Integrative analysis of transcriptome and metabolome provides insights into the effects on different tissues by overexpression and knockout of NtLHT1

Abstract NtLHT1 is a multifunctional amino acid transporter involved in plant development and defense responses. This study investigated the effects of NtLHT1 knockout (LHT1-KO) and overexpression (LHT1-OE) on metabolic and transcriptomic profiles across three tobacco organs-leaves, stems and roots. Metabolomics analysis showed LHT1-KO and LHT1-OE caused significant changes in metabolites from various pathways, particularly amino acids, flavonoids, lipids, and terpenoids, with the specific effects differing across organs. RNA-seq transcriptomics revealed major organ-specific transcriptional changes caused by LHT1-KO and LHT1-OE. In leaves, LHT1-KO specifically downregulated genes involved in photosynthesis like MENG and TMN7, while LHT1-OE upregulated DNA replication and photosynthesis genes. In stems, LHT1-OE induced phenylpropanoid biosynthesis genes but in roots it induced carbon metabolism and oxidative phosphorylation. Taken together, these multi-omics analyses demonstrate that NtLHT1 has heterogeneous effects across different tobacco organs, highlighting the complexity of its functional roles in plant amino acid transport, vegetative growth and Secondary metabolite biosynthesis.