Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Data Mining
2.3. DNA, RNA Extraction and cDNA Synthesis
2.4. Full-Length cDNA and Gene Cloning from Anemonia viridis
2.5. Sequence and Phylogenetic and Structural Analyses
2.6. Anemonia viridis Translationally Controlled Tumour Protein Tissue-Specific Expression Pattern
2.7. Challenging Sea Anemone with Environmental Elicitors
2.8. Quantitative Reverse Transcription PCR (RT-qPCR)
3. Results and Discussion
3.1. Anemonia viridis cDNA Characterisation and Identification of TCTPs in Cnidarians
3.2. Phylogenetic and Structural Analysis of Cnidarian TCTPs
3.3. Phylogenetic Analysis with other Eumetazoa and Structural Inferences
3.4. Tissue Expression Pattern of AvTCTP
3.5. Expression Profiles in Response to Thermal, Chemical and Biotic Challenges
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Primers | Sequences (5′–3′) | Amplicon Size (bp) |
---|---|---|
3′ RACE | GACCGCTTTAATGGAGTCTTC F | - |
Fl-TCTP | GAGGTCGAGCTGTACCAACAA F | 877 |
TTGTTCACGACGAACTTCCTAC R | ||
RCC2 | GGTTCCAAATCCTCCACAAACC F | 83 |
TGTCCCAATCCGCACGTTAC R | ||
COP γ | GCCTGTTGGACACCGATGAT F | 142 |
TGCAAGGCTCTCTCCAGTCC R | ||
qTCTP | GGATGAAATGTTCGGAGGAAAC F | 133 |
CATAGTGGGCTGTTCGCTGTAT R | ||
F Forward primer | ||
R Reverse primer |
Species | Accession Number | Taxonomic Group |
---|---|---|
Homo sapiens | AAQ01550.1 | Mammalia |
Mus musculus | NP033455.1 | Mammalia |
Sus scrofa | AAL68965.1 | Mammalia |
Rattus norvegicus | NP446319.1 | Mammalia |
Gallus gallus | NP990729.1 | Aves |
Xenopus tropicalis | NP_001008074.1 | Amphibia |
Pogona vitticeps | XP_020652710.1 | Reptilia |
Danio rerio | NP937783.1 | Osteichtyes |
Salmo salar | ACI68686.1 | Osteichtyes |
Xiphophorus maculatus | XP005807723.1 | Osteichtyes |
Takifugu rubripes | XP003962088.1 | Osteichtyes |
Petromyzon marinus | EB084009.1 | Agnata |
Branchiostoma floridae | XP_002592847.1 | Cephalochordata |
Ciona intestinalis | FK151528.1 | Tunicata |
Apostichopus japonicus | ABC87996.1 | Echinodermata |
Stichopus monotuberculatus | AID69538.1 | Echinodermata |
Strongylocentrotus purpuratus | XP795619.2 | Echinodermata |
Nilaparvata lugens | XP_022184371.1 | Insecta |
Drosophila melanogaster | NP001303431.1 | Insecta |
Anopheles sinensis | KFB46001.1 | Insecta |
Spodoptera frugiperda | ADK56158.1 | Insecta |
Harpegnathos saltator | XP011150938.1 | Insecta |
Megachile rotundata | XP_003700051.1 | Insecta |
Fenneropenaeus chinensis | ABB05535.1 | Crustacea |
Penaeus monodon | ACD13588.1 | Crustacea |
Lepeophtheirus salmonis | ACO12977.1 | Crustacea |
Octopus bimaculoides | XP_014780570.1 | Mollusca |
Aplysia californica | XP_005092645.1 | Mollusca |
Crassostrea virginica | XP_022338092.1 | Mollusca |
Caenorhabditis elegans | Q93573.1 | Nematoda |
Caenorhabditis remanei | EFP12520.1 | Nematoda |
Dictyocaulus viviparus | KJH46926.1 | Nematoda |
Brugia malayi | XP001897741 | Nematoda |
Clonorchis sinensis | AAX84199.1 | Platyhelmintes |
Macrostomum lignano | PAA86325.1 | Platyhelmintes |
Hydra vulgaris 1 | NM_001309745.1 | Hydrozoa |
Hydra vulgaris 2 | XM_002157314.3 | Hydrozoa |
