Analysis of High Molecular Mass Compounds from the Spider Pamphobeteus verdolaga Venom Gland. A Transcriptomic and MS ID Approach
Abstract
:1. Introduction
2. Results
2.1. Transcriptomic Findings
2.2. MS Findings
rp-HPLC | Peptide Sequence | Similarity | Best Match | Protein Family |
---|---|---|---|---|
6 | Y-GMDFVPLLKSYGILV-N | 100% | c51925_g1_i1 | Hyaluronidase |
6 | R-TIKDWYK-G | 80% | c40556_g1_i1 | Lycotoxin |
21–22 | K-SFPTVLTSSSMSFTK-K | 84.6% | c9919_g1_i1 | CRISP |
R-TGPQVKGEK-S | 77.8% | c9919_g1_i1 | ||
K-DWYKEIK-D | 55.2% | c9919_g1_i1 | ||
K-VATGKETQYSMPK-A | 100% | c9919_g1_i1 | ||
7 | R-DSANGFINK-I | 73% | c14372_g1_i1 | Phospholipases D |
K-ESGYNDK-Y | ||||
6 | P-STYGGGLSVSSR-F | 42.6% | c66767_g1_i1 | Kunitz-type |
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Spider Collection and Venom Extraction
5.2. Venom Fractionation
5.3. Proteomic Analysis
LC-MS/MS
5.4. Data Analysis
5.5. Transcriptomic Analysis
5.6. Nomenclature
5.7. Signal Peptide and Disulfide Bond Prediction
5.8. Data Availability
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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A. Phospholipase A2-Like Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c3142 | PhospholipaseA2-1-pverdolaga | Calcium-independent phospholipase A2 | A0A087UHX4 | Stegodyphus mimosarum | 173.33 | 7.09 × 10−50 | 5.79 |
c4865 | PhospholipaseA2-2-pverdolaga | Cytosolic phospholipase A2 | XP_003214621.2 | Anolis carolinensis | 112.08 | 2.93 × 10−25 | 5.45 |
c15998 | PhospholipaseA2-3-pverdolaga | Group XV phospholipase A2 | A0A087U096 | S. mimosarum | 560.84 | 0.00 × 10+00 | 28.76 |
c33599 | PhospholipaseA2-4-pverdolaga | Cytosolic phospholipase A2 | A0A087UL94 | S. mimosarum | 139.04 | 5.33 × 10−39 | 1.51 |
c45513 | PhospholipaseA2-5-pverdolaga | Calcium-independent phospholipase A2 | A0A087UHX4 | S. mimosarum | 275.02 | 7.49 × 10−88 | 3.09 |
c10524 | PhospholipaseA2-6-pverdolaga | Calcium-independent phospholipase A2 | A0A0J7L0J5 | Lasius niger | 101.29 | 1.51 × 10−18 | 6.49 |
c11106 | PhospholipaseA2-7-pverdolaga | Phospholipase A2 | A0A087SVA4 | S. mimosarum | 149.06 | 3.02 × 10−41 | 8.04 |
c12950 | PhospholipaseA2-8-pverdolaga | Phospholipase A2 | A0A087TLC5 | S. mimosarum | 87.04 | 2.14 × 10−17 | 58.98 |
c18752 | PhospholipaseA2-9-pverdolaga | Group XIIA secretory phospholipase A2 | XP_011150082.1 | Harpegnathos saltator | 135.58 | 3.87 × 10−35 | 138.53 |
c21159 | PhospholipaseA2-10-pverdolaga | Calcium-independent phospholipase A2 | E2B1P4 | Camponotus floridanus | 114.39 | 3.47 × 10−24 | 2.68 |
c42153 | PhospholipaseA2-11-pverdolaga | Cytosolic phospholipase A2 | A0A087UL97 | S. mimosarum | 117.86 | 1.08 × 10−31 | 2.65 |
c20465 | PhospholipaseA2-12-pverdolaga | Calcium-independent phospholipase A2 | XP_002399324.1 | Ixodes scapularis | 342.81 | 1.19 × 10−105 | 2.66 |
c29120 | PhospholipaseA2-13-pverdolaga | Group 3 secretory phospholipase A2 | XP_012259279.1 | Athalia rosae | 137.89 | 6.44 × 10−36 | 1.4 |
c57457 | PhospholipaseA2-14-pverdolaga | Phospholipase A2 | A0A087UYP4 | S. mimosarum | 118.24 | 1.83 × 10−29 | 2.01 |
