In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes
Abstract
:1. Introduction
2. Results—Discussion
3. Materials and Methods
3.1. Animals
3.2. Ethical Statement
3.3. Haemolymph Collection and Challenge with Heat-Killed Bacteria
3.4. Illumina Sequencing
3.5. Bioinformatic Analysis
3.5.1. Transcriptome Assembly
3.5.2. Transcriptome Annotation
3.5.3. PepTraq
3.5.4. In-Depth In Silico Search
3.6. Peptide Synthesis
3.7. Antimicrobial Assay
3.8. Haemolytic Assay
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Transcript | Name | Transcript Length (nt) | Protein Length (aa) | Expression (TPM) | Fold Change | |
---|---|---|---|---|---|---|
c-hct | Vs-hct | |||||
TR5906|c0_g1_i2 | TLRγ | 2861 | 833 | 3.55 | 4.58 | 1.29 |
TR31922|c0_g2_i3 | TLR-h (partial) | 1741 | 536 | 0.31 | 4.71 | 15.11 |
TR20767|c0_g1_i1 | MyD88 | 1938 | 338 | 12.13 | 14.50 | 1.20 |
TR42010|c1_g1_i1 | IRAK4 | 1939 | 319 | 8.56 | 10.63 | 1.24 |
TR37884|c0_g2_i2 | TRAF6 | 2364 | 547 | 2.53 | 3.05 | 1.21 |
TR17535|c0_g1_i1 | IκB | 2609 | 337 | 233.96 | 230.08 | 0.98 |
TR34670|c0_g1_i1 | IKK-h | 2724 | 476 | 10.64 | 12.29 | 1.16 |
TR41212|c6_g1_i2 | Rel/NF-κB-h | 2614 | 491 | 1.85 | 2.56 | 1.39 |
TR24628|c0_g1_i1 | iNOS-h (partial) | 4137 | 1106 | 0.00 | 0.52 | - |
TR41722|c24_g56_i1 | PGRP-h1 | 873 | 213 | 254.12 | 466.71 | 1.84 |
TR14900|c0_g1_i1 | PGRP-h2 | 956 | 204 | 87.28 | 154.73 | 1.77 |
TR40338|c3_g2_i1 | BPI/LPB | 2342 | 537 | 134.38 | 149.31 | 1.11 |
TR32087|c0_g2_i1 | Gal-2 (partial) | 817 | 236 | 86.15 | 120.87 | 1.40 |
Transcript Name | Length (aa) | Expression (TPM) | Fold Change | SP | AMP Name | |
---|---|---|---|---|---|---|
c-hct | Vs-hct | |||||
TR42258|c1_g1_i1 | 54 | 8.92 | 7.57 | 0.85 | Yes | AV19 |
TR27534|c0_g1_i1 | 48 | 17.39 | 23.79 | 1.37 | Yes | GK28 |
TR36613|c0_g1_i1 | 47 | 20.28 | 17.01 | 0.84 | Yes | NF19 |
TR42563|c7_g3_i1 | 40 | 1.99 | 0.78 | 0.39 | Yes | II19 |
TR5654|c0_g1_i1 | 45 | 9.77 | 17.33 | 1.77 | Yes | LV25 |
Name | Sequence | Length (aa) | MW | C | HR | α-Helix Prediction and NRH | CAMP Algorithms | |||
---|---|---|---|---|---|---|---|---|---|---|
SVM | RFC | ANN | DAC | |||||||
AV19 | ASSFLTPRLSSLGKRSWAV | 19 | 2063.38 | +3 | 42% | Yes-2 | 0.75 | 0.8 | AMP | 0.91 |
GK28 | GFCNFMHLKPISRELRRELYGRTRRRRK | 28 | 3577.25 | +8 | 28% | No | 0.69 | 0.31 | AMP | 0.8 |
NF19 | NYWLLVLRRLLITKKVMWF | 19 | 2493.14 | +4 | 63% | Yes-7 | 0.43 | 0.71 | AMP | 0.65 |
II19 | IYFHLFRKINFNLRIYYFI | 19 | 2581.1 | +3 | 52% | Yes-6 | 0.13 | 0.65 | AMP | 0.87 |
LV25 | LKALKLPKGSTSTEVRRILVLEIRV | 25 | 2820.45 | +4 | 44% | Yes-4 | 0.68 | 0.88 | NAMP | 0.84 |
Name | Gram Negative | Gram Positive | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vibrio alginolyticus | Vibrio splendidus | Vibrio aestueranius | Vibrio anguillarum | Vibrio parahaemo-lyticus | Escherichia coli | Halomonas aquamarina | Aeromonas salmonicida | Enterococcus faecalis | Lactococcus garvieae | |||||||||||
MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | MIC | MBC | |
AV19 | - | - | 10–20 | 10–20 | - | - | - | - | 10–20 | 20–50 | - | - | - | - | - | - | - | - | - | - |
GK28 | ≤5 | 20–50 | ≤5 | ≤5 | 10–20 | >50 | 10–20 | 20–50 | ≤5 | 10–20 | ≤5 | 20–50 | - | - | - | - | - | - | - | - |
NF19 | - | - | 5–10 | 10–20 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
II19 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
LV25 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
SYN | 10–20 | >20 | 5–10 | 10–20 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Ox | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | ≤5 | >10 | - | ≤5 | ≤5 | ≤5 | 5–10 | ≤5 | > 10 |
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Benoist, L.; Houyvet, B.; Henry, J.; Corre, E.; Zanuttini, B.; Zatylny-Gaudin, C. In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes. Mar. Drugs 2020, 18, 439. https://doi.org/10.3390/md18090439
Benoist L, Houyvet B, Henry J, Corre E, Zanuttini B, Zatylny-Gaudin C. In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes. Marine Drugs. 2020; 18(9):439. https://doi.org/10.3390/md18090439
Chicago/Turabian StyleBenoist, Louis, Baptiste Houyvet, Joël Henry, Erwan Corre, Bruno Zanuttini, and Céline Zatylny-Gaudin. 2020. "In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes" Marine Drugs 18, no. 9: 439. https://doi.org/10.3390/md18090439
APA StyleBenoist, L., Houyvet, B., Henry, J., Corre, E., Zanuttini, B., & Zatylny-Gaudin, C. (2020). In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes. Marine Drugs, 18(9), 439. https://doi.org/10.3390/md18090439