Multiomic Approach for Bioprospection: Investigation of Toxins and Peptides of Brazilian Sea Anemone Bunodosoma caissarum
Abstract
:1. Introduction
2. Results
2.1. Tentacle Transcriptome
2.2. Mucus and Tentacle Proteome
2.3. Mucus and Tentacle Peptidome
Non-Reduced and Non-Alkylated Samples
2.4. Peptidome with Reduced and Alkylated Cysteine Residues
2.5. Analysis of Cleavage Site in the Peptidome
3. Discussion
3.1. Considerations about the Mucus Collection Protocol and Omic Techniques
3.2. Tentacle and Mucus Composition
3.2.1. Toxins
Toxin | Trinity Code | Transcript (Identity) | E-Value | Toxin Family | Tentacle/Mucus | Omic Approach |
---|---|---|---|---|---|---|
* U-actitoxin-Bcs3d | TRINITY_DN72667 | U-actitoxin-Bgr3d (42.3%) | 4.4E−13 | Sea anemone type 3 (BDS) potassium channel toxin | −/+ | Proteome, RA peptidome |
* U-actitoxin-Bcs3a | TRINITY_DN10015 TRINITY_DN5917 TRINITY_DN38124 | U-actitoxin-Bgr3a (38.1%) | 4.8E−06 | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome, RA peptidome |
* U-actitoxin-Bcs2c | TRINITY_DN42790 | U-actitoxin-Ael2c (45.7%) | 1.8E−09 | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome |
* Κ-actitoxin-Bcs4m | TRINITY_DN4181 | Kappa-actitoxin-Avd4m (50%) | 1.4E−16 | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome, RA peptidome |
U-actitoxin-Bcs2a | TRINITY_DN14686 | U-actitoxin-Bcs2a (100%) | 1.3E−30 | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome, RA peptidome |
Bcs Tx3 | TRINITY_DN1024 | type III potassium channel toxin protein, partial (96%) | 1.4E−47 | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome, RA peptidome |
* Κ-actitoxin-Bcs2a | TRINITY_DN58216 | Kappa-actitoxin-Ael2a (50%) | 1.2E−08 | Sea anemone type 3 (BDS) potassium channel toxin | −/+ | RA peptidome |
* ΚΠ-actitoxin-Bcs3e | TRINITY_DN13254 | kappaPI-actitoxin-Avd3e-like (73.5%) | 4.9E−90 | Venom Kunitz type. Sea anemone type 2 potassium channel toxin. | +/+ | Proteome |
* Π-actitoxin-Bcs2e | TRINITY_DN217 | PI-stichotoxin-Hcr2e (56.4%) | 2.5E−28 | Venom Kunitz type. Sea anemone type 2 potassium channel toxin. | +/− | Proteome |
* U-actitoxin-Bcs3n | TRINITY_DN6572 | U-actitoxin-Avd3n (74.7%) | 1.6E−51 | Venom Kunitz type. Sea anemone type 2 potassium channel toxin. | +/+ | Proteome, RA peptidome |
* Π-actitoxin-Bcs3a | TRINITY_DN10770 | PI-actitoxin-Aeq3a-like (85.9%) | 1.2E−59 | Venom Kunitz type. Sea anemone type 2 potassium channel toxin. | −/+ | Proteome |
* U-actitoxin-Bcs12a | TRINITY_DN7989 | U-actitoxin-Avd12a (74.4%) | 9.4E−38 | EGF-domain peptide | +/+ | Proteome |
Turripeptide Pal 9.2-like | TRINITY_DN4295 | Turripeptide Pal 9.2 (38.2%) | 1.2E−12 | Kazal-type serine protease inhibitor domain | +/+ | Proteome, RA peptidome |
* Π-actitoxin-Bcs5a | TRINITY_DN713 | PI-actitoxin-Avd5a (67.4%) | 8E−24 | Kazal-type serine protease inhibitor domain | +/+ | Proteome |
Basic phospholipase A2 pseudexin A chain-like | TRINITY_DN24551 | Basic phospholipase A2 pseudexin A chain-like (72.8%) | 7.8E−108 | Phospholipase A2 | −/+ | Proteome |
* Κ-actitoxin-Bcs1a | TRINITY_DN3227 | Kappa-actitoxin-Bgr1a (89.2%) | 1.4E−20 | Sea anemone type 1 potassium channel toxin | −/+ | Proteome |