c61053 | PhospholipaseA2-15-pverdolaga | Calcium-independent phospholipase A2-γ | A0A087TW26 | S. mimosarum | 479.56 | 1.22 × 10−158 | 10.53 |
c60448 | PhospholipaseA2-16-pverdolaga | Phospholipase A2-activating protein | B7PWX1 | Ixodes scapularis | 624 | 0.00 × 10+00 | 5.76 |
B. Phospholipase D-Like Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c46024 | PhospholipaseD-1-pverdolaga | Phospholipase D LiSicTox-betaID1 | Q1W694 | Loxosceles intermedia | 319.70 | 3.17 × 10−100 | 9.24 |
c14372 | PhospholipaseD-2-pverdolaga | Phospholipase D StSicTox-betaIF1 | C0JB54 | Sicarius terrosus | 214.54 | 4.16 × 10−61 | 16.94 |
c45658 | PhospholipaseD-3-pverdolaga | Phospholipase D1 | KFM64830.1 | S. mimosarum | 165 | 1 × 10−48 | 1.98 |
c54699 | PhospholipaseD-4-pverdolaga | Phospholipase D1 | XP_003744259.1 | Metaseiulus occidentalis | 353 | 4.94 × 10−118 | 2.34 |
C. Phospholipase B-Like Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c17591 | Phospholipase-B-1-pverdolaga | Putative phospholipase B-like 2 | XP_015925352.1 | Parasteatoda tepidariorum | 752 | 0.00 × 10+00 | 31.29 |
D. KTPSI-Like Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c1808 | Kunitz-1-pverdolaga | Kunitz-type serine protease inhibitor huwentoxin-11g11 | B2ZBB6 | H. schmidti | 75.87 | 9.22 × 10−15 | 5.22 |
c8989 | Kunitz-2-pverdolaga | Kunitz-type serine protease inhibitor kunitz-1 | W4VSH9 | Trittame loki | 66.24 | 4.76 × 10−10 | 23.43 |
c12801 | Kunitz-3-pverdolaga | Kunitz-type serine protease inhibitor HWTX-XI-IS4 | P0DJ76 | H. schmidti | 99.37 | 5.62 × 10−23 | 157.37 |
c15163 | Kunitz-4-pverdolaga | Kunitz-type serine protease inhibitor kunitz-1 | W4VSH9 | Trittame loki | 128.26 | 2.03 × 10−32 | 38.26 |
c16277 | Kunitz-5-pverdolaga | Kunitz-type serine protease inhibitor 6-like | KFM65460.1 | S. mimosarum | 137.50 | 1 × 10−38 | 13.39 |
c30159 | Kunitz-6-pverdolaga | Kunitz-type serine protease inhibitor huwentoxin-11g11 | B2ZBB6 | H. schmidti | 92.82 | 4.50 × 10−22 | 76.26 |
c41726 | Kunitz-7-pverdolaga | Protein with kunitz domain | XP_002435922.1 | Ixodes scapularis | 74.33 | 1.38 × 10−16 | 2.85 |
c59058 | Kunitz-8-pverdolaga | Kunitz-type serine protease inhibitor huwentoxin-11g11 | B2ZBB6 | H. schmidti | 64.70 | 1.40 × 10−09 | 4.26 |
c66767 | Kunitz-9-pverdolaga | Kunitz-type protease inhibitor AXPI-I-like | XP_011135446.1 | Harpegnathos saltator | 63.16 | 4.85 × 10−10 | 1.58 |
c43290 | Kunitz-10-pverdolaga | Kunitz-type protease inhibitor kalicludine-3-like | XP_012273912.1 | Orussus abietinus | 51.99 | 1.71 × 10−06 | 1.66 |
c52646 | Kunitz-11-pverdolaga | Kunitz-type serine protease inhibitor huwentoxin-11g11 | B2ZBB6 | H. schmidti | 84.73 | 2.64 × 10−17 | 144.34 |
c6182 | Kunitz-12-pverdolaga | Kunitz-type serine protease inhibitor kunitz-1 | W4VSH9 | Trittame loki | 64.31 | 9.75 × 10−10 | 3.02 |
c9496 | Kunitz-13-pverdolaga | Kunitz-type serine protease inhibitor huwentoxin-11 | P68425 | H. schmidti | 119.78 | 1.02 × 10−30 | 325.15 |
