Mutation and gene editing

📚The biology

Types of gene mutation

A gene mutation is a structural change to a gene at the molecular level: a change in its base sequence. There are three types:

Consequences of base substitutions

A base substitution changes only one codon. Because the genetic code is degenerate — most amino acids have several codons — the consequence depends on the new codon:

• Silent (same-sense): the new codon codes for the same amino acid, so the polypeptide is unchanged. Example: GAA → GAG, both glutamic acid.
• Missense: the new codon codes for a different amino acid, changing one amino acid in the polypeptide. The effect may be negligible, or it may change the protein’s shape and function, as in sickle cell anaemia (D1.2).
• Nonsense: the new codon is a stop codon, so translation ends early and the polypeptide is truncated, usually non-functional.

Single-nucleotide polymorphisms (SNPs) — positions where individuals of a species differ by a single base — are the result of base substitution mutations that have become established in a population. Because of degeneracy, a SNP may or may not change an amino acid.

Consequences of insertions and deletions

mRNA is read in consecutive triplets from the start codon. Inserting or deleting a single base (or any number not a multiple of three) shifts the reading frame for every codon after it: a frameshift. Every amino acid downstream is likely to change, and a stop codon often appears early. The polypeptide is very likely to cease to function.

Insertions or deletions of three bases (or a multiple of three) add or remove whole codons without a frameshift, but major insertions or deletions of many codons are still likely to destroy the polypeptide’s function.

Causes of gene mutation

Mutations arise in two main ways.

Randomness in mutation

Mutations can occur anywhere in the base sequence of a genome. They are random in the sense that their position and effect are not directed: some bases do have a higher probability of mutating than others (for example cytosines that are methylated, or sequences that are frequently repeated), but no position is protected. Importantly, no natural mechanism is known that makes a deliberate change to a particular base in order to change a trait. An organism in a cold environment does not produce mutations for cold tolerance; mutations happen regardless of whether they would be useful, and selection then acts on whatever arises.

Germ cells and somatic cells

Mutation as the source of variation

Gene mutation is the original source of all genetic variation. Every allele of every gene first arose by mutation. Sexual reproduction reshuffles existing alleles into new combinations, but only mutation creates new ones.

For an individual organism, most mutations are either neutral (no effect, for instance silent substitutions or changes in non-coding DNA) or harmful. Only occasionally is a mutation beneficial. But in a species, over the long term, mutation is essential: without a continual supply of new variation, natural selection would have nothing to act on, and populations could not adapt to changing environments (D4.1).

Commercial genetic tests, sold directly to consumers, analyse SNPs to estimate a person’s risk of certain diseases. Without expert interpretation, this information can be problematic: an increased relative risk may sound alarming but still be small in absolute terms; a negative result may give false reassurance because the test examines only some variants; and results can cause anxiety or affect relatives.

Gene knockout AHL

One way to find out what a gene does is to stop it working and see what changes. Gene knockout is a technique in which a gene is altered to make it inoperative in an organism. Comparing the knockout organism with a normal one reveals the gene’s function: if mice lacking a particular gene become obese, for example, that gene is involved in regulating appetite or metabolism. For some model species used in research, such as mice, fruit flies, zebrafish, yeast and the plant Arabidopsis, libraries of knockout organisms are available, with a separate strain for many genes. (You do not need to know the details of how knockouts are made.)

CRISPR–Cas9 gene editing AHL

CRISPR–Cas9 is a technique for editing the genome at a precise location. It uses two components, originally from a bacterial defence system:

• Guide RNA, designed with a sequence of about 20 bases complementary to the target DNA sequence. It directs the enzyme to exactly that place in the genome.
• Cas9, an enzyme (a nuclease) that cuts both strands of the DNA at the site where the guide RNA binds.

After the cut, the cell repairs the break. Repair is often imperfect, introducing small insertions or deletions that knock out the gene. Alternatively, if a piece of DNA with the desired sequence is supplied, the cell can use it as a template during repair, inserting or correcting a sequence. CRISPR is faster, cheaper and far more precise than earlier methods.

An example of successful use: in sickle cell disease and beta thalassaemia, a patient’s own blood stem cells are removed and edited with CRISPR–Cas9 to switch back on the production of foetal haemoglobin, which does not sickle. The edited cells are returned to the patient. In clinical trials most patients no longer needed blood transfusions or suffered painful crises, and the first such therapy was approved for medical use in 2023.

Some potential uses raise serious ethical issues that must be addressed before implementation — above all, editing human embryos or germ cells, which would change the genes of future generations who cannot consent, and which in 2018 was carried out without approval. Scientists in different countries are subject to different regulatory systems, so there is an international effort to harmonize regulation of genome-editing technologies.

Conserved sequences AHL

Conserved sequences are base sequences that are identical or very similar across a species or a group of species. Highly conserved sequences are identical or similar over long periods of evolution, across distantly related organisms — for example the genes for histones, ribosomal RNA and cytochrome c. Two hypotheses account for them:

The two can be distinguished by evidence. If a sequence is conserved because of selection, then silent changes within it (which do not alter the protein) should still accumulate, while changes to amino acids should not. Comparisons of this kind generally support the functional-requirement hypothesis for most conserved coding sequences.