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...

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Autores principales:	Tammy J Bullwinkle, Daniel Samorodnitsky, Rayna C Rosati, Gerald B Koudelka
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a4721036d113456ab2e536d40efefacc
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spelling	oai:doaj.org-article:a4721036d113456ab2e536d40efefacc2021-11-18T07:23:21ZDeterminants of bacteriophage 933W repressor DNA binding specificity.1932-620310.1371/journal.pone.0034563https://doaj.org/article/a4721036d113456ab2e536d40efefacc2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22509323/?tool=EBIhttps://doaj.org/toc/1932-6203We 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.Tammy J BullwinkleDaniel SamorodnitskyRayna C RosatiGerald B KoudelkaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34563 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tammy J Bullwinkle Daniel Samorodnitsky Rayna C Rosati Gerald B Koudelka Determinants of bacteriophage 933W repressor DNA binding specificity.
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.
format	article
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
title	Determinants of bacteriophage 933W repressor DNA binding specificity.
title_short	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_sort	determinants of bacteriophage 933w repressor dna binding specificity.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/a4721036d113456ab2e536d40efefacc
work_keys_str_mv	AT tammyjbullwinkle determinantsofbacteriophage933wrepressordnabindingspecificity AT danielsamorodnitsky determinantsofbacteriophage933wrepressordnabindingspecificity AT raynacrosati determinantsofbacteriophage933wrepressordnabindingspecificity AT geraldbkoudelka determinantsofbacteriophage933wrepressordnabindingspecificity
_version_	1718423553228931072

Determinants of bacteriophage 933W repressor DNA binding specificity.

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