Fig 1.
Some relevant abbreviations used in this paper.
Detailed domain sturcture for each abbreviation can be found in Fig 3. FBG: fibrinogen domain; EGF-like: epidermal growth factor (EGF)-like domain; IgSF1: Immunoglobulin Superfamily Member 1; IgSF2: Immunoglobulin Superfamily Member 2; ICR: interceding region (<150aa) between IgSF and FBG domains that form coiled coils; long ICR: long interceding region (150~320aa).
Fig 2.
Workflow to predict FBG and IgSF domains in the genome assembly of BB02 B. glabrata.
The colored boxes highlight some of the important steps/results in the workflow.
Table 1.
Summary of 39 FREPs discussed in this study.
Table 2.
Summary of predicted FReD proteins in B. glabrata BB02 strain.
Fig 3.
Predicted domain architectures of FReD proteins in B. glabrata BB02.
Three main categories are indicated: sFReD (FBG), FReM (EGF-like + FBG), 1-IgSF FREP (1 IgSF loop + FBG), and 2-IgSF FREP (2 IgSF loops + FBG). FBG: fibrinogen domain; EGF-like: epidermal growth factor (EGF)-like domain; PAN/Apple: PAN/Apple domain; IgSF1: Immunoglobulin Superfamily Member 1; IgSF2: Immunoglobulin Superfamily Member 2; ICR: interceding region (<150aa) between IgSF and FBG domains that form coiled coils; long ICR: long interceding region (150~320aa).
Fig 4.
Gene tree and representative protein domain architecture of 73 B. glabrata FReDs.
A. Maximum likelihood tree with 1000 bootstrap tests was constructed using full length representative protein sequences of 73 FReD genes in B. glabrata. Nodes with bootstrap support of 75 or higher are marked with black squares. The gene IDs of the 73 FReDs were followed with number of IgSF domains and the best hit with any published FREP genes (BLASTp hit with at least 150 aa aligned with ≥ 90% identity was considered as the same FREP; or considered a “FREP-like” gene if identity was 85% ~ 90%; identity <85% was not assigned to any published FREP). Any FReD genes with best hit to FREPs from the genome paper [32] are labeled with a red dot at the corresponding gene ID. Complete FREP or FReD genes fitting the criteria in this study were highlighted in blue text. B. Domain architectures were predicted using InterProScan and lineage specific HMM models. “Peptide sequences” represent multiple peptide sequences extracted from a proteomics study [49]. Colored small horizontal bars above or below some protein domain structures highlight the matched location of peptide sequences with binding affinity to S. mansoni sporocyst membrane-enriched and larval transformation proteins, from either schistosome-susceptible NMRI strain (SUS in green) or -resistant BS-90 strain (RES in red) of B. glabrata. The dashed gray line was manually added to distinguish most “sFReD clades” from “FREP clades”.
Fig 5.
Violin plots of protein sequence-pairwise identity analyses of IgSF1, IgSF2, and FBG domains in B. glabrata FReD genes.
The 26 complete FREP protein sequences, and complete FBG domain sequences from all FReD genes in B. glabrata were used for pairwise blast identity analysis. Number under each Violin plot at x-axis is the number used for each assigned analysis, and y-axis represents percentage of protein sequence identity (%).
Fig 6.
Domain tree comparisons of IgSF1, IgSF2 and FBG domains from complete 2-IgSF FREPs in B. glabrata. A.
Domain structure of 2-IgSF FREPs; B. Tree distances were measured by Robinson-Foulds or symmetric distance among trees of IgSF1, IgSF2 and FBG domains from 2-IgSF FREPs; C. Tanglegram plot of a side by side ML (Maximum Likelihood) trees for IgSF1 and IgSF2 domains from 2-IgSF FREPs; D. Tanglegram plot of ML trees for IgSF1 and FBG domains from the 2-IgSF FREPs; E. Tanglegram plot of ML trees for IgSF2 and FBG domains from the 2-IgSF FREPs. The colored connection lines in 6C, 6D and 6E highlighted some common subtrees.
Fig 7.
Unrooted Maximum Likelihood (ML) trees of IgSF domains identified in B. glabrata with new HMM profile search.
A: ML tree with all IgSF domains from search using the 38 new IgSF HMM profiles (in Fig 2). Gray branches in panel A represent other IgSFs predicted with 36 new HMM profiles, which are not associated with FBG domain; B: An ML tree for only IgSF1 and IgSF2 domains from B. glabrata. ML trees with 1000 bootstrap tests were constructed using IQ-TREE. Nodes with bootstrap support of 75 or higher were highlighted with black squares at the nodes in panel B. Any domains associated with FBG domain are colored in red (IgSF1) or in blue (IgSF2) and followed with name of best hit to published FREPs. IgSF1 or IgSF2 domains without association with FBG domain are colored in pink (IgSF1) or in light blue (IgSF2). Gene has been identified previously in the genome paper [32] is labelled with an asterisk next to the corresponding gene ID. 1-IgSF FREPs are labeled with a green dot at the end of the branches. All FREPs identified in this study were named with IgSF domain, the Vectorbase ID and the best hit to published FREPs.
Table 3.
Summary of expression levels of FReD genes in RES and SUS B. glabrata: Constitutive and post-exposure responses to S. mansoni.
Fig 8.
Single nucleotide variant (SNV) analysis in B. glabrata FREPs between SUS and RES with RNA-Seq sequences.
SNV analysis of (A) FREP2 (Bg28617-PA); (B) FREP4 (Bg125-PA); (C) FREP3.1 (Bg96-PA); and (D) FREP3.2 (Bg204-PB). “Ref_BB02”, “SUS”, and “RES” are protein sequences of corresponding FREPs; in which RES and SUS are regenerated based on SNVs in their transcriptome data with BB02 as reference. Four featured sequences of “Signal peptide”, “IgSF1”, “IgSF2” and “FBG” are highlighted in colors. Each SNVs in RES from the two susceptible strains of BB02 and SUS are boxed in red. Any absolute matched sequences to identified peptides from FREP2, FREP3.2 of the plasma of SUS or RES from the pull-down experiments by the Li et al. [47] are framed in gray boxes with solid line. Sequences in FREP3.2 absolutely matched to the two RES-specific peptides from the pull-down experiments by Wu et al. [49] are framed in gray boxes with dash line.