Suppressor mutation

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A suppressor mutation is a second mutation that alleviates or reverts the phenotypic effects of an already existing mutation in a process defined synthetic rescue. Genetic suppression therefore restores the phenotype seen prior to the original background mutation. [1] Suppressor mutations are useful for identifying new genetic sites which affect a biological process of interest. They also provide evidence between functionally interacting molecules and intersecting biological pathways. [2]

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Intragenic vs. intergenic suppression

Intragenic suppression

Intragenic suppression results from suppressor mutations that occur in the same gene as the original mutation. In a classic study, Francis Crick (et al.) used intragenic suppression to study the fundamental nature of the genetic code. From this study it was shown that genes are expressed as non-overlapping triplets (codons). [1]

Researchers showed that mutations caused by either a single base insertion (+) or a single base deletion (-) could be "suppressed" or restored by a second mutation of the opposite sign, as long as the two mutations occurred in the same vicinity of the gene. This led to the conclusion that genes needed to be read in a specific "reading frame" and a single base insertion or deletion would shift the reading frame (frameshift mutation) in such a way that the remaining DNA would code for a different polypeptide than the one intended. Therefore, researchers concluded that the second mutation of opposite sign suppresses the original mutation by restoring the reading frame, as long as the portion between the two mutations is not critical for protein function. [1]

In addition to the reading frame, Crick also used suppressor mutations to determine codon size. It was found that while one and two base insertions/deletions of the same sign resulted in a mutant phenotype, deleting or inserting three bases could give a wild type phenotype. From these results it was concluded that an inserted or deleted triplet does not disturb the reading frame and the genetic code is in fact a triplet. [1]

Intergenic suppression

Intergenic (also known as extragenic) suppression relieves the effects of a mutation in one gene by a mutation somewhere else within the genome. The second mutation is not on the same gene as the original mutation. [2] Intergenic suppression is useful for identifying and studying interactions between molecules, such as proteins. For example, a mutation which disrupts the complementary interaction between protein molecules may be compensated for by a second mutation elsewhere in the genome that restores or provides a suitable alternative interaction between those molecules. Several proteins of biochemical, signal transduction, and gene expression pathways have been identified using this approach. Examples of such pathways include receptor-ligand interactions as well as the interaction of components involved in DNA replication, transcription, and translation. [1]

These Intergenic suppressions are also likely to persist in the population. When these compensatory mutations are established in organisms like E. coli making it resistant to the drug due to the presence of a drug, and the drug usage is halted, the resistant strains are not easily able to evolve back into strains that can then once again be sensitive to the drug they had incurred resistance to. [3] These strains are likely not subject to losing these compensatory mutations and which would greatly decrease the fitness in the strain resulting in the intermediate strains. These intermediate strains are subjected to bottlenecking and thus making it difficult for the alleles to be reverted prior to Intergenic suppressions. Consequently, when drugs are halted it can be seen that these mutations are likely to persist in the population.

Tevenphage Tevenphage.svg
Tevenphage

Suppressor mutations also occur in genes that code for virus structural proteins. To create a viable phage T4 virus (see image), a balance of structural components is required. An amber mutant of phage T4 contains a mutation that changes a codon for an amino acid in a protein to the nonsense stop codon TAG (see stop codon and nonsense mutation). If, upon infection, an amber mutant defective in a gene encoding a needed structural component of phage T4 is weakly suppressed (in an E. coli host containing a specific altered tRNA – see nonsense suppressor), it will produce a reduced number of the needed structural component. As a consequence few if any viable phage are formed. However, it was found that viable phage could sometimes be produced in the host with the weak nonsense suppressor if a second amber mutation in a gene that encodes another structural protein is also present in the phage genome. [4] It was found that the reason the second amber mutation could suppress the first one is that the two numerically reduced structural proteins would now be in balance. For instance, if the first amber mutation caused a reduction of tail fibers to one tenth the normal level, most phage particles produced would have insufficient tail fibers to be infective. However, if a second amber mutation is defective in a base plate component and causes one tenth the number of base plates to be made, this may restore the balance of tail fibers and base plates, and thus allow infective phage to be produced. [4]

Revertant

In microbial genetics, a revertant is a mutant that has reverted to its former genotype or to the original phenotype by means of a suppressor mutation, or else by compensatory mutation somewhere in the gene (second site reversion).

