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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number5
JournalClinical Proteomics
Volume11
Issue number1
DOIs
StatePublished - 2014

Fingerprint

Cryptococcus neoformans
Yeast
Mass spectrometry
Mass Spectrometry
Genes
Yeasts
Pathogens
Proteomics
Proteins
Genome
Reading Frames
Meningitis
Introns
Fungi
Proteogenomics
Polymerase Chain Reaction
Pharmaceutical Preparations

Keywords

  • Antifungal drugs
  • Computational prediction
  • Cryptococcal meningitis
  • Fungal genomics
  • Fungal infection
  • Genome annotation

ASJC Scopus subject areas

  • Molecular Biology
  • Molecular Medicine
  • Clinical Biochemistry

Cite this

Selvan, L. D. N., Kaviyil, J. E., Nirujogi, R. S., Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., ... Prasad, T. S. K. (2014). Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics, 11(1), [5]. https://doi.org/10.1186/1559-0275-11-5

Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry. / Selvan, Lakshmi Dhevi Nagarajha; Kaviyil, Jyothi Embekkat; Nirujogi, Raja Sekhar; Muthusamy, Babylakshmi; Puttamallesh, Vinuth N.; Subbannayya, Tejaswini; Syed, Nazia; Radhakrishnan, Aneesha; Kelkar, Dhanashree S.; Ahmad, Sartaj; Pinto, Sneha M.; Kumar, Praveen; Madugundu, Anil K.; Nair, Bipin; Chatterjee, Aditi; Pandey, Akhilesh; Ravikumar, Raju; Gowda, Harsha; Prasad, Thottethodi Subrahmanya Keshava.

In: Clinical Proteomics, Vol. 11, No. 1, 5, 2014.

Research output: Contribution to journalArticle

Selvan, LDN, Kaviyil, JE, Nirujogi, RS, Muthusamy, B, Puttamallesh, VN, Subbannayya, T, Syed, N, Radhakrishnan, A, Kelkar, DS, Ahmad, S, Pinto, SM, Kumar, P, Madugundu, AK, Nair, B, Chatterjee, A, Pandey, A, Ravikumar, R, Gowda, H & Prasad, TSK 2014, 'Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry', Clinical Proteomics, vol. 11, no. 1, 5. https://doi.org/10.1186/1559-0275-11-5
Selvan, Lakshmi Dhevi Nagarajha ; Kaviyil, Jyothi Embekkat ; Nirujogi, Raja Sekhar ; Muthusamy, Babylakshmi ; Puttamallesh, Vinuth N. ; Subbannayya, Tejaswini ; Syed, Nazia ; Radhakrishnan, Aneesha ; Kelkar, Dhanashree S. ; Ahmad, Sartaj ; Pinto, Sneha M. ; Kumar, Praveen ; Madugundu, Anil K. ; Nair, Bipin ; Chatterjee, Aditi ; Pandey, Akhilesh ; Ravikumar, Raju ; Gowda, Harsha ; Prasad, Thottethodi Subrahmanya Keshava. / Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry. In: Clinical Proteomics. 2014 ; Vol. 11, No. 1.
@article{c0b13fc4d210484096210dc9a171c61d,
title = "Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry",
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.",
keywords = "Antifungal drugs, Computational prediction, Cryptococcal meningitis, Fungal genomics, Fungal infection, Genome annotation",
author = "Selvan, {Lakshmi Dhevi Nagarajha} and Kaviyil, {Jyothi Embekkat} and Nirujogi, {Raja Sekhar} and Babylakshmi Muthusamy and Puttamallesh, {Vinuth N.} and Tejaswini Subbannayya and Nazia Syed and Aneesha Radhakrishnan and Kelkar, {Dhanashree S.} and Sartaj Ahmad and Pinto, {Sneha M.} and Praveen Kumar and Madugundu, {Anil K.} and Bipin Nair and Aditi Chatterjee and Akhilesh Pandey and Raju Ravikumar and Harsha Gowda and Prasad, {Thottethodi Subrahmanya Keshava}",
year = "2014",
doi = "10.1186/1559-0275-11-5",
language = "English (US)",
volume = "11",
journal = "Clinical Proteomics",
issn = "1542-6416",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Proteogenomic analysis of pathogenic yeast cryptococcus neoformans using high resolution mass spectrometry

AU - Selvan, Lakshmi Dhevi Nagarajha

AU - Kaviyil, Jyothi Embekkat

AU - Nirujogi, Raja Sekhar

AU - Muthusamy, Babylakshmi

AU - Puttamallesh, Vinuth N.

AU - Subbannayya, Tejaswini

AU - Syed, Nazia

AU - Radhakrishnan, Aneesha

AU - Kelkar, Dhanashree S.

AU - Ahmad, Sartaj

AU - Pinto, Sneha M.

AU - Kumar, Praveen

AU - Madugundu, Anil K.

AU - Nair, Bipin

AU - Chatterjee, Aditi

AU - Pandey, Akhilesh

AU - Ravikumar, Raju

AU - Gowda, Harsha

AU - Prasad, Thottethodi Subrahmanya Keshava

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - Antifungal drugs

KW - Computational prediction

KW - Cryptococcal meningitis

KW - Fungal genomics

KW - Fungal infection

KW - Genome annotation

UR - http://www.scopus.com/inward/record.url?scp=84903795994&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84903795994&partnerID=8YFLogxK

U2 - 10.1186/1559-0275-11-5

DO - 10.1186/1559-0275-11-5

M3 - Article

C2 - 24484775

AN - SCOPUS:84903795994

VL - 11

JO - Clinical Proteomics

JF - Clinical Proteomics

SN - 1542-6416

IS - 1

M1 - 5

ER -