Comparative Proteomic Analysis of Candida albicans and Candida glabrata

Prasad, T. S. Keshava; Keerthikumar, Shivakumar; Chaerkady, Raghothama; Kandasamy, Kumaran; Renuse, Santosh; Marimuthu, Arivusudar; Venugopal, Abhilash; Thomas, Joji Kurian; Jacob, Harrys K.C.; Goel, Renu; Pawar, Harsh; Sahasrabuddhe, Nandini A.; Krishna, V.; Nair, Bipin; Guček, Marjan; Cole, Robert N.; Ravikumar, Raju; Harsha, H. C.; Pandey, Akhilesh

doi:10.1007/s12014-010-9057-9

Cited by 3 publications

(4 citation statements)

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“…Previously, we had described a comparative proteomic analysis to identify differentially expressed proteins between proteomes of C. albicans and C. glabrata, particularly to provide a discovery platform for diagnostics. 27 For this, we used iTRAQ reagents for in vitro labeling, SCX chromatography for fractionation, a quadrupole time-of-flight mass spectrometer (QSTAR/Pulsar, Applied Biosystems) for MS/MS and ProteinPilot software for MS/ MS data analysis. While analyzing the proteomic data for the previous study, we realized that most of the predicted proteins in C. glabrata genome are hypothetical.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Mass spectrometry-derived data was searched using two search algorithmsSequest and X!Tandemagainst (i) a protein database comprising of protein sequences of C. glabrata from databases of Genolevures () and NCBI RefSeq and (ii) a database of six frame translated genome of C. glabrata . Previously, we had described a comparative proteomic analysis to identify differentially expressed proteins between proteomes of C. albicans and C. glabrata , particularly to provide a discovery platform for diagnostics . For this, we used iTRAQ reagents for in vitro labeling, SCX chromatography for fractionation, a quadrupole time-of-flight mass spectrometer (QSTAR/Pulsar, Applied Biosystems) for MS/MS and ProteinPilot software for MS/MS data analysis.…”

Section: Resultsmentioning

confidence: 99%

“…19−26 In a recent study, we described a comparative proteomic strategy to identify differentially expressed proteins between proteomes of C. albicans and C. glabrata, with the goal of developing a discovery platform for diagnostics. 27 In contrast to C. albicans, which is the most studied organism among Candida species, only limited proteomic studies have been carried out in C. glabrata. 7,28 Significantly, although the complete genome sequence of C. glabrata was published in the year 2004, 29 the large majority of protein-coding genes annotated in its genome are still labeled as hypothetical.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Candida glabrata has gained importance as an opportunistic human pathogen owing to its resistance to broad-spectrum antimycotic drugs. , C. glabrata , otherwise considered as a nonpathogenic saprophytic organism, has been increasingly reported from patients suffering from acquired immunodeficiency syndrome or undergoing immunosuppressive therapy . It causes higher mortality when compared to other nonalbicans Candida species with a reported mortality rate ranging from 50 to 100% among those with cancer, septicaemia or in bone-marrow transplant patients. − In contrast, C. glabrata exhibits low virulence in animal models. , Virulence factors of C. glabrata have not been well understood at the molecular level, when compared to that of C. albicans . , Aspartyl proteinases and phospholipases, which are associated with the virulence of other Candida species, have not been observed to play a role in the pathogenesis of C. glabrata infections. − In a recent study, we described a comparative proteomic strategy to identify differentially expressed proteins between proteomes of C. albicans and C. glabrata , with the goal of developing a discovery platform for diagnostics . In contrast to C. albicans , which is the most studied organism among Candida species, only limited proteomic studies have been carried out in C. glabrata . , Significantly, although the complete genome sequence of C. glabrata was published in the year 2004, the large majority of protein-coding genes annotated in its genome are still labeled as hypothetical.…”

