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Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry |
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| Authors: | Lakshmi Dhevi Nagarajha Selvan Jyothi Embekkat Kaviyil Raja Sekhar Nirujogi Babylakshmi Muthusamy Vinuth N Puttamallesh Tejaswini Subbannayya Nazia Syed Aneesha Radhakrishnan Dhanashree S Kelkar Sartaj Ahmad Sneha M Pinto Praveen Kumar Anil K Madugundu Bipin Nair Aditi Chatterjee Akhilesh Pandey Raju Ravikumar Harsha Gowda Thottethodi Subrahmanya Keshava Prasad |
| Affiliation: | 1. Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India 2. Amrita School of Biotechnology, Amrita University, Kollam, 690 525, India 3. Department of Neuromicrobiology, National Institute of Mental Health and Neuro Sciences, Bangalore, 560 029, India 4. Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605 014, India 5. Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605 014, India 6. Manipal University, Madhav Nagar, Manipal, 576 104, India 10. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA 7. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA 8. Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA 9. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA |
| Abstract: | BackgroundCryptococcus 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.ResultsWe 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.ConclusionsProteogenomic 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. |
| Keywords: | Fungal infection Fungal genomics Antifungal drugs Cryptococcal meningitis Computational prediction Genome annotation |
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