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Evolutionary conservation levels of subunits of histone-modifying protein complexes in fungi.

Nishida H - Comp. Funct. Genomics (2009)

Bottom Line: The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes.Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific.In contrast, in the fungal histone methylation system, both the catalytic and the associated subunits are evolutionary lineage-specific.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACT
Eukaryotes possess a variety of histone-modifying protein complexes. Generally, a histone-modifying protein complex consists of multiple subunits, that is, a catalytic subunit and the associated subunits. In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific. In contrast, in the fungal histone methylation system, both the catalytic and the associated subunits are evolutionary lineage-specific.

No MeSH data available.


Boxplots of combined evolutionary conservation levels of Saccharomyces and Schizosaccharomyces subunits of histone-modifying protein complexes. Based on the E values of the BLASTP search results, I classified 6 evolutionary conservation levels and scored them as follows: score 0, not detected; score 1, E value   > 100; score 2, 10−50 < E value  ≤ 100; score 3, 10−100 < E value  ≤ 10−50; score 4, 10−150 < E value  ≤ 10−100; score 5, E value  ≤ 10−150.  Each circle indicates the total of the scores of each protein.  Boxes are composed of medians with first and third quartiles from the scores of the subunits.  HATc, histone acetyltransferase (HAT) catalytic subunits; HATa, HAT-associated subunits; HDACc, histone deacetylase (HDAC) catalytic subunits; HDACa, HDAC-associated subunits; HMTc, histone methyltransferase (HMT) catalytic subunits; HMTa, HMT-associated subunits; HDMTc, histone demethylase catalytic subunits.
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fig3: Boxplots of combined evolutionary conservation levels of Saccharomyces and Schizosaccharomyces subunits of histone-modifying protein complexes. Based on the E values of the BLASTP search results, I classified 6 evolutionary conservation levels and scored them as follows: score 0, not detected; score 1, E value > 100; score 2, 10−50 < E value ≤ 100; score 3, 10−100 < E value ≤ 10−50; score 4, 10−150 < E value ≤ 10−100; score 5, E value ≤ 10−150. Each circle indicates the total of the scores of each protein. Boxes are composed of medians with first and third quartiles from the scores of the subunits. HATc, histone acetyltransferase (HAT) catalytic subunits; HATa, HAT-associated subunits; HDACc, histone deacetylase (HDAC) catalytic subunits; HDACa, HDAC-associated subunits; HMTc, histone methyltransferase (HMT) catalytic subunits; HMTa, HMT-associated subunits; HDMTc, histone demethylase catalytic subunits.

Mentions: The evolutionary conservation levels of the HAT and histone deacetylase (HDAC) catalytic subunits are higher than those of the associated subunits, respectively, in Saccharomyces and Schizosaccharomyces (Figure 2). However, the conservation levels of the HMT catalytic subunits are similar to those of the associated subunits, especially in Schizosaccharomyces (Figure 2). In order to elucidate the difference in evolutionary conservation levels, I analyzed the combined data of the conservation scores of the HAT catalytic and the associated subunits, HDAC catalytic and the associated subunits, HMT catalytic and the associated subunits, and the histone demethylase (HDMT) catalytic subunits of Saccharomyces and Schizosaccharomyces. Distributions of the conservation levels of the combined data are shown in Figure 3. The P values obtained by the Wilcoxon rank-sum test for the difference between the conservation levels of the HAT catalytic and the associated subunits, HDAC catalytic and the associated subunits, and HMT catalytic and the associated subunits were .043 (<.05), .0027 (<.05), and .90 (>.05), respectively. Thus, the hypothesis (conservation levels of catalytic and the associated subunits are equal) was rejected in the case of the histone acetylation and deacetylation systems, but not for the histone methylation system.


Evolutionary conservation levels of subunits of histone-modifying protein complexes in fungi.

Nishida H - Comp. Funct. Genomics (2009)

Boxplots of combined evolutionary conservation levels of Saccharomyces and Schizosaccharomyces subunits of histone-modifying protein complexes. Based on the E values of the BLASTP search results, I classified 6 evolutionary conservation levels and scored them as follows: score 0, not detected; score 1, E value   > 100; score 2, 10−50 < E value  ≤ 100; score 3, 10−100 < E value  ≤ 10−50; score 4, 10−150 < E value  ≤ 10−100; score 5, E value  ≤ 10−150.  Each circle indicates the total of the scores of each protein.  Boxes are composed of medians with first and third quartiles from the scores of the subunits.  HATc, histone acetyltransferase (HAT) catalytic subunits; HATa, HAT-associated subunits; HDACc, histone deacetylase (HDAC) catalytic subunits; HDACa, HDAC-associated subunits; HMTc, histone methyltransferase (HMT) catalytic subunits; HMTa, HMT-associated subunits; HDMTc, histone demethylase catalytic subunits.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2683545&req=5

fig3: Boxplots of combined evolutionary conservation levels of Saccharomyces and Schizosaccharomyces subunits of histone-modifying protein complexes. Based on the E values of the BLASTP search results, I classified 6 evolutionary conservation levels and scored them as follows: score 0, not detected; score 1, E value > 100; score 2, 10−50 < E value ≤ 100; score 3, 10−100 < E value ≤ 10−50; score 4, 10−150 < E value ≤ 10−100; score 5, E value ≤ 10−150. Each circle indicates the total of the scores of each protein. Boxes are composed of medians with first and third quartiles from the scores of the subunits. HATc, histone acetyltransferase (HAT) catalytic subunits; HATa, HAT-associated subunits; HDACc, histone deacetylase (HDAC) catalytic subunits; HDACa, HDAC-associated subunits; HMTc, histone methyltransferase (HMT) catalytic subunits; HMTa, HMT-associated subunits; HDMTc, histone demethylase catalytic subunits.
Mentions: The evolutionary conservation levels of the HAT and histone deacetylase (HDAC) catalytic subunits are higher than those of the associated subunits, respectively, in Saccharomyces and Schizosaccharomyces (Figure 2). However, the conservation levels of the HMT catalytic subunits are similar to those of the associated subunits, especially in Schizosaccharomyces (Figure 2). In order to elucidate the difference in evolutionary conservation levels, I analyzed the combined data of the conservation scores of the HAT catalytic and the associated subunits, HDAC catalytic and the associated subunits, HMT catalytic and the associated subunits, and the histone demethylase (HDMT) catalytic subunits of Saccharomyces and Schizosaccharomyces. Distributions of the conservation levels of the combined data are shown in Figure 3. The P values obtained by the Wilcoxon rank-sum test for the difference between the conservation levels of the HAT catalytic and the associated subunits, HDAC catalytic and the associated subunits, and HMT catalytic and the associated subunits were .043 (<.05), .0027 (<.05), and .90 (>.05), respectively. Thus, the hypothesis (conservation levels of catalytic and the associated subunits are equal) was rejected in the case of the histone acetylation and deacetylation systems, but not for the histone methylation system.

Bottom Line: The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes.Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific.In contrast, in the fungal histone methylation system, both the catalytic and the associated subunits are evolutionary lineage-specific.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACT
Eukaryotes possess a variety of histone-modifying protein complexes. Generally, a histone-modifying protein complex consists of multiple subunits, that is, a catalytic subunit and the associated subunits. In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific. In contrast, in the fungal histone methylation system, both the catalytic and the associated subunits are evolutionary lineage-specific.

No MeSH data available.