DNA Mutations and Mutagens

DNA Mutations

• Change in DNA sequence, resulting from replication errors or DNA damage
• Can affect the protein product if it is a mutation in a protein-coding region
• Mechanisms exist to correct mutations, but errors can bypass proofreading by DNA polymerase
• Mistakes occur frequently during DNA replication and other processes
• DNA sequence changes can be unavoidable
• Few mechanisms can fix mistakes, such as replacing a wrongly paired base

Causes of Mutation

• Spontaneous mutations occur naturally due to replication errors or mismatches
  • No known cause or triggers
• Induced mutations occur when an organism's DNA is exposed to a mutagen
  • Mutagens are chemical or physical agents capable of inducing DNA changes

Mutagens

• Physical agents like radiation and sunlight
  • Ionizing radiation is dangerous because it induces changes in germ cells, altering genetic material that can be transmitted across generations and cause double-strand breaks (DSB)
  • Non-ionizing radiation causes vibrations in atoms, leading to heat
• Chemical agents like cigarette smoke, junk food, fast food preservatives, and grilled food
• Biological agents like Human papilloma virus and Helicobacter pylori cause double-strand breaks

Point Mutation

• Base substitution where single bases are substituted
• Arise when bases pair with an inappropriate partner during DNA replication
  • Example: A pairs with C or G pairs with T
• Transitions: Purine/pyrimidine replaced by another
• Transversions: Purine substituted for pyrimidine

Possible Effects of Point Mutation

• Silent Mutation: Nucleotide change that still results in the same amino acid
• Missense Mutation: Change of a nucleotide in a codon of protein coding region results in new codon for a different amino acid
• Nonsense Mutation: Codon changed to a stop codon, resulting in early termination of protein synthesis

Missense Mutation Causing Sickle Cell Anemia

• A missense mutation changes the template strand sequence, CAC which should be CTC
• Normal conversion would be CTC to GAG, coding for Glutamic Acid
• In sickle cell anemia, CAC becomes GUG, coding for Valine
• Red blood cells assume a sickle shape

Insertion & Deletion

• Insertions: Addition of one or more base pairs
• Deletions: Removal of one or more base pairs
• Frameshift Mutations: Results from the loss or addition of a single nucleotide that is not multiples of three

DNA Repair

• Direct Repair: Enzyme recognizes and directly converts an incorrect alteration in DNA structure
• Base Excision Repair: Corrects a base damaged by oxidation or chemical modification that are not significant as distortions to DNA helix
  • DNA glycosylase recognizes and excises a damaged base
• Nucleotide Excision Repair: Removes bulky lesions caused by UV radiation or damage from chemotherapeutic agents
  • Deficiency results in human skin diseases
  • Involves removal of several nucleotides
• Mismatch Repair: Biological pathway with specificity for base-base mismatches and insertion/deletion mispairs generated during DNA replication and recombination
  • Mismatch is recognized, repair mechanisms excise or remove the mismatch, filling the gap

Nucleotide Excision Repair (NER) Deficiency

• Results in inability to repair UV-induced lesions, leading to susceptibility to skin diseases

Xeroderma Pigmentosum

• Increased sensitivity to sunlight
• May have pigmentation abnormalities
• Many premalignant lesions
• High predisposition to skin cancer

Cancer

• Disease resulting in uncontrollable growth of body cells that spread to other parts of the body
• Mostly arises due to changes in DNA

HeLa Cells

• Henrietta Lacks' cells came from the human source who died from cervical cancer
• "Immortal cells" used to study cancer
• First immortal human cell line able to reproduce indefinitely
• Used to study the effects of toxins used to kill cancer cells
• Line of cells were durable and prolific, obtained during Henrietta's cancer treatment by Dr. George Gey in 1951

Carcinogenesis

• Normal/healthy cells transform into cancer cells through mutations
• Stages: initiation, promotion, and progression

Carcinogenesis Stages

• Initiation: Exposure of cells to a sufficient dose of a carcinogenic agent, causing permanent DNA damage (mutations)
  • Substances initiate DNA damage
  • Carcinogens cause DNA damage resulting in irreversible genetic alteration that cannot be repaired
• Promotion: Promoters can induce tumors to arise from initiated cells
  • Transformed/initiated cells are stimulated to divide
  • Environment within and outside the cell influences cancer development
  • Transformation of cells into malignancy involves more than one step requiring repeated exposures
• Progression: Final stage with genetic and phenotypic changes
  • Proliferation occurs involving an increase in tumor size
  • Cells may undergo further mutations that improve or aggravate the invasive and metastatic potential

Genome Evolution

• Processes that lead to variation among populations and species
• First step is change in the DNA sequence referred to as mutation

