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Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach
Gene editing is one of the most promising tools in science. It enables precise modifications of an organism's genetic material. Metagenomics is considered a powerful tool that unlocks the broad genetic potential found in uncultured microbial communities. Exploring the genetic diversity of uncultured...
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AUC Knowledge Fountain
2025
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| _version_ | 1867613424444243968 |
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| access_status_str | Open Access |
| author | Ghonaim, Lobna Abdallah |
| author_browse | Ghonaim, Lobna Abdallah |
| author_facet | Ghonaim, Lobna Abdallah |
| author_sort | Ghonaim, Lobna Abdallah |
| collection | Thesis |
| description | Gene editing is one of the most promising tools in science. It enables precise modifications of an organism's genetic material. Metagenomics is considered a powerful tool that unlocks the broad genetic potential found in uncultured microbial communities. Exploring the genetic diversity of uncultured microbial communities helps identify novel functional proteins with unique properties and make the best use of these diverse microbial ecosystems.
We developed and employed a metagenomic-based approach to mine more than 1000 metagenomes for prokaryotic argonaute proteins (pAgos), a potential gene editing machinery encoded in bacterial and archaeal genomes. Our workflow involved strict quality control, sequence assembly, taxonomic classification, profiling and analysis, and annotation. We then identified the presence of key domains such as PIWI and MID. Our methodology ensured effective screening and identification of these proteins across metagenomes from 25 different ecosystems. We analyzed 1,011 publicly available metagenomic datasets from which we identified 905 putative pAgos across these diverse environments by building a custom Hidden Markov Model (HMM) profile. Our analysis identified proteins with substantial diversity and considerable abundance in diverse microbial environments and included novel variants with unique functional characteristics. Our work highlights the power of metagenomics to discover novel functional proteins and presents promising applications for gene editing. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-3499 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:55.364Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-3499 Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach Ghonaim, Lobna Abdallah Gene editing is one of the most promising tools in science. It enables precise modifications of an organism's genetic material. Metagenomics is considered a powerful tool that unlocks the broad genetic potential found in uncultured microbial communities. Exploring the genetic diversity of uncultured microbial communities helps identify novel functional proteins with unique properties and make the best use of these diverse microbial ecosystems. We developed and employed a metagenomic-based approach to mine more than 1000 metagenomes for prokaryotic argonaute proteins (pAgos), a potential gene editing machinery encoded in bacterial and archaeal genomes. Our workflow involved strict quality control, sequence assembly, taxonomic classification, profiling and analysis, and annotation. We then identified the presence of key domains such as PIWI and MID. Our methodology ensured effective screening and identification of these proteins across metagenomes from 25 different ecosystems. We analyzed 1,011 publicly available metagenomic datasets from which we identified 905 putative pAgos across these diverse environments by building a custom Hidden Markov Model (HMM) profile. Our analysis identified proteins with substantial diversity and considerable abundance in diverse microbial environments and included novel variants with unique functional characteristics. Our work highlights the power of metagenomics to discover novel functional proteins and presents promising applications for gene editing. 2025-02-19T08:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/2452 https://fount.aucegypt.edu/context/etds/article/3499/viewcontent/lobna_abdallah_ghonaim_thesis.pdf Theses and Dissertations AUC Knowledge Fountain metagenomics argonaute proteins genetic editing gene silencing bioinformatics. Bioinformatics Biotechnology Computational Biology Genetics Genomics Molecular Genetics |
| spellingShingle | metagenomics argonaute proteins genetic editing gene silencing bioinformatics. Bioinformatics Biotechnology Computational Biology Genetics Genomics Molecular Genetics Ghonaim, Lobna Abdallah Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title | Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title_full | Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title_fullStr | Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title_full_unstemmed | Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title_short | Identification of Novel Argonaute Proteins Using a Metagenomic Mining Approach |
| title_sort | identification of novel argonaute proteins using a metagenomic mining approach |
| topic | metagenomics argonaute proteins genetic editing gene silencing bioinformatics. Bioinformatics Biotechnology Computational Biology Genetics Genomics Molecular Genetics |
| url | https://fount.aucegypt.edu/etds/2452 https://fount.aucegypt.edu/context/etds/article/3499/viewcontent/lobna_abdallah_ghonaim_thesis.pdf |
| work_keys_str_mv | AT ghonaimlobnaabdallah identificationofnovelargonauteproteinsusingametagenomicminingapproach |