See also

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Genetic code Rules by which information encoded within genetic material is translated into proteins.

The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.

Stop codon Codon that marks the end of a protein-coding sequence

In molecular biology, a stop codon is a codon that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.

A genetic screen or mutagenesis screen is an experimental technique used to identify and select for individuals who possess a phenotype of interest in a mutagenized population. Hence a genetic screen is a type of phenotypic screen. Genetic screens can provide important information on gene function as well as the molecular events that underlie a biological process or pathway. While genome projects have identified an extensive inventory of genes in many different organisms, genetic screens can provide valuable insight as to how those genes function.

Frameshift mutation Mutation that shifts codon alignment

A frameshift mutation is a genetic mutation caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame, resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein. A frameshift mutation is not the same as a single-nucleotide polymorphism in which a nucleotide is replaced, rather than inserted or deleted. A frameshift mutation will in general cause the reading of the codons after the mutation to code for different amino acids. The frameshift mutation will also alter the first stop codon encountered in the sequence. The polypeptide being created could be abnormally short or abnormally long, and will most likely not be functional.

In genetics, a nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product. The functional effect of a nonsense mutation depends on the location of the stop codon within the coding DNA. For example, the effect of a nonsense mutation depends on the proximity of the nonsense mutation to the original stop codon, and the degree to which functional subdomains of the protein are affected.

<i>Escherichia virus T4</i> species of virus

Escherichia virus T4 is a species of bacteriophages that infect Escherichia coli bacteria. It is a double-stranded DNA virus in the subfamily Tevenvirinae from the family Myoviridae. T4 is capable of undergoing only a lytic lifecycle and not the lysogenic lifecycle. The species was formerly named T-even bacteriophage, a name which also encompasses, among other strains, Enterobacteria phage T2, Enterobacteria phage T4 and Enterobacteria phage T6.

Sup35p is the Saccharomyces cerevisiae eukaryotic translation release factor. More specifically, it is the yeast eukaryotic release factor 3 (eRF3), which forms the translation termination complex with eRF1. This complex recognizes and catalyzes the release of the nascent polypeptide chain when the ribosome encounters a stop codon. While eRF1 recognizes stop codons, eRF3 facilitates the release of the polypeptide chain through GTP hydrolysis.

Silent mutation

Silent mutations are mutations in DNA that do not have an observable effect on the organism's phenotype. They are a specific type of neutral mutation. The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are not always silent, nor vice versa. Synonymous mutations can affect transcription, splicing, mRNA transport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent. The substrate specificity of the tRNA to the rare codon can affect the timing of translation, and in turn the co-translational folding of the protein. This is reflected in the codon usage bias that is observed in many species. Mutations that cause the altered codon to produce an amino acid with similar functionality are often classified as silent; if the properties of the amino acid are conserved, this mutation does not usually significantly affect protein function.

This is a list of topics in molecular biology. See also index of biochemistry articles.

Genetics, a discipline of biology, is the science of heredity and variation in living organisms.

In genetics, complementation occurs when two strains of an organism with different homozygous recessive mutations that produce the same mutant phenotype have offspring that express the wild-type phenotype when mated or crossed. Complementation will ordinarily occur if the mutations are in different genes. Complementation may also occur if the two mutations are at different sites within the same gene, but this effect is usually weaker than that of intergenic complementation. In the case where the mutations are in different genes, each strain's genome supplies the wild-type allele to "complement" the mutated allele of the other strain's genome. Since the mutations are recessive, the offspring will display the wild-type phenotype. A complementation test can be used to test whether the mutations in two strains are in different genes. Complementation ordinarily will occur more weakly or not at all if the mutations are in the same gene. The convenience and essence of this test is that the mutations that produce a phenotype can be assigned to different genes without the exact knowledge of what the gene product is doing on a molecular level. The complementation test was developed by American geneticist Edward B. Lewis.

