The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters
Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we found that the essential cell cycle regulator...
| Main Authors: | , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Cold Spring Harbor Laboratory Press
2016
|
| Online Access: | http://hdl.handle.net/1721.1/105365 https://orcid.org/0000-0002-4668-1695 https://orcid.org/0000-0003-0492-4895 https://orcid.org/0000-0002-8288-7607 |
| _version_ | 1826194773992538112 |
|---|---|
| author | Haakonsen, Diane Laure Yuan, Andy Han Laub, Michael T |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Haakonsen, Diane Laure Yuan, Andy Han Laub, Michael T |
| author_sort | Haakonsen, Diane Laure |
| collection | MIT |
| description | Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we found that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active σ[superscript 70]-dependent promoters in vivo but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ[superscript 70] interact with domain 4, GcrA interfaces with domain 2, the region that binds the −10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrated that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identified a regulon of ∼200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than recruitment exclusively. |
| first_indexed | 2024-09-23T10:01:35Z |
| format | Article |
| id | mit-1721.1/105365 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:01:35Z |
| publishDate | 2016 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/1053652022-09-26T15:17:01Z The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters The bacterial cell cycle regulator GcrA is a σ70 cofactor that drives gene expression from a subset of methylated promoters Haakonsen, Diane Laure Yuan, Andy Han Laub, Michael T Massachusetts Institute of Technology. Department of Biology Haakonsen, Diane Laure Yuan, Andy Han Laub, Michael T Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we found that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active σ[superscript 70]-dependent promoters in vivo but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ[superscript 70] interact with domain 4, GcrA interfaces with domain 2, the region that binds the −10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrated that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identified a regulon of ∼200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than recruitment exclusively. Howard Hughes Medical Institute (International Predoctural Fellowship) National Institutes of Health (U.S.) (Grant R01GM082899) 2016-11-18T18:59:43Z 2016-11-18T18:59:43Z 2015-11 2015-10 Article http://purl.org/eprint/type/JournalArticle 0890-9369 1549-5477 http://hdl.handle.net/1721.1/105365 Haakonsen, Diane L., Andy H. Yuan, and Michael T. Laub. “The Bacterial Cell Cycle Regulator GcrA Is a σ[superscript 70] Cofactor That Drives Gene Expression from a Subset of Methylated Promoters.” Genes & Development 29.21 (2015): 2272–2286. https://orcid.org/0000-0002-4668-1695 https://orcid.org/0000-0003-0492-4895 https://orcid.org/0000-0002-8288-7607 en_US http://dx.doi.org/10.1101/gad.270660.115 Genes & Development Creative Commons Attribution-NonCommercial 4.0 International http://creativecommons.org/licenses/by-nc/4.0/ application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Haakonsen, Diane Laure Yuan, Andy Han Laub, Michael T The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title | The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title_full | The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title_fullStr | The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title_full_unstemmed | The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title_short | The bacterial cell cycle regulator GcrA is a σ[superscript 70] cofactor that drives gene expression from a subset of methylated promoters |
| title_sort | bacterial cell cycle regulator gcra is a σ superscript 70 cofactor that drives gene expression from a subset of methylated promoters |
| url | http://hdl.handle.net/1721.1/105365 https://orcid.org/0000-0002-4668-1695 https://orcid.org/0000-0003-0492-4895 https://orcid.org/0000-0002-8288-7607 |
| work_keys_str_mv | AT haakonsendianelaure thebacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT yuanandyhan thebacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT laubmichaelt thebacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT haakonsendianelaure thebacterialcellcycleregulatorgcraisas70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT yuanandyhan thebacterialcellcycleregulatorgcraisas70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT laubmichaelt thebacterialcellcycleregulatorgcraisas70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT haakonsendianelaure bacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT yuanandyhan bacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters AT laubmichaelt bacterialcellcycleregulatorgcraisassuperscript70cofactorthatdrivesgeneexpressionfromasubsetofmethylatedpromoters |