scholarly journals Evolutionary Conservation Levels of Subunits of Histone-Modifying Protein Complexes in Fungi

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
Hiromi Nishida
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Acetylation ◽  
Histone Methylation ◽  
Protein Complex ◽  
Histone Acetyltransferase ◽  
Protein Complexes ◽  
Evolutionary Conservation ◽  
Catalytic Subunits ◽  
Evolutionary Lineage ◽  
Conservation Level

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 ofSaccharomyces cerevisiaeandSchizosaccharomyces 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.

scholarly journals Asf1 Can Promote Trimethylation of H3 K36 by Set2

2010 ◽  
Vol 30 (5) ◽  
pp. 1116-1129 ◽  
Author(s):  
Ling-ju Lin ◽  
Laura V. Minard ◽  
Gerald C. Johnston ◽  
Richard A. Singer ◽  
Michael C. Schultz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Histone Acetylation ◽  
Rna Polymerase Ii ◽  
Posttranslational Modification ◽  
Protein Complexes ◽  
Histone H3 ◽  
Cross Linking ◽  
Coding Region ◽  
Repressive Chromatin

ABSTRACT Asf1 is a conserved histone H3/H4 chaperone that can assemble and disassemble nucleosomes and promote histone acetylation. Set2 is an H3 K36 methyltransferase. The functions of these proteins intersect in the context of transcription elongation by RNA polymerase II: both contribute to the establishment of repressive chromatin structures that inhibit spurious intragenic transcription. Here we characterize further interactions between budding yeast (Saccharomyces cerevisiae) Asf1 and Set2 using assays of intragenic transcription, H3/H4 posttranslational modification, coding region cross-linking of Asf1 and Set2, and cooccurrence of Asf1 and Set2 in protein complexes. We find that at some genes Asf1 and Set2 control chromatin metabolism as components of separate pathways. However, the existence of a low-abundance complex containing both proteins suggests that Asf1 and Set2 can more directly collaborate in chromatin regulation. Consistent with this possibility, we show that Asf1 stimulates Set2 occupancy of the coding region of a highly transcribed gene by a mechanism that depends on Asf1 binding to H3/H4. This function of Asf1 promotes the switch from di- to trimethylation of H3 K36 at that gene. These results support the view that Set2 function in chromatin metabolism can intimately involve histone chaperone Asf1.

scholarly journals The ADA Complex Is a Distinct Histone Acetyltransferase Complex in Saccharomyces cerevisiae

1999 ◽  
Vol 19 (10) ◽  
pp. 6621-6631 ◽  
Author(s):  
Anton Eberharter ◽  
David E. Sterner ◽  
David Schieltz ◽  
Ahmed Hassan ◽  
John R. Yates ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Acetyltransferase ◽  
Protein Complexes ◽  
Personal Communication ◽  
Mass Spectrometry Analysis ◽  
Cold Sensitivity ◽  
Adapter Proteins ◽  
Histone H2a ◽  
Saga Complex ◽  
Spectrometry Analysis

ABSTRACT We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyces cerevisiae, the 0.8-MDa ADA complex and the 1.8-MDa SAGA complex. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex contains several subunits which also function as part of other protein complexes, including a subset of TATA box binding protein-associated factors (TAFIIs) and Tra1. These observations raise the question of whether the 0.8-MDa ADA complex is a subcomplex of SAGA or whether it is a distinct HAT complex that also shares subunits with SAGA. To address this issue, we sought to determine if the ADA complex contained subunits that are not present in the SAGA complex. In this study, we report the purification of the ADA complex over 10 chromatographic steps. By a combination of mass spectrometry analysis and immunoblotting, we demonstrate that the adapter proteins Ada2, Ada3, and Gcn5 are indeed integral components of ADA. Furthermore, we identify the product of the S. cerevisiae gene YOR023C as a novel subunit of the ADA complex and name it Ahc1 for ADA HAT complex component 1. Biochemical functions of YOR023C have not been reported. However,AHC1 in high copy numbers suppresses the cold sensitivity caused by particular mutations in HTA1 (I. Pinto and F. Winston, personal communication), which encodes histone H2A (J. N. Hirschhorn et al., Mol. Cell. Biol. 15:1999–2009, 1995). Deletion ofAHC1 disrupted the integrity of the ADA complex but did not affect SAGA or give rise to classic Ada− phenotypes. These results indicate that Gcn5, Ada2, and Ada3 function as part of a unique HAT complex (ADA) and represent shared subunits between this complex and SAGA.

