Histone variants in archaea – An undiscovered country

Stevens, Kathryn M; Warnecke, Tobias

doi:10.1016/j.semcdb.2022.02.016

Cited by 12 publications

(14 citation statements)

References 74 publications

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“…1a, Table S1). Like their archaeal homologs, most bacterial singlets also lack the long, disordered N-terminal tails that are characteristic of eukaryotic histones (Henneman et al 2018;Stevens and Warnecke 2022). Amino acid conservation across the three domains of life is particularly high in the L2 loop (RKTV).…”

Section: Histones Are Phylogenetically Entrenched In Several Bacteria...mentioning

confidence: 99%

Histone-organized chromatin in bacteria

Hocher

Laursen

Radford

et al. 2023

Preprint

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Histones are the principal constituents of chromatin in eukaryotes and most archaea, while bacteria generally rely on an orthogonal set of proteins to organize their chromosomes. However, several bacterial genomes encode proteins with putative histone fold domains. Whether these proteins are structurally and functionally equivalent to archaeal and eukaryotic histones is unknown. Here, we demonstrate that histones are essential and are major components of chromatin in the bacteriaBdellovibrio bacteriovorusandLeptospira interrogans. Patterns of sequence evolution suggest important roles in several additional bacterial clades. Structural analysis of theB. bacteriovorushistone (Bd0055) dimer shows that histone fold topology is conserved between bacteria, archaea, and eukaryotes. Yet, unexpectedly, Bd0055 binds DNA end-on and forms a sheath of tightly packed histone dimers to encase straight DNA. This binding mode is in stark contrast to that employed by archaeal, eukaryotic, and viral histones, which invariably bend and wrap DNA around their outer surface. Our results demonstrate that histones are integral chromatin components across the tree of life and highlight organizational innovation in the domain Bacteria.

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Section: Histones Are Phylogenetically Entrenched In Several Bacteria...mentioning

confidence: 99%

Histone-organized chromatin in bacteria

Hocher

Laursen

Radford

et al. 2023

Preprint

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“…Therefore, PTM studies are one of the major forefronts or proteomics research and their widespread use is not limited only to mammals or eukaryota. PTM types and sites in bacteria, archaea, and even viral proteins have been characterized and reported in an extensive number of studies 24-26 . These PTMs can modulate protein turnover 27 , stability/solubility 2, 8, 28, 29 , folding and localization of proteins, the interactions between proteins 30 , genome function 31 , the trafficking of molecules 32 , cell signaling 33 and the activation of receptors 34 .…”

Section: Discussionmentioning

confidence: 99%

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Nickchi

Mirzaie

Baumann

et al. 2022

Preprint

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Post-translational modifications (PTMs) are under significant focus in molecular biomedicine due to their importance in signal transduction in most cellular and organismal processes. Characterization of PTMs, discrimination between functional and inert PTMs, quantification of their occupancies and PTM crosstalk are demanding tasks in each biosystem. On top of that, the study of each PTM often necessitates a particular laborious experimental design. Here, we present a PTM-centric proteome informatic pipeline for prediction of most probable and relevant PTMs in mass spectrometry-based proteomics data. Upon prediction, such PTMs can be incorporated in a refined database search. To demonstrate the applicability of our approach, using expression profiling, we identified cellular proteins that are differentially regulated in response to multikinase inhibitors dasatinib and staurosporine. Computational enrichment analysis was employed to determine the potential PTMs of protein targets for both drugs. Finally, we conducted an additional round of database search with the predicted probable PTMs. Our pipeline helped analyze the enriched PTMs and even detected proteins that were not picked up in the initial search. Our findings support the idea of PTM-centric searching of MS data in proteomics based on computational enrichment analysis and we believe this strategy should be incorporated in futuristic proteomics search engines.

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“…Following the initial discovery of histones in archaea, further homologs -usually one or two copies -have been found in most archaeal lineages (Ammar et al ., 2012, Maruyama et al ., 2013, Pereira et al ., 1997, Reeve et al ., 1997, Sandman & Reeve, 2000, 2006, Sanders et al ., 2021), including the Asgard superphylum, whose members are the closest prokaryotic relatives of eukaryotes (Henneman et al ., 2018, Stevens et al ., 2020). Archaeal histones assemble both into homo- and hetero-oligomers and have varying sizes, with some even possessing N- or C-terminal tails similar to eukaryotic histones (Henneman et al ., 2018, Stevens & Warnecke, 2023). This diversity observed in archaeal histones suggests that they serve distinct roles in genome organization and regulation (Peeters et al ., 2015, Sanders et al ., 2021, Stevens et al ., 2020, Kouzarides, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…Archaeal histones can assemble into both homo-and hetero-oligomers and exhibit varying sizes, with some even possessing N-or C-terminal tails akin to eukaryotic histones (8,18).…”

Section: Introductionmentioning

confidence: 99%

Bacterial histone HBb fromBdellovibrio bacteriovoruscompacts DNA by bending

Hu¹,

Deiss²,

Joiner³

et al. 2023

Preprint

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Histones are DNA-binding proteins that play a crucial role in DNA packaging and gene regulation in eukaryotes and archaea. In eukaryotes, histones form octamers that constitute the core of the nucleosome, the fundamental unit of chromatin. Archaeal histones, on the other hand, form tetramers that assemble into extended superhelices upon DNA binding. Although previously thought to occur only in archaea and eukaryotes, histone homologs have recently been discovered in bacteria. This work presents the dimeric crystal structure of the bacterial histone HBb from Bdellovibrio bacteriovorus determined at a resolution of 1.06 Angstrom, representing the first-ever structure of any histone protein determined at atomic resolution. Furthermore, this study shows that HBb binds DNA and is essential for bacterial viability, suggesting that bacterial histone homologs likely have a similar biological function as their eukaryotic and archaeal counterparts. These findings have important implications for our understanding of the fundamental processes of DNA organization and regulation in all domains of life.

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Histone variants in archaea – An undiscovered country

Cited by 12 publications

References 74 publications

Histone-organized chromatin in bacteria

Histone-organized chromatin in bacteria

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Bacterial histone HBb fromBdellovibrio bacteriovoruscompacts DNA by bending

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