DNA Repair Mechanisms in Bacteria

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Questions and Answers

What is the core sequence of Chi sites in enteric bacteria such as E. coli and Salmonella?

5'-GCTGATGG-3’

5'-GCTGGTAG-3’

5'-GCTGGTGG-3’ (correct)

5'-GCTGCTGG-3’

What function does the N-terminal domain of the RecB protein serve?

Dimerization

DNA recognition

Nuclease activity

Helicase function (correct)

Which key catalytic residues are found in the nuclease motif of RecB?

Serine and threonine

Aspartate and lysine (correct)

Cysteine and histidine

Arginine and glutamate

Which protein is responsible for recognizing the Chi site and how many amino acids does it contain?

RecC, 1122 aa Signup and view all the answers

Which of the following motifs are characteristic of the SF1 helicase found in the RecB protein?

1, 1a, 2, 3, 4, 5, 6 Signup and view all the answers

What is the first step in the process of homologous recombination?

Strand exchange Signup and view all the answers

What structural formation results from strand invasion during homologous recombination?

Holliday junction Signup and view all the answers

During which part of homologous recombination is heteroduplex DNA formed?

Strand exchange Signup and view all the answers

What happens during the branch migration step of recombination?

Regions of heteroduplex DNA are extended Signup and view all the answers

What enzymatic complex processes DNA ends following a double-strand break?

RecBCD Signup and view all the answers

What is the function of RecBCD at a Chi site during recombination?

It loads RecA onto the DNA tail Signup and view all the answers

How are Holliday junctions typically resolved?

By endonucleolytic cleavage Signup and view all the answers

Chi sites, also known as recombination hotspots, are characterized by which feature?

They increase the likelihood of homologous recombination Signup and view all the answers

What is the primary function of the Ku heterodimer in the C-NHEJ pathway?

To bind to double-stranded DNA ends and initiate DNA repair Signup and view all the answers

Which components are essential for forming the DNA-PK holoenzyme in C-NHEJ?

Ku70/80 and DNA-PKcs Signup and view all the answers

Which statement correctly describes the characteristics of the Ku protein?

It is essential for maintaining genome integrity and is found in both prokaryotes and eukaryotes Signup and view all the answers

What is the primary role of DNA-PKcs in the C-NHEJ mechanism?

It acts as a catalytic subunit to facilitate DNA end joining Signup and view all the answers

Which of the following enzymes is NOT involved in the processing of DNA ends during C-NHEJ?

DNA polymerase I Signup and view all the answers

What distinguishes C-NHEJ from other DNA repair mechanisms regarding DNA ends?

C-NHEJ requires free DNA ends for effective binding Signup and view all the answers

What is the role of the LIG4/XRCC4/XLF complex in the C-NHEJ pathway?

To rejoin the processed DNA ends after repair Signup and view all the answers

Which of these choices is a consequence of Ku's initial binding to DNA ends?

It improves the binding of other repair components like nucleases Signup and view all the answers

What characterizes the mechanistic flexibility of the NHEJ process?

Iterative loading and independent DNA end processing Signup and view all the answers

Which statement accurately describes the role of A-NHEJ?

A-NHEJ is considered a backup pathway for DSB repair Signup and view all the answers

What suppresses the activity of A-EJ?

C-NHEJ and possibly HRR Signup and view all the answers

What has been proposed about the factors involved in A-EJ?

They engage in multiple sub-pathways at each DSB Signup and view all the answers

When does A-EJ typically engage in DSB processing?

Only after C-NHEJ and HRR have failed Signup and view all the answers

What is the relationship between A-EJ and C-NHEJ?

A-EJ actively competes with C-NHEJ for DSB processing Signup and view all the answers

Which of the following best describes the speed of A-EJ compared to C-NHEJ?

A-EJ is slower than C-NHEJ Signup and view all the answers

What is one of the implications of the functional diversity of A-EJ factors?

Several sub-pathways may exist depending on the DSB Signup and view all the answers

In which phase of the cell cycle is the dependency on BRCA1/CtIP/MRN more likely?

