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N-terminal domain of nuclear IL-1α shows structural similarity to the C-terminal domain of Snf1 and binds to the HAT/core module of the SAGA complex.

Zamostna B, Novak J, Vopalensky V, Masek T, Burysek L, Pospisek M - PLoS ONE (2012)

Bottom Line: Interestingly, a significant proportion of IL-1α is translocated to the cell nucleus, in which it interacts with histone acetyltransferase complexes.We also predicted the 3-D structure of the IL-1α N-terminal domain, and by employing structure similarity searches, we found a similar structure in the C-terminal regulatory region of the catalytic subunit of the AMP-activated/Snf1 protein kinases, which interact with HAT complexes both in mammals and yeast, respectively.Finally, the careful evaluation of our data together with other published data in the field allows us to hypothesize a new function for the ADA complex in SAGA complex assembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.

ABSTRACT
Interleukin-1α (IL-1α) is a proinflammatory cytokine and a key player in host immune responses in higher eukaryotes. IL-1α has pleiotropic effects on a wide range of cell types, and it has been extensively studied for its ability to contribute to various autoimmune and inflammation-linked disorders, including rheumatoid arthritis, Alzheimer's disease, systemic sclerosis and cardiovascular disorders. Interestingly, a significant proportion of IL-1α is translocated to the cell nucleus, in which it interacts with histone acetyltransferase complexes. Despite the importance of IL-1α, little is known regarding its binding targets and functions in the nucleus. We took advantage of the histone acetyltransferase (HAT) complexes being evolutionarily conserved from yeast to humans and the yeast SAGA complex serving as an epitome of the eukaryotic HAT complexes. Using gene knock-out technique and co-immunoprecipitation of the IL-1α precursor with TAP-tagged subunits of the yeast HAT complexes, we mapped the IL-1α-binding site to the HAT/Core module of the SAGA complex. We also predicted the 3-D structure of the IL-1α N-terminal domain, and by employing structure similarity searches, we found a similar structure in the C-terminal regulatory region of the catalytic subunit of the AMP-activated/Snf1 protein kinases, which interact with HAT complexes both in mammals and yeast, respectively. This finding is further supported with the ability of the IL-1α precursor to partially rescue growth defects of snf1Δ yeast strains on media containing 3-Amino-1,2,4-triazole (3-AT), a competitive inhibitor of His3. Finally, the careful evaluation of our data together with other published data in the field allows us to hypothesize a new function for the ADA complex in SAGA complex assembly.

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The structure of IL-1αNTP resembles the C-terminal portion of the catalytical subunit of the eukaryotic AMP-activated protein kinase.(A) Prediction of the 3-D structure of the first N-terminal 112 amino acid residues of the IL-1α precursor (IL-1αNTP). Acidic amino acid residues are depicted in red. (B) The 3-D structure of the INL domain of the yeast Snf1 protein kinase (PDB ID: 3T4N). (C) A superimposition of IL-1αNTP (blue) and the C-terminal INL domain of the yeast Snf1 protein kinase (green). (D) A superimposition of the INL domains of yeast Snf1 (green, PDB ID: 3T4N) and rat AMP-activated protein kinase (grey, PDB ID: 2V92). Acidic amino acid residues are depicted in red tones. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.
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pone-0041801-g003: The structure of IL-1αNTP resembles the C-terminal portion of the catalytical subunit of the eukaryotic AMP-activated protein kinase.(A) Prediction of the 3-D structure of the first N-terminal 112 amino acid residues of the IL-1α precursor (IL-1αNTP). Acidic amino acid residues are depicted in red. (B) The 3-D structure of the INL domain of the yeast Snf1 protein kinase (PDB ID: 3T4N). (C) A superimposition of IL-1αNTP (blue) and the C-terminal INL domain of the yeast Snf1 protein kinase (green). (D) A superimposition of the INL domains of yeast Snf1 (green, PDB ID: 3T4N) and rat AMP-activated protein kinase (grey, PDB ID: 2V92). Acidic amino acid residues are depicted in red tones. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.