Section: Introductionmentioning

confidence: 99%

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Proteogenomic Analysis ofCandida glabratausing High Resolution Mass Spectrometry

et al. 2011

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Candida glabrata is a common opportunistic human pathogen leading to significant mortality in immunosuppressed and immunodeficient individuals. We carried out proteomic analysis of C. glabrata using high resolution Fourier transform mass spectrometry with MS resolution of 60,000 and MS/MS resolution of 7500. On the basis of 32,453 unique peptides identified from 118,815 peptide-spectrum matches, we validated 4421 of the 5283 predicted protein-coding genes (83%) in the C. glabrata genome. Further, searching the tandem mass spectra against a six frame translated genome database of C. glabrata resulted in identification of 11 novel protein coding genes and correction of gene boundaries for 14 predicted gene models. A subset of novel protein-coding genes and corrected gene models were validated at the transcript level by RT-PCR and sequencing. Our study illustrates how proteogenomic analysis enabled by high resolution mass spectrometry can enrich genome annotation and should be an integral part of ongoing genome sequencing and annotation efforts.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Proteogenomic Analysis ofCandida glabratausing High Resolution Mass Spectrometry

et al. 2011

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Quantitative proteomics for identifying biomarkers for tuberculous meningitis

et al. 2012

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IntroductionTuberculous meningitis is a frequent extrapulmonary disease caused by Mycobacterium tuberculosis and is associated with high mortality rates and severe neurological sequelae. In an earlier study employing DNA microarrays, we had identified genes that were differentially expressed at the transcript level in human brain tissue from cases of tuberculous meningitis. In the current study, we used a quantitative proteomics approach to discover protein biomarkers for tuberculous meningitis.MethodsTo compare brain tissues from confirmed cased of tuberculous meningitis with uninfected brain tissue, we carried out quantitative protein expression profiling using iTRAQ labeling and LC-MS/MS analysis of SCX fractionated peptides on Agilent’s accurate mass QTOF mass spectrometer.Results and conclusionsThrough this approach, we identified both known and novel differentially regulated molecules. Those described previously included signal-regulatory protein alpha (SIRPA) and protein disulfide isomerase family A, member 6 (PDIA6), which have been shown to be overexpressed at the mRNA level in tuberculous meningitis. The novel overexpressed proteins identified in our study included amphiphysin (AMPH) and neurofascin (NFASC) while ferritin light chain (FTL) was found to be downregulated in TBM. We validated amphiphysin, neurofascin and ferritin light chain using immunohistochemistry which confirmed their differential expression in tuberculous meningitis. Overall, our data provides insights into the host response in tuberculous meningitis at the molecular level in addition to providing candidate diagnostic biomarkers for tuberculous meningitis.

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iTRAQ-based proteomic profiling of Vibrio parahaemolyticus under various culture conditions

et al. 2015

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BackgroundVibrio parahaemolyticus is a common pathogen infecting humans and marine animals; this pathogen has become a major concern of marine food products and trade. In this study, V. parahaemolyticus isolated from sewage was exposed to different culture conditions and analyzed by isobaric tag for relative and absolute quantitation (iTRAQ) based reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Our goal is to gain further insights into the proteomics of V. parahaemolyticus, particularly differentially expressed proteins closely correlated with growth conditions and pathogenicity associated proteins.ResultsIn this study, a total of 2,717 proteins including numerous membrane proteins were significantly identified, and 616 proteins displayed significant differential expression under different conditions. Of them, 12 proteins mainly participating in metabolism showed the most elastic expression differentiation between different culture conditions. Some membrane proteins such as type I secretion outer membrane protein, TolC, lipoprotein, efflux system proteins iron-regulated protein A and putaive Fe-regulated protein B, ferric siderophore receptor homolog and several V. parahaemolyticus virulence-associated proteins were differentially regulated under different conditions. Some differentially regulated proteins were analyzed and confirmed at gene expression level by quantitative real time polymerase chain reaction (qRT-PCR).ConclusionsProteomics analysis results revealed the characteristics of V. parahaemolyticus proteome expression, provided some promising biomarkers related with growth conditions, the results likely advance insights into the mechanism involved in the response of V. parahaemolyticus to different conditions. Some virulence-associated proteins were discovered to be differentially expressed under different conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12953-015-0075-4) contains supplementary material, which is available to authorized users.

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Comparative Proteomic Analysis of Candida albicans and Candida glabrata

Cited by 3 publications

References 64 publications

Proteogenomic Analysis ofCandida glabratausing High Resolution Mass Spectrometry

Proteogenomic Analysis ofCandida glabratausing High Resolution Mass Spectrometry

Quantitative proteomics for identifying biomarkers for tuberculous meningitis

iTRAQ-based proteomic profiling of Vibrio parahaemolyticus under various culture conditions

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