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Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry
Lakshmi Dhevi Nagarajha Selvan, Jyothi Embekkat Kaviyil, Raja Sekhar Nirujogi
1Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. harsha@ibioinformatics.org.
Background:
Cryptococcus neoformans, a basidiomycetous fungus of universal occurrence, is a significant opportunistic human pathogen causing meningitis. Owing to an increase in the number of immunosuppressed individuals along with emergence of drug-resistant strains, C. neoformans is gaining importance as a pathogen. Although, whole genome sequencing of three varieties of C. neoformans has been completed recently, no global proteomic studies have yet been reported.
Results:
We performed a comprehensive proteomic analysis of C. neoformans var. grubii (Serotype A), which is the most virulent variety, in order to provide protein-level evidence for computationally predicted gene models and to refine the existing annotations. We confirmed the protein-coding potential of 3,674 genes from a total of 6,980 predicted protein-coding genes. We also identified 4 novel genes and corrected 104 predicted gene models. In addition, our studies led to the correction of translational start site, splice junctions and reading frame used for translation in a number of proteins. Finally, we validated a subset of our novel findings by RT-PCR and sequencing.
Conclusions:
Proteogenomic investigation described here facilitated the validation and refinement of computationally derived gene models in the intron-rich genome of C. neoformans, an important fungal pathogen in humans.
Insights
This study presents a proteogenomic analysis of Cryptococcus neoformans var. grubii, validating and refining gene models in this important fungal pathogen. Findings confirm protein-coding potential for thousands of genes and identify novel genetic elements.
Area of Science:
- Fungal genomics
- Proteomics
- Medical mycology
Background:
- Cryptococcus neoformans is a major opportunistic fungal pathogen causing meningitis, particularly in immunocompromised individuals.
- Emergence of drug-resistant strains and increasing numbers of immunosuppressed patients heighten the importance of C. neoformans as a pathogen.
- Despite whole-genome sequencing, global proteomic studies for C. neoformans were lacking.
Purpose of the Study:
- To conduct a comprehensive proteomic analysis of Cryptococcus neoformans var. grubii (Serotype A).
- To provide protein-level evidence for computationally predicted gene models.
- To refine existing gene annotations in the C. neoformans genome.
Main Methods:
- Comprehensive proteomic analysis of C. neoformans var. grubii.
- Validation of novel findings using RT-PCR and sequencing.
- Comparison of proteomic data with computationally predicted gene models.
Main Results:
- Confirmed protein-coding potential for 3,674 out of 6,980 predicted genes.
- Identified 4 novel genes and corrected 104 predicted gene models.
- Corrected translational start sites, splice junctions, and reading frames for several proteins.
Conclusions:
- Proteogenomic investigation validated and refined computationally derived gene models in C. neoformans.
- This study provides crucial protein-level evidence for the intron-rich genome of this significant human fungal pathogen.
- Refined gene annotations improve our understanding of C. neoformans biology and pathogenesis.
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