Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect

The inhibitors of growth (ING) family of tumor suppressors consists of five homologous proteins involved in chromatin remodeling. They form part of different acetylation and deacetylation complexes and are thought to direct them to specific regions of the chromatin, through the recognition of H3K4me3 (trimethylated K4 in the histone 3 tail) by their conserved plant homeodomain (PHD). We have determined the crystal structure of ING4-PHD bound to H3K4me3, which reveals a tight complex stabilized by numerous interactions. NMR shows that there is a reduction in the backbone mobility on the regions of the PHD that participate in the peptide binding, and binding affinities differ depending on histone tail lengths Thermodynamic analysis reveals that the discrimination in favor of methylated lysine is entropydriven, contrary to what has been described for chromodomains. The molecular basis of H3K4me3 recognition by ING4 differs from that of ING2, which is consistent with their different affinities for methylated histone tails. These differences suggest a distinct role in transcriptional regulation for these two ING family members because of the antagonistic effect of the complexes that they recruit onto chromatin. Our results illustrate the versatility of PHD fingers as readers of the histone code.Regulation of chromatin dynamics dictates the outcome of fundamental nuclear processes such as DNA transcription replication and repair (1-3). It is central to cell homeostasis, because alterations in chromatin structure contribute to the development of cancer and other human diseases (4). The ING 6 family of tumor suppressors consists of five homologous proteins implicated in chromatin remodeling, growth arrest, and, in cooperation with p53, senescence and apoptosis (5-7). They are frequently deregulated in different types of cancer (8) and contain a conserved C-terminal PHD finger (9) that is present in many nuclear proteins involved in gene expression regulation and chromatin remodeling (10). They form stable histone acetylation or deacetylation complexes (11) and are thought to direct them to specific regions of the chromatin through binding of their PHD fingers to histone 3 N-terminal tails trimethylated at lysine 4 (12, 13). These binding properties link ING proteins with actively transcribed genes, because H3K4 trimethylation is a hallmark of active genes (14). The recognition of H3K4me3 by ING2 is critical for the occupancy of the mSin3A-HDAC1 complex at the promoter of the cyclin D1 gene, which results in histone deacetylation and transcriptional repression of the active gene in response to DNA damage (15). This result suggests a general active transcriptional repression role for ING2; nonetheless, the biological outcome of the recognition of methylated histone tails by the other ING proteins is still unclear. Different PHD fingers link H3K4me3 recognition with gene activation, such as the PHD of the bromodomain PHD finger transcription factor, which helps to recruit the nucleosome remodeling factor complex to target ...

Section: Dynamics and Thermodynamics Of The Recognition Of H3k4me3 Bymentioning

confidence: 96%

Molecular Basis of Histone H3K4me3 Recognition by ING4

Palacios

Muñoz

Pantoja-Uceda

et al. 2008

“…1B). Three aromatic residues were shown to be necessary for assembling a methyllysine binding aromatic cage in HP1 and Polycomb chromodomains (11,12,16). Interestingly, the chromodomains of the CDYL proteins do not have the first aromatic cage residue, suggesting substantial difference in the function of this factor.…”

Section: Variability In Binding To H3 Methylated On Lys-9-mentioning

confidence: 99%

“…ability of CDY to establish more favorable polar interactions with the H3 tail than those used by HP1. Previous studies have shown that recognition of methyllysine by the HP1 chromodomain is driven by cation-interactions between the methylated ammonium group of methylated H3K9 and the side chains of three aromatic residues (11,16). The magnitude of the cationinteraction depends on the electron density of the aromatic ring, which can substantially vary from a tyrosine to a phenylalanine as well as the degree of solvent exposure in the interaction site (37,38).…”

Section: Table 2 Thermodynamic Parameters For Binding To H3 Peptides mentioning

confidence: 99%

See 1 more Smart Citation

Specificity of the Chromodomain Y Chromosome Family of Chromodomains for Lysine-methylated ARK(S/T) Motifs

