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Histone H3 serine 57 and lysine 56 interplay in transcription elongation and recovery from S-phase stress.

Aslam A, Logie C - PLoS ONE (2010)

Bottom Line: Because phosphorylated human histone H3 serine 57 peptides have been detected by mass spectrometry we examined whether H3-S57 phosphorylation interplays with H3-K56 acetylation in vivo.Strikingly, opposite results were obtained in the context of a serine to alanine substitution at position 57 of histone H3.We speculate that histone H3-S57 couples H3-K56 acetylation to histone quaternary structures involving arginine 40 on histone H4 helix 1.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.

ABSTRACT

Background: Acetylation of lysine 56 of histone H3 plays an important role in the DNA damage response and it has been postulated to play an as yet undefined role in transcription, both in yeast and in higher eukaryotes. Because phosphorylated human histone H3 serine 57 peptides have been detected by mass spectrometry we examined whether H3-S57 phosphorylation interplays with H3-K56 acetylation in vivo.

Methodology/principal findings: To explore the physiological role of H3-S57, H3-K56 was mutated to mimic constitutively (un)acetylated forms of H3-K56 and these were combined with constitutively (un)phosphorylated mimics of H3-S57, in yeast. A phosphorylated serine mimic at position 57 lessened sensitivities to a DNA replication fork inhibitor and to a transcription elongation inhibitor that were caused by an acetylated lysine mimic at position 56, while the same substitution exacerbated sensitivities due to mimicking a constitutive non-acetylated lysine at position 56. Strikingly, opposite results were obtained in the context of a serine to alanine substitution at position 57 of histone H3.

Conclusions/significance: The phenotypes elicited and the context-dependent interplay of the H3-K56 and -S57 point mutations that mimic their respective modification states suggest that serine 57 phosphorylation promotes a nucleosomal transaction when lysine 56 is acetylated. We speculate that histone H3-S57 couples H3-K56 acetylation to histone quaternary structures involving arginine 40 on histone H4 helix 1.

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Regulatory and atomic context of histone H3 serine 57.A. Theoretical scheme imbricating the acetylation cycle of H3-K56 with the putative phosphorylation cycle of H3-S57. Double point mutations introduced to constitutively mimic the 4 possible modification states are indicated in red. The observed fitness upon induction of S-phase double strand breaks by MMS (Figure 3A) is shown as smileys next to the mutations. B. Ribbon view of one nucleosomal molecule of histone H3 (blue) and of histone H4 (green) as well as the first 14 base pairs of nucleosomal DNA, displaying the H3-K56, H3-S57 and H4-R40 residue atoms as ball and stick. H3-K56 makes a water mediated contact with bp 9 of the DNA and H3-S57 is linked by a hydrogen bridge to H4-R40 on histone H4 helix 1. This figure was built using Yasara (http://www.yasara.org) and PDB file 1ID3 [2]. The same hydrogen bridges are visible in all the nucleosome crystal structures we examined [1], [2], [54].
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pone-0010851-g005: Regulatory and atomic context of histone H3 serine 57.A. Theoretical scheme imbricating the acetylation cycle of H3-K56 with the putative phosphorylation cycle of H3-S57. Double point mutations introduced to constitutively mimic the 4 possible modification states are indicated in red. The observed fitness upon induction of S-phase double strand breaks by MMS (Figure 3A) is shown as smileys next to the mutations. B. Ribbon view of one nucleosomal molecule of histone H3 (blue) and of histone H4 (green) as well as the first 14 base pairs of nucleosomal DNA, displaying the H3-K56, H3-S57 and H4-R40 residue atoms as ball and stick. H3-K56 makes a water mediated contact with bp 9 of the DNA and H3-S57 is linked by a hydrogen bridge to H4-R40 on histone H4 helix 1. This figure was built using Yasara (http://www.yasara.org) and PDB file 1ID3 [2]. The same hydrogen bridges are visible in all the nucleosome crystal structures we examined [1], [2], [54].

Mentions: We have not ruled out the possibility that the serine 57 substitutions we employed affect the capacity of yeast to acetylate or subsequently deacetylate H3-K56. However, this does not affect our conclusions much as they are based on the phenotypes of double mutants that constitutively mimic the (un)modified state of both lysine 56 and serine 57, entirely bypassing the need to modify H3-K56 (Figure 5A). To mimic H3-S57ph we substituted glutamate for serine 57. Glutamate closely mimics the length of the R chain of a phosphorylated serine which is about 4.8 Å from Cα to the furthest oxygen. An alternative would have been to substitute aspartate [39]. We predict that substituting aspartate would result in less pronounced effects because it is shorter by about 1.1 Å. If our results were to be duplicated using aspartate mutants obtained from site directed [39] or random mutagenesis [33] this would strengthen the tentative conclusions we draw below. Positive identification of H3-S57 putative kinase and phosphatase activities [30] would shed more light on the role of H3-S57 in chromatin metabolism. Until then alternative interpretations of our results that do not invoke phosphorylation of H3-S57 must also be considered.


