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AtEAF1 is a potential platform protein for Arabidopsis NuA4 acetyltransferase complex.

Bieluszewski T, Galganski L, Sura W, Bieluszewska A, Abram M, Ludwikow A, Ziolkowski PA, Sadowski J - BMC Plant Biol. (2015)

Bottom Line: Plants carrying a T-DNA insertion in one of the genes encoding AtEAF1 showed decreased FLC expression and early flowering, similarly to Atyaf9 mutants.Chromatin immunoprecipitation analyses of the single mutant Ateaf1b-2 and artificial miRNA knock-down Ateaf1 lines showed decreased levels of H4K5 acetylation in the promoter regions of major flowering regulator genes, further supporting the role of AtEAF1 as a subunit of the plant NuA4 complex.Growing evidence suggests that the molecular functions of the NuA4 and SWR1 complexes are conserved in plants and contribute significantly to plant development and physiology.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Histone acetyltransferase complex NuA4 and histone variant exchanging complex SWR1 are two chromatin modifying complexes which act cooperatively in yeast and share some intriguing structural similarities. Protein subunits of NuA4 and SWR1-C are highly conserved across eukaryotes, but form different multiprotein arrangements. For example, the human TIP60-p400 complex consists of homologues of both yeast NuA4 and SWR1-C subunits, combining subunits necessary for histone acetylation and histone variant exchange. It is currently not known what protein complexes are formed by the plant homologues of NuA4 and SWR1-C subunits.

Results: We report on the identification and molecular characterization of AtEAF1, a new subunit of Arabidopsis NuA4 complex which shows many similarities to the platform protein of the yeast NuA4 complex. AtEAF1 copurifies with Arabidopsis homologues of NuA4 and SWR1-C subunits ARP4 and SWC4 and interacts physically with AtYAF9A and AtYAF9B, homologues of the YAF9 subunit. Plants carrying a T-DNA insertion in one of the genes encoding AtEAF1 showed decreased FLC expression and early flowering, similarly to Atyaf9 mutants. Chromatin immunoprecipitation analyses of the single mutant Ateaf1b-2 and artificial miRNA knock-down Ateaf1 lines showed decreased levels of H4K5 acetylation in the promoter regions of major flowering regulator genes, further supporting the role of AtEAF1 as a subunit of the plant NuA4 complex.

Conclusions: Growing evidence suggests that the molecular functions of the NuA4 and SWR1 complexes are conserved in plants and contribute significantly to plant development and physiology. Our work provides evidence for the existence of a yeast-like EAF1 platform protein in A. thaliana, filling an important gap in the knowledge about the subunit organization of the plant NuA4 complex.

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Arabidopsis thalianaAtEAF1 and PIE1 represent two distinct protein families that share highly similar HSA and SANT domains and do not coexist outside plants. (a) Protein alignment of domain relatives of Arabidopsis thaliana (At) AtEAF1 and PIE1, found in Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Brachypodium distachyon (Bd), Selaginella moellendorffii (Sm), Physcomitrella patens (Pp) and Homo sapiens (Hs). A dotted rectangle depicts the region of yeast EAF1 that recruits ARP4 and actin, according to Szerlong et al. [28]. Columns containing over 75% gaps were removed from the alignment for clarity. Similarity shading of the alignments in (a) and (b) was done using the Blosum62 matrix. White indicates < 60% similarity, light grey 60 to 80%, dark grey 80 to 100% and black 100%. (b) A close-up of the conserved fragments of the HSA domain and the SANT domain. (c) Protein domains HSA, ATPase and SANT form three different domain architectures, which occur in various combinations across eukaryotes. All sequences and alignments used in this figure can be found in the Additional file 3. * Mean pairwise identity over all pairs in the column. A sliding window of 5 was used in the histogram.
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Fig1: Arabidopsis thalianaAtEAF1 and PIE1 represent two distinct protein families that share highly similar HSA and SANT domains and do not coexist outside plants. (a) Protein alignment of domain relatives of Arabidopsis thaliana (At) AtEAF1 and PIE1, found in Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Brachypodium distachyon (Bd), Selaginella moellendorffii (Sm), Physcomitrella patens (Pp) and Homo sapiens (Hs). A dotted rectangle depicts the region of yeast EAF1 that recruits ARP4 and actin, according to Szerlong et al. [28]. Columns containing over 75% gaps were removed from the alignment for clarity. Similarity shading of the alignments in (a) and (b) was done using the Blosum62 matrix. White indicates < 60% similarity, light grey 60 to 80%, dark grey 80 to 100% and black 100%. (b) A close-up of the conserved fragments of the HSA domain and the SANT domain. (c) Protein domains HSA, ATPase and SANT form three different domain architectures, which occur in various combinations across eukaryotes. All sequences and alignments used in this figure can be found in the Additional file 3. * Mean pairwise identity over all pairs in the column. A sliding window of 5 was used in the histogram.

Mentions: According to published data for other species, the presence of ARP4 and SWC4 subunits is restricted to protein complexes closely related to NuA4, SWR1-C and TIP60-p400. Therefore, we considered proteins copurified with both baits as potential subunits of a hypothetical plant TIP60-p400-like complex (Table 1). One uncharacterized protein in this category had a domain architecture similar to that of yeast EAF1 (Figure 1a). We therefore named it AtEAF1.Figure 1


AtEAF1 is a potential platform protein for Arabidopsis NuA4 acetyltransferase complex.

