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Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health

Keshava K Datta1,2, Arun H Patil1,2, Krishna Patel1,3

  • 11 Institute of Bioinformatics , International Technology Park, Bangalore, India.

Omics : a Journal of Integrative Biology
|April 20, 2016
PubMed

Insights

This study used proteomics to validate and refine the genome annotation of Candida tropicalis, an emerging fungal pathogen. Proteogenomic analysis identified novel genes and corrected existing models, aiding future efforts against rising Candida infections.

Area of Science:

  • Mycology
  • Proteomics
  • Genomics

Background:

  • Candida infections are increasing globally, worsened by azole resistance in fungal pathogens.
  • Candida tropicalis, a non-albicans Candida species, is an opportunistic pathogen frequently causing infections in immunocompromised individuals.
  • Existing genome annotation for C. tropicalis lacks experimental validation.

Purpose of the Study:

  • To perform comprehensive proteomics profiling of Candida tropicalis.
  • To validate computationally predicted protein-coding genes using experimental evidence.
  • To refine the current genome annotation of C. tropicalis through proteogenomic analysis.

Main Methods:

  • High-resolution Fourier transform mass spectrometry was employed for proteomics profiling.
  • Proteome analysis was conducted on both cell lysate and conditioned media of C. tropicalis.
  • Mass spectrometry data underwent proteogenomic analysis to identify novel genetic elements and correct gene models.

Main Results:

  • Identified 2743 proteins, validating approximately 44% of predicted protein-coding genes at the peptide level.
  • Analyzed 2591 proteins in cell lysate and 780 proteins in conditioned media, including unique secreted proteins.
  • Discovered 86 novel genes, 12 novel exons, and corrected 49 computationally predicted gene models.

Conclusions:

  • This study represents the first high-throughput proteomics investigation to validate C. tropicalis genes and refine its genome annotation.
  • The proteogenomic findings provide crucial experimental evidence for the C. tropicalis genome.
  • These results can contribute to future global health strategies for combating Candida infections.

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