Topic 3: Mutation (mostly) and recombination Introduction MUTATIONS are changes to hereditary material (DNA or RNA) that arise If you are looking at a population and a either by an error in replication, or an error in a repair process. In migrant from another population brings molecular evolution (and population genetics) we are interested in the with it a new genetic variant, then the mechanisms of mutation as it is the ultimate source of novel genetic source of the new variation can be said variation. The scale of the change in DNA or RNA is hugely variable, it to be migration. However its ultimate can be at an individual nucleotide, at the level of an entire gene, part of origin was mutation. a chromosome, or doubling of the entire genome; we call all of these events mutations. We make a strict separation between the processes that generates mutation from the processes that influence the evolutionary fate of a mutation. Darwin made the same logical distinction in the first edition of the Origin of Species: “Whatever the cause may be for each slight difference in the offspring from their parents ⎯and a cause for each must exist⎯ it is the steady accumulation, through natural selection, of such differences, when beneficial to the individual that give rise to all the more important modification of structure …” This distinction has become the central principle of modern evolutionary theory. The processes of mutation and recombination operate at random with respect to the fitness of the molecule, cell or organism. Adaptations arise only as a consequence of the sorting of this random variation by natural selection. The ultimate fate of a mutation is either (i) FIXATION in a population, or (ii) complete loss from a population. During the period of time when a new genetic variant has arisen by mutation but has not yet been fixed or lost in a population, we refer to such genetic variation as POLYMORPHISM. We may use the term polymorphism at the level of the species as well, and, more rarely, above the species level. We use the term MUTATION only to refer to the result of a mutagenic event, and its use makes no claim to the ultimate fate of that mutation. We use the term SUBSTITUTION to refer to a mutation that has completed the process of being fixed in a population. For example, we use the term NUCLEOTIDE SUBSTITUTION to refer to a single nucleotide mutation that grew in frequency in a population until it replaced all other alternative nucleotide variants at that particular site. Mutations may be divided into two very broad categories: 1. Point mutations (nucleotide mutations). 2. Insertion, deletion, or rearrangement of nucleotides. The objective of this lecture is to review the causes and types of mutations. We also introduce the process of recombination, which functions to “shuffle” the pre-existing variants that arose via mutation. The processes that determine the evolutionary fate of such genetic variation will be covered in future lectures. Point mutation 1. Transitions and transversions: Nucleotides can be divided into two classes: (i) purines (A and G) and (ii) pyrimidines (C and T). In many genomes, point mutations are more likely to occur within these classes A G than between them, so their rates are often estimated separately. TV When a mutation is within a class, e.g., from A to G, we say that a TRANSITION (TS) has occurred (blue arrows in figure to the right). When a mutation is between classes, e.g., from A to T, we say a C T TS TRANSVERSION (TV) has occurred (red arrows in figure to the right). If such mutations go to fixation, we can say that either a transitional or transversional substitution has occurred. This class of point mutation applies to all types of nucleotide sequences, coding and non-coding. 2. Synonymous and nonsynonymous: If a mutation occurs in a protein-coding region then they are classified according to its effect on the protein product of the gene. Due to the redundancy of the genetic code, we can classify all mutations into two categories. SYNONYMOUS (SILENT) mutations result in a change among codons that code for the same amino acid; hence, such mutations have no effect on the protein product of the gene. NONSYNONYMOUS (also called REPLACEMENT or MISSENCE) mutations result in a change among codons that code for different amino acids, thus changing the polypeptide encoded by the gene. 3. Nonsense: Another type of mutation in a coding region is one that changes a codon from one that encodes an amino acid to one that encodes a termination signal. This can be a dramatic change if it occurs anywhere other than near the natural end of the polypeptide, as it causes premature end to translation and a truncated polypeptide. Ser Ter Seq 1 ATG CTG GTC