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

来源：

CLINICAL PROTEOMICS | 2014年 / 11卷

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.

引用

页数：16

共 52 条

[51] Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger [J].

Wright, James C. ;

Sugden, Deana ;

Francis-McIntyre, Sue ;

Riba-Garcia, Isabel ;

Gaskell, Simon J. ;

Grigoriev, Igor V. ;

Baker, Scott E. ;

Beynon, Robert J. ;

Hubbard, Simon J. .

BMC GENOMICS, 2009, 10

[52] Molecular and genetic analysis of the Cryptococcus neoformans MET3 gene and a met3 mutant [J].

Yang, ZH ;

Pascon, RC ;

Alspaugh, JA ;

Cox, GM ;

McCusker, JH .

MICROBIOLOGY-SGM, 2002, 148 :2617-2625

← 1 2 3 4 5 6 →