Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health.
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.
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|2 School of Biotechnology, KIIT University , Bhubaneswar, India .
Keshava K
KK
Datta
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|2 School of Biotechnology, KIIT University , Bhubaneswar, India .
Arun H
AH
Patil
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|3 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham , Kollam, India .
Krishna
K
Patel
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|4 Manipal University , Madhav Nagar, Manipal, India .
Gourav
G
Dey
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|5 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India .
Anil K
AK
Madugundu
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|3 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham , Kollam, India .
Santosh
S
Renuse
6 Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India .
Jyothi E
JE
Kaviyil
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|5 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India .
Raja
R
Sekhar
2 School of Biotechnology, KIIT University , Bhubaneswar, India .
Aryashree
A
Arunima
7 National Institute for Research in Reproductive Health (ICMR) , Parel, Mumbai, India .
Bhavna
B
Daswani
8 Malaria Research Group, International Center for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, India .
Inderjeet
I
Kaur
9 ICAR-Central Institute of Freshwater Aquaculture , Kausalyaganga, Bhubaneswar, India .
Jyotirmaya
J
Mohanty
10 ITC LSTC , Bangalore, India .
Ranjana
R
Sinha
2 School of Biotechnology, KIIT University , Bhubaneswar, India .
Sangeeta
S
Jaiswal
11 Department of Ocular Pathology, Vision Research Foundation , Chennai, India .
S
S
Sivapriya
12 Great Eastern Medical School & Hospital , Ragolu, Srikakulam, India .
Yeshwanth
Y
Sonnathi
13 Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, The M. S. University of Baroda , Vadodara, India .
Bharat B
BB
Chattoo
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|2 School of Biotechnology, KIIT University , Bhubaneswar, India .|14 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .
Harsha
H
Gowda
6 Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India .
Raju
R
Ravikumar
1 Institute of Bioinformatics , International Technology Park, Bangalore, India.|14 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .|15 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India .
T S Keshava
TS
Prasad
D041022:Candida tropicalis / Q000235:genetics / Q000378:metabolism*; D017077:Culture Media, Conditioned; D005656:Fungal Proteins / Q000235:genetics*; D016681:Genome, Fungal; D014943:Global Health; D013058:Mass Spectrometry
D017077:Culture Media, Conditioned; D005656:Fungal Proteins