Show Notes
Zahid S et al., Nature Communications, doi:10.1038/s41467-025-65609-y - Cryo-EM and biophysical analyses show Mycobacterium tuberculosis Ku assembles into DNA-bound oligomeric filaments that synapse DNA ends and are required for survival under DNA-damaging conditions. Key terms: Ku-Mtb, non-homologous end joining, cryo-EM, DNA synapsis, Mycobacterium tuberculosis.
Study Highlights:
Deletion of ku in M. smegmatis causes marked survival defects after methyl methanesulfonate exposure and desiccation that are rescued by complementation. Cryo-EM structures of apo-Ku-Mtb (4.04 Å) and DNA-bound Ku-Mtb (2.96 Å) reveal a homodimer that assembles into extended filaments with a minimal repeating unit of two homodimers per DNA duplex. Biophysical assays (mass photometry, FIDA, AFM) and positive-stain EM confirm DNA-induced oligomerisation and show Ku can circularize DNA ends, holding them ~40 Å apart. Mutation of hydrophobic loop residues L13/V14 abolishes filament formation while preserving DNA binding and reduces bacterial survival, and the C-terminal α-helix blocks the filament interface in the apo state and is displaced on DNA binding to enable LigD recruitment.
Conclusion:
Ku oligomerisation mediates DNA end synapsis during bacterial NHEJ and is critical for mycobacterial survival under DNA-damaging stresses
Music:
Enjoy the music based on this article at the end of the episode.
Article title:
Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis
First author:
Zahid S
Journal:
Nature Communications, doi:10.1038/s41467-025-65609-y
DOI:
10.1038/s41467-025-65609-y
Reference:
Zahid S, Baconnais S, Smith H, Atwal S, Bates L, Read H, Chadda A, Morati F, Stender EGP, Westerlund F, Galburt E, Mukamolova GV, Chaplin AK, et al. Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis. Nature Communications. 2025;16:10568. https://doi.org/10.1038/s41467-025-65609-y
License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00
Official website https://basebybase.com
On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.
Episode link: https://basebybase.com/episodes/ku-mtb-dna-synapsis
QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-14.
QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content covering MTB NHEJ, Ku-Mtb filament formation on DNA, cryo-EM structural details, mutational analyses, functional assays, and therapeutic implications.
- transcript topics: Ku essential for mycobacterial survival under MMS-induced DNA DSBs; Desiccation tolerance and MTB DNA repair via NHEJ; apo-Ku-Mtb structure by cryo-EM (4.04 Å) and DNA-bound filament (2.96 Å); DNA synapsis by Ku-Mtb filament; ~40 Å end-to-end distance; Minimal repeating unit: two Ku-Mtb homodimers per DNA duplex; Role of C-terminal helix and L13/V14 hydrophobic interface in filament regulation
QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0
Metadata Audited:
- article_doi
- article_title
- article_journal
- license
Factual Items Audited:
- Ku-Mtb forms an extended filament on DNA and synapses DNA ends; minimal unit is two Ku-Mtb homodimers per DNA duplex
- DNA ends are held at a distance of approximately 40 Å within the filament
- Leu13 and Val14 form a hydrophobic interface critical for filament formation; L13A/V14A abolishes filament formation
- The C-terminus acts as an autoinhibitory regulatory arm; displacement upon DNA binding enables filament formation and LigD recruitment
- MTB NHEJ is a minimalist system lacking vWA domains and DNA-PKcs, capable of synapsis without the large human machinery
- Mutational analysis in vivo (L23A/L24A equivalent) reduces survival under DNA-damaging stress
QC result: Pass.
