custom interproscan annotation  (InterPro Inc)

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Putative glycan receptor genes identified in the Aplysia . Conserved protein domains identified by InterProScan used to identify each immune gene set are listed under “Required Domains.” The Strict column contains diagnostic domains know from vertebrate orthologs of target genes. The relaxed column represents more relaxed criteria, using family level annotation for domains that are more divergent in invertebrate lineages. The count column contains the number of genes identified for each group based on mining IPS results for requisite domains and then vetting with OrthoFinder predicted orthologs. Genes with fewer than 5 representatives per group have their gene identifiers listed, otherwise readers are encouraged to access Supplemental File SFile3 for full gene and protein identifier lists

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Glycoproteomics, Diagnostic Assay

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Conserved domains of Variable Immunoglobulin-like (VIgL) genes in Aplysia californica . Multiple sequence alignment of two previously identified Aplysia FREP proteins (NP_001191528/LOC100533300 and NP_001191643/LOC100533436) and two putative CREP proteins (XP_005106994/ LOC101862063 and XP_005100118/ LOC101860578) identified by InterProScan conserved domains. Above the alignment, a set of lines demarcate the protein domains of the two previously described Aplysia FREPs as reported in . Dashed line above sequence alignments demarcates signal peptide. Dotted line demarcates immunoglobulin superfamily (IgSf) domains. Solid line demarcates the carbohydrate binding domains. Conserved cysteine residues of VIgLs IgSf domains are highlighted in yellow. Note that the putative CREPs only contain one IgSf domain and thus the signal peptides alignments extend into the region demarcated as IgSF1 for the FREPs

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Sequencing, Binding Assay

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Conserved domains of RIG-I-like receptors in Aplysia and other animals. Proteins are represented by black line segments and labeled according to species with gene identifiers provided in parentheses (Nv = Nematostella vectensis, Hs = Homo sapiens, Cg = Crassostraea gigas, Bg = Biomphalaria glabrata, Ac = Aplysia californica ). Colored boxes along gene line segments represent conserved protein domains identified by InterProScan. Numbers inside boxes representing conserved domains are Pfam identifiers with “PF” trimmed off (e.g. PF00270 ➔ 00270)

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Labeling

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Orthologous components of the antiviral signaling cascade in Aplysia californica and other animals. Immune genes of interest were extracted from a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on InterPro domains detailed in supplementary data Supplemental File . Results were further refined using sequence similarity search among listed proteomes and predicted protein models using OrthoFinder and BLASTP. Columns of the table represent a single species, while rows represent proteins known to play key roles in antiviral signaling in mammals. Proteins are grouped according to their functional roles in antiviral signaling: viral nucleotide receptors, signaling cascade components such as adapters like STING and MAVS, antiviral effector genes such as ADAR, and components of RNA interference (RNAi) known to play a major role in arthropod viral response. Numbers in each cell represent the number of protein hits to each protein type, and thus differ from gene level numbers present in the main text. Note that hits are to Uniprot KB proteomes and as such differ from previously reported numbers for C. gigas and S. purpuratus which used predicted gene models. While Aplysia retains many viral sensors and antiviral effectors, key signaling adapters STING and MAVS are absent despite being retained in Oyster. Pyrin and hematopoietic interferon-inducible nuclear (HIN) domain (PYHIN) proteins (AIM2-like/IFI16-like); Leucine-rich repeat flightless-interacting protein 1-like (LRRFIP1); Double-strand break repair protein MRE11-like (MRE11); DNA repair protein RAD50 (RAD50); DNA-dependent protein kinase-like (DNAPK); ATP-dependent DNA helicase II/X-ray repair cross-complementing protein 5/6 (Ku70/80); 2′-5′-oligoadenylate synthetase (OAS); High mobility group box proteins (HMGBs); EIF2AK2/PKR-like (PKR); ATP-dependent RNA helicase DDX41 (DDX41); Z-DNA-binding proteins (ZBP/DAI); Cyclic GMP-AMP synthase (cGAS); DNA-directed RNA polymerase III (RNApol_III); RIG-I-like receptors (RLR); Mitochondrial Antiviral-Signaling Protein (MAVS); Stimulator of interferon genes (STING/MITA); TRAF family member-associated NF-kappa-B activator (TANK); Nck-associated_protein-1 (NAP1); TANK-binding kinase 1-binding protein 1 (TBKBP1/SINTBAD); TANK-binding kinase 1/ NFkB activated Kinase (TBK1/NAK); Interferon regulatory factor (IRF); Double-stranded RNA-specific adenosine deaminase (ADAR); Apolipoprotein B Editing Complex 3 proteins (APOBEC3); Tetherines (Bone marrow stromal antigen 2-like) (BST2L); Caveolin (CAV); Gilt (Gilt); Interferon-induced GTP-binding protein Mx (Mx); Interferon-induced protein 44 (IFI44); Interferon-induced transmembrane protein-like (IFITML); Protein mono-ADP-ribosyltransferase (PARPs); Ribonuclease L (RNASEL); viperins (Radical S-adenosyl methionine domain-containing proteins) (RSADs); Deoxynucleoside triphosphate triphosphohydrolase SAMHD (SAMHD); Tripartite motif-containing protein 5 (TRIM5); zinc finger NFX1-type containing 1 (ZNFX1); Zinc-finger antiviral proteins (ZAP); Argonaute (AGO); Dicer (Dicer); Piwi-like (PIWI); RISC-loading complex subunit TARBP (TRBP)

