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

被引:15
作者
Selvan, Lakshmi Dhevi Nagarajha [1 ,2 ]
Kaviyil, Jyothi Embekkat [3 ]
Nirujogi, Raja Sekhar [1 ,4 ]
Muthusamy, Babylakshmi [1 ,4 ]
Puttamallesh, Vinuth N. [1 ]
Subbannayya, Tejaswini [1 ,2 ]
Syed, Nazia [1 ,5 ]
Radhakrishnan, Aneesha [1 ,5 ]
Kelkar, Dhanashree S. [1 ,2 ]
Ahmad, Sartaj [1 ,6 ]
Pinto, Sneha M. [1 ,6 ]
Kumar, Praveen [1 ]
Madugundu, Anil K. [1 ]
Nair, Bipin [2 ]
Chatterjee, Aditi [1 ,6 ]
Pandey, Akhilesh [7 ,8 ,9 ,10 ]
Ravikumar, Raju [3 ]
Gowda, Harsha [1 ]
Prasad, Thottethodi Subrahmanya Keshava [1 ,2 ,4 ,6 ]
机构
[1] Inst Bioinformat, Int Technol Pk, Bangalore 560066, Karnataka, India
[2] Amrita Univ, Amrita Sch Biotechnol, Kollam 690525, India
[3] Natl Inst Mental Hlth & Neurosci, Dept Neuromicrobiol, Bangalore 560029, Karnataka, India
[4] Pondicherry Univ, Sch Life Sci, Ctr Excellence Bioinformat, Pondicherry 605014, India
[5] Pondicherry Univ, Sch Life Sci, Dept Biochem & Mol Biol, Pondicherry 605014, India
[6] Manipal Univ, Manipal 576104, Karnataka, India
[7] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Sch Med, Baltimore, MD 21205 USA
[8] Johns Hopkins Univ, Dept Biol Chem, Sch Med, Baltimore, MD 21205 USA
[9] Johns Hopkins Univ, Dept Pathol, Sch Med, Baltimore, MD 21205 USA
[10] Johns Hopkins Univ, Dept Oncol, Sch Med, Baltimore, MD 21205 USA
关键词
Fungal infection; Fungal genomics; Antifungal drugs; Cryptococcal meningitis; Computational prediction; Genome annotation; GENOME ANNOTATION; PROTEOMIC DATA; VAR; GRUBII; GENE; IDENTIFICATION; SEROTYPE; ACCURACY; SEQUENCE; ELEGANS;
D O I
10.1186/1559-0275-11-5
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
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页数:16
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