that stop-codon recognition by RFs induces a structural rearrangement of the decoding center that is productive for peptide release (Youngman et al., 2007). RF3 decreases the fidelity of nearly-cognate codon recognition by RF1 and RF2 (Freistroffer et al., 2000); notwithstanding, the consequence is much larger when a mismatched peptidyl–tRNA is present in the P site (Zaher and Light-green, 2009a,b).

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Inherited metabolic disease

, in

Clinical Biochemistry: Metabolic and Clinical Aspects (Tertiary Edition), 2014

Other molecular therapies

Nonsense mutations create a premature
stop codon
thus producing a truncated, unremarkably non-operation, protein. It is estimated that nonsense mutations business relationship for 5–15% of disease-causing mutations. It was recognized that aminoglycosides could influence the ability to read through the premature stop codon and so produce a normal length functioning protein. Chiefly, this affects only premature, and not normal, stop codons. Subsequent evolution of minor read-through molecules has shown that boosting the affected enzyme by small amounts can significantly reduce disease severity. Clinical trials in cystic fibrosis have been promising and potential trials for patients with IMDs secondary to nonsense mutations are currently existence planned.

Exon skipping is some other technique to heave functioning protein production, by masking the faulty exon harboring a frameshift mutation, using small-scale pieces of Deoxyribonucleic acid (antisense oligonucleotides). Bypassing the frameshift mutation facilitates reading of the remaining exons. Animal piece of work confirmed the principal in mouse models and now clinical trials have started in Duchenne muscular dystrophy and Huntington disease.

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RNA Modification

, …
, in

Methods in Enzymology, 2015



All naturally occurring ORF
stop codons, UAA, UGA, and UAG, contain a uridine in the start position. To study Ψ-mediated nonsense suppression, we cull a plasmid containing a C-terminally tagged (3C-HA-HIS6X-Protein A) reporter factor,

TRM4, which, when transformed into yeast cells, is highly expressed (Chernyakov, Whipple, Kotelawala, Grayhack, & Phizicky, 2008). Using PCR-based site-directed mutagenesis, we then innovate a PTC into the ORF of
at codon 602 (TTT-to-TAA change), as shown in
Fig. one.

Figure i.
Schematic representation of pTRM4-TAA
expression plasmid. The wild-type
gene is mutated at F602 position (TTT converted to TAA) to generate a premature termination codon (PTC) (indicated). The plasmid-borne
gene is fused with a multicomponent C-terminal tag to facilitate the detection and purification of full-length Trm4 product. The tag contains a 3C protease cleavage site that tin can be used to release the purified poly peptide from the tag. The expression of
gene is under the control of Gal promoter, which is galactose-inducible.
is an auxotroph selective marker in yeast. This is a loftier copy 2
μ plasmid.

To introduce Ψs into PTC, we generate an artificial box H/ACA guide RNA (based on yeast
box H/ACA RNA) (Ma et al., 2005), in which the guide sequences are designed to target the uridine of the PTC codon for pseudouridylation. The artificial box H/ACA RNA is amplified by PCR with four overlapping primers. The get-go primer (snR81-TRM4-TAA-F1) is a sense forrard primer and the other three (snR81-TRM4-TAA-R1,
snR81-TRM4-TAA-R2, and
snR81-TRM4-TAA-R3) are antisense reverse primers (Figs. two and 3). Within each primer, at that place is a tract of nucleotides that represents the guide sequence (indicated as guide1, guide1′, guide2, and guide2′ in
Figs. 2 and 3). Guide1 and guide1′ form the first (5′) pseudouridylation pocket, and guide2 and guide2′ form the 2d (iii′) pseudouridylation pocket in the guide RNA (Fig. 2). The guide sequences in both pseudouridylation pockets of the artificial guide RNA (snR81-TRM4-TAA) are designed to target the PTC site in
TRM4-TAA. Like to
construct, a control
guide RNA construct is generated past PCR with iv overlapping primers,
snR81-Control-R2, and
snR81-Control-R3. The guide sequences in
snR81-Control do non target the PTC of
and have no targets in yeast genome.

Figure 2.
Schematic representation of box H/ACA guide RNA and its interaction with its substrate RNAs. The guide RNA (ruby) folds into a hairpin-hinge-hairpin-tail construction. The pseudouridylation pockets responsible for target site specification are the internal loops (thick ruby lines) within the hairpin structures. The H and ACA boxes and the guide sequences (guide1, guide1′, guide2, and guide2′) are indicated. The mRNA substrates (bluish) are paired with the guide sequences of the guide RNA, every bit indicated by short lines between strands. The pseudouridylated uridine (Ψ) and its downstream residue (Due north) in the mRNA substrates are left unpaired. The 4 overlapping primers, used for guide RNA construction (see text), are also shown (black lines). The dotted black lines denote specific guide sequences.

Effigy iii.
The strategy for cloning artificial
using four primers overlapping PCR (also run into
Fig. 2). The structure is based on naturally occurring yeast
box H/ACA RNA. The v′-nigh primer is sense-strand sequence (forward), while the other primers have antisense sequences (reverse). The guide sequences (guide1, guide1′, guide2, and guide2′) are changed to base of operations pair with substrate mRNAs, while the residuum of the
sequence remain unchanged. The amplified artificial
is digested with
BamHowdy and
HindIII and subsequently cloned into pSEC plasmid under the control of the Gal promoter. LEU2 is an auxotroph selective marker in yeast.

Finally, yeast BY4741 strain is cotransformed with the
reporter and one of the guide RNA constructs (control or PTC-specific). It is expected that only the PTC-specific guide RNA (snR81-TRM4-TAA) will directly
mRNA pseudouridylation at the PTC codon.

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, in

Encyclopedia of Genetics, 2001

Other Compensatory Changes Outcome in Suppression

When the ribosome reaches a
stop codon, translational release factors facilitate hydrolysis of the fully synthesized protein from the peptidyl-tRNA. In improver to genetic suppression through altered tRNAs, variants of release factors have besides been identified that produce suppression phenotypes. Mutations are primarily within the C-terminal regions of the release factors, and likely prevent sequence-dependent recognition of stop codons.

Certain ribosomal proteins and regions of rRNA accept long been implicated in translational accuracy command. For instance, mutations in small subunit proteins S4, S5, and S12 lead to ribosomes that are either hyperaccurate or error-decumbent. Errors in protein synthesis include increased levels of stop codon readthrough, frameshifting, and missense errors. Codon-specific suppression variants accept also been identified inside ribosomal components. A single C to A substitution inside the small subunit rRNA (Eastward. coli
C1054A) results in UGA readthrough without affecting other termination events or causing missense or frameshift suppression. This mutation decreases the bounden affinity of release cistron two for the ribosome, resulting in the observed genetic suppression.

Finally, suppression of genetic mutations can be the result of compensatory changes in partner molecules. Mitochondria interpret a limited number of proteins from a minor genome that likewise contains a complete fix of tRNA genes. A nucleotide substitution in the acceptor stem of yeast mitochondrial tRNAAsp
was shown recently to exist suppressed by a variant of aspartyl-tRNA synthetase (AspRS). The unmarried amino acid subsitution in the nuclear-encoded AspRS enzyme is in a region known to contact the acceptor stem of its cognate tRNAAsp. New contacts between the variant tRNAAsp
and AspRS event in enhanced aminoacylation efficiency and genetic suppression of the tRNA defect.

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Which Type of Mutation Always Produces a Stop Codon

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