Histone divergence in<i>Trypanosoma brucei</i>results in unique alterations to nucleosome structure

Deák, Gauri; Wapenaar, Hannah; Sandoval, Gorka; Chen, Ruofen; Taylor, Mark RD; Burdett, H.; Watson, James A.; Tuijtel, Maarten W.; Webb, Shaun; Wilson, Marcus D.

doi:10.1101/2023.04.17.536592

Cited by 3 publications

(2 citation statements)

References 109 publications

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“…Here, we explored their potential to engage acetylated histone peptides experimentally in an unbiased manner, using an array that could be probed with recombinant bromodomains. As kinetoplastid histone tails are significantly divergent from those of mammalian orthologues, 41 , 42 a custom peptide microarray was developed. In the absence of a comprehensive data set of Leishmania histone PTMs, the microarray represented a panel of around 1000 unmodified, pan-acetylated, and monoacetylated peptides derived from the 25 N-terminal residues of L. donovani histones, tiled in 15-mer duplicates to cover the full sequence.…”

Section: Resultsmentioning

confidence: 99%

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

Russell,

Carter,

Borgia

et al. 2023

ACS Infect. Dis.

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Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC–CBP30, bromosporine, and I-BRD9; moreover, SGC–CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.

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Section: Resultsmentioning

confidence: 99%

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

Russell,

Carter,

Borgia

et al. 2023

ACS Infect. Dis.

View full text Add to dashboard Cite

show abstract

“…Here, we explored their potential to engage acetylated histone peptides experimentally in an unbiased manner, using an array that could be probed with recombinant bromodomains. As kinetoplastid histone tails are significantly divergent from those of mammalian orthologues 41,42 , a custom peptide microarray was developed. In the absence of a comprehensive dataset of Leishmania histone PTMs, the microarray represented a panel of around 1000 unmodified, pan-acetylated and mono-acetylated peptides derived from the 25 N-terminal residues of L. donovani histones, tiled in 15-mer duplicates to cover the full sequence.…”

Section: Identifying Histone Binding Interactions Of Ldbdf5mentioning

confidence: 99%

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

Russell,

Carter,

Borgia

et al. 2023

Preprint

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Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarisation assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarisation and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine and I-BRD9, moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a drug target in Leishmania and provide a foundation for the future development of optimised antileishmanial compounds targeting this epigenetic reader protein.

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The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment

Wapenaar,

Clifford,

Rolls

et al. 2023

Preprint

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DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns. However, the mechanisms underlying DNMT3A recruitment to and function within different chromatin environments remain unclear. Using a combination of biochemical and structural approaches we find that DNMT3A interacts using multiple interfaces with chromatin; directly binding generic nucleosome features as well as site-specific post-translational histone modifications. The N-terminal region, unique to the DNMT3A1 isoform, is essential for these interactions and stabilises H3K36me2-nucleosome recruitment. Intriguingly, in the same region critical for nucleosome binding we also map a ubiquitylation-dependent recruitment motif (UDR). The UDR binds specifically to ubiquitylated H2AK119, explaining the previously observed recruitment to Polycomb-occupied heterochromatin. A cryo-EM structure of DNMT3A1-DNMT3L with a modified nucleosome reveals that the UDR interacts with the nucleosome surface including the acidic patch. Previously unexplained disease-associated mutations are present in the UDR and ablate nucleosome interactions. This leads to an increased understanding of how DNMT3A1 recruitment occurs in the genome and highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome.

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Histone divergence inTrypanosoma bruceiresults in unique alterations to nucleosome structure

Cited by 3 publications

References 109 publications

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery

The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment

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