BULLETIN 1
Supercharged Tool for Developing Tastier, More Resilient Crops

China Agricultural University researchers reported their success in improving prime editing, a powerful technique for editing genes. The enhanced prime editing system allows researchers to make specific changes to rice genes, potentially leading to tastier, more disease-resistant, or higher-yielding varieties. The results are available in the Journal of Integrative Plant Biology.
The research team developed versions of the prime editing tool using four types of prime editors generated using evolved and engineered reverse transcriptase (RT) variants from three various sources. One version, called PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposons, showed the highest editing efficiency reaching over 3 times more than the previous tool. The other types also showed promising prime-editing efficiencies, indicating that all the prime editors tested has the potential to help breeders develop rice varieties with desirable traits.
Read the open-access research article in the Journal of Integrative Plant Biology.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20899

 

BULLETIN 2
GeneMAP Discovery Platform Identifies Functions of Metabolic Proteins

Figure: Researchers from Vanderbilt University Medical Center (VUMC) produced GeneMAP, a platform that analyzes the role of genes involved in metabolism. The platform discovered a gene that is important for mitochondrial choline transport.

Metabolic reactions play crucial roles in life-sustaining chemical reactions, such as nutrient absorption, waste disposal, and energy production. Approximately 20% of genes that code for proteins are involved in metabolism. However, many of these genes have unknown molecular substrates due to a wide variety of structure and function of proteins.
Researchers from Vanderbilt University Medical Center (VUMC) combined genomics and metabolism to develop the GeneMAP discovery platform, which can identify the role of proteins with unknown substrates. The platform can study existing gene-metabolite associations as well as reveal new ones. Their results also showed that the GeneMAP-derived metabolic networks may be utilized to deduce the biochemical properties of uncharacterized metabolites. Their research demonstrates great potential in the field of health and medicine.
For more information, read the news article of VUMC.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20894

 

BULLETIN 3
PE6c greatly enhances prime editing in transgenic rice plants

 

Zhenghong Cao, Wei Sun, Dexin Qiao, Junya Wang, Siyun Li, Xiaohan Liu, Cuiping Xin, Yu Lu, Syeda Leeda Gul, Xue-Chen Wang, Qi-Jun Chen
Journal of Integrative Plant Biology. First published: 09 July 2024; https://doi.org/10.1111/jipb.13738

ABSTRACT
Prime editing is a versatile CRISPR/Cas-based precise genome-editing technique for crop breeding. Four new types of prime editors (PEs) named PE6a–d were recently generated using evolved and engineered reverse transcriptase (RT) variants from three different sources. In this study, we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double-RT modules in transgenic rice (Oryza sativa) plants. PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposon, yielded the highest prime-editing efficiency. The average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 genes. We also demonstrated the feasibility of using two RT modules to improve prime-editing efficiency. Our results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot plants. In addition, our findings have laid a foundation for prime-editing-based breeding of rice varieties with enhanced agronomically important traits.
See https://onlinelibrary.wiley.com/doi/full/10.1111/jipb.13738

 

Figure: Editing efficiencies of seven types of duplex prime editors (PEs) in transgenic rice plants

(A) Diagram of the T-DNAs for the seven types of duplex PEs used to generate transgenic rice lines. E9t, OCSt, and HSPt are terminators from pea (Pisum sativum), Agrobacterium, and Arabidopsis, respectively. Hyg, hygromycin-resistance gene. RB and LB, right and left T-DNA borders, respectively. tGly and tMet, tRNA(Gly) and tRNA(Met), respectively. HDV, Hepatitis delta virus ribozyme. (B) Editing efficiencies of seven types of duplex PEs at 18 agronomically important targets from 15 genes. Ho, He, and Chi are homozygous, heterozygous, and chimeric mutant lines, respectively. Re, DNA repair-derived byproducts with only some of the target bases edited when installing multiple-base substitution edits. Sc, pegRNA scaffold-derived byproducts. K161, TAP, and GP represent three targets of EPSPS. TAP-IVS, T173I, A174V, and P177S; GP-AS, G172A, and P177S. W548 and P171 represent two targets of ALS. Lines with 100% deep-sequencing reads representing only one type of mutation with desired edits were scored as homozygous. Non-homozygous lines containing more than one type of mutation with desired edits were scored as heterozygous (≥45% desired edits) or chimeric (<45% desired edits). When the main mutation type in a chimeric line was Re byproducts, it was scored as Re lines; when the main mutation type was InDel byproducts, it was scored as InDel lines; when the main mutation type in a chimeric line was Sc byproducts, it was scored as Sc lines. The sorting-based mutation efficiency was calculated based on the ratio of the number of mutants to the total number of transgenic plants.