Identification and characterisation of sPEPs in Cryptococcus neoformans

Paige E Erpf; Sheena M H Chua; Toan K Phung; Edward D Kerr; Joseph A Rothnagel; Benjamin L Schulz; James A Fraser

doi:10.1016/j.fgb.2022.103688

Identification and characterisation of sPEPs in Cryptococcus neoformans

Fungal Genet Biol. 2022 May:160:103688. doi: 10.1016/j.fgb.2022.103688. Epub 2022 Mar 23.

Authors

Paige E Erpf¹, Sheena M H Chua¹, Toan K Phung¹, Edward D Kerr¹, Joseph A Rothnagel², Benjamin L Schulz³, James A Fraser⁴

Affiliations

¹ The University of Queensland, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia; The University of Queensland, Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia.
² The University of Queensland, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia.
³ The University of Queensland, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia; The University of Queensland, Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia; The University of Queensland, Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, St Lucia, Queensland 4072, Australia.
⁴ The University of Queensland, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia; The University of Queensland, Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, St Lucia, Queensland 4072, Australia. Electronic address: jafraser@uq.edu.au.

PMID: 35339703
DOI: 10.1016/j.fgb.2022.103688

Abstract

Short open reading frame (sORF)-encoded peptides (sPEPs) have been found across a wide range of genomic locations in a variety of species. To date, their identification, validation, and characterisation in the human fungal pathogen Cryptococcus neoformans has been limited due to a lack of standardised protocols. We have developed an enrichment process that enables sPEP detection within a protein sample from this polysaccharide-encapsulated yeast, and implemented proteogenomics to provide insights into the validity of predicted and hypothetical sORFs annotated in the C. neoformans genome. Novel sORFs were discovered within the 5' and 3' UTRs of known transcripts as well as in "non-coding" RNAs. One novel candidate, dubbed NPB1, that resided in an RNA annotated as "non-coding", was chosen for characterisation. Through the creation of both specific point mutations and a full deletion allele, the function of the new sPEP, Npb1, was shown to resemble that of the bacterial trans-translation protein SmpB.

Keywords: Cryptococcus neoformans; Fungi; Genetics; Pathogen; Proteogenomics; Proteomics; Small peptides; sPEPs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cryptococcus neoformans* / genetics
Fungal Proteins* / genetics
Genomics
Open Reading Frames
Peptides / genetics

Substances

Fungal Proteins
Peptides