Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression
Abstract Archaeal methanogenesis is a dynamic process regulated by various cellular and environmental signals. However, understanding this regulation is technically challenging due to the difficulty of measuring gene expression dynamics in individual archaeal cells. Here, we develop a multi-round hy...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-57159-0 |
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| author | Yijing Dong Lanting Qi Fei Zhao Yifan Chen Lewen Liang Jing Wang Weishu Zhao Fengping Wang Heng Xu |
| author_facet | Yijing Dong Lanting Qi Fei Zhao Yifan Chen Lewen Liang Jing Wang Weishu Zhao Fengping Wang Heng Xu |
| author_sort | Yijing Dong |
| collection | DOAJ |
| description | Abstract Archaeal methanogenesis is a dynamic process regulated by various cellular and environmental signals. However, understanding this regulation is technically challenging due to the difficulty of measuring gene expression dynamics in individual archaeal cells. Here, we develop a multi-round hybridization chain reaction (HCR)-assisted single-molecule fluorescence in situ hybridization (FISH) method to quantify the transcriptional dynamics of 12 genes involved in methanogenesis in individual cells of Methanococcoides orientis. Under optimal growth condition, most of these genes appear to be expressed in a temporal order matching metabolic reaction order. Interestingly, an important environmental factor, Fe(III), stimulates cellular methane production without upregulating methanogenic gene expression, likely through a Fenton-reaction-triggered mechanism. Through single-cell clustering and kinetic analyses, we associate these gene expression patterns to a dynamic mixture of distinct cellular states, potentially regulated by a set of shared factors. Our work provides a quantitative framework for uncovering the mechanisms of metabolic regulation in archaea. |
| format | Article |
| id | doaj-art-7de32d4656e04610acdaa34ce8a88128 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-7de32d4656e04610acdaa34ce8a881282025-08-20T01:57:49ZengNature PortfolioNature Communications2041-17232025-03-0116111510.1038/s41467-025-57159-0Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expressionYijing Dong0Lanting Qi1Fei Zhao2Yifan Chen3Lewen Liang4Jing Wang5Weishu Zhao6Fengping Wang7Heng Xu8School of Physics and Astronomy, Shanghai Jiao Tong UniversitySchool of Physics and Astronomy, Shanghai Jiao Tong UniversitySchool of Physics and Astronomy, Shanghai Jiao Tong UniversityState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityKey Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, and School of Oceanography, Shanghai Jiao Tong UniversityKey Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, and School of Oceanography, Shanghai Jiao Tong UniversityState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityState Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversitySchool of Physics and Astronomy, Shanghai Jiao Tong UniversityAbstract Archaeal methanogenesis is a dynamic process regulated by various cellular and environmental signals. However, understanding this regulation is technically challenging due to the difficulty of measuring gene expression dynamics in individual archaeal cells. Here, we develop a multi-round hybridization chain reaction (HCR)-assisted single-molecule fluorescence in situ hybridization (FISH) method to quantify the transcriptional dynamics of 12 genes involved in methanogenesis in individual cells of Methanococcoides orientis. Under optimal growth condition, most of these genes appear to be expressed in a temporal order matching metabolic reaction order. Interestingly, an important environmental factor, Fe(III), stimulates cellular methane production without upregulating methanogenic gene expression, likely through a Fenton-reaction-triggered mechanism. Through single-cell clustering and kinetic analyses, we associate these gene expression patterns to a dynamic mixture of distinct cellular states, potentially regulated by a set of shared factors. Our work provides a quantitative framework for uncovering the mechanisms of metabolic regulation in archaea.https://doi.org/10.1038/s41467-025-57159-0 |
| spellingShingle | Yijing Dong Lanting Qi Fei Zhao Yifan Chen Lewen Liang Jing Wang Weishu Zhao Fengping Wang Heng Xu Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression Nature Communications |
| title | Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression |
| title_full | Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression |
| title_fullStr | Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression |
| title_full_unstemmed | Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression |
| title_short | Uncovering dynamic transcriptional regulation of methanogenesis via single-cell imaging of archaeal gene expression |
| title_sort | uncovering dynamic transcriptional regulation of methanogenesis via single cell imaging of archaeal gene expression |
| url | https://doi.org/10.1038/s41467-025-57159-0 |
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