Identification and functional analysis of novel protein-encoding sequences related to stress-resistance
Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extrem...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1268315/full |
| _version_ | 1797671508023181312 |
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| author | Joshelin Huanca-Juarez Joshelin Huanca-Juarez Edson Alexandre Nascimento-Silva Edson Alexandre Nascimento-Silva Ninna Hirata Silva Rafael Silva-Rocha María-Eugenia Guazzaroni |
| author_facet | Joshelin Huanca-Juarez Joshelin Huanca-Juarez Edson Alexandre Nascimento-Silva Edson Alexandre Nascimento-Silva Ninna Hirata Silva Rafael Silva-Rocha María-Eugenia Guazzaroni |
| author_sort | Joshelin Huanca-Juarez |
| collection | DOAJ |
| description | Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance. |
| first_indexed | 2024-03-11T21:16:34Z |
| format | Article |
| id | doaj.art-0c2e034637c244c4a54d1e9babeb3130 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-11T21:16:34Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-0c2e034637c244c4a54d1e9babeb31302023-09-28T16:52:36ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-09-011410.3389/fmicb.2023.12683151268315Identification and functional analysis of novel protein-encoding sequences related to stress-resistanceJoshelin Huanca-Juarez0Joshelin Huanca-Juarez1Edson Alexandre Nascimento-Silva2Edson Alexandre Nascimento-Silva3Ninna Hirata Silva4Rafael Silva-Rocha5María-Eugenia Guazzaroni6Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, BrazilDepartment of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, BrazilDepartment of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, BrazilDepartment of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, BrazilDepartment of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, BrazilByMyCell Inova Simples, São Paulo, BrazilDepartment of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, BrazilCurrently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1268315/fullstress resistancebacterial robustnessindustrial biotechnologysynthetic biologymetagenomics |
| spellingShingle | Joshelin Huanca-Juarez Joshelin Huanca-Juarez Edson Alexandre Nascimento-Silva Edson Alexandre Nascimento-Silva Ninna Hirata Silva Rafael Silva-Rocha María-Eugenia Guazzaroni Identification and functional analysis of novel protein-encoding sequences related to stress-resistance Frontiers in Microbiology stress resistance bacterial robustness industrial biotechnology synthetic biology metagenomics |
| title | Identification and functional analysis of novel protein-encoding sequences related to stress-resistance |
| title_full | Identification and functional analysis of novel protein-encoding sequences related to stress-resistance |
| title_fullStr | Identification and functional analysis of novel protein-encoding sequences related to stress-resistance |
| title_full_unstemmed | Identification and functional analysis of novel protein-encoding sequences related to stress-resistance |
| title_short | Identification and functional analysis of novel protein-encoding sequences related to stress-resistance |
| title_sort | identification and functional analysis of novel protein encoding sequences related to stress resistance |
| topic | stress resistance bacterial robustness industrial biotechnology synthetic biology metagenomics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1268315/full |
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