Mentions: Previously, we provided evidence that both N-terminal and C-terminal helices of IL-1αNTP are important for its nuclear function and interaction with both the mammalian and yeast histone acetyltransferase complexes [40]. The structure of the SAGA complex is evolutionarily conserved from yeast to mammals. If one expects a similar or identical mode of interaction between human IL-1αNTP and both the yeast SAGA complex and its human analog, one would also expect that yeast cells may naturally contain some peptide structures similar to IL-1αNTP. To test this hypothesis, we performed structure similarity searches with IL-1αNTP against known structures in the Protein Data Bank (PDB). The structures of IL-1αNTP and full-length pre-IL-1α have yet not been determined. Therefore, we employed the Robetta server [45] to obtain ab initio models of IL-1αNTP. For prediction, we used the first 112 N-terminal amino acid residues of human pre-IL-1α (NCBI Reference Sequence: NP_000566.3). We obtained five predicted structures, which we used for structure similarity searches using the Dali server at the Institute of Biotechnology, University of Helsinki [46]. The best-scored and only meaningful hit returned by one of the IL-1αNTP structure predictions was the C-terminal regulatory domain of the Snf1 kinase alpha subunit (Figure 3). The Snf1 kinase is a founding member of the AMP-activated protein kinase family (AMPK). Yeast with a deleted SNF1 gene are viable; however, its loss leads to reduced fitness under various stress conditions, an inability to grow on sucrose, galactose, maltose, melibiose and non-fermentable carbon sources and sporulation defects (Saccharomyces Genome Database). Snf1 has been shown to functionally and physically interact with members of the SAGA complex (Gcn5, Sgf73, Spt3, Spt8 and Ubp8) and Ahc1, an identifying member of the ADA complex [47], [48], [49]. Snf1 phosphorylates Gcn5 and can undergo deubiquitination by Ubp8, which is another member of the SAGA complex. As depicted in Figure 3C, an overlay of IL-1αNTP and the Snf1 C-terminal regulatory domain demonstrates the high extent of their structural similarity in 3-D. The AMPK/Snf1 protein family displays a high degree of similarity in amino acid sequences across all eukaryotes [50], [51]. We investigated whether the AMPK/Snf1 C-terminal Interleukin-1αNTP-Like domain (INL domain) was structurally similar in yeast and mammals. We superimposed the INL domains of yeast Snf1 (PDB ID: 3T4N) and the rat AMP-activated protein kinase (PDB ID: 2V92), and this overlay revealed that both structures were almost identical, including the positions of some acidic residues. The AMPK/Snf1 INL domains span amino acid residues 406 to 559 and 505 to 630, respectively. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.


N-terminal domain of nuclear IL-1α shows structural similarity to the C-terminal domain of Snf1 and binds to the HAT/core module of the SAGA complex.

Zamostna B, Novak J, Vopalensky V, Masek T, Burysek L, Pospisek M - PLoS ONE (2012)

The structure of IL-1αNTP resembles the C-terminal portion of the catalytical subunit of the eukaryotic AMP-activated protein kinase.(A) Prediction of the 3-D structure of the first N-terminal 112 amino acid residues of the IL-1α precursor (IL-1αNTP). Acidic amino acid residues are depicted in red. (B) The 3-D structure of the INL domain of the yeast Snf1 protein kinase (PDB ID: 3T4N). (C) A superimposition of IL-1αNTP (blue) and the C-terminal INL domain of the yeast Snf1 protein kinase (green). (D) A superimposition of the INL domains of yeast Snf1 (green, PDB ID: 3T4N) and rat AMP-activated protein kinase (grey, PDB ID: 2V92). Acidic amino acid residues are depicted in red tones. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3412866&req=5