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Sequencing, Functional Assay, DNA Binding Assay, Binding Assay

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Neighbor Joining Tree of putative Aplysia Toll-like Receptor TLR domains. Neighbor joining tree generated using the Jones-Taylor-Thornton model and bootstrapped with 1000 iterations (see ) using the TIR domains of the longest protein isoform of all putative Aplysia TLR genes. Corresponding orthogroups identified in OrthoFinder analysis demarcate member proteins with strips and orthogroup identifier. Heatmap to the right of the tree represents presences (black square) or absence (light grey square) of key protein domains identified by InterProScan. Domain category is demarcated with a strip above the heatmap columns. Domains without a category include SP (signal peptide, Phobius), TIR (Toll-interleukin Receptor homology domain, IPR000157), TM (transmembrane domain, Phobius). Domains demarcated as LRRs represent various leucine-rich repeat subtypes: LRR1 (single LRR, IPR001611), T (typical type, IPR003591, SM00369), S (bacterial type, SM00364), SD22 (sds22-like, SM00365), BspA (BspA type, IPR026906), RI (Ribonuclease inhibitor, G3DSA:3.80.10.10), and CT (Cysteine-rich c-terminal flanking region of LRR, IPR000483, SM00082). Domains demarcated as “Novel Domains” represent domains found in Aplysia TLRs not typically associated with vertebrate TLRS, including MBT (malignant brain tumor repeat, IPR004092), ROC (Ras of complex small GTPase domain, IPR020859), COR (C-terminal of ROC, IPR032171), and EF (EF-hand, IPR002048). Only the TIR domains of XP_012942443.2 and XP_005112480.1 do not cluster with their Orthogroup. The TLRS contain Roc and Cor (ROCO) domains as well as other accessory domains, suggesting possible novel function. Only two TLRs contain c-terminal flanking regions

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Generated, Stripping Membranes

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Multi-species Neighbor Joining Tree of Toll-like Receptor proteins. Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains. Protein sequences were aligned and used to generate a neighbor joining tree with the JTT model. Branches and leaf nodes are colored based on the species from which the sequence originated. Arcs describe major groupings of TLRs in the tree: a S. purpuratus dominated branch, a set of TLRs containing mostly human TLRs (dubbed vertebrate-like), a major branch that contains sequences only from the protostomes assessed (as well as lone TLR from Nematostella ), and a branch containing only molluscan representatives. This tree corroborates earlier findings that massive TLR expansions in S. purpuratus and mollusks represent distinct, lineage specific radiations of TLR genes

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Sequencing

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Conserved domains of TIR and COR domain containing proteins in Aplysia . Proteins are represented by black line segments labeled with RefSeq protein identifiers and gene locus number underneath in parentheses. Colored boxes along gene line segments represent conserved protein domains identified by InterProScan. Domains are labeled above (COR = C-terminal of Roc domain, Death = Death domain, EF-hand = EF-hand calcium-binding domain, LRR = Leucine-rich repeat, Mbt = Mbt repeat, NHR Neuralized homology repeat domain, ROC = Roc domain, TIR = Toll/interleukin-1 receptor homology domain)

