Table 1.
Accession numbers, source databases, and original references where used. CDS, coding sequence; NCBI SRA, National Centre for Biotechnology Information Sequence Read Archive.
Fig 1.
Schematic of the method for identifying coproantigens of Strongyloides stercoralis using ‘omic’ data and computational analyses.
Filled shapes represent datasets, colours represent analyses against three characteristics of a candidate coproantigen. E/S, excreted and secreted; MSA, multiple sequence alignment; Ss, Strongyloides stercoralis; BLAST, basic local alignment search tool; DE, differentially expressed.
Fig 2.
Strongyloides stercoralis life stages.
Asterisks indicate life stages for which transcriptomic data were obtained by Stoltzfus et al. (2012). We grouped these transcriptomic data by presence in the host gut (boxed asterisks), and outside the host gut. P Females, parasitic females; PP, post parasitic; FL, Free-living; PFL, post free-living; L1, stage 1 larva; L3, stage 3 larva; iL3, infectious third stage larva; L3+, tissue-migrating larva; L3a, autoinfective L3. Figure modified from Stoltzfus et al. (2012) [37] under a CC BY license. Accession numbers are given for NCBI SRA for the triplicate reads in Table 1.
Table 2.
Outgroup species used for phylogenetic comparison to S. stercoralis.
Fig 3.
Strongyloides stercoralis proteins differentially expressed (DE) between gut-dwelling and non-gut-dwelling life stages and their overlap with other analyses.
Panel A; DE proteins grouped by sequence similarity with protein families identified. Colours refer to features or families; the 5 priority protein families analysed in depth (SCP/TAPS; TTL; AChE; aspartic peptidases, and POP) are labelled with an asterisk and boxed text; pale grey indicates proteins not identified by any method, dark grey indicates disordered proteins. Panel B, overlap, in numbers of proteins, between the DE proteins and other analyses. In both panels, labels indicate: a, the 328 S. stercoralis DE proteins; b, proteins orthologous to S. ratti E/S proteins; c, proteins containing epitopes predicted by BcePred (left in Panel A) and BepiPred (right in Panel A); d, the 203 proteins that were DE in gut-dwelling life stages. Gene accession numbers and all protein family names for the DE proteins can be found in S2 and S4 Files for E/S orthologues. These results originate from methods in Fig 1, boxes C-H and M).
Fig 4.
Phylogenetic alignment of Strongyloides stercoralis high priority family proteins with other S. stercoralis proteins and outgroups.
Proteins of the five priority families of S. stercoralis (dark green), from the differentially expressed dataset, in phylogenetic alignment with BLAST hits from S. stercoralis itself (black) and outgroups (other colours). Colours reaching the outer edge represent Strongyloides species, whereas shorter colour bands are non-Strongyloides outgroups. (A) SCP/TAPS, (B) transthyretin-like (TTL), (C) acetylcholinesterase (AChE), (D) aspartic peptidase, (E) prolyl oligopeptidase (POP). Arrows indicate clusters of S. stercoralis proteins containing species-specific regions; derived from both gut- and non-gut-dwelling differential expression data, augmenting detection of lack of species specificity. These results originate from methods in Fig 1, box K.
Table 3.
Candidate coproantigens of S. stercoralis based on upregulation in parasitism, amino acid sequence specificity to Strongyloides or S. stercoralis, and containing a predicted epitope.
Gene accession numbers can be found in WormBase ParaSite or UniProtKB. Amino acid sequences are given in S6 File. PF: parasitic female, E/S: excretory/secretory.
Fig 5.
A transthyretin-like (TTL) protein of Strongyloides stercoralis in rotated view showing surface-exposed epitope regions and N-linked glycosylation sites.
Accession number SSTP_0000700800. Blue, BepiPred predicted epitope aa’s 124–143; pink, bcepred predicted epitope aa’s 99–123; green, predicted N-linked glycosylation site at N165 in the motif NVS. The bcepred epitope (pink) extends to residue 141 but has been shortened to show the BepiPred epitope (blue), which overlaps with it. These results originate from methods shown in Fig 1, boxes M-P.
Fig 6.
Strongyloides stercoralis acetylcholinesterase in rotated views showing surface-exposed epitope regions and N-linked glycosylation sites.
Accession number SSTP_0000509400. Predicted features indicated in colour: blue, BepiPred 2.0 predicted epitope at residues 85–103; and yellow at 390–411; green, predicted N-linked glycosylation sites at N38 (NVT), N89 (NFS) and N319 (NLT). The site at N89 is within the blue epitope sequence. Both predicted epitope regions (blue and yellow) were selected as candidate coproantigens in this study. These results originate from methods shown in Fig 1, boxes M-P.