Cosmin SaveanuOct 4, 2024

New #paper! Structural and functional data from the Marc Graille lab, together with in vitro experiments from the Le Hir lab and our #yeast experiments, identified specific interactions between Upf1, the core #NMD RNA helicase and Nmd4, the yeast equivalent of SMG6 (the NMD #endonuclease in many organisms). Another surprising result showing how conserved NMD mechanisms are!

https://pubmed.ncbi.nlm.nih.gov/39331656/
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002821

#rna #plosbiol #research

Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans - PubMed

The nonsense-mediated mRNA decay (NMD) pathway clears eukaryotic cells of mRNAs containing premature termination codons (PTCs) or normal stop codons located in specific contexts. It therefore plays an important role in gene expression regulation. The precise molecular mechanism of the NMD pathway ha …

PubMed
Show threadkatch wreckSep 23, 2024
"Overall, the set of tools presented in this study facilitates the application of #TnpB as an ultracompact programmable #endonuclease in research and therapeutics."
katch wreckJul 4, 2024

i did a Summer internship studying homing introns in college. big advance!

"This work demonstrates how a homing endonuclease can be deployed in interference competition among viruses and provide a relative fitness advantage. Given the ubiquity of homing endonucleases, this selective advantage likely has widespread evolutionary implications in diverse plasmid and viral competition as well as virus-host interactions."

#homing #endonuclease #phage #bacteriophage #virus

https://www.science.org/doi/10.1126/science.adl1356

CellBioNewsSep 3, 2023

Researchers determine how type II restriction #endonuclease #Sau3AI cleaves #DNA.

https://phys.org/news/2023-08-ii-restriction-endonuclease-sau3ai-cleaves.html

Researchers determine how type II restriction endonuclease Sau3AI cleaves DNA

Sau3AI is a type II restriction enzyme widely used for genetic manipulation, such as genome library construction. Sau3AI consists of two domains, the N-terminal domain (Sau3AI-N) and the C-terminal domain (Sau3AI-C). How these two domains work together to cut DNA remains unclear.

Phys.org
CellBioNewsJul 14, 2023

Molecular scissors caught in the act: Describing the function of #tRNA splicing #endonuclease #TSEN based on its structure.

https://phys.org/news/2023-07-molecular-scissors-caught-function-trna.html

Molecular scissors caught in the act: Describing the function of tRNA splicing endonuclease TSEN based on its structure

In all living organisms, the biomolecule transfer RNA (tRNA) plays a fundamental role in protein production. tRNAs are generated from precursor molecules in several steps. The enzyme tRNA splicing endonuclease (TSEN), among other things, catalyzes one step in this process. Mutations in TSEN lead to a neurodegenerative disorder called pontocerebellar hypoplasia, which is associated with severe disabilities and early death.

Phys.org
β„΅β‚€ πŸ³οΈβ€βš§οΈπŸ΄β€β˜ οΈJul 10, 2023

#Fanzor is a #eukaryotic #programmable #RNA-guided #endonuclease

https://www.nature.com/articles/s41586-023-06356-2

#biology #geneticengineering #crisprcas #CRISPR #naturescientificreports

Fanzor is a eukaryotic programmable RNA-guided endonuclease - Nature

Fanzor is shown to be an RNA-guided DNA endonuclease, demonstrating that such endonucleases are found in all domains of life and indicating a potential new tool for genome engineering applications.

Nature
The EMBO JournalJan 9, 2023

What is the #molecular basis of #syntheticlethality between loss of Werner #helicase #WRN and #mismatchrepair #MMR proteins particularly in #cancer cells with #microsatellite instability?

Using #biochemcial assays, Petr Cejka and colleages, Bellinzona LRB, show how they synergistically and independently unfold #cruciform #DNA structures, with WRN preventing their cleavage by #SLX1-#SLX4 structure-specific #endonuclease and DNA breakage

https://www.embopress.org/doi/10.15252/embj.2022111998

Vivek MutalikDec 14, 2022

Cells with stochastically increased #methyltransferase to #restriction #endonuclease ratio provide an entry for #bacteriophage into protected cell population -

https://pubmed.ncbi.nlm.nih.gov/36477901/

#phage #phages

Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population - PubMed

The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites. We here show that protection from phage infe …

PubMed