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Single-cell metabolome and RNA-seq multiplexing on single plant cells
Moonyoung Kang1, Anh Hai Vu1, Abbie L Casper2
1Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.
Summary
Researchers developed a new method to measure gene expression and metabolite levels in the same plant cell. This breakthrough allows direct correlation of biosynthetic genes with natural product compounds in individual cells.
Area of Science:
- Plant biochemistry
- Molecular biology
- Genomics
Background:
- Plants synthesize valuable natural products crucial for various industries.
- Understanding plant biosynthetic pathways is of significant interest.
- Gene-to-metabolite networks, derived from transcriptomic and metabolomic data, aid pathway identification.
- Single-cell RNA sequencing (scRNA-seq) and single-cell mass spectrometry metabolomics (scMS) measure gene expression or metabolite levels individually.
- Current methods only allow indirect correlation between gene expression and metabolite levels at the single-cell level.
Purpose of the Study:
- To demonstrate the feasibility of applying both scRNA-seq and scMS to the same plant cell.
- To enable direct comparison of gene expression and metabolite levels within individual cells.
- To reveal correlations between metabolite concentrations and biosynthetic gene expression in single plant cells.
Main Methods:
- Utilized protoplasts from *Catharanthus roseus* leaves.
- Employed a microfluidics-based robot for sorting protoplasts into 96-well plates.
- Developed lysis conditions compatible with both scMS and SMART-seq single-cell protocols.
- Applied a multiplexing approach for simultaneous gene expression and metabolite analysis.
Main Results:
- Successfully applied scRNA-seq and scMS to the same plant cell.
- Enabled direct, single-cell level comparisons between gene expression and metabolite levels.
- Revealed both qualitative and quantitative correlations between metabolite levels and biosynthetic gene expression.
- Provided insights into the regulatory mechanisms of plant biosynthesis at the single-cell level.
Conclusions:
- The integrated scRNA-seq and scMS approach is a powerful proof-of-concept for plant science.
- This method facilitates a deeper understanding of complex plant biosynthetic pathways.
- It opens new avenues for studying natural product formation in plants at an unprecedented resolution.
