From the 2-yeast genome databases, I extracted 62 and 48 subunits of histone-modifying protein complexes of S. cerevisiae and S. pombe, respectively. Among the 110 subunits, 34 Saccharomyces and 24 Schizosaccharomyces proteins were catalytic subunits; the others were associated complex subunits. The evolutionary conservation levels of the 62 Saccharomyces and 48 Schizosaccharomyces proteins are shown in and , respectively.
Evolutionary conservation levels of Saccharomyces proteins related to histone modifications.
Evolutionary conservation levels of Schizosaccharomyces proteins related to histone modifications.
The histone acetyltransferase (HAT) catalytic subunit ELP3 was found to be the most conserved among the 62 Saccharomyces
and 48 Schizosaccharomyces
subunits. The main acetylation sites of ELP3 are lysine-14 of histone H3 and lysine-8 of histone H4 [10
]. In addition, ELP3 is an integral subunit of elongating RNA polymerase II holoenzyme in S. cerevisiae
, which is involved in transcription-associated chromatin modification and remodeling [11
]. The deletion of ELP3
gene in yeast confers slow growth adaptation, slow gene activation, and temperature sensitivity [11
]. The ELP3 protein's function may be so important for fungi (eukaryotes) that it is the most conserved.
The phylogenetic tree based on ELP3 and its homologues show that these proteins are present across eukaryotes ( and ). The phylogenetic relationships among fungal ELP3 and its homologues are consistent with the fungal classification [13
]. Interestingly, the microsporidium E. cuniculi
is not included in the fungal lineage in the neighbor-joining tree (), but it is included in the maximum likelihood tree with 44% bootstrap support ().
Figure 1 Phylogenetic relationships among the histone acetyltransferase catalytic subunit ELP3 and its homologues. A total of 496 amino acid sites were considered from multiple alignments with all the gap sites deleted. (a) Neighbor-joining tree was generated (more ...)
There are some lineage-specific subunits of histone-modifying protein complexes. For example, homologues of Dot1, the histone methyltransferase (HMT) catalytic subunit of Saccharomyces
are present in K. lactis
and Y. lipolytica
—2 ascomycetous yeasts (). Dot1 methylates the histone H3 at lysine-79, which is related to gene silencing in S. cerevisiae
]. This modification system is also found in mammals [14
]. However, S. pombe
has no homologue of Dot1 ().
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 (). However, the conservation levels of the HMT catalytic subunits are similar to those of the associated subunits, especially in Schizosaccharomyces (). 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 . 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 null 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.
Figure 2 Boxplots of evolutionary conservation levels of 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 (more ...)
Figure 3 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 (more ...)
The results of this study show that histone acetylase and deacetylase catalytic subunits are more conserved than other subunits ( and ). In fact, out of the 10 most abundant proteins of Saccharomyces and Schizosaccharomyces, 9 were histone acetylation or deacetylation related proteins, that is, 4 HAT catalytic, 3 HDAC catalytic, 1 HAT associated, 1 HDAC associated, and 1 HMT catalytic subunits ( and ). In fungal histone acetylation and deacetylation, the catalytic subunits of protein complexes are conserved and the associated subunits are evolutionary lineage-specific. However, in fungal histone methylation, both the catalytic and the associated subunits are evolutionary lineage-specific. Although the histone modification systems work cooperatively, these results strongly suggest that the evolution of the fungal histone acetylation/deacetylation system was different from that of the histone methylation system.