AAG TTG AGA AGT TAA ↓ (1) (A) Seq 2 ATG CTG GTC AAG TTG AGA AGC TAA Ser Leu Ter Seq 1 ATG CTG GTC AAG TTG AGA AGT TAA ↓ (2) (B) Seq 2 ATG GTG GTC AAG TTG AGA ACT TAA Val Lys Ter Seq 1 ATG CTG GTC AAG TTG AGA AGT TAA ↓ (3) Seq 2 ATG CTG GTC TAG Ter Two sequences showing the different types of mutations (1) synonymous mutation, (2) nonsynonymous mutation, (3) nonsense mutation, (A) transition, (B) transversion. We can compute the expected proportions of mutation types in coding regions if we are willing to assume all nucleotide mutations occur at the same rate (ts = tv) and all codons are used equally frequently (1/61). Although very unrealistic assumptions for most genes, the expected proportions are useful in giving us a rough idea of the relative “mutational opportunities” for these different types of change. There are 61 sense codons in the standard code, and 9 ways for each to change to another codon (3 alternative nucleotides × 3 codon positions); so there are 61 × 9 = 549 possible mutational pathways to consider. The table below shows the expected proportions of each type of change. Relative proportion of different types of mutations in hypothetical protein coding sequence. Expected number of changes (proportion) Type All 3 Positions 1st positions 2nd positions 3rd positions Total mutations 549 (100) 183 (100) 183 (100) 183 (100) Synonymous 134 (25) 8 (4) 0 (0) 126 (69) Nonsyonymous 392 (71) 166 (91) 176 (96) 50 (27) nonsense 23 (4) 9 (5) 7 (4) 7 (4) Modified from Li and Graur (1991). Note that we assume a hypothetical model where all codons are used equally and that all types of point mutations are equally likely. Molecular basis of point mutation is varied. Replication errors can give rise to mismatches between strands of DNA which can be incorrectly repaired, or proofreading enzymes can simply fail to recognize an error. UV or a variety of chemicals can lead to direct damage to DNA. The process of transcription can leave the non-coding strand vulnerable to damage by, for example, spontaneous decay. Single stranded DNA has much higher rates of spontaneous decay by process such as deamination, as compared with double stranded DNA. Insertion, deletion, or rearrangement 1. Nucleotide indels: The term “INDEL” is an informal way of referring to an insertion or deletion mutation. When nucleotide indels occur within a coding region they cause FRAME-SHIFT mutations. A frame shift mutation usually has a very dramatic effect on the encoded polypeptide, as translation is not terminated, but all the encoded amino acids downstream of the frame-shift are altered. insert T 1↓23 Leu Arg Ser Ter Seq 1 ATG CTG AAG TTG AGA AGT TAA … ↓ Seq 2 ATG CTG ATA GTT GAG AAG TTA AGA Val Glu Lys Leu Arg The insertion of a T causes the amino acids encoded beyond the insertion to change and since no stop codon is found it would continue until one is reached resulting in a longer polypeptide. 2. Genic indels: Entire genes can be inserted or deleted. A gene originating from another organisms genome might be inserted by a process called LATERAL GENE TRANSFER (LGT). A gene may originate from within an organism’s own genome via the process of gene duplication. When gene indels are compared among different lineages the variation is often referred to as gene PRESENCE-ABSENCE POLYMORPHISM. Presence-absence polymorphism is an important area of research; e.g., it is critical to understanding the evolution of bacterial pathogenicity. Specific sets of genes are often involved in conferring the capabilities for pathogenicity. When such sets of genes are located together in a genome they are called PATHOGENICITY ISLANDS, and they often are present in a genome as the result of a LGT event. 3. Chromosomal rearrangements: CHROMOSOMAL MUTATIONS include any change from the normal number and condition of the chromosomes. Entire segments of chromosomes can be DELETED, DUPLICATED, INVERTED, or TRANSLOCATED. The figure to the right illustrates some broad classes of chromosomal rearrangement. Although the examples in this figure are based on eukaryotic chromosomes, chromosomal mutations occur in prokaryotes and viruses as well. As long as the brakes in the DNA do not fall within a gene, chromosomal mutations do not directly alter the gene. However, there is a possible contextual effect on the phenotype of a gene known as the POSITION EFFECT. In such cases the chromosomal context (i.e., what genes are found Figure courtesy of national health museum near it) defines the expression of a gene and a chromosomal mutation that affects the location of such a gene results in a change of its regulation and expression, and ultimately the phenotype of the organism. A classic example of position effect is an eye colour gene in Drosophila.