pone-0041801-g003: The structure of IL-1αNTP resembles the C-terminal portion of the catalytical subunit of the eukaryotic AMP-activated protein kinase.(A) Prediction of the 3-D structure of the first N-terminal 112 amino acid residues of the IL-1α precursor (IL-1αNTP). Acidic amino acid residues are depicted in red. (B) The 3-D structure of the INL domain of the yeast Snf1 protein kinase (PDB ID: 3T4N). (C) A superimposition of IL-1αNTP (blue) and the C-terminal INL domain of the yeast Snf1 protein kinase (green). (D) A superimposition of the INL domains of yeast Snf1 (green, PDB ID: 3T4N) and rat AMP-activated protein kinase (grey, PDB ID: 2V92). Acidic amino acid residues are depicted in red tones. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.
Mentions: Previously, we provided evidence that both N-terminal and C-terminal helices of IL-1αNTP are important for its nuclear function and interaction with both the mammalian and yeast histone acetyltransferase complexes [40]. The structure of the SAGA complex is evolutionarily conserved from yeast to mammals. If one expects a similar or identical mode of interaction between human IL-1αNTP and both the yeast SAGA complex and its human analog, one would also expect that yeast cells may naturally contain some peptide structures similar to IL-1αNTP. To test this hypothesis, we performed structure similarity searches with IL-1αNTP against known structures in the Protein Data Bank (PDB). The structures of IL-1αNTP and full-length pre-IL-1α have yet not been determined. Therefore, we employed the Robetta server [45] to obtain ab initio models of IL-1αNTP. For prediction, we used the first 112 N-terminal amino acid residues of human pre-IL-1α (NCBI Reference Sequence: NP_000566.3). We obtained five predicted structures, which we used for structure similarity searches using the Dali server at the Institute of Biotechnology, University of Helsinki [46]. The best-scored and only meaningful hit returned by one of the IL-1αNTP structure predictions was the C-terminal regulatory domain of the Snf1 kinase alpha subunit (Figure 3). The Snf1 kinase is a founding member of the AMP-activated protein kinase family (AMPK). Yeast with a deleted SNF1 gene are viable; however, its loss leads to reduced fitness under various stress conditions, an inability to grow on sucrose, galactose, maltose, melibiose and non-fermentable carbon sources and sporulation defects (Saccharomyces Genome Database). Snf1 has been shown to functionally and physically interact with members of the SAGA complex (Gcn5, Sgf73, Spt3, Spt8 and Ubp8) and Ahc1, an identifying member of the ADA complex [47], [48], [49]. Snf1 phosphorylates Gcn5 and can undergo deubiquitination by Ubp8, which is another member of the SAGA complex. As depicted in Figure 3C, an overlay of IL-1αNTP and the Snf1 C-terminal regulatory domain demonstrates the high extent of their structural similarity in 3-D. The AMPK/Snf1 protein family displays a high degree of similarity in amino acid sequences across all eukaryotes [50], [51]. We investigated whether the AMPK/Snf1 C-terminal Interleukin-1αNTP-Like domain (INL domain) was structurally similar in yeast and mammals. We superimposed the INL domains of yeast Snf1 (PDB ID: 3T4N) and the rat AMP-activated protein kinase (PDB ID: 2V92), and this overlay revealed that both structures were almost identical, including the positions of some acidic residues. The AMPK/Snf1 INL domains span amino acid residues 406 to 559 and 505 to 630, respectively. See also File S1 for cordinates of IL-1αNTP prediction and File S2 for primary sequences of all proteins used in this analysis.

Bottom Line: Interestingly, a significant proportion of IL-1α is translocated to the cell nucleus, in which it interacts with histone acetyltransferase complexes.We also predicted the 3-D structure of the IL-1α N-terminal domain, and by employing structure similarity searches, we found a similar structure in the C-terminal regulatory region of the catalytic subunit of the AMP-activated/Snf1 protein kinases, which interact with HAT complexes both in mammals and yeast, respectively.Finally, the careful evaluation of our data together with other published data in the field allows us to hypothesize a new function for the ADA complex in SAGA complex assembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.

ABSTRACT
Interleukin-1α (IL-1α) is a proinflammatory cytokine and a key player in host immune responses in higher eukaryotes. IL-1α has pleiotropic effects on a wide range of cell types, and it has been extensively studied for its ability to contribute to various autoimmune and inflammation-linked disorders, including rheumatoid arthritis, Alzheimer's disease, systemic sclerosis and cardiovascular disorders. Interestingly, a significant proportion of IL-1α is translocated to the cell nucleus, in which it interacts with histone acetyltransferase complexes. Despite the importance of IL-1α, little is known regarding its binding targets and functions in the nucleus. We took advantage of the histone acetyltransferase (HAT) complexes being evolutionarily conserved from yeast to humans and the yeast SAGA complex serving as an epitome of the eukaryotic HAT complexes. Using gene knock-out technique and co-immunoprecipitation of the IL-1α precursor with TAP-tagged subunits of the yeast HAT complexes, we mapped the IL-1α-binding site to the HAT/Core module of the SAGA complex. We also predicted the 3-D structure of the IL-1α N-terminal domain, and by employing structure similarity searches, we found a similar structure in the C-terminal regulatory region of the catalytic subunit of the AMP-activated/Snf1 protein kinases, which interact with HAT complexes both in mammals and yeast, respectively. This finding is further supported with the ability of the IL-1α precursor to partially rescue growth defects of snf1Δ yeast strains on media containing 3-Amino-1,2,4-triazole (3-AT), a competitive inhibitor of His3. Finally, the careful evaluation of our data together with other published data in the field allows us to hypothesize a new function for the ADA complex in SAGA complex assembly.

Show MeSH
Related in: MedlinePlus