Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX
<p>Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C<sub>1</sub>) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert c...
محفوظ في:
| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | , , , , , , |
| منشور في: |
2024
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| الموضوعات: | |
| الوسوم: |
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| _version_ | 1852024940871548928 |
|---|---|
| author | Ugochi Jennifer Nwaokorie (15467270) |
| author2 | Kristina Reinmets (5340758) Lorena Azevedo de Lima (12403306) Pratik Rajendra Pawar (15467273) Kurshedaktar Majibullah Shaikh (15467276) Audrey Harris (446383) Michael Köpke (405397) Kaspar Valgepea (4901794) |
| author2_role | author author author author author author author |
| author_facet | Ugochi Jennifer Nwaokorie (15467270) Kristina Reinmets (5340758) Lorena Azevedo de Lima (12403306) Pratik Rajendra Pawar (15467273) Kurshedaktar Majibullah Shaikh (15467276) Audrey Harris (446383) Michael Köpke (405397) Kaspar Valgepea (4901794) |
| author_role | author |
| dc.creator.none.fl_str_mv | Ugochi Jennifer Nwaokorie (15467270) Kristina Reinmets (5340758) Lorena Azevedo de Lima (12403306) Pratik Rajendra Pawar (15467273) Kurshedaktar Majibullah Shaikh (15467276) Audrey Harris (446383) Michael Köpke (405397) Kaspar Valgepea (4901794) |
| dc.date.none.fl_str_mv | 2024-11-25T13:51:14Z |
| dc.identifier.none.fl_str_mv | 10.3389/fbioe.2023.1167892.s004 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Table3_Deletion_of_genes_linked_to_the_C1-fixing_gene_cluster_affects_growth_by-products_and_proteome_of_Clostridium_autoethanogenum_XLSX/27901524 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biotechnology Biological Engineering Genetic Engineering Biomarkers Biomaterials Biomechanical Engineering Biomedical Engineering not elsewhere classified Synthetic Biology Agricultural Marine Biotechnology Bioremediation Bioprocessing, Bioproduction and Bioproducts Industrial Biotechnology Diagnostics (incl. Biosensors) Industrial Microbiology (incl. Biofeedstocks) Industrial Molecular Engineering of Nucleic Acids and Proteins Industrial Biotechnology not elsewhere classified Medical Biotechnology Diagnostics (incl. Biosensors) Medical Molecular Engineering of Nucleic Acids and Proteins Regenerative Medicine (incl. Stem Cells and Tissue Engineering) Medical Biotechnology not elsewhere classified gas fermentation acetogen CRISPR/Cas9 genetic engineering metabolomics proteomics chemostat syngas |
| dc.title.none.fl_str_mv | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p>Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C<sub>1</sub>) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO<sub>2</sub>) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C<sub>1</sub>-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions—hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)—directly adjacent and expressed at similar levels to the C<sub>1</sub>-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO<sub>2</sub> and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C<sub>1</sub>-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_18a89492432ba767609d5a7e6ab4b8b1 |
| identifier_str_mv | 10.3389/fbioe.2023.1167892.s004 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27901524 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSXUgochi Jennifer Nwaokorie (15467270)Kristina Reinmets (5340758)Lorena Azevedo de Lima (12403306)Pratik Rajendra Pawar (15467273)Kurshedaktar Majibullah Shaikh (15467276)Audrey Harris (446383)Michael Köpke (405397)Kaspar Valgepea (4901794)BiotechnologyBiological EngineeringGenetic EngineeringBiomarkersBiomaterialsBiomechanical EngineeringBiomedical Engineering not elsewhere classifiedSynthetic BiologyAgricultural Marine BiotechnologyBioremediationBioprocessing, Bioproduction and BioproductsIndustrial Biotechnology Diagnostics (incl. Biosensors)Industrial Microbiology (incl. Biofeedstocks)Industrial Molecular Engineering of Nucleic Acids and ProteinsIndustrial Biotechnology not elsewhere classifiedMedical Biotechnology Diagnostics (incl. Biosensors)Medical Molecular Engineering of Nucleic Acids and ProteinsRegenerative Medicine (incl. Stem Cells and Tissue Engineering)Medical Biotechnology not elsewhere classifiedgas fermentationacetogenCRISPR/Cas9genetic engineeringmetabolomicsproteomicschemostatsyngas<p>Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C<sub>1</sub>) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO<sub>2</sub>) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C<sub>1</sub>-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions—hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)—directly adjacent and expressed at similar levels to the C<sub>1</sub>-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO<sub>2</sub> and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C<sub>1</sub>-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.</p>2024-11-25T13:51:14ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fbioe.2023.1167892.s004https://figshare.com/articles/dataset/Table3_Deletion_of_genes_linked_to_the_C1-fixing_gene_cluster_affects_growth_by-products_and_proteome_of_Clostridium_autoethanogenum_XLSX/27901524CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/279015242024-11-25T13:51:14Z |
| spellingShingle | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX Ugochi Jennifer Nwaokorie (15467270) Biotechnology Biological Engineering Genetic Engineering Biomarkers Biomaterials Biomechanical Engineering Biomedical Engineering not elsewhere classified Synthetic Biology Agricultural Marine Biotechnology Bioremediation Bioprocessing, Bioproduction and Bioproducts Industrial Biotechnology Diagnostics (incl. Biosensors) Industrial Microbiology (incl. Biofeedstocks) Industrial Molecular Engineering of Nucleic Acids and Proteins Industrial Biotechnology not elsewhere classified Medical Biotechnology Diagnostics (incl. Biosensors) Medical Molecular Engineering of Nucleic Acids and Proteins Regenerative Medicine (incl. Stem Cells and Tissue Engineering) Medical Biotechnology not elsewhere classified gas fermentation acetogen CRISPR/Cas9 genetic engineering metabolomics proteomics chemostat syngas |
| status_str | publishedVersion |
| title | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| title_full | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| title_fullStr | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| title_full_unstemmed | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| title_short | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| title_sort | Table3_Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum.XLSX |
| topic | Biotechnology Biological Engineering Genetic Engineering Biomarkers Biomaterials Biomechanical Engineering Biomedical Engineering not elsewhere classified Synthetic Biology Agricultural Marine Biotechnology Bioremediation Bioprocessing, Bioproduction and Bioproducts Industrial Biotechnology Diagnostics (incl. Biosensors) Industrial Microbiology (incl. Biofeedstocks) Industrial Molecular Engineering of Nucleic Acids and Proteins Industrial Biotechnology not elsewhere classified Medical Biotechnology Diagnostics (incl. Biosensors) Medical Molecular Engineering of Nucleic Acids and Proteins Regenerative Medicine (incl. Stem Cells and Tissue Engineering) Medical Biotechnology not elsewhere classified gas fermentation acetogen CRISPR/Cas9 genetic engineering metabolomics proteomics chemostat syngas |