Histone H3 serine 57 and lysine 56 interplay in transcription elongation and recovery from S-phase stress.

Aslam A, Logie C - PLoS ONE (2010)

Regulatory and atomic context of histone H3 serine 57.A. Theoretical scheme imbricating the acetylation cycle of H3-K56 with the putative phosphorylation cycle of H3-S57. Double point mutations introduced to constitutively mimic the 4 possible modification states are indicated in red. The observed fitness upon induction of S-phase double strand breaks by MMS (Figure 3A) is shown as smileys next to the mutations. B. Ribbon view of one nucleosomal molecule of histone H3 (blue) and of histone H4 (green) as well as the first 14 base pairs of nucleosomal DNA, displaying the H3-K56, H3-S57 and H4-R40 residue atoms as ball and stick. H3-K56 makes a water mediated contact with bp 9 of the DNA and H3-S57 is linked by a hydrogen bridge to H4-R40 on histone H4 helix 1. This figure was built using Yasara (http://www.yasara.org) and PDB file 1ID3 [2]. The same hydrogen bridges are visible in all the nucleosome crystal structures we examined [1], [2], [54].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2877106&req=5

pone-0010851-g005: Regulatory and atomic context of histone H3 serine 57.A. Theoretical scheme imbricating the acetylation cycle of H3-K56 with the putative phosphorylation cycle of H3-S57. Double point mutations introduced to constitutively mimic the 4 possible modification states are indicated in red. The observed fitness upon induction of S-phase double strand breaks by MMS (Figure 3A) is shown as smileys next to the mutations. B. Ribbon view of one nucleosomal molecule of histone H3 (blue) and of histone H4 (green) as well as the first 14 base pairs of nucleosomal DNA, displaying the H3-K56, H3-S57 and H4-R40 residue atoms as ball and stick. H3-K56 makes a water mediated contact with bp 9 of the DNA and H3-S57 is linked by a hydrogen bridge to H4-R40 on histone H4 helix 1. This figure was built using Yasara (http://www.yasara.org) and PDB file 1ID3 [2]. The same hydrogen bridges are visible in all the nucleosome crystal structures we examined [1], [2], [54].
Mentions: We have not ruled out the possibility that the serine 57 substitutions we employed affect the capacity of yeast to acetylate or subsequently deacetylate H3-K56. However, this does not affect our conclusions much as they are based on the phenotypes of double mutants that constitutively mimic the (un)modified state of both lysine 56 and serine 57, entirely bypassing the need to modify H3-K56 (Figure 5A). To mimic H3-S57ph we substituted glutamate for serine 57. Glutamate closely mimics the length of the R chain of a phosphorylated serine which is about 4.8 Å from Cα to the furthest oxygen. An alternative would have been to substitute aspartate [39]. We predict that substituting aspartate would result in less pronounced effects because it is shorter by about 1.1 Å. If our results were to be duplicated using aspartate mutants obtained from site directed [39] or random mutagenesis [33] this would strengthen the tentative conclusions we draw below. Positive identification of H3-S57 putative kinase and phosphatase activities [30] would shed more light on the role of H3-S57 in chromatin metabolism. Until then alternative interpretations of our results that do not invoke phosphorylation of H3-S57 must also be considered.

Bottom Line: Because phosphorylated human histone H3 serine 57 peptides have been detected by mass spectrometry we examined whether H3-S57 phosphorylation interplays with H3-K56 acetylation in vivo.Strikingly, opposite results were obtained in the context of a serine to alanine substitution at position 57 of histone H3.We speculate that histone H3-S57 couples H3-K56 acetylation to histone quaternary structures involving arginine 40 on histone H4 helix 1.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.

ABSTRACT

Background: Acetylation of lysine 56 of histone H3 plays an important role in the DNA damage response and it has been postulated to play an as yet undefined role in transcription, both in yeast and in higher eukaryotes. Because phosphorylated human histone H3 serine 57 peptides have been detected by mass spectrometry we examined whether H3-S57 phosphorylation interplays with H3-K56 acetylation in vivo.

Methodology/principal findings: To explore the physiological role of H3-S57, H3-K56 was mutated to mimic constitutively (un)acetylated forms of H3-K56 and these were combined with constitutively (un)phosphorylated mimics of H3-S57, in yeast. A phosphorylated serine mimic at position 57 lessened sensitivities to a DNA replication fork inhibitor and to a transcription elongation inhibitor that were caused by an acetylated lysine mimic at position 56, while the same substitution exacerbated sensitivities due to mimicking a constitutive non-acetylated lysine at position 56. Strikingly, opposite results were obtained in the context of a serine to alanine substitution at position 57 of histone H3.

Conclusions/significance: The phenotypes elicited and the context-dependent interplay of the H3-K56 and -S57 point mutations that mimic their respective modification states suggest that serine 57 phosphorylation promotes a nucleosomal transaction when lysine 56 is acetylated. We speculate that histone H3-S57 couples H3-K56 acetylation to histone quaternary structures involving arginine 40 on histone H4 helix 1.

Show MeSH
Related in: MedlinePlus