Abstract
Recently a likely prion was found in the proteome of Arabidopsis thaliana based on inclusive compositional similarity to known yeast prion-like domains (PrLDs) and gene ontology analysis. A total of 474 proteins in the Arabidopsis thaliana proteome showed significant compositional similarity to known PrLDs in yeast warranting further analysis. In this chapter, we describe the use and limitations of the PLAAC (Prion-Like Amino Acid Composition) software for the identification of prions, specifically as it has recently been applied to identifying the first prion in plants. Our interest in this method, though presented from a plant-based perspective here, is broad and is primarily in using the method for comparative assessment with novel prion identification algorithms currently under development in our lab. This chapter is not meant to serve as a replete description of the architecture and use of HMM in prion prediction in general but is intended to serve as a reference for implementation and interpretation of output from PLAAC and its application to plant proteomes.
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Dixson, J.D., Azad, R.K. (2022). A Protocol for Prion Discovery in Plants. In: Shulaev, V. (eds) Plant Metabolic Engineering. Methods in Molecular Biology, vol 2396. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1822-6_16
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DOI: https://doi.org/10.1007/978-1-0716-1822-6_16
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