Hydractinia echinata | DT623491.1 | Hydrozoa |
Podocoryna carnea | DY451741.1 | Hydrozoa |
Clytia hemisphaerica | FP985759.1 | Hydrozoa |
Polypodium hydriforme | GBGH01019625.1 | Hydrozoa |
Kudoa iwatai | GBGI01001069.1 | Myxozoa |
Aurelia aurita | GBRG01251580.1 | Scyphozoa |
Alatina alata | GEUJ01004399.1 | Cubozoa |
Haliclystus sanjuanensis | HAHB01030183.1 | Staurozoa |
Haliclystus auricula | HAHA01057349.1 | Staurozoa |
Calvadosia cruxmelitensis | HAHC01090444.1 | Staurozoa |
Acanthogiorgia aspera | GETB01037007.1 | Anthozoa Octocorallia |
Heliopora coerulea | IABP01022130.1 | Anthozoa Octocorallia |
Acropora digitifera | XP_015766473.1 | Anthozoa Hexacorallia |
Acropora millepora | JR988252.1 | Anthozoa Hexacorallia |
Acropora palmata | GW212294.1 | Anthozoa Hexacorallia |
Montastraea faveolata | GW258989.1 | Anthozoa Hexacorallia |
Nematostella vectensis | XM_001624752.1 | Anthozoa Hexacorallia |
Metridiumsenile | FC834313.1 | Anthozoa Hexacorallia |
Anemonia viridis | FK734027.1 | Anthozoa Hexacorallia |
Aiptasia pulchella | CK662981.1 | Anthozoa Hexacorallia |
Exaiptasia pallida | XP_020911835.1 | Anthozoa Hexacorallia |
Amphimedon qeenslandica | XP_003382650.1 | Porifera |
Organism | Protein Length a | Molecular Weight b | pI c | Templates d |
---|---|---|---|---|
A. millepora | 173 | 19,436.99 | 4.60 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
1TXJ (P. knowlesi) | ||||
A. digitifera | 173 | 19,392.98 | 4.65 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
1TXJ (P. knowlesi) | ||||
A. viridis | 180 | 20,553.34 | 4.54 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
N. vectensis | 181 | 20,715.78 | 4.78 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
E. pallida | 185 | 21,076.87 | 4.73 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
H. vulgaris 1 | 184 | 20,950.68 | 4.76 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
1TXJ (P. knowlesi) | ||||
H. vulgaris 2 | 180 | 20,854.76 | 5.48 | 1H6Q (S. pombe) |
2KWB (C. elegans) | ||||
1YZ1 (H. sapiens) | ||||
1TXJ (P. knowlesi) |
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Nicosia, A.; Bennici, C.; Biondo, G.; Costa, S.; Di Natale, M.; Masullo, T.; Monastero, C.; Ragusa, M.A.; Tagliavia, M.; Cuttitta, A. Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. Genes 2018, 9, 30. https://doi.org/10.3390/genes9010030
Nicosia A, Bennici C, Biondo G, Costa S, Di Natale M, Masullo T, Monastero C, Ragusa MA, Tagliavia M, Cuttitta A. Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. Genes. 2018; 9(1):30. https://doi.org/10.3390/genes9010030
Chicago/Turabian StyleNicosia, Aldo, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, and Angela Cuttitta. 2018. "Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues" Genes 9, no. 1: 30. https://doi.org/10.3390/genes9010030
APA StyleNicosia, A., Bennici, C., Biondo, G., Costa, S., Di Natale, M., Masullo, T., Monastero, C., Ragusa, M. A., Tagliavia, M., & Cuttitta, A. (2018). Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. Genes, 9(1), 30. https://doi.org/10.3390/genes9010030