G2 Signup and view all the answers

What starts Non-Homologous End Joining (NHEJ) in the repair process?

Ku70/80 heterodimer Signup and view all the answers

Which enzyme can trim incompatible DNA ends during NHEJ?

Artemis Signup and view all the answers

After DSB resection in homologous recombination, what is the first protein that coats the single-stranded DNA?

RPA Signup and view all the answers

What is the role of Rad51 in homologous recombination?

Mediate strand invasion Signup and view all the answers

What complex seals the break in Non-Homologous End Joining?

XRCC4-DNA Ligase IV-XLF Signup and view all the answers

What happens to the break after resection in homologous recombination?

It can no longer be repaired by NHEJ. Signup and view all the answers

Which protein assists Rad51 in the replacement of RPA during homologous recombination?

BRCA2 Signup and view all the answers

Study Notes

Chi Sites and DNA Repair in Bacteria

Chi sites are unique sequences that stimulate DNA double-strand break (DSB) repair in bacteria.
In enteric bacteria like E. coli and Salmonella, the core sequence of the Chi site is 5'-GCTGGTGG-3’.
The Chi site includes an additional 4 to 7 nucleotides on the 3' side, essential for function.

RecBCD Enzyme Structure

RecBCD enzyme is crucial for processing DSBs in bacteria.
Comprised of three proteins:
- RecB: 1180 amino acids, features:
  - N-terminal domain with seven SF1 helicase motifs.
  - C-terminal domain with nuclease motifs containing key aspartate and lysine residues.
- RecC: 1122 amino acids, contains the Chi recognition site.
- RecD: 608 amino acids, also has seven conserved SF1 helicase motifs.

Homologous Recombination Process

Homologous recombination involves three key steps:
- Strand exchange: Pairing of broken DNA with homologous sister chromatid regions.
- Branch migration: Extends regions of heteroduplex DNA formed during crossover.
- Resolution: Cleavage of Holliday junctions to separate duplex DNA.

Key Processes in Homologous Recombination

Resection creates 3' single-stranded DNA tails necessary for strand invasion.
Strand invasion uses free 3' ends to form Holliday junctions, initiating DNA synthesis.
Branch migration translocates the Holliday junction along the DNA, extending heteroduplex areas.

Non-Homologous End Joining (NHEJ) Pathways

Canonical Non-Homologous End Joining (C-NHEJ):
- Dependent on Ku70/80 heterodimer and DNA-PK catalytic subunit (DNA-PKcs).
- Ku binds DSBs, providing a docking site for DNA-PKcs and facilitating repair.
- Various nucleases, such as Artemis, process DNA ends for ligation by the LIG4/XRCC4/XLF complex.
Alternative End Joining (A-EJ):
- Functions alongside C-NHEJ as a backup repair pathway if standard processes fail.
- Typically engaged at DSBs where C-NHEJ or homologous recombination have been ineffective.
- A-EJ is more prevalent in G2 phase cells due to dependencies on repair factors present.

General Mechanisms of DSB Repair

Non-homologous end joining begins with Ku recognition of DNA ends.
End processing by nucleases like Artemis can occur if ends are incompatible.
Ligase IV complex finalizes the break sealing.
Homologous recombination requires MRN-CtIP complex to initiate resection and generate ssDNA coated by RPA, later replaced by Rad51 for strand invasion.

Importance of DNA Repair Mechanisms

Ku proteins are essential for both prokaryotic and eukaryotic genome integrity.
Multi-faceted repair pathways like C-NHEJ and A-EJ allow cells to adapt to varied DNA break configurations.
Understanding these processes enhances knowledge of genetic repair mechanisms and potential cancer therapies.

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Description

This quiz explores the role of Chi sites in the DNA double-strand break repair process in enteric bacteria such as E. coli and Salmonella. It examines the unique core sequence and the importance of the RecBCD enzyme in these organisms. Test your knowledge of bacterial DNA repair and genetic sequences.