E. Hyaluronidase-Like Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c17398 | Hyaluronidase-1-pverdolaga | Hyaluronidase-3 | A0A0F8AST4 | Larimichthys crocea | 79.34 | 4.21 × 10−13 | 14.8 |
c51925 | Hyaluronidase-2-pverdolaga | Hyaluronidase | J9XYC6 | Brachypelma vagans | 816.99 | 0.00 × 10+00 | 1107.75 |
F. Lycotoxin-Like Peptides. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c3316 | Lycotoxin-1-pverdolaga | U15-lycotoxin-Ls1d | B6DD42 | Lycosa singoriensis | 50.1 | 6 × 10−06 | 7.36 |
c28990 | Lycotoxin-2-pverdolaga | U16-lycotoxin-Ls1b | B6DD53 | Lycosa singoriensis | 42 | 8 × 10−7 | 2.35 |
c13977 | Lycotoxin-3-pverdolaga | U20-lycotoxin-Ls1c-like | A0A087UBG5 | S. mimosarum | 52.37 | 2.96 × 10−06 | 6.38 |
G. CRISP Proteins. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c9788 | CRISP-1- pverdolaga | GTx-CRISP1 | BAN13537.1 | Grammostola rosea | 518 | 0.00 × 10+00 | 1388.9 |
C9919 | CRISP-2- pverdolaga | GTx-VA1 | BAN13538.1 | G. rosea | 590 | 0.00 × 10+00 | 18191.29 |
c18710 | CRISP-3- pverdolaga | GTx-CRISP1 | BAN13537.1 | G. rosea | 322 | 4 × 10−108 | 12.97 |
H. Hephaestin-Like Protein. | |||||||
Contig Number | Given Name | Similarity with | Accession number | Organism | Score | E-Value | TPM |
c5907 | hephaestin-1- pverdolaga | Hephaestin-like protein | XP_021003833.1 | Parasteatoda tepidariorum | 1017 | 0.00 × 10+00 | 4.18 |
c20814 | hephaestin-2- pverdolaga | Hephaestin | PRD23536.1 | Nephila clavipes | 193 | 1 × 10−59 | 3.16 |
I. Venom Metalloproteinase. | |||||||
Contig Number | Given Name | Similarity with | Accession Number | Organism | Score | E-Value | TPM |
c728 | Metalloproteinase-1- pverdolaga | A disintegrin and metalloproteinase with thrombospondin motifs 1 | KFM63257.1 | S. mimosarum | 758 | 0.00 × 10+00 | 20.99 |
rp-HPLC | Protein Family | Protein Name | Organism |
---|---|---|---|
6 | Hyaluronidase | Hyaluronidase, partial | Brachypelma vagans |
6 | Lycotoxin | U16-lycotoxin-Ls1a | Lycosa singoriensis |
21–22 | CRISP | GTx-VA1 | Grammostola rosea |
CRISP | GTx-VA1 | ||
CRISP | GTx-VA1 | ||
CRISP | GTx-VA1 | ||
7 | Phospholipases D | Phospholipase D isoform 1 | Loxosceles laeta |
Phospholipases D | Phospholipase D LlSicTox-alphaIII1i | ||
6 | No match | No match | No match |
Sequences | % Similarity | ID | Match |
---|---|---|---|
AGFAGDDAPR | 100 | c6436_g1_i1 | Actin |
AVFPSIVGRPR | |||
DSYVGDEAQSKR | |||
HQGVMVGMGQKDSYVGDEAQSK | |||
RGILTLK | |||
EITALAPSTMK | 100 | c62193_g1_i1 | Actin |
VAPEEHPVLLTEAPLNPK | 100 | c13011_g1_i1 | Actin |
MTQIMFETFNSPAMYVAIQAVLSLYASGR | 96.55 | ||
ESRSE | 100 | c15096_g1_i3 | Cytosolic purine 5′-nucleotidase |
GKPKIQVEYK | 100 | c27174_g1_i1 | Heat shock protein |
LSKEEIER | 100 | ||
SENVQDLLLLDVAPLSLGIETAGGVMTALIK | 90.32 | ||
SENVQDLLLLDVAPLSLGIETAGGVMTSLIK | 90.32 | ||
GVPQIEVTFDLDANGILQVSAQDKSTGK | 89.29 | ||
QTQIFTTYSDNQPGVLIQVYEGER | 95.8 | ||
QTQTFITYSDNQPGVLIQVYEGER | 95.8 | ||
GVPQIEVTFDIDANGILNVTATDK | 91.67 | ||
EIAEAYLGYPVTNAVITVPAYFNDSQR | 88.89 | ||
LLQDFFNGR | 88.89 | ||
SENVQDLLLLDVAPLSLGLETAGGVMTALIK | 87.1 | ||
