Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i>
The red palm weevil, <i>Rhynchophorus ferrugineus</i>, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-04-01
|
| Series: | Insects |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4450/16/4/421 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849713892195827712 |
|---|---|
| author | Nazmi Harith-Fadzilah Mohammad Nihad Mohammed Ali AlSaleh Abdulqader Yaslam Bazeyad Subash-Babu Pandurangan Kashif Munawar Arya Vidyawan Hattan A. Alharbi Jernej Jakše Arnab Pain Binu Antony |
| author_facet | Nazmi Harith-Fadzilah Mohammad Nihad Mohammed Ali AlSaleh Abdulqader Yaslam Bazeyad Subash-Babu Pandurangan Kashif Munawar Arya Vidyawan Hattan A. Alharbi Jernej Jakše Arnab Pain Binu Antony |
| author_sort | Nazmi Harith-Fadzilah |
| collection | DOAJ |
| description | The red palm weevil, <i>Rhynchophorus ferrugineus</i>, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target <i>R. ferrugineus</i> proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes, annotated DE-related genes from the <i>R. ferrugineus</i> gut and abdomen, manually annotated the DE gene family from the recently available genome and our transcriptome data, and reported 34 glycosidases, 85 lipases, and 201 proteases. We identified several tandem duplicates and allelic variants from the lipase and protease families, notably, 10 RferLip and 21 RferPro alleles, which emerged primarily through indels and single-site substitution. These alleles may confer enhanced digestive lipolysis and proteolysis. Phylogenetic analyses identified and classified different subfamilies of DEs and revealed close evolutionary relationships with other coleopterans. We assessed select candidate DEs’ activity and the potential for inhibition in silico to better understand the herbivory arsenal. In silico analysis revealed that the selected enzymes exhibited similar ligand-binding affinity to their corresponding substrate, except for protease aminopeptidase N, RferPro40, which exhibited poorer affinity to the inhibitor bestatin. Overall, our study serves as a foundation for further functional analysis and offers a novel target for the development of a novel bio-rational insecticide for <i>R. ferrugineus</i>. |
| format | Article |
| id | doaj-art-acd3540a84574f9bbc8c2b3918872dec |
| institution | DOAJ |
| issn | 2075-4450 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Insects |
| spelling | doaj-art-acd3540a84574f9bbc8c2b3918872dec2025-08-20T03:13:50ZengMDPI AGInsects2075-44502025-04-0116442110.3390/insects16040421Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i>Nazmi Harith-Fadzilah0Mohammad Nihad1Mohammed Ali AlSaleh2Abdulqader Yaslam Bazeyad3Subash-Babu Pandurangan4Kashif Munawar5Arya Vidyawan6Hattan A. Alharbi7Jernej Jakše8Arnab Pain9Binu Antony10School of Agriculture Sciences and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut 22200, MalaysiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaAgronomy Department, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, SloveniaPathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah 23955, Saudi ArabiaDepartment of Plant Protection, Center for Chemical Ecology and Functional Genomics, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi ArabiaThe red palm weevil, <i>Rhynchophorus ferrugineus</i>, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target <i>R. ferrugineus</i> proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes, annotated DE-related genes from the <i>R. ferrugineus</i> gut and abdomen, manually annotated the DE gene family from the recently available genome and our transcriptome data, and reported 34 glycosidases, 85 lipases, and 201 proteases. We identified several tandem duplicates and allelic variants from the lipase and protease families, notably, 10 RferLip and 21 RferPro alleles, which emerged primarily through indels and single-site substitution. These alleles may confer enhanced digestive lipolysis and proteolysis. Phylogenetic analyses identified and classified different subfamilies of DEs and revealed close evolutionary relationships with other coleopterans. We assessed select candidate DEs’ activity and the potential for inhibition in silico to better understand the herbivory arsenal. In silico analysis revealed that the selected enzymes exhibited similar ligand-binding affinity to their corresponding substrate, except for protease aminopeptidase N, RferPro40, which exhibited poorer affinity to the inhibitor bestatin. Overall, our study serves as a foundation for further functional analysis and offers a novel target for the development of a novel bio-rational insecticide for <i>R. ferrugineus</i>.https://www.mdpi.com/2075-4450/16/4/421red palm weevilherbivorydigestive enzymegene duplicationphylogenymolecular docking |
| spellingShingle | Nazmi Harith-Fadzilah Mohammad Nihad Mohammed Ali AlSaleh Abdulqader Yaslam Bazeyad Subash-Babu Pandurangan Kashif Munawar Arya Vidyawan Hattan A. Alharbi Jernej Jakše Arnab Pain Binu Antony Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> Insects red palm weevil herbivory digestive enzyme gene duplication phylogeny molecular docking |
| title | Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> |
| title_full | Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> |
| title_fullStr | Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> |
| title_full_unstemmed | Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> |
| title_short | Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, <i>Rhynchophorus ferrugineus</i> |
| title_sort | genome wide identification and expression profiling of glycosidases lipases and proteases from invasive asian palm weevil i rhynchophorus ferrugineus i |
| topic | red palm weevil herbivory digestive enzyme gene duplication phylogeny molecular docking |
| url | https://www.mdpi.com/2075-4450/16/4/421 |
| work_keys_str_mv | AT nazmiharithfadzilah genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT mohammadnihad genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT mohammedalialsaleh genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT abdulqaderyaslambazeyad genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT subashbabupandurangan genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT kashifmunawar genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT aryavidyawan genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT hattanaalharbi genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT jernejjakse genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT arnabpain genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi AT binuantony genomewideidentificationandexpressionprofilingofglycosidaseslipasesandproteasesfrominvasiveasianpalmweevilirhynchophorusferrugineusi |