* Κ-actitoxin-Bcs3a | TRINITY_DN4127 | Kappa-actitoxin-Aer3a (55.4%) | 1.3E−28 | Sea anemone type 1 potassium channel toxin | +/+ | Proteome |
* U-actitoxin-Bcs8a | TRINITY_DN1939 | U-actitoxin-Avd8a-like (82.3%) | 1.9E−51 | Sea anemone 8 toxin | +/+ | Proteome |
* Δ-actitoxin-Bcs2a | TRINITY_DN24411 | Delta-stichotoxin-Sgt2a (48.2%) | 3.1E−15 | Anemone neurotoxin | −/+ | Proteome, RA peptidome |
Zinc-metalloproteinase nas-13-like | TRINITY_DN24501 | Zinc-metalloproteinase nas-13-like (84.9%) | 3.5E−80 | Astacin | −/+ | Proteome |
Zinc metalloproteinase nas-4-like | TRINITY_DN2272 | Zinc metalloprotease nas-4-like isoform X2 (82.9%) | 4E−269 | Astacin | +/+ | Proteome |
Zinc metalloproteinase nas-15-like | TRINITY_DN1535 | Zinc-metalloproteinase nas-15-like (68.2%) | 1.2E−221 | Astacin | +/+ | Proteome |
Cystatin | TRINITY_DN6968 | Cystatin-like (57.2%) | 7.3E−65 | Cystatin domain | +/+ | Proteome |
Trinity Code | Transcript (Identity) | E-Value | Toxin Family | Tentacle/Mucus | Omic Approach |
---|---|---|---|---|---|
TRINITY_DN4279 | - | - | Sea anemone type 3 (BDS) potassium channel toxin | +/+ | Proteome, RA peptidome |
TRINITY_DN14881 | Carboxypeptidase inhibitor SmCl-like (64.1%) | 3E−32 | Venom Kunitz type. Sea anemone type 2 potassium channel toxin | −/+ | Proteome |
TRINITY_DN4129 | Neurogenic locus notch homolog protein 1 (37.1%) | 7.9E−12 | EGF-domain | +/+ | Proteome |
TRINITY_DN3459 | Agrin-like (42.5%) | 4.1E−71 | Kazal-type serine protease inhibitor domain | −/+ | Proteome |
TRINITY_DN322 | Fibrilin-2-like isoform X3 (69.5%) | 4.3E−70 | Kazal-type serine protease inhibitor domain | +/+ | Proteome |
TRINITY_DN14498 | Neurogenic locus notch homolog protein 1-like isoform X6 (81.8%) | 2.4E−55 | Kazal-type serine protease inhibitor domain | +/+ | Proteome |
TRINITY_DN1312 | Uncharacterized protein ZK643.6-like (47.2%) | 6.4E−52 | ShK domain-like | +/+ | Proteome |
TRINITY_DN22515 | Uncharacterized protein LOC116291117 (72.1%) | 3.5E−75 | ShK domain-like | +/+ | Proteome |
TRINITY_DN10788 | Uncharacterized protein LOC116293550 (67.9%) | 2.2E−227 | ShK domain-like | +/− | Proteome |
TRINITY_DN10521 | Uncharacterized protein LOC116287301 (52.2%) | 1.9E−48 | ShK domain-like | +/+ | Proteome, RA peptidome, NRNA peptidome |
TRINITY_DN4363 | Uncharacterized protein LOC116301037 (80.4%) | 0 | ShK domain-like | +/− | Proteome |
TRINITY_DN19291 | Uncharacterized protein LOC116291117 (61.8%) | 1.3E−135 | ShK domain-like | +/+ | Proteome |
TRINITY_DN2326 | mRNA, partial (76%) | 5.9E−45 | Anemone neurotoxin | −/+ | RA peptidome |
TRINITY_DN52114 | Uncharacterized protein LOC116291022 (70.8%) | 6.6E−102 | F5/8 C domain | −/+ | Proteome |
TRINITY_DN16749 | Uncharacterized protein LOC116297803 isoform X6 (67.5%) | 1.4E−50 | F5/8 C domain | −/+ | Proteome |
TRINITY_DN8245 | Uncharacterized protein LOC116298543 (67.6%) | 5.2E−70 | F5/8 C domain | +/+ | Proteome |
TRINITY_DN37576 | Uncharacterized protein LOC116297953 (65.3%) | 6.2E−44 | F5/8 C domain | −/+ | RA peptidome, NRNA peptidome |
TRINITY_DN10809 | Perlucin-like protein (65.7%) | 1.2E−98 | Lectin C-type domain | +/+ | Proteome |