scholarly journals Requirement for Three Novel Protein Complexes in the Absence of the Sgs1 DNA Helicase in Saccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 103-118 ◽  
Author(s):  
Janet R Mullen ◽  
Vivek Kaliraman ◽  
Samer S Ibrahim ◽  
Steven J Brill
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Stability ◽  
Protein Complexes ◽  
Ring Finger ◽  
Dna Helicase ◽  
Open Reading Frames ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Dna Helicases ◽  
Cell Extracts

Abstract The Saccharomyces cerevisiae Sgs1 protein is a member of the RecQ family of DNA helicases and is required for genome stability, but not cell viability. To identify proteins that function in the absence of Sgs1, a synthetic-lethal screen was performed. We obtained mutations in six complementation groups that we refer to as SLX genes. Most of the SLX genes encode uncharacterized open reading frames that are conserved in other species. None of these genes is required for viability and all SLX null mutations are synthetically lethal with mutations in TOP3, encoding the SGS1-interacting DNA topoisomerase. Analysis of the null mutants identified a pair of genes in each of three phenotypic classes. Mutations in MMS4 (SLX2) and SLX3 generate identical phenotypes, including weak UV and strong MMS hypersensitivity, complete loss of sporulation, and synthetic growth defects with mutations in TOP1. Mms4 and Slx3 proteins coimmunoprecipitate from cell extracts, suggesting that they function in a complex. Mutations in SLX5 and SLX8 generate hydroxyurea sensitivity, reduced sporulation efficiency, and a slow-growth phenotype characterized by heterogeneous colony morphology. The Slx5 and Slx8 proteins contain RING finger domains and coimmunoprecipitate from cell extracts. The SLX1 and SLX4 genes are required for viability in the presence of an sgs1 temperature-sensitive allele at the restrictive temperature and Slx1 and Slx4 proteins are similarly associated in cell extracts. We propose that the MMS4/SLX3, SLX5/8, and SLX1/4 gene pairs encode heterodimeric complexes and speculate that these complexes are required to resolve recombination intermediates that arise in response to DNA damage, during meiosis, and in the absence of SGS1/TOP3.

scholarly journals Upstream – News in Genomics

2002 ◽  
Vol 3 (3) ◽  
pp. 221-225
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ovarian Cancer ◽  
Oryza Sativa ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Proteomic Analysis ◽  
Large Scale ◽  
Protein Complexes ◽  
The Other ◽  
Blood Samples

In recent months a bumper crop of genomes has been completed, including the fission yeast (Schizosaccharomyces pombe) and rice (Oryza sativa). Two large-scale studies ofSaccharomyces cerevisiaeprotein complexes provided a picture of the eukaryotic proteome as a network of complexes. Amongst the other stories of interest was a demonstration that proteomic analysis of blood samples can be used to detect ovarian cancer, perhaps even as early as stage I.

scholarly journals Interaction with Tap42 Is Required for the Essential Function of Sit4 and Type 2A Phosphatases

2003 ◽  
Vol 14 (11) ◽  
pp. 4342-4351 ◽  
Author(s):  
Huamin Wang ◽  
Xiaodong Wang ◽  
Yu Jiang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Amino Acid Substitution ◽  
Binding Domain ◽  
Charge Amino Acid ◽  
Catalytic Subunits ◽  
Regulatory Subunits ◽  
Terminal Domain ◽  
Major Form ◽  
Essential Function

In Saccharomyces cerevisiae, Pph21 and Pph22 are the two catalytic subunits of type 2A phosphatase (PP2Ac), and Sit4 is a major form of 2A-like phosphatase. The function of these phosphatases requires their association with different regulatory subunits. In addition to the conventional regulatory subunits, namely, the A and B subunits for Pph21/22 and the Sap proteins for Sit4, these phosphatases have been found to associate with a protein termed Tap42. In this study, we demonstrated that Sit4 and PP2Ac interact with Tap42 via an N-terminal domain that is conserved in all type 2A and 2A-like phosphatases. We found that the Sit4 phosphatase in the sit4-102 strain contains a reverse-of-charge amino acid substitution within its Tap42 binding domain and is defective for formation of the Tap42-Sit4 complex. Our results suggest that the interaction with Tap42 is required for the activity as well as for the essential function of Sit4 and PP2Ac. In addition, we showed that Tap42 is able to interact with two other 2A-like phosphatases, Pph3 and Ppg1.

scholarly journals Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae

Genetics ◽  
2017 ◽  
Vol 207 (1) ◽  
pp. 347-355 ◽  
Author(s):  
Mackenzie B. D. Lawrence ◽  
Nicolas Coutin ◽  
Jennifer K. Choi ◽  
Benjamin J. E. Martin ◽  
Nicholas A. T. Irwin ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Acetylation ◽  
Linker Histone ◽  
Histone Binding
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