Microbial Physiology and Genetics I - DNA Repair and Adaptation
DNA Repair Mechanisms Overview
Focus on the intricate mechanisms that repair damaged DNA before potential heritable mutations can occur, ensuring genetic integrity across generations. Prokaryotes such as bacteria are the primary organisms under study for DNA repair due to their simplicity and rapid replication rates, allowing for real-time analysis of repair processes.
Types of DNA Repair Mechanisms
Error-Proof and Error-Prone Repair
Error-Proof: These mechanisms operate with high fidelity, effectively correcting errors without introducing new mutations. They utilize homologous sequences and other cellular machinery to ensure that any damage is meticulously repaired according to the original template.
Error-Prone: This involves the action of specialized, less accurate DNA polymerases that are activated in response to significant DNA damage, allowing cells to bypass lesions at the cost of introducing mutations. This mechanism serves as a last resort to maintain cell viability under stress.
DNA Replication
DNA replication is classified as semi-conservative, meaning each of the two new helices contains one original (parental) strand and one newly synthesized (daughter) strand. This process relies on a family of enzymes known as DNA polymerases that catalyze the formation of new DNA strands, ensuring accurate duplication of genetic material.
Methyl Mismatch Repair (MMR)
In bacteria, parental DNA strands are tagged by specific methylation marks, enabling the discrimination of original from new strands during the replication process. Upon incorporation of incorrect bases, the mismatch is recognized by a set of methyl-directed repair enzymes, including MutS, MutL, and MutH. These enzymes detect mismatches by identifying distortions in the DNA helix and create loops in the strand to facilitate repair processes.
Process of Methyl Mismatch Repair
MutH cleaves the unmethylated strand at the site of the error.
DNA helicase unwinds the cleaved strand, facilitating access for exonucleases that degrade the erroneous strand.
DNA polymerase I synthesizes a new strand to fill in the gap, while DNA ligase seals the final nick to restore DNA integrity.
Base Excision Repair (BER)
Base excision repair involves glycosylase enzymes that identify and cleave the bonds connecting damaged bases to the sugar-phosphate backbone. After the damaged base is removed, AP endonuclease cuts at the apurinic/apyrimidinic (AP) site. Subsequently, DNA polymerase I not only degrades the downstream strand but also synthesizes a replacement one, which is completed by DNA ligase finalizing the repair.
Homologous Recombination (HR)
This critical repair mechanism utilizes an intact copy of DNA, often from a homologous chromosome, to accurately mend double-strand breaks. It involves the invasion of an adjacent undamaged DNA strand, using it as a template to initiate the resynthesis of the damaged segment, which is essential for maintaining genomic stability.
SOS Response in Bacteria
The SOS response is a global response to DNA damage that activates numerous genes responsible for DNA repair and mutagenesis. Key players include the proteins LexA and RecA, where RecA facilitates the cleavage of LexA, leading to the expression of repair enzymes. Notably, DNA polymerase V is involved in bypassing lesions, inserting nucleotides without regard for accuracy which can lead to increased mutagenesis.
Non-Homologous End Joining (NHEJ)
In contrast to HR, non-homologous end joining repairs double-strand breaks by directly ligating the ends of the broken DNA. The Ku protein first binds to the DNA ends, recruiting LigD, which possesses several enzymatic activities needed to fill gaps and ligate the broken ends. Although NHEJ is a quick repair response, it can be error-prone, often resulting in nucleotide additions, removals, or misjoined sequences.
Limitations and Mutagenesis
Despite their importance, DNA repair pathways are not infallible, and imperfections in the repair processes can introduce mutations into the genome. Such variability is a double-edged sword: while it promotes adaptability and evolution, it can also lead to deleterious mutations.
Experiments and Concepts
Luria-Delbruck Experiment (1943)
This landmark experiment aimed to determine the nature of spontaneous mutations occurring within bacterial populations subjected to selective stress, providing insights into mutation rates and mechanisms.
The Ames Test
An essential assay for evaluating the mutagenic potential of chemical compounds. This test uses strains of Salmonella that require histidine, assessing the frequency of mutations caused by various substances, especially for potential carcinogenicity in humans.
Evolution Theories Comparison
Lamarck vs. Darwin
Lamarck: Proposed that species evolve over time, emphasizing the idea of directed mutation based on environmental demands, with adaptive traits acquired during an organism's lifetime being passed on to offspring.
Darwin: Championed natural selection as the revolutionary process by which organisms survive and reproduce based on favorable traits, operating on the premise of random mutations rather than directed changes.
The key distinction between the two lies in Lamarck’s notion of directed mutation versus Darwin’s concept of random selection and survival of the fittest, laying the foundation for modern evolutionary biology.
Bacteriophage Characteristics
Bacteriophages, viruses that specifically infect bacteria, hijack the host's cellular machinery to replicate viral components, ultimately leading to bacterial cell lysis. Similarly, antibiotic resistance in bacteria can emerge through mechanisms akin to those used by phages, linking mutation, adaptation, and survival strategies in these microorganisms.