Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions
Gastropods are among the most diverse animals. Gastropod mucus contains several glycoproteins and peptides that vary by species and habitat. Some bioactive peptides from gastropod mucus were identified only in a few species. Therefore, using biochemical, mass spectrometric, and bioinformatics approa...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-06-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/26/11/3475 |
| _version_ | 1797531002503954432 |
|---|---|
| author | Viroj Tachapuripunya Sittiruk Roytrakul Pramote Chumnanpuen Teerasak E-kobon |
| author_facet | Viroj Tachapuripunya Sittiruk Roytrakul Pramote Chumnanpuen Teerasak E-kobon |
| author_sort | Viroj Tachapuripunya |
| collection | DOAJ |
| description | Gastropods are among the most diverse animals. Gastropod mucus contains several glycoproteins and peptides that vary by species and habitat. Some bioactive peptides from gastropod mucus were identified only in a few species. Therefore, using biochemical, mass spectrometric, and bioinformatics approaches, this study aimed to comprehensively identify putative bioactive peptides from the mucus proteomes of seven commonly found or commercially valuable gastropods. The mucus was collected in triplicate samples, and the proteins were separated by 1D-SDS-PAGE before tryptic digestion and peptide identification by nano LC-MS/MS. The mucus peptides were subsequently compared with R scripts. A total of 2818 different peptides constituting 1634 proteins from the mucus samples were identified, and 1218 of these peptides (43%) were core peptides found in the mucus of all examined species. Clustering and correspondence analyses of 1600 variable peptides showed unique mucous peptide patterns for each species. The high-throughput k-nearest neighbor and random forest-based prediction programs were developed with more than 95% averaged accuracy and could identify 11 functional categories of putative bioactive peptides and 268 peptides (9.5%) with at least five to seven bioactive properties. Antihypertensive, drug-delivering, and antiparasitic peptides were predominant. These peptides provide an understanding of gastropod mucus, and the putative bioactive peptides are expected to be experimentally validated for further medical, pharmaceutical, and cosmetic applications. |
| first_indexed | 2024-03-10T10:37:54Z |
| format | Article |
| id | doaj.art-40c530d99beb414c87c08a184bb41841 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T10:37:54Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-40c530d99beb414c87c08a184bb418412023-11-21T23:09:32ZengMDPI AGMolecules1420-30492021-06-012611347510.3390/molecules26113475Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics PredictionsViroj Tachapuripunya0Sittiruk Roytrakul1Pramote Chumnanpuen2Teerasak E-kobon3Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandFunctional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, ThailandDepartment of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandDepartment of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, ThailandGastropods are among the most diverse animals. Gastropod mucus contains several glycoproteins and peptides that vary by species and habitat. Some bioactive peptides from gastropod mucus were identified only in a few species. Therefore, using biochemical, mass spectrometric, and bioinformatics approaches, this study aimed to comprehensively identify putative bioactive peptides from the mucus proteomes of seven commonly found or commercially valuable gastropods. The mucus was collected in triplicate samples, and the proteins were separated by 1D-SDS-PAGE before tryptic digestion and peptide identification by nano LC-MS/MS. The mucus peptides were subsequently compared with R scripts. A total of 2818 different peptides constituting 1634 proteins from the mucus samples were identified, and 1218 of these peptides (43%) were core peptides found in the mucus of all examined species. Clustering and correspondence analyses of 1600 variable peptides showed unique mucous peptide patterns for each species. The high-throughput k-nearest neighbor and random forest-based prediction programs were developed with more than 95% averaged accuracy and could identify 11 functional categories of putative bioactive peptides and 268 peptides (9.5%) with at least five to seven bioactive properties. Antihypertensive, drug-delivering, and antiparasitic peptides were predominant. These peptides provide an understanding of gastropod mucus, and the putative bioactive peptides are expected to be experimentally validated for further medical, pharmaceutical, and cosmetic applications.https://www.mdpi.com/1420-3049/26/11/3475gastropodmucusbioactive peptidesmachine-learning predictionproteomics |
| spellingShingle | Viroj Tachapuripunya Sittiruk Roytrakul Pramote Chumnanpuen Teerasak E-kobon Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions Molecules gastropod mucus bioactive peptides machine-learning prediction proteomics |
| title | Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions |
| title_full | Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions |
| title_fullStr | Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions |
| title_full_unstemmed | Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions |
| title_short | Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions |
| title_sort | unveiling putative functions of mucus proteins and their tryptic peptides in seven gastropod species using comparative proteomics and machine learning based bioinformatics predictions |
| topic | gastropod mucus bioactive peptides machine-learning prediction proteomics |
| url | https://www.mdpi.com/1420-3049/26/11/3475 |
| work_keys_str_mv | AT virojtachapuripunya unveilingputativefunctionsofmucusproteinsandtheirtrypticpeptidesinsevengastropodspeciesusingcomparativeproteomicsandmachinelearningbasedbioinformaticspredictions AT sittirukroytrakul unveilingputativefunctionsofmucusproteinsandtheirtrypticpeptidesinsevengastropodspeciesusingcomparativeproteomicsandmachinelearningbasedbioinformaticspredictions AT pramotechumnanpuen unveilingputativefunctionsofmucusproteinsandtheirtrypticpeptidesinsevengastropodspeciesusingcomparativeproteomicsandmachinelearningbasedbioinformaticspredictions AT teerasakekobon unveilingputativefunctionsofmucusproteinsandtheirtrypticpeptidesinsevengastropodspeciesusingcomparativeproteomicsandmachinelearningbasedbioinformaticspredictions |