ABSTRACT

Unintended effects of gene edit crops may pose safety issues. Omics is a useful tool for researchers to evaluate these unexpected effects. Transcriptome and proteomics analyses were performed for two gene editors, CRISPR-Cas9 and adenine base editor (ABE) gene edit rice, as well as corresponding wild-type plants (Nipponbare). Transcriptome revealed 520 and 566 rice differentially expressed genes (DEGs) in the Cas9/Nip and ABE/Nip comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEGs participated in metabolism of terpenoids and polyketones, plant–pathogen interactions, and plant signal transduction. It mainly belongs to environmental adaptation. Proteomics revealed 298 and 54 rice differentially expressed proteins (DEPs) in the Cas9/Nip and ABE/Nip comparisons, respectively. KEGG pathway enrichment analysis showed that most DEPs participated in the biosynthesis of secondary metabolite and metabolic pathways.

According to integrated transcriptomes and proteomics analysis, the results showed that no newly generated genes were identified as new transcripts of these differentially expressed genes, and gene edit tools had little effect on rice transcription levels and no new proteins were generated in the gene-edited rice.

摘要

基因编辑作物的意外影响可能会带来安全问题。组学是研究人员评估这些意外影响的有用工具。对两种基因编辑器 CRISPR-Cas9 和腺嘌呤碱基编辑器 (ABE) 基因编辑水稻以及相应的野生型植物 (Nipponbare) 进行了转录组和蛋白质组学分析。转录组显示 Cas9/Nip 和 ABE/Nip 比较中分别有 520 个和 566 个水稻差异表达基因 (DEG)。京都基因与基因组百科全书（KEGG）通路富集分析表明，大多数DEG参与萜类化合物和聚酮的代谢、植物与病原体的相互作用以及植物信号转导。主要属于环境适应。蛋白质组学在 Cas9/Nip 和 ABE/Nip 比较中分别揭示了 298 个和 54 个水稻差异表达蛋白 (DEP)。

根据转录组和蛋白质组学综合分析，结果表明，没有新产生的基因被鉴定为这些差异表达基因的新转录本，基因编辑工具对水稻转录水平影响很小，基因编辑的水稻中没有产生新的蛋白质。