3.2.2. Cysteine Rich Proteins
3.2.3. Neuropeptides
3.2.4. Intracellular Peptides (InPeps)
4. Materials and Methods
4.1. Collection and Maintenance of Specimens
4.2. Transcriptomic
4.2.1. RNA Extraction, mRNA Library Synthesis and Illumina Sequencing
4.2.2. Transcriptome Assembly, Annotation and Functional Enrichment
4.3. Proteomic and Peptidomic
Protein and Peptide Fractions Preparation
4.4. NanoLC and Mass Spectrometry
4.5. Protein and Peptide Identification
4.6. Quantitative Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trinity | TransDecoder | |
---|---|---|
Transcripts | 186,978 | 150,493 |
N50 | 1900 | 501 |
Genes | 111,386 | 61,465 |
TRINITY | Name | Peptide | Mucus Sample Area | Tentacle Sample Area |
---|---|---|---|---|
TRINITY_DN1213 | - | DCRGKHCQTGPFGD | 9.06E+09 | 4.84E+08 |
TRINITY_DN58641 | - | TLASSIQCVGKCKIKTSSGQCRTDLRCMLANKGAS | 1.70E+09 | 3.88E+08 |
TRINITY_DN14686 | U-actitoxin-Bcs2a | GLPCDCHGHTGTYWLNYYSKCPKGYGYTGRCRYLVGSCCYK | 1.32E+09 | - |
TRINITY_DN3092 | - | MATSCRKCKPGYGCWAVPCPKR | 1.09E+09 | - |
TRINITY_DN557 | Lamin-A | EELSFKRSVYDKE | 5.92E+08 | - |
TRINITY_DN1213 | - | DCRGKHCQTGPF | 3.56E+08 | 1.38E+06 |
TRINITY_DN14686 | U-actitoxin-Bcs2a | GLPCDCHGHTGTY | 2.59E+08 | - |
TRINITY_DN3092 | - | MATSCRKCKPGYGCWAVPCPKR | 2.16E+08 | - |
TRINITY_DN3092 | - | ATSCRKCKPGYGCWAVPCPKR | 1.71E+08 | - |
TRINITY_DN14686 | U-actitoxin-Bcs2a | WLNYYSKCPKGYGYTGRCRYLVGSCCYK | 1.68E+08 | - |
TRINITY | Name | Peptide | Mucus Sample Area | Tentacle Sample Area |
---|---|---|---|---|
TRINITY_DN1213 | - | DCRGKHCQTGPFGD | 9.06E+09 | 4.84E+08 |
TRINITY_DN282 | Histone H2B | LPGELAKHAVSEGTKAVTKYTSSK | - | 3.99E+08 |
TRINITY_DN58641 | - | TLASSIQCVGKCKIKTSSGQCRTDLRCMLANKGAS | 1.7E+09 | 3.88E+08 |
TRINITY_DN3037 | - | NPPYEEILEPAFFHIR | - | 2.61E+08 |
TRINITY_DN10521 | - | APPDTSILDKLGKL | 7.26E+06 | 2.13E+08 |
TRINITY_DN12562 | - | DEAGLLKYKTAAGAALVNERLKNLAERY | - | 1.81E+08 |
TRINITY_DN3037 | - | QPPFLGGPAYFHIR | - | 1.52E+08 |
TRINITY_DN282 | Histone H2B | LLLPGELAKHAVSEGTKAVTKYTSSK | 8.66E+06 | 1.52E+08 |
TRINITY_DN25490 | U-actitoxin-Aeq6a | KERCDLLGDPCVKG | - | 1.51E+08 |
TRINITY_DN1828 | - | AAAYVCDVARNLDCSAH | - | 1.43E+08 |
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Mazzi Esquinca, M.E.; Correa, C.N.; Marques de Barros, G.; Montenegro, H.; Mantovani de Castro, L. Multiomic Approach for Bioprospection: Investigation of Toxins and Peptides of Brazilian Sea Anemone Bunodosoma caissarum. Mar. Drugs 2023, 21, 197. https://doi.org/10.3390/md21030197
Mazzi Esquinca ME, Correa CN, Marques de Barros G, Montenegro H, Mantovani de Castro L. Multiomic Approach for Bioprospection: Investigation of Toxins and Peptides of Brazilian Sea Anemone Bunodosoma caissarum. Marine Drugs. 2023; 21(3):197. https://doi.org/10.3390/md21030197
Chicago/Turabian StyleMazzi Esquinca, Maria Eduarda, Claudia Neves Correa, Gabriel Marques de Barros, Horácio Montenegro, and Leandro Mantovani de Castro. 2023. "Multiomic Approach for Bioprospection: Investigation of Toxins and Peptides of Brazilian Sea Anemone Bunodosoma caissarum" Marine Drugs 21, no. 3: 197. https://doi.org/10.3390/md21030197