MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase

Abstract

The subcellular location of a protein is a key factor in determining the molecular function of the protein in an organism. MetazSecKB is a secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. The protein sequence data, consisting of over 4 million entries with 121 species having a complete proteome, were retrieved from UniProtKB. Protein subcellular locations including secreted and 15 other subcellular locations were assigned based on either curated experimental evidence or prediction using seven computational tools. The protein or subcellular proteome data can be searched and downloaded using several different types of identifiers, gene name or keyword(s), and species. BLAST search and community annotation of subcellular locations are also supported. Our primary analysis revealed that the proteome sizes, secretome sizes and other subcellular proteome sizes vary tremendously in different animal species. The proportions of secretomes vary from 3 to 22% (average 8%) in metazoa species. The proportions of other major subcellular proteomes ranged approximately 21–43% (average 31%) in cytoplasm, 20–37% (average 30%) in nucleus, 3–19% (average 12%) as plasma membrane proteins and 3–9% (average 6%) in mitochondria. We also compared the protein families in secretomes of different primates. The Gene Ontology and protein family domain analysis of human secreted proteins revealed that these proteins play important roles in regulation of human structure development, signal transduction, immune systems and many other biological processes.Database URL: http://proteomics.ysu.edu/secretomes/animal/index.php

Global mRNA sequencing of human skeletal muscle: Search for novel exercise-regulated myokines

“…To identify transcripts encoding secreted proteins, we used the MetazSecKB knowledgebase [30]. MetazSecKB identifies secretory proteins based on either curated evidence of secretion (annotated and reviewed in the UniProtKB/Swiss-Prot dataset) or being “highly likely” to be secreted based on computationally predicted secretory protein sequences, without containing transmembrane domains or endoplasmic reticulum (ER) retention signals, by several tools (SignalP4, Phobius, TargetP and WoLF PSORT).…”

In silicoprediction of the secretome from the invasive neurotoxic marine dinoflagellateAlexandrium catenella

“…To predict the A. catenella secretome, we applied bioinformatics tools to the total proteome obtained from the A. catenella transcriptome (Zhang et al ., ). This secretome contains 2 779 proteins depicting 2.4% of the total proteome, which is similar to the proportions reported for: (i) the brown algae Ectocarpus siliculosus (3.4%) (Terauchi et al ., ), (ii) the plant pathogenic fungus Fusarium graminearum (4.2%) (Brown et al ., ), (iii) a nematode (9.2%) (Gahoi and Gautam, ) and (iv) human/animals (8.1%) (Meinken et al ., ). This similarity shows that generally < 10% of the total proteins are secreted, regardless of the eukaryotic kingdom considered.…”

Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses

“…Table 11). We therefore intersected this group of genes with curated and highly-likely predicted secreted proteins from the MetazSecKB database (Meinken, Walker, Cooper, & Min, 2015) and found that secreted proteins were highly enriched (59 of the 236 common genes (25%), p<0.0001). We subdivided these genes into those with concordant or discordant regulation between CPT treatment and Irf4 -/-(Supp .…”