NQVALNPQNTVFDAK | 86.67 | ||
SENVQDLLLLDVAALSLGLETAGGVMTALIK | 83.87 | ||
DVLLVDVAPLSLGIETAGGVMTK | 100 | c15743_g1_i1 | Heat shock protein |
KLFNPEEISAMVLTK | 100 | ||
LFNPEEISAMVLTK | 100 | ||
DAGVIAGLNVLR | 91.67 | ||
TTPSYVAFTDTER | 100 | c10792_g1_i2 | Heat shock protein |
YRPGTVALREIR | 100 | c2143_g1_i2 | Histone |
TITLEVEPSDTIENVK | 100 | c16774_g1_i2 | Polyubiquitin-B |
AGFAGDDAPRAVFPSIVGRPR | 100 | c17180_g4_i1 | Actin |
DLYANTVLSGGTTMYPGIADRMQK | 100 | ||
MQKEITALAPSTMK | 100 | ||
SYELPDGQVITIGNER | 100 | ||
YSVWIGGSI | 100 | ||
TTGIVLDSGDGVSHTVPIYEGYALPHAILWLDLAGRDLTDYLMK | 97.73 | ||
MQKEITALAPSQMK | 92.86 | ||
MQKEITALAPSWMK | 92.86 | ||
MQKEITALAPSYMK | 92.86 | ||
SINPDEAVAYGAAVQAAILMGDK | 95.65 | c16820_g1_i1 | Heat shock protein |
IINEPTAAALAYGLDR | 93.75 | c9831_g1_i1 | Heat shock protein |
TITLEVEPSDTAENVK | 93.75 | c16774_g1_i2 | Polyubiquitin-B |
FELSGIPPAPR | 90.91 | c14336_g1_i1 | Heat shock protein |
AASSSSTEK | 88.89 | c51913_g1_i1 | Actin |
MAATKQTAR | 88.89 | c2143_g1_i2 | Histone |
KSAMATGGVK | 80 | ||
MAGTKQTAR | 88.89 | c4667_g1_i1 | Histone |
MANTKQTAR | 88.89 | ||
AVTKQTAR | 87.5 | ||
KSAAATGGVK | 80 | ||
KSACATGGVK | 80 | ||
KSAEATGGVK | 80 | ||
KSAGATGGVK | 80 | ||
KSAHATGGVK | 80 | ||
KSASATGGVK | 80 | ||
KSASATGGVK | 80 | ||
KSAWATGGVK | 80 | ||
KSAYATGGVK | 80 | ||
SAIATGGVKKPHR | 84.62 | ||
CNDMMNVGRLQGFEGK | 87.5 | c15300_g1_i1 | Triple functional domain protein |
ELEEAER | 85.71 | c34105_g1_i1 | Ubiquitin |
QAAEAAPEDK | 80 | c5964_g1_i2 | PDZ and LIM domain protein Zasp |
GSSSGGGYSSGSSSYGSGGR | 80 | c14908_g1_i2 | Protein phosphatase |
LENEIQTYR | 77.78 | c4688_g1_i1 | Dystonin |
CKINFCLK | 75 | c14491_g1_i2 | AN1-type zinc finger protein |
SPATREGK | 75 | c9864_g1_i1 | Cip1-interacting zinc finger protein |
KVLPLPQR | 75 | c62910_g1_i1 | Developmental protein |
EDQEQRER | 75 | c29740_g1_i1 | Intersectin-1 |
KLMEMVNN | 75 | c11572_g1_i1 | Serine/threonine-protein kinase |
IPCCGKSR | 75 | c5016_g1_i1 | Ubiquitin |
VQGHSHSK | 75 | c17992_g1_i1 | Uncharacterized protein |
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Estrada-Gómez, S.; Vargas-Muñoz, L.J.; Segura Latorre, C.; Saldarriaga-Cordoba, M.M.; Arenas-Gómez, C.M. Analysis of High Molecular Mass Compounds from the Spider Pamphobeteus verdolaga Venom Gland. A Transcriptomic and MS ID Approach. Toxins 2021, 13, 453. https://doi.org/10.3390/toxins13070453
Estrada-Gómez S, Vargas-Muñoz LJ, Segura Latorre C, Saldarriaga-Cordoba MM, Arenas-Gómez CM. Analysis of High Molecular Mass Compounds from the Spider Pamphobeteus verdolaga Venom Gland. A Transcriptomic and MS ID Approach. Toxins. 2021; 13(7):453. https://doi.org/10.3390/toxins13070453
Chicago/Turabian StyleEstrada-Gómez, Sebastian, Leidy Johana Vargas-Muñoz, Cesar Segura Latorre, Monica Maria Saldarriaga-Cordoba, and Claudia Marcela Arenas-Gómez. 2021. "Analysis of High Molecular Mass Compounds from the Spider Pamphobeteus verdolaga Venom Gland. A Transcriptomic and MS ID Approach" Toxins 13, no. 7: 453. https://doi.org/10.3390/toxins13070453