Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity
Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when gr...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1075609/full |
| _version_ | 1797956460596953088 |
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| author | Jonathan R. Humphreys Bisrat J. Debebe Stephen P. Diggle Klaus Winzer |
| author_facet | Jonathan R. Humphreys Bisrat J. Debebe Stephen P. Diggle Klaus Winzer |
| author_sort | Jonathan R. Humphreys |
| collection | DOAJ |
| description | Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network. |
| first_indexed | 2024-04-10T23:49:37Z |
| format | Article |
| id | doaj.art-d48c08edafee46cca0214a0068821778 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-10T23:49:37Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-d48c08edafee46cca0214a00688217782023-01-10T21:14:19ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-01-011310.3389/fmicb.2022.10756091075609Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activityJonathan R. Humphreys0Bisrat J. Debebe1Stephen P. Diggle2Klaus Winzer3BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United KingdomDeepSeq, Centre for Genetics and Genomics, The University of Nottingham, Nottingham, United KingdomCenter for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United StatesBBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United KingdomSolventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1075609/fullstrain degenerationsolventogenic clostridiaultra-deep sequencingcomparative genomicsbiofuels |
| spellingShingle | Jonathan R. Humphreys Bisrat J. Debebe Stephen P. Diggle Klaus Winzer Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity Frontiers in Microbiology strain degeneration solventogenic clostridia ultra-deep sequencing comparative genomics biofuels |
| title | Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity |
| title_full | Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity |
| title_fullStr | Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity |
| title_full_unstemmed | Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity |
| title_short | Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity |
| title_sort | clostridium beijerinckii strain degeneration is driven by the loss of spo0a activity |
| topic | strain degeneration solventogenic clostridia ultra-deep sequencing comparative genomics biofuels |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1075609/full |
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