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Open AccessArticle

Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays

by 1,2 and 1,3,*
1
Graduate Institute of Systems Biology and Bioinformatics, and Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Jhongli 32001, Taiwan
2
Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
3
Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2021, 22(2), 760; https://doi.org/10.3390/ijms22020760
Received: 31 October 2020 / Revised: 8 December 2020 / Accepted: 9 December 2020 / Published: 13 January 2021
(This article belongs to the Special Issue Peptides for Health Benefits 2020)
Antimicrobial peptides (AMPs) are intensively studied in terms of alternative drugs. Sub5 is a synthetic 12-mer AMP with substitutions of five amino acids of bactenecin 2A (Bac2A), a linear-ized bactenecin variant of bovine. Sub5 is highly effective against fungi with an ability to trans-locate cell membrane, but its targets are unknown. Systematic analysis of Sub5 targets will facil-itate our understanding on its mechanism of action. In this study, we used high-throughput Saccharomyces cerevisiae proteome microarrays to explore the potential protein targets of Sub5. The screening results showed 128 potential protein targets of Sub5. Bioinformatics analysis of protein targets of Sub5 revealed significant gene ontology (GO) enrichment in actin related pro-cess of “actin filament-based process”, “actin filament organization”, “actin cortical patch or-ganization”, regulation of “actin filament bundle assembly”. Moreover, the other enriched cat-egories in GO enrichment mostly contained actin associate proteins. In total, 11 actin-associated proteins were identified in the protein targets of Sub5. Protein family (PFAM) enrichment anal-ysis shows protein domain enriched in actin binding, i.e., “Cytoskeletal-regulatory complex EF hand (helix E-loop-helix F motif)”. Being consistent with GO analysis, Search Tool for the Re-trieval of Interacting Genes/Proteins (STRING) analysis of the protein targets of Sub5 showed ac-tin network with involvement of 15 protein targets. Along with actin-network, STRING analysis showed protein–protein interaction network in ribonucleoprotein, transcription and translation, chromosome, histone, and ubiquitin related, DNA repair, and chaperone. Multiple Expression motifs for Motif Elicitation (MEME) suite provided a consensus binding motif of [ED][ED]EEE[ED][ED][ED][ED][ED], in total of 75 protein targets of Sub5. This motif was present in 9 out of 15 actin-related proteins identified among protein targets of Sub5. View Full-Text
Keywords: Sub5; antifungal activity; antimicrobial peptides (AMPs); proteome microarray; target identification Sub5; antifungal activity; antimicrobial peptides (AMPs); proteome microarray; target identification
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MDPI and ACS Style

Shah, P.; Chen, C.-S. Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays. Int. J. Mol. Sci. 2021, 22, 760. https://doi.org/10.3390/ijms22020760

AMA Style

Shah P, Chen C-S. Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays. International Journal of Molecular Sciences. 2021; 22(2):760. https://doi.org/10.3390/ijms22020760

Chicago/Turabian Style

Shah, Pramod; Chen, Chien-Sheng. 2021. "Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays" Int. J. Mol. Sci. 22, no. 2: 760. https://doi.org/10.3390/ijms22020760

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