Determinants of bacteriophage 933W repressor DNA binding specificity.
We reported previously that 933W repressor apparently does not cooperatively bind to adjacent sites on DNA and that the relative affinities of 933W repressor for its operators differ significantly from that of any other lambdoid bacteriophage. These findings indicate that the operational details of...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22509323/?tool=EBI |
| _version_ | 1818851841355546624 |
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| author | Tammy J Bullwinkle Daniel Samorodnitsky Rayna C Rosati Gerald B Koudelka |
| author_facet | Tammy J Bullwinkle Daniel Samorodnitsky Rayna C Rosati Gerald B Koudelka |
| author_sort | Tammy J Bullwinkle |
| collection | DOAJ |
| description | We reported previously that 933W repressor apparently does not cooperatively bind to adjacent sites on DNA and that the relative affinities of 933W repressor for its operators differ significantly from that of any other lambdoid bacteriophage. These findings indicate that the operational details of the lysis-lysogeny switch of bacteriophage 933W are unique among lambdoid bacteriophages. Since the functioning of the lysis-lysogeny switch in 933W bacteriophage uniquely and solely depends on the order of preference of 933W repressor for its operators, we examined the details of how 933W repressor recognizes its DNA sites. To identify the specificity determinants, we first created a molecular model of the 933W repressor-DNA complex and tested the predicted protein-DNA interactions. These results of these studies provide a picture of how 933W repressor recognizes its DNA sites. We also show that, opposite of what is normally observed for lambdoid phages, 933W operator sequences have evolved in such a way that the presence of the most commonly found base sequences at particular operator positions serves to decrease, rather than increase, the affinity of the protein for the site. This finding cautions against assuming that a consensus sequence derived from sequence analysis defines the optimal, highest affinity DNA binding site for a protein. |
| first_indexed | 2024-12-19T07:11:26Z |
| format | Article |
| id | doaj.art-a4721036d113456ab2e536d40efefacc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T07:11:26Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a4721036d113456ab2e536d40efefacc2022-12-21T20:31:12ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0174e3456310.1371/journal.pone.0034563Determinants of bacteriophage 933W repressor DNA binding specificity.Tammy J BullwinkleDaniel SamorodnitskyRayna C RosatiGerald B KoudelkaWe reported previously that 933W repressor apparently does not cooperatively bind to adjacent sites on DNA and that the relative affinities of 933W repressor for its operators differ significantly from that of any other lambdoid bacteriophage. These findings indicate that the operational details of the lysis-lysogeny switch of bacteriophage 933W are unique among lambdoid bacteriophages. Since the functioning of the lysis-lysogeny switch in 933W bacteriophage uniquely and solely depends on the order of preference of 933W repressor for its operators, we examined the details of how 933W repressor recognizes its DNA sites. To identify the specificity determinants, we first created a molecular model of the 933W repressor-DNA complex and tested the predicted protein-DNA interactions. These results of these studies provide a picture of how 933W repressor recognizes its DNA sites. We also show that, opposite of what is normally observed for lambdoid phages, 933W operator sequences have evolved in such a way that the presence of the most commonly found base sequences at particular operator positions serves to decrease, rather than increase, the affinity of the protein for the site. This finding cautions against assuming that a consensus sequence derived from sequence analysis defines the optimal, highest affinity DNA binding site for a protein.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22509323/?tool=EBI |
| spellingShingle | Tammy J Bullwinkle Daniel Samorodnitsky Rayna C Rosati Gerald B Koudelka Determinants of bacteriophage 933W repressor DNA binding specificity. PLoS ONE |
| title | Determinants of bacteriophage 933W repressor DNA binding specificity. |
| title_full | Determinants of bacteriophage 933W repressor DNA binding specificity. |
| title_fullStr | Determinants of bacteriophage 933W repressor DNA binding specificity. |
| title_full_unstemmed | Determinants of bacteriophage 933W repressor DNA binding specificity. |
| title_short | Determinants of bacteriophage 933W repressor DNA binding specificity. |
| title_sort | determinants of bacteriophage 933w repressor dna binding specificity |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22509323/?tool=EBI |
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