More Like this

1. Targeted editing and evolution of engineered ribosomes in vivo by filtered editing

   https://doi.org/10.1038/s41467-021-27836-x  

   Radford, Felix; Elliott, Shane D.; Schepartz, Alanna; Isaacs, Farren J. (January 2022, Nature Communications)

   Abstract Genome editing technologies introduce targeted chromosomal modifications in organisms yet are constrained by the inability to selectively modify repetitive genetic elements. Here we describe filtered editing, a genome editing method that embeds group 1 self-splicing introns into repetitive genetic elements to construct unique genetic addresses that can be selectively modified. We introduce intron-containing ribosomes into theE. coligenome and perform targeted modifications of these ribosomes using CRISPR/Cas9 and multiplex automated genome engineering. Self-splicing of introns post-transcription yields scarless RNA molecules, generating a complex library of targeted combinatorial variants. We use filtered editing to co-evolve the 16S rRNA to tune the ribosome’s translational efficiency and the 23S rRNA to isolate antibiotic-resistant ribosome variants without interfering with native translation. This work sets the stage to engineer mutant ribosomes that polymerize abiological monomers with diverse chemistries and expands the scope of genome engineering for precise editing and evolution of repetitive DNA sequences. 

   more » « less
2. Hypercompact CRISPR–Cas12j2 (CasΦ) enables genome editing, gene activation, and epigenome editing in plants

   https://doi.org/10.1016/j.xplc.2022.100453  

   Liu, Shishi; Sretenovic, Simon; Fan, Tingting; Cheng, Yanhao; Li, Gen; Qi, Aileen; Tang, Xu; Xu, Yang; Guo, Weijun; Zhong, Zhaohui; et al (November 2022, Plant Communications)
3. Imaging and Editing the Phospholipidome

   https://doi.org/10.1021/acs.accounts.2c00510  

   Chiu, Din-Chi; Baskin, Jeremy M. (November 2022, Accounts of Chemical Research)
4. Collaborative networks in gene editing

   https://doi.org/10.1038/s41587-019-0275-z  

   Huang, Ying; Porter, Alan; Zhang, Yi; Barrangou, Rodolphe (October 2019, Nature Biotechnology)
5. Sexual stage–specific A-to-I mRNA editing is mediated by tRNA-editing enzymes in fungi

   https://doi.org/10.1073/pnas.2319235121  

   Bian, Zhuyun; Wang, Zeyi; Wang, Diwen; Xu, Jin-Rong (March 2024, Proceedings of the National Academy of Sciences)

   A-to-I RNA editing catalyzed by adenosine-deaminase-acting-on-RNA (ADARs) was assumed to be unique to metazoans because fungi and plants lack ADAR homologs. However, genome-wide messenger RNA (mRNA) editing was found to occur specifically during sexual reproduction in filamentous ascomycetes. Because systematic characterization of adenosine/cytosine deaminase genes has implicated the involvement ofTAD2andTAD3orthologs in A-to-I editing, in this study, we used genetic and biochemical approaches to characterize the role ofFgTAD2, an essential adenosine-deaminase-acting-on-tRNA (ADAT) gene, in mRNA editing inFusarium graminearum.FgTAD2had a sexual-stage-specific isoform and formed heterodimers with enzymatically inactiveFgTAD3. Using a repeat-induced point (RIP) mutation approach, we identified 17 mutations inFgTAD2that affected mRNA editing during sexual reproduction but had no effect on transfer RNA (tRNA) editing and vegetative growth. The functional importance of the H352Y and Q375*(nonsense) mutations in sexual reproduction and mRNA editing were confirmed by introducing specific point mutations into the endogenousFgTAD2allele in the wild type. An in vitro assay was developed to show that FgTad2-His proteins purified from perithecia, but not from vegetative hyphae, had mRNA editing activities. Moreover, the H352Y mutation affected the enzymatic activity of FgTad2 to edit mRNA but had no effect on its ADAT activity. We also identified proteins co-purified with FgTad2-His by mass spectrometry analysis and found that two of them have the RNA recognition motif. Taken together, genetic and biochemical data from this study demonstrated that FgTad2, an ADAT, catalyzes A-to-I mRNA editing with the stage-specific isoform and cofactors during sexual reproduction in fungi. 

   more » « less