Dissecting Candida Pathobiology: Post-Translational Modifications on the Candida tropicalis Proteome

Abstract

Candida tropicalis belongs to the non-albicans group of Candida, and causes epidermal, mucosal, or systemic candidiasis in immunocompromised individuals. Although the prevalence of candidiasis has increased worldwide and non-albicans Candida (NAC) are becoming more significant, there are very few studies that focus on the NAC biology. Proteins and their post-translational modifications (PTMs) are an integral aspect in the pathobiology of such medically important fungi. Previously, we had reported the largest proteomic catalog of C. tropicalis. Notably, PTMs can be identified from proteomics data without a priori enrichment for a particular PTM, thus allowing broad-scale omics analyses. In this study, we developed the "PTM-Pro," a graphical user interface-based tool for identification and summary of high-confidence PTM sites based on statistical threshold of users' choice. We mined available proteomic data of C. tropicalis, and using PTM-Pro identified nearly 600 high-confidence PTM sites. The PTMs identified include phosphorylation of serine, threonine, and tyrosine; acetylation, crotonylation, methylation, and succinylation of lysine. These PTMs reside on biologically significant molecules, including histones, enzymes, and transcription factors. To our knowledge, this is the first report of PTMs in C. tropicalis and lays a foundation for future investigations of C. tropicalis PTMs. In addition, the PTM-Pro offers a graphical user interface tool for research on PTM sites in the field of proteomics.

Triton X‐114 Fractionated Subcellular Proteome of Leptospira interrogans Shows Selective Enrichment of Pathogenic and Outer Membrane Proteins in the Detergent Fraction

“…The intensity‐based absolute quantification (iBAQ) value was generated using the iBAQ algorithm, which estimates the relative abundance of proteins within each sample. [ 27 ] The proteomic data obtained by MS analysis were deposited to the ProteomeXchange Consortium via the PRoteomics IDEntifications database, [ 28,29 ] a partner repository, under the dataset identifiers PXD009050 and PXD016204.…”

Temporal Quantitative Proteomics Reveals Proteomic and Phosphoproteomic Alterations Associated with Adaptive Response to Hypoxia in Melanoma Cells

“…We identified and quantified 13,269 phosphosites corresponding to 2796 proteins. A phosphoRS score of 75% was used as a threshold to identify phosphosites that were mapped reliably with high confidence [ 36 ]. Using this stringent threshold, we identified 9456 phosphosites.…”

Temporal Quantitative Phosphoproteomics Profiling of Interleukin-33 Signaling Network Reveals Unique Modulators of Monocyte Activation

“…Phosphopeptides with a log2-fold change ≥±0.58496 were considered to be differentially regulated. An online post-translational modification-profiling (PTM-Pro) (Version 2.0) tool ( , accessed on 26 December 2021) was employed for summarizing the high-confidence PTMs with a ptmRS site probability >75%, in accordance with previous research [ 25 ].…”