Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry.
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.
Lakshmi Dhevi
LD
Nagarajha Selvan
Jyothi Embekkat
JE
Kaviyil
Raja Sekhar
RS
Nirujogi
Babylakshmi
B
Muthusamy
Vinuth N
VN
Puttamallesh
Tejaswini
T
Subbannayya
Nazia
N
Syed
Aneesha
A
Radhakrishnan
Dhanashree S
DS
Kelkar
Sartaj
S
Ahmad
Sneha M
SM
Pinto
Praveen
P
Kumar
Anil K
AK
Madugundu
Bipin
B
Nair
Aditi
A
Chatterjee
Akhilesh
A
Pandey
Raju
R
Ravikumar
Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. harsha@ibioinformatics.org.
Harsha
H
Gowda
Thottethodi Subrahmanya Keshava
TS
Prasad