Bieluszewski T, Galganski L, Sura W, Bieluszewska A, Abram M, Ludwikow A, Ziolkowski PA, Sadowski J - BMC Plant Biol. (2015)

Arabidopsis thalianaAtEAF1 and PIE1 represent two distinct protein families that share highly similar HSA and SANT domains and do not coexist outside plants. (a) Protein alignment of domain relatives of Arabidopsis thaliana (At) AtEAF1 and PIE1, found in Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Brachypodium distachyon (Bd), Selaginella moellendorffii (Sm), Physcomitrella patens (Pp) and Homo sapiens (Hs). A dotted rectangle depicts the region of yeast EAF1 that recruits ARP4 and actin, according to Szerlong et al. [28]. Columns containing over 75% gaps were removed from the alignment for clarity. Similarity shading of the alignments in (a) and (b) was done using the Blosum62 matrix. White indicates < 60% similarity, light grey 60 to 80%, dark grey 80 to 100% and black 100%. (b) A close-up of the conserved fragments of the HSA domain and the SANT domain. (c) Protein domains HSA, ATPase and SANT form three different domain architectures, which occur in various combinations across eukaryotes. All sequences and alignments used in this figure can be found in the Additional file 3. * Mean pairwise identity over all pairs in the column. A sliding window of 5 was used in the histogram.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358907&req=5

Fig1: Arabidopsis thalianaAtEAF1 and PIE1 represent two distinct protein families that share highly similar HSA and SANT domains and do not coexist outside plants. (a) Protein alignment of domain relatives of Arabidopsis thaliana (At) AtEAF1 and PIE1, found in Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Brachypodium distachyon (Bd), Selaginella moellendorffii (Sm), Physcomitrella patens (Pp) and Homo sapiens (Hs). A dotted rectangle depicts the region of yeast EAF1 that recruits ARP4 and actin, according to Szerlong et al. [28]. Columns containing over 75% gaps were removed from the alignment for clarity. Similarity shading of the alignments in (a) and (b) was done using the Blosum62 matrix. White indicates < 60% similarity, light grey 60 to 80%, dark grey 80 to 100% and black 100%. (b) A close-up of the conserved fragments of the HSA domain and the SANT domain. (c) Protein domains HSA, ATPase and SANT form three different domain architectures, which occur in various combinations across eukaryotes. All sequences and alignments used in this figure can be found in the Additional file 3. * Mean pairwise identity over all pairs in the column. A sliding window of 5 was used in the histogram.
Mentions: According to published data for other species, the presence of ARP4 and SWC4 subunits is restricted to protein complexes closely related to NuA4, SWR1-C and TIP60-p400. Therefore, we considered proteins copurified with both baits as potential subunits of a hypothetical plant TIP60-p400-like complex (Table 1). One uncharacterized protein in this category had a domain architecture similar to that of yeast EAF1 (Figure 1a). We therefore named it AtEAF1.Figure 1

Bottom Line: Plants carrying a T-DNA insertion in one of the genes encoding AtEAF1 showed decreased FLC expression and early flowering, similarly to Atyaf9 mutants.Chromatin immunoprecipitation analyses of the single mutant Ateaf1b-2 and artificial miRNA knock-down Ateaf1 lines showed decreased levels of H4K5 acetylation in the promoter regions of major flowering regulator genes, further supporting the role of AtEAF1 as a subunit of the plant NuA4 complex.Growing evidence suggests that the molecular functions of the NuA4 and SWR1 complexes are conserved in plants and contribute significantly to plant development and physiology.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Histone acetyltransferase complex NuA4 and histone variant exchanging complex SWR1 are two chromatin modifying complexes which act cooperatively in yeast and share some intriguing structural similarities. Protein subunits of NuA4 and SWR1-C are highly conserved across eukaryotes, but form different multiprotein arrangements. For example, the human TIP60-p400 complex consists of homologues of both yeast NuA4 and SWR1-C subunits, combining subunits necessary for histone acetylation and histone variant exchange. It is currently not known what protein complexes are formed by the plant homologues of NuA4 and SWR1-C subunits.

Results: We report on the identification and molecular characterization of AtEAF1, a new subunit of Arabidopsis NuA4 complex which shows many similarities to the platform protein of the yeast NuA4 complex. AtEAF1 copurifies with Arabidopsis homologues of NuA4 and SWR1-C subunits ARP4 and SWC4 and interacts physically with AtYAF9A and AtYAF9B, homologues of the YAF9 subunit. Plants carrying a T-DNA insertion in one of the genes encoding AtEAF1 showed decreased FLC expression and early flowering, similarly to Atyaf9 mutants. Chromatin immunoprecipitation analyses of the single mutant Ateaf1b-2 and artificial miRNA knock-down Ateaf1 lines showed decreased levels of H4K5 acetylation in the promoter regions of major flowering regulator genes, further supporting the role of AtEAF1 as a subunit of the plant NuA4 complex.

Conclusions: Growing evidence suggests that the molecular functions of the NuA4 and SWR1 complexes are conserved in plants and contribute significantly to plant development and physiology. Our work provides evidence for the existence of a yeast-like EAF1 platform protein in A. thaliana, filling an important gap in the knowledge about the subunit organization of the plant NuA4 complex.

Show MeSH