TY - JOUR
T1 - Proteogenomics of Candida tropicalis - An Opportunistic Pathogen with Importance for Global Health
AU - Datta, Keshava K.
AU - Patil, Arun H.
AU - Patel, Krishna
AU - Dey, Gourav
AU - Madugundu, Anil K.
AU - Renuse, Santosh
AU - Kaviyil, Jyothi E.
AU - Sekhar, Raja
AU - Arunima, Aryashree
AU - Daswani, Bhavna
AU - Kaur, Inderjeet
AU - Mohanty, Jyotirmaya
AU - Sinha, Ranjana
AU - Jaiswal, Sangeeta
AU - Sivapriya, S.
AU - Sonnathi, Yeshwanth
AU - Chattoo, Bharat B.
AU - Gowda, Harsha
AU - Ravikumar, Raju
AU - Prasad, T. S.Keshava
N1 - Publisher Copyright:
© Copyright 2016, Mary Ann Liebert, Inc.
PY - 2016/4/1
Y1 - 2016/4/1
N2 - The frequency of Candida infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens. Candida tropicalis is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of Candida that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of C. tropicalis was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of C. tropicalis validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against Candida infections.
AB - The frequency of Candida infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens. Candida tropicalis is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of Candida that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of C. tropicalis was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of C. tropicalis validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against Candida infections.
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U2 - 10.1089/omi.2015.0197
DO - 10.1089/omi.2015.0197
M3 - Article
C2 - 27093108
AN - SCOPUS:84966650467
SN - 1536-2310
VL - 20
SP - 239
EP - 247
JO - OMICS A Journal of Integrative Biology
JF - OMICS A Journal of Integrative Biology
IS - 4
ER -