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Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens
Published on: June 6, 2020
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A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to
Carolyn J Schultz1, Yue Wu2, Ute Baumann2
1School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia. carolyn.schultz@adelaide.edu.au.
Mycorrhiza
|January 15, 2022
Summary
Arbuscular mycorrhizal fungi (AMF) diversity enhances ecosystems. Researchers identified novel, highly variable intrinsically disordered proteins (IDPs) in AMF, suggesting a molecular basis for functional complementarity and ecosystem resilience.
Area of Science:
- Mycology
- Plant-microbe interactions
- Bioinformatics
Background:
- Arbuscular mycorrhizal fungi (AMF) are crucial for ecosystem health and agricultural productivity.
- Functional complementarity in AMF symbiosis is observed but lacks molecular explanation.
- Intrinsically disordered proteins (IDPs) are hypothesized to contribute due to their flexible nature and potential for diverse interactions.
Purpose of the Study:
- To investigate the molecular basis of functional complementarity in AMF.
- To identify and characterize intrinsically disordered proteins (IDPs), specifically arabinogalactan-protein-like proteins (AGLs), in AMF.
- To develop a bioinformatics approach for discovering variable IDPs in AMF RNA-sequence data.
Main Methods:
- A targeted bioinformatics approach combining modified k-mer assembly (Oases) and targeted sequence capture/assembly (mirabait-mira).
- Analysis of RNA-sequence datasets from various AMF species, including the ancestral Paraglomeraceae family.
- Bioinformatic identification of proteins rich in disorder-promoting amino acids (proline, glycine, asparagine).
Main Results:
- Identified small families of highly variable, disorder-rich proteins (AGLs/IDPs) across all analyzed AMF species.
- Found glycine- and asparagine-rich proteins in Geosiphon pyriformis, a related symbiont.
- Predicted functional diversity in AGLs based on the physical properties of their tandem repeats and broad pI ranges.
Conclusions:
- Sequence diversity in AGLs/IDPs likely underlies functional complementarity in AMF.
- These proteins may contribute to nutrient retention, soil stability, and water movement.
- The developed bioinformatics approach is effective for identifying variable IDPs in AMF, advancing our understanding of fungal symbiosis.
