Group Final Project

Team & credit
Team members: Alireza Hekmati and Yousif Graytee (Baghdad, Iraq).
Yousif is affiliated with the Designer Cells Lab at Yonsei University (Incheon, South Korea). Page text credit: Yousif Graytee. :contentReference[oaicite:0]{index=0}
Lab site: https://designercells.yonsei.ac.kr

Our goal

Make lysis independent of DnaJ by separating the C-terminal from the N-terminal of the MS2 L-protein. :contentReference[oaicite:1]{index=1}

Core idea (high level)

The L-protein’s productive interaction is believed to depend on DnaJ. Its N-terminal is highly soluble and has been reported dispensable for function, while the functional, transmembrane region resides toward the C-terminal. The MS2 lys gene substantially overlaps with the coat protein (cp) and replicase (rep) genes, but a 33-nt (11-codon) window exists with no overlap. :contentReference[oaicite:2]{index=2}

Figures (from our analysis)

1. Genome context & overlaps (Benchling view)
   :contentReference[oaicite:3]{index=3}

2. Non-overlapping 33-nt region highlighted
   :contentReference[oaicite:4]{index=4}

3. N-terminal extent vs. overlaps
   :contentReference[oaicite:5]{index=5}

4. C-terminal/replicase overlap context
   :contentReference[oaicite:6]{index=6}

5. Zoom on the non-overlapping window
   :contentReference[oaicite:7]{index=7}

Explanation (from our notes)

• The lys coding region overlaps with both cp and rep genes for most of its length. :contentReference[oaicite:8]{index=8}
• There is a 33-nt region that does not overlap any other gene and maps to part of the N-terminal (not the functional C-terminal transmembrane domain). :contentReference[oaicite:9]{index=9}
• Idea: introduce a stop codon within that non-overlapping window so the N-terminal is translated separately from the C-terminal segment, avoiding changes to cp/rep while allowing the C-terminal to function independently for lysis. :contentReference[oaicite:10]{index=10}
• This mirrors prior observations that C-terminal truncations can be sufficient for lysis; here, rather than deleting the N-terminal, it is separated to minimize effects on overlapping genes. Hypothesis: DnaJ-dependence and steric hindrance relate to the N-terminal; separating termini could let the C-terminal act without DnaJ. :contentReference[oaicite:11]{index=11}

What we plan to document next

• Rationale and design sketches (already above).
• In-silico checks & controls (non-overlapping region annotations, reading-frame sanity).
• Literature pointers on MS2 L-protein function and DnaJ dependence (to be added as we curate references).
• Evaluation plan outline (conceptual only).