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Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry

Ahmad, Sartaj and Pinto, Sneha M and Chatterjee, Aditi and Prasad, Keshava TS (2014) Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics, 11 (5). pp. 1-16.

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Abstract

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.

Item Type: Article
Uncontrolled Keywords: Fungal infection; fungal genomics; antifungal drugs; cryptococcal meningitis; computational prediction; genome annotation
Subjects: Research > Research Center - Health Sciences
Depositing User: KMC Manipal
Date Deposited: 13 Feb 2015 06:25
Last Modified: 13 Feb 2015 06:25
URI: http://eprints.manipal.edu/id/eprint/141896

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