In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins
Abstract Background Plant-parasitic nematodes (PPNs) that cause most damage include root-knot nematodes (RKNs) which are a major impediment to crop production. Root-knot nematodes, like other parasites, secrete proteins which are required for parasite proliferation and survival within the host durin...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09366-6 |
| _version_ | 1827933845221015552 |
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| author | Teresia Nyambura Macharia Tuan A. Duong Lucy Novungayo Moleleki |
| author_facet | Teresia Nyambura Macharia Tuan A. Duong Lucy Novungayo Moleleki |
| author_sort | Teresia Nyambura Macharia |
| collection | DOAJ |
| description | Abstract Background Plant-parasitic nematodes (PPNs) that cause most damage include root-knot nematodes (RKNs) which are a major impediment to crop production. Root-knot nematodes, like other parasites, secrete proteins which are required for parasite proliferation and survival within the host during the infection process. Results Here, we used various computational tools to predict and identify classically and non-classically secreted proteins encoded in the Meloidogyne javanica genome. Furthermore, functional annotation analysis was performed using various integrated bioinformatic tools to determine the biological significance of the predicted secretome. In total, 7,458 proteins were identified as secreted ones. A large percentage of this secretome is comprised of small proteins of ≤ 300 aa sequence length. Functional analyses showed that M. javanica secretome comprises cell wall degrading enzymes for facilitating nematode invasion, and migration by disintegrating the complex plant cell wall components. In addition, peptidases and peptidase inhibitors are an important category of M. javanica secretome involved in compatible host-nematode interactions. Conclusion This study identifies the putative secretome encoded in the M. javanica genome. Future experimental validation analyses can greatly benefit from this global analysis of M. javanica secretome. Equally, our analyses will advance knowledge of the interaction between plants and nematodes. |
| first_indexed | 2024-03-13T07:30:23Z |
| format | Article |
| id | doaj.art-4aad0b9e2e0f47ee9652440ca09e72d7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-13T07:30:23Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-4aad0b9e2e0f47ee9652440ca09e72d72023-06-04T11:07:21ZengBMCBMC Genomics1471-21642023-06-0124111410.1186/s12864-023-09366-6In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteinsTeresia Nyambura Macharia0Tuan A. Duong1Lucy Novungayo Moleleki2Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaDepartment of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaDepartment of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaAbstract Background Plant-parasitic nematodes (PPNs) that cause most damage include root-knot nematodes (RKNs) which are a major impediment to crop production. Root-knot nematodes, like other parasites, secrete proteins which are required for parasite proliferation and survival within the host during the infection process. Results Here, we used various computational tools to predict and identify classically and non-classically secreted proteins encoded in the Meloidogyne javanica genome. Furthermore, functional annotation analysis was performed using various integrated bioinformatic tools to determine the biological significance of the predicted secretome. In total, 7,458 proteins were identified as secreted ones. A large percentage of this secretome is comprised of small proteins of ≤ 300 aa sequence length. Functional analyses showed that M. javanica secretome comprises cell wall degrading enzymes for facilitating nematode invasion, and migration by disintegrating the complex plant cell wall components. In addition, peptidases and peptidase inhibitors are an important category of M. javanica secretome involved in compatible host-nematode interactions. Conclusion This study identifies the putative secretome encoded in the M. javanica genome. Future experimental validation analyses can greatly benefit from this global analysis of M. javanica secretome. Equally, our analyses will advance knowledge of the interaction between plants and nematodes.https://doi.org/10.1186/s12864-023-09366-6Secretome predictionPlant-nematode interactionRoot-knot nematodeBioinformaticsEffectors. |
| spellingShingle | Teresia Nyambura Macharia Tuan A. Duong Lucy Novungayo Moleleki In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins BMC Genomics Secretome prediction Plant-nematode interaction Root-knot nematode Bioinformatics Effectors. |
| title | In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins |
| title_full | In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins |
| title_fullStr | In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins |
| title_full_unstemmed | In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins |
| title_short | In silico secretome analyses of the polyphagous root-knot nematode Meloidogyne javanica: a resource for studying M. javanica secreted proteins |
| title_sort | in silico secretome analyses of the polyphagous root knot nematode meloidogyne javanica a resource for studying m javanica secreted proteins |
| topic | Secretome prediction Plant-nematode interaction Root-knot nematode Bioinformatics Effectors. |
| url | https://doi.org/10.1186/s12864-023-09366-6 |
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