This glossary of genetics is a list of definitions of terms and concepts commonly used in the study of genetics and related disciplines in biology, including molecular biology and evolutionary biology. It is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term. For related terms, see Glossary of evolutionary biology.

A nonsense suppressor is a factor which can inhibit the effect of the nonsense mutation. Nonsense suppressors can be generally divided into two classes: a) a mutated tRNA which can bind with a termination codon on mRNA; b) a mutation on ribosomes decreasing the effect of a termination codon. It's believed that nonsense suppressors keep a low concentration in the cell and do not disrupt normal translation most of the time. In addition, many genes do not have only one termination codon, and cells commonly use ochre codons as the termination signal, whose nonsense suppressors are usually inefficient.

Temperature-sensitive mutants are variants of genes that allow normal function of the organism at low temperatures, but altered function at higher temperatures. Cold sensitive mutants are variants of genes that allow normal function of the organism at higher temperatures, but altered function at low temperatures.

Lethal alleles are alleles that cause the death of the organism that carries them. They are usually a result of mutations in genes that are essential for growth or development. Lethal alleles may be recessive, dominant, or conditional depending on the gene or genes involved. Lethal alleles can cause death of an organism prenatally or any time after birth, though they commonly manifest early in development.

The phage group was an informal network of biologists centered on Max Delbrück that contributed heavily to bacterial genetics and the origins of molecular biology in the mid-20th century. The phage group takes its name from bacteriophages, the bacteria-infecting viruses that the group used as experimental model organisms. In addition to Delbrück, important scientists associated with the phage group include: Salvador Luria, Alfred Hershey, Seymour Benzer, Charles Steinberg, Gunther Stent, James D. Watson, Frank Stahl, and Renato Dulbecco.

Synthetic rescue refers to a genetic interaction in which a cell that is nonviable, sensitive to a specific drug, or otherwise imparied due to the presence of a genetic mutation becomes viable when the original mutation is combined with a second mutation in a different gene. The second mutation can either be a loss-of-function mutation or a gain-of-function mutation.

Epistasis refers to genetic interactions in which the mutation of one gene masks the phenotypic effects of a mutation at another locus. Systematic analysis of these epistatic interactions can provide insight into the structure and function of genetic pathways. Examining the phenotypes resulting from pairs of mutations helps in understanding how the function of these genes intersects. Genetic interactions are generally classified as either Positive/Alleviating or Negative/Aggravating. Fitness epistasis is positive when a loss of function mutation of two given genes results in exceeding the fitness predicted from individual effects of deleterious mutations, and it is negative when it decreases fitness. Ryszard Korona and Lukas Jasnos showed that the epistatic effect is usually positive in Saccharomyces cerevisiae. Usually, even in case of positive interactions double mutant has smaller fitness than single mutants. The positive interactions occur often when both genes lie within the same pathway Conversely, negative interactions are characterized by an even stronger defect than would be expected in the case of two single mutations, and in the most extreme cases the double mutation is lethal. This aggravated phenotype arises when genes in compensatory pathways are both knocked out.

Epistasis Dependence of a gene mutations phenotype on mutations in other genes

Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears. Epistatic mutations therefore have different effects on their own than when they occur together. Originally, the term epistasis specifically meant that the effect of a gene variant is masked by that of a different gene.

Charles M. Steinberg was an immunobiologist and permanent member of the Basel Institute for Immunology. He was a former student of Max Delbrück. Notably he hosted Richard Feynman at Caltech when the physicist studied molecular biology, leading Feynman to remark that Charlie was “...the smartest guy I know”. He was instrumental in the discovery of V(D)J recombination, bacteriophage genetics as part of the phage group and co-discoverer of the amber-mutant of the T4 bacteriophage that led to the recognition of stop codons.

References

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