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Labeling, Binding Assay

Journal: BMC Genomics

Article Title: In search of the Aplysia immunome: an in silico study

doi: 10.1186/s12864-022-08780-6

Figure Lengend Snippet: Orthologous components of the TLR signaling cascade in Aplysia californica and other animals. Immune genes of interest were extracted from a custom InterProScan annotation of the Aplysia californcia RefSeq predicted protein models (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on InterPro domains detailed in supplementary data Supplemental File . Results were further refined using sequence similarity search among listed proteomes and predicted protein models using OrthoFinder and BLASTP. Columns of the table represent a single species, while rows represent proteins known to play key roles in TLR signaling in mammals. Proteins are grouped according to their functional roles in TLR signaling: TLR receptors, Adapter proteins like MyD88, E3 Ubiquitin ligases, Kinase signaling complexes and components, and Transcription factors and associated proteins. Numbers in each cell represent the number of protein hits to each protein type, and thus differ from gene level numbers present in the main text. Note that hits are to Uniprot KB proteomes and as such differ from previously reported numbers for C. gigas and S. purpuratus which used predicted gene models. Aplysia protein numbers for major components are broadly similar to other animals, although TLRs appear to be highly diversified compared to mammals and arthropods, but still fewer in number than in S. purpuratus and previously reported numbers for C. gigas (83 genes vs the 18 identified proteins with out methods in Uniprot KB). Similarly, TLR/Interleukin-1 receptor domain (TIR) containing adapters are much more diverse in Aplysia compared to human, but again less diverse than that of S. purpuratus and C. gigas . Toll-like receptor (TLR); Myeloid differentiation primary response protein (MyD88); NAD(+) hydrolase SARM1 (SARM); TIR domain-containing adapter molecule 1 (TRIF/TICAM1); TIR domain-containing adapter molecule 2 (TRAM/TICAM2); Toll/interleukin-1 receptor domain-containing adapter protein (TIRAP/Mal); Armadillo fold and TIR domain containing proteins (ARM-TIR); Epidermal growth factor and TIR domain containing proteins (EGF-TIR); Imunoglobulin and TIR domain containing proteins (IG-TIR); Orphan TIR proteins (OrTIR); Evolutionarily conserved signaling intermediate in Toll pathway (ECSIT); Toll-interacting protein (TOLLIP); TNF receptor-associated factors (TRAF); E3 ubiquitin ligase Pellino (Pellino); E3 ubiquitin-protein ligase RNF31 (HOIP); RanBP-type and C3HC4-type zinc finger-containing protein 1 RBCK1 (HOIL1); Sharpin (SHARPIN); Interleukin-1 receptor-associated kinase 1 (IRAK); TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 (TAB1); TGF-beta-activated kinase 1 and MAP3K7-binding protein 2/3 (TAB2/3); MAP3K7/TGF-beta-activated kinase 1 (TAK1); Inhibitor of nuclear factor kappa-B kinase subunit alpha (IKK); NF-kappa-B essential modulator (IKKg/NEMO); p38 MAPK/ MAPK14 (p38); Mitogen-activated protein kinase 8 (JNK); Inhibitor of NFkB (IkB); Major Vault Protein (MVP); Nuclear factor kB (NFkB); Activating protein 1 family (AP-1); Activating protein 1 JUN (JUN)

Article Snippet: Toll-like receptor genes were extracted a custom InterProScan annotation of the Aplysia californcia RefSeq protein modles (AplCal, GCF_000002075.1) and publicly available InterPro annotations of proteins from the UniprotKB data base for Biomphalaria glabrata (Bglab, UP000076420_IPS), Crassosteraea gigas (Cgig, UP000005408), Nematostella vectensis (Nvect, UP000001593), Drosophila melanogaster (Dromel, UP000000803), Strongylocentrotus purpuratus (Spurp, UP000007110) , and human (Hs, UP000005640) based on presence of TIR and LRR domains.

Techniques: Sequencing, Functional Assay, Ubiquitin Proteomics, Binding Assay