Mutation in Genome Evolution

• Arises from a change in the genetic sequence which serves as a cause of diversity among organisms
• May be introduced through replication error or DNA damage
• Characterized by effect on the polypeptide product as synonymous and non-synonymous mutation if it happens in a protein-coding region

Synonymous vs. Non-Synonymous Mutation

• Synonymous Mutation: No change in amino acid sequence
  • Accumulate more rapidly
  • May be a silent mutation
• Non-Synonymous Mutation: Change in amino acid sequence
  • Missense mutation: Resulting codon codes for a different amino acid, changing the sequence
  • Nonsense mutation: Substitution mutation which results in a stop codon

Fixation of Mutation

• Mutation becomes a feature of entire phylogenetic unit
• Usually nucleotide substitutions

Regulatory Sequences

• Contain information on the timing (when) and intensity of gene expression

Retroposition

• Reverse-transcription of mRNAs with the cDNAs being inserted into the genome
  • Generates retroposed gene copies that do not have introns and lack regulatory elements

Duplication

• DNA-Based Duplication: Copying and pasting of DNA sequence from one genomic region to another

Gene Duplication

• Gene transcript is used to generate retroposed gene copies, which are either functional or non-functional
• Whole Genome Duplication (WGD): Offspring having twice the number of chromosomes in each cell as their diploid parents

Duplications are formed by unequal crossing-over and rolling-circle amplification

• Unequal Crossing Over: Homologous chromosomes are misaligned
• Rolling-Circle Amplification: A short DNA/RNA primer is amplified to form along single-stranded DNA/RNA using a circular DNA template and special DNA/RNA polymerases

De Novo Origination

• Emergence of genes from a non-functional DNA sequence that was previously not a gene
• A mutation from a previously non-functional sequence led to the formation of new gene

Horizontal Gene Transfer

• New genes can be generated from pre-existing genes
• Exchange of genes between genomes from distantly related taxa
  • DNA can be acquired from the genome of one cell to another
• Serves as a major mechanism for the addition of new genes to prokaryotic genomes
  • Horizontal gene transfer is one of the leading mechanisms for pathogenic bacteria to acquire antibiotic resistance

Gene Recombination

• Modification of existing exons or domains to produce new chimeric genes
• Gene recombination involves the combination of portions of existing coding sequences to create a new gene

Recombinant Gene Creation

• Jingwei is a young chimeric processed gene identified in the common ancestor of two African Drosophila species
• Formed due to the recombination of a retroposed alcohol dehydrogenase (Adh)-derived enzymatic domain, with the yellow emperor (Ymp) hydrophobic domain of the Ymp gene

New Gene Regulatory Systems

• A transcription regulatory system must be acquired to ensure certain temporal and spatial expression patterns
  • e.g. temporal regulation (a gene is only expressed at a specific time) and spatial are spatial regulation (a gene is only expressed at a specific location)

Transposable Elements

• Elements that can move from one place in a chromosome to another site
• Can contribute to functional divergence in duplicate genes
• Can mediate gene recombination through carrying coding sequences from a part of genome to other sites of the genome included to existing coding sequences

Molecular Evolution of Repetitive Sequences

• Repetitive Sequences: Homologous DNA fragments present in multiple copies on the genome, generated by molecular mechanisms
  • Used to differentiate species that are related
  • The evolution rate is correlated with their copy number
    • High copy number: Heterogenous and evolve quickly
    • Low copy number: Homogenous and evolve slowly

Evolution of the Prokaryotic Genome

• Prokaryotes live with gene sets are much more reduced in comparison to eukaryotes
• In free-living prokaryotes, natural selection favors genome reduction
• Free-living prokaryotes evolve strategies through:
  • The Streamlining Hypothesis
  • The Muller's Ratchet

The Streamlining Hypothesis

• Smaller genomes are favored for cellular economization
• Free-living prokaryotes have a small intergenic regions and small cell size
• A low G+C content is favored if these free-living prokaryotes live in low nutrient environment
  • Genes unneeded are lost during cellular conditions

The Muller's Ratchet

• Genome reduction through the accumulation of slightly deleterious mutations
• Populations undergoing constant bottlenecks and no recombination have: genome reduction occurs through the accumulation of slightly deleterious mutations
• Genes constant accumulation of mutations become inactive and eventually deleted
• Happens in asexual populations since there is no recombination happening among them

Genome Reduction in Endosymbiotic Prokaryotes

• Host-associated bacteria
• Endosymbiotic prokaryotes function with a reduced gene set through three ways
  • (1) Gene modification
  • (2) Complementary genes
  • (3) Genes coded in genome of host