Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in
We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid-associated protein Rok of Bacillus subtilis. DnaA binds directly to clusters of DnaA boxes at the origin of replication and elsewhere, including the promoters of several Dn...
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| Format: | Article |
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Wiley-Blackwell
2018
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| Online Access: | http://hdl.handle.net/1721.1/116408 https://orcid.org/0000-0001-8212-467X https://orcid.org/0000-0001-7983-5534 https://orcid.org/0000-0002-8235-7227 |
| _version_ | 1826213802613407744 |
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| author | Seid, Charlotte Allen Grossman, Alan Davis Smith, Janet L. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Seid, Charlotte Allen Grossman, Alan Davis Smith, Janet L. |
| author_sort | Seid, Charlotte Allen |
| collection | MIT |
| description | We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid-associated protein Rok of Bacillus subtilis. DnaA binds directly to clusters of DnaA boxes at the origin of replication and elsewhere, including the promoters of several DnaA-regulated genes. Rok, an analog of H-NS from gamma-proteobacteria that affects chromosome architecture and of Lsr2 from Mycobacteria, binds A+T-rich sequences throughout the genome and represses expression of many genes. Using crosslinking and immunoprecipitation followed by deep sequencing (ChIP-seq), we found that DnaA was associated with eight previously identified regions containing clusters of DnaA boxes, plus 36 additional regions that were also bound by Rok. Association of DnaA with these additional regions appeared to be indirect as it was dependent on Rok and independent of the DNA-binding domain of DnaA. Gene expres sion and mutant analyses support a model in which DnaA and Rok cooperate to repress transcription of yxaJ, the yybNM operon and the sunA-bdbB operon. Our results indicate that DnaA modulates the activity of Rok. We postulate that this interaction might affect nucleoid architecture. Furthermore, DnaA might interact similarly with Rok analogues in other organisms. |
| first_indexed | 2024-09-23T15:55:04Z |
| format | Article |
| id | mit-1721.1/116408 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T15:55:04Z |
| publishDate | 2018 |
| publisher | Wiley-Blackwell |
| record_format | dspace |
| spelling | mit-1721.1/1164082022-09-29T17:03:25Z Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in Seid, Charlotte Allen Grossman, Alan Davis Smith, Janet L. Massachusetts Institute of Technology. Department of Biology Seid, Charlotte Allen Smith, Janet Grossman, Alan Davis We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid-associated protein Rok of Bacillus subtilis. DnaA binds directly to clusters of DnaA boxes at the origin of replication and elsewhere, including the promoters of several DnaA-regulated genes. Rok, an analog of H-NS from gamma-proteobacteria that affects chromosome architecture and of Lsr2 from Mycobacteria, binds A+T-rich sequences throughout the genome and represses expression of many genes. Using crosslinking and immunoprecipitation followed by deep sequencing (ChIP-seq), we found that DnaA was associated with eight previously identified regions containing clusters of DnaA boxes, plus 36 additional regions that were also bound by Rok. Association of DnaA with these additional regions appeared to be indirect as it was dependent on Rok and independent of the DNA-binding domain of DnaA. Gene expres sion and mutant analyses support a model in which DnaA and Rok cooperate to repress transcription of yxaJ, the yybNM operon and the sunA-bdbB operon. Our results indicate that DnaA modulates the activity of Rok. We postulate that this interaction might affect nucleoid architecture. Furthermore, DnaA might interact similarly with Rok analogues in other organisms. United States. Public Health Service (Grant GM41934) 2018-06-19T14:41:41Z 2018-06-19T14:41:41Z 2016-11 2016-11 2018-06-18T17:40:14Z Article http://purl.org/eprint/type/JournalArticle 0950-382X 1365-2958 http://hdl.handle.net/1721.1/116408 Seid, Charlotte A. et al. “Genetic and Biochemical Interactions Between the Bacterial Replication Initiator DnaA and the Nucleoid-Associated Protein Rok inBacillus Subtilis.” Molecular Microbiology 103, 5 (January 2017): 798–817 © 2016 John Wiley & Sons Ltd https://orcid.org/0000-0001-8212-467X https://orcid.org/0000-0001-7983-5534 https://orcid.org/0000-0002-8235-7227 http://dx.doi.org/10.1111/MMI.13590 Molecular Microbiology Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Wiley-Blackwell PMC |
| spellingShingle | Seid, Charlotte Allen Grossman, Alan Davis Smith, Janet L. Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title | Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title_full | Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title_fullStr | Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title_full_unstemmed | Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title_short | Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in |
| title_sort | genetic and biochemical interactions between the bacterial replication initiator dnaa and the nucleoid associated protein rok in |
| url | http://hdl.handle.net/1721.1/116408 https://orcid.org/0000-0001-8212-467X https://orcid.org/0000-0001-7983-5534 https://orcid.org/0000-0002-8235-7227 |
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