Mechanisms of Genetic Variation

Mechanisms of Genetic Variation

I. Mutations

• Definition: Changes in the genetic code.
• Mutation: Heritable changes in the DNA sequences.

A. Causes of Mutations

1. Spontaneous Mutations
   • Random changes in the DNA due to:
     • Errors in replication.
     • Spontaneously occurring lesions in the DNA.
     • Movement of a transposon (jumping DNA).
   • Characteristics:
     • Short stretches of nucleotide repeats are problematic.
     • Purines and pyrimidines can lose their bases, affecting base pairing.
2. Induced Mutations
   • Result from exposure to known mutagens, physical or chemical agents disrupting DNA.

B. Types of Mutagens

1. Base Analogues
   • Structurally similar to normal nitrogenous bases.
   • Example: 5-bromouracil (analogue of thymine) binds with guanine instead of adenine.
   • Effect: Can cause stable mutations due to incorrect pairing.
2. DNA Modifying Agents
   • Change a base’s base pairing ability; example includes methylnitrosoguanidine which methylates guanine causing mispairing with thymine.
3. Intercalating Agents
   • Distort DNA structure, inducing single nucleotide pair insertions and deletions by inserting themselves between the bases.

C. Categories of Point Mutations

• Point Mutations: One single pair of nucleotides is altered, being the most common type of mutation.
• Substitution Mutations:
  1. Missense Mutation: Causes a change in a single amino acid.
  2. Nonsense Mutation: Changes a normal codon into a stop codon.
  3. Silent Mutation: Alters a base but does not change the amino acid due to degeneracy.
• Frameshift Mutation: Reading frame of the mRNA codons is altered; caused by insertion or deletion of bases.

D. Screening for Mutants

1. Direct Selection:
   • Detection of mutant cells by inhibiting the growth of wild-type cells (e.g., adding Penicillin selects for resistant microbes).
2. Indirect Selection:
   • Using methods such as replica plating to distinguish between mutant and wild-type strains based on growth ability.
   • Auxotroph: A mutant microbe having specific nutrient requirements absent in wild-type.

II. DNA Repair Mechanisms

• Purpose: Maintains genome stability.

A. Types of DNA Repair

1. Proofreading
   • Carried out by DNA Pol I and III, correcting mistakes during replication by removing an error and inserting the correct nucleotide.
   • Prevents many spontaneous mutations but does not repair induced mutations.
2. Mismatch Repair
   • Enzymes like MutS and MutH in E. coli scan DNA for mismatches, excising the incorrect segment, which is replaced by DNA polymerase.
3. Excision Repair:
   • Nucleotide Excision Repair: UvrABC endonuclease removes damaged nucleotides and adjacent ones, then filled by DNA polymerase I and sealed by ligase.
   • Base Excision Repair: DNA glycosylases remove damaged nucleotides; AP endonucleases nick the backbone, followed by nucleotide replacement and ligation.
4. Direct Repair
   • Repairs specific lesions like thymine dimers using photolyase and alkyltransferase for alkylated bases.
5. Recombinational Repair
   • RecA protein helps incorporate template DNA from a sister molecule into gaps.
6. SOS Response
   • Activates when DNA damage is extensive and normal repair fails; involves a control network of over 50 genes.
   • Key elements of SOS response:
     • LexA: A repressor that initiates SOS response when destroyed.
     • RecA: Binds to damaged sites to initiate recombinational repair.
     • SfiA: Blocks cellular division until repairs are substantially completed.
     • After 40 minutes, if still unrepaired, translesion DNA synthesis is activated by DNA polymerase IV and V, which can introduce errors by lacking proofreading.

III. Horizontal Gene Transfer and Molecular Recombination

• Definition: Acquisition and expression of genes from another organism, typically unidirectional (donor to recipient).
• Three Means of Horizontal Gene Transfer in Bacteria:
  1. Conjugation: Direct cell-to-cell contact transfer.
  2. Transformation: Uptake of “naked” DNA.
  3. Transduction: Phage-mediated DNA transfer.

A. Molecular Recombination:

• Integrating donor DNA into recipient chromosome akin to crossing over in meiosis.
• Homologous Recombination: Common type involving long sequence similarities.
• Site-Specific Recombination: Occurs at specific sites, facilitating close, non-homologous DNA connections, catalyzed by recombinases.

IV. Conjugation

• Definition: Transfer of plasmid or chromosomal fragment from a living donor to a living recipient cell via a direct connection.
• Conjugative Plasmids: Best studied is the F factor, which encodes for sex pilus formation and plasmid transfer.

A. Types of Conjugation

1. F factor transfer (F+ x F- mating):
   • Donor has the F factor, allowing transfer via sex pilus and rolling circle replication.
   • Recipient becomes F+ after transfer.
2. Hfr Conjugation:
   • Involves integrated F plasmid allowing chromosomal gene transfer without changing recipient to F+.
   • Takes about 100 minutes to transfer entire chromosome but is often interrupted, leaving the recipient F-.
3. F’ Conjugation:
   • Results when the F factor leaves the chromosome, sometimes excising a part of the host DNA.
   • Involves transfer of additional bacterial genes on the F’ plasmid.
   • Recipient becomes partially diploid, retaining both original genes and those on the plasmid.

V. Summary of Horizontal Gene Transfer Mechanisms

• Note: Direct means donor and recipient are in contact during exchange; indirect means they are not.