Fischle

Franz

Jacobs

et al. 2008

Self Cite

107

Previous studies have shown two homologous chromodomain modules in the HP1 and Polycomb proteins exhibit discriminatory binding to related methyllysine residues (embedded in ARKS motifs) of the histone H3 tail. Methylated ARK(S/T) motifs have recently been identified in other chromatin factors (e.g. linker histone H1.4 and lysine methyltransferase G9a). These are thought to function as peripheral docking sites for the HP1 chromodomain. In vertebrates, HP1-like chromodomains are also present in the chromodomain Y chromosome (CDY) family of proteins adjacent to a putative catalytic motif. The human genome encodes three CDY family proteins, CDY, CDYL, and CDYL2. These have putative functions ranging from establishment of histone H4 acetylation during spermiogenesis to regulation of transcription co-repressor complexes. To delineate the biochemical functions of the CDY family chromodomains, we analyzed their specificity of methyllysine recognition. We detected substantial differences among these factors. The CDY chromodomain exhibits discriminatory binding to lysinemethylated ARK(S/T) motifs, whereas the CDYL2 chromodomain binds with comparable strength to multiple ARK(S/T) motifs. Interestingly, subtle amino acid changes in the CDYL chromodomain prohibit such binding interactions in vitro and in vivo. However, point mutations can rescue binding. In support of the in vitro binding properties of the chromodomains, the full-length CDY family proteins exhibit substantial variability in chromatin localization. Our studies underscore the significance of subtle sequence differences in a conserved signaling module for diverse epigenetic regulatory pathways.The human Y chromosome has been thoroughly sequenced and compared with partially sequenced Y chromosomes of chimpanzee and mouse (1-3). The Y chromosomes are believed to be enriched in genes essential for spermatogenesis and testis development. Interstitial Y chromosome deletions are associated with spermatogenic failure and male infertility (1,4,5). One gene that is present in multiple copies on the human Y chromosome is CDY, 5 which exhibits testis-specific expression (1). Interestingly, the mouse Y chromosome does not encode CDY, suggesting a developmentally advanced usage of CDY in primates (3).The human CDY gene seems to be derived from the autosomal homologs CDYL or CDYL2 (Fig. 1, A and B) (6). CDYL is ubiquitously expressed, whereas CDYL2 exhibits selective expression in tissues of testis, prostate, spleen, and leukocytes (6). The mouse genome also encodes related CDYL and CDYL2 genes (Fig. 1B). The presence of CDY-like genes appears to be a hallmark of echinoderm and vertebrate genomes. In sea urchin and chicken genomes we found only one CDY-like gene that corresponds to mammalian CDYL2 (Fig. 1B).CDY family proteins have two conserved domains implicated in histone modification and recognition; that is, a chromodomain followed by an enoyl-coenzyme A hydratase/isomerase (ECH) putative catalytic domain (Fig. 1A). Previously, it was shown that the chromodomain of hum...

“…For example, trimethylation in calmodulin has been shown to modulate NAD kinase (38). Similarly, trimethylation was shown to promote interaction with polynucleotides (39) and participate in histone lysine methylation-mediated chromatin remodeling (40). A number of trimethyllysine-binding domains have been found in recent years (41).…”

Section: Monomethylation Dimethylationmentioning

confidence: 99%

Multimethylation of Rickettsia OmpB Catalyzed by Lysine Methyltransferases

Abeykoon

Wang

Chao

et al. 2014

Background: Methylation of OmpB has been implicated in rickettsial virulence. Results: Native OmpBs purified from Rickettsia contain mono-and trimethyllysine at specific locations that coincide with those catalyzed by methyltransferases in vitro. Conclusion: The number of trimethyllysine clusters in OmpBs correlates with degree of virulence. Significance: This study provides new insight into methylation of OmpB and its correlation with virulence.