scholarly journals N- and C-terminal Domains Determine Differential Nucleosomal Binding Geometry and Affinity of Linker Histone Isotypes H10 and H1c

2012 ◽  
Vol 287 (15) ◽  
pp. 11778-11787 ◽  
Author(s):  
Payal Vyas ◽  
David T. Brown
Keyword(s):  
Fluorescent Proteins ◽  
Dynamic Properties ◽  
Linker Histone ◽  
Chromatin Interaction ◽  
Globular Domain ◽  
Binding Characteristics ◽  
Domain Swap ◽  
Terminal Domain ◽  
Terminal Domains

Eukaryotic linker or H1 histones modulate DNA compaction and gene expression in vivo. In mammals, these proteins exist as multiple isotypes with distinct properties, suggesting a functional significance to the heterogeneity. Linker histones typically have a tripartite structure composed of a conserved central globular domain flanked by a highly variable short N-terminal domain and a longer highly basic C-terminal domain. We hypothesized that the variable terminal domains of individual subtypes contribute to their functional heterogeneity by influencing chromatin binding interactions. We developed a novel dual color fluorescence recovery after photobleaching assay system in which two H1 proteins fused to spectrally separable fluorescent proteins can be co-expressed and their independent binding kinetics simultaneously monitored in a single cell. This approach was combined with domain swap and point mutagenesis to determine the roles of the terminal domains in the differential binding characteristics of the linker histone isotypes, mouse H10 and H1c. Exchanging the N-terminal domains between H10 and H1c changed their overall binding affinity to that of the other variant. In contrast, switching the C-terminal domains altered the chromatin interaction surface of the globular domain. These results indicate that linker histone subtypes bind to chromatin in an intrinsically specific manner and that the highly variable terminal domains contribute to differences between subtypes. The methods developed in this study will have broad applications in studying dynamic properties of additional histone subtypes and other mobile proteins.

scholarly journals MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Katarzyna Zawadzka ◽  
Pawel Zawadzki ◽  
Rachel Baker ◽  
Karthik V Rajasekar ◽  
Florence Wagner ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Chromosome Segregation ◽  
Atp Hydrolysis ◽  
Helix Bundle ◽  
Terminal Domain ◽  
Terminal Domains

The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes.

scholarly journals Tau consists of a set of proteins with repeated C-terminal microtubule-binding domains and variable N-terminal domains.

1989 ◽  
Vol 9 (4) ◽  
pp. 1381-1388 ◽  
Author(s):  
A Himmler ◽  
D Drechsel ◽  
M W Kirschner ◽  
D W Martin
Keyword(s):  
Polyclonal Antibodies ◽  
Bovine Brain ◽  
Tau Proteins ◽  
In Vitro Translation ◽  
Cdna Clones ◽  
Terminal Domain ◽  
Binding Domains ◽  
Terminal Domains

Tau proteins consist of a family of proteins, heterogeneous in size, which associate with microtubules in vivo and are induced during neurite outgrowth. In humans, tau is one of the major components of the pathognomonic neurofibrillary tangles in Alzheimer's disease brain. Screening of a cDNA library prepared from bovine brain led to the isolation of several cDNA clones encoding tau proteins with different N termini and differing by insertions or deletions, suggesting differential splicing of the tau transcripts. One of the N-terminal domains and the repeated C-terminal domain of the encoded tau proteins are recognized by polyclonal antibodies to bovine tau. The bovine tau proteins are highly homologous to murine and human tau, especially within the repeated C-terminal domain. Compared with murine and human tau, bovine tau contains the insertion of three longer segments, one of which is an additional characteristic repeat. Portions of tau proteins generated by in vitro translation were used to show that these repeats represent tubulin-binding domains, two of which are sufficient to bind to microtubules assembled from purified tubulin in the presence of taxol.

scholarly journals Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X

2016 ◽  
Vol 36 (21) ◽  
pp. 2681-2696 ◽  
Author(s):  
Mitsuru Okuwaki ◽  
Mayumi Abe ◽  
Miharu Hisaoka ◽  
Kyosuke Nagata
Keyword(s):  
Binding Site ◽  
Dynamic Behavior ◽  
Histone Variants ◽  
Linker Histone ◽  
Site Preference ◽  
Globular Domain ◽  
Linker Histones ◽  
Terminal Domain ◽  
Site Preferences ◽  
Linker Histone Variants

Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histonesin vivo. Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones.

scholarly journals Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle

2020 ◽  
Author(s):  
Hao Wu ◽  
Yamini Dalal ◽  
Garegin A. Papoian
Keyword(s):  
Regulatory Protein ◽  
Conformational Dynamics ◽  
Histone H1 ◽  
Linker Histone ◽  
Coarse Grained ◽  
Globular Domain ◽  
Linker Histone H1 ◽  
Eukaryotic Chromatin ◽  
Cancer Phenotype ◽  
Terminal Domains

AbstractLinker histone H1 is an essential regulatory protein for many critical biological processes, such as eukaryotic chromatin packaging and gene expression. Mis-regulation of H1s is commonly observed in tumor cells, where the balance between different H1 subtypes has been shown to alter the cancer phenotype. Consisting of a rigid globular domain and two highly charged terminal domains, H1 can bind to multiple sites on a nucleosomal particle to alter chromatin hierarchical condensation levels. In particular, the disordered H1 amino- and carboxyl-terminal domains (NTD/CTD) are believed to enhance this binding affinity, but their detailed dynamics and functions remain unclear. In this work, we used a coarse-grained computational model AWSEM-DNA to simulate the H1.0b-nucleosome complex, namely chromatosome. Our results demonstrate that H1 disordered domains restrict the dynamics of both globular H1 and linker DNA arms, resulting in a more compact and rigid chromatosome particle. Furthermore, we identified regions of H1 disordered domains that are tightly tethered to DNA near the entry-exit site. Overall, our study elucidates at near atomic resolution the way the disordered linker histone H1 modulates nucleosome’s structural preferences and conformational dynamics.

scholarly journals Inter- and intra-molecular interactions of Arabidopsis thaliana DELLA protein RGL1

2011 ◽  
Vol 435 (3) ◽  
pp. 629-639 ◽  
Author(s):  
David J. Sheerin ◽  
Jeremy Buchanan ◽  
Chris Kirk ◽  
Dawn Harvey ◽  
Xiaolin Sun ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dissociation Kinetics ◽  
Della Protein ◽  
Terminal Domain ◽  
Della Proteins ◽  
F Box Protein ◽  
Key Aspects ◽  
Terminal Domains

The phytohormone gibberellin and the DELLA proteins act together to control key aspects of plant development. Gibberellin induces degradation of DELLA proteins by recruitment of an F-box protein using a molecular switch: a gibberellin-bound nuclear receptor interacts with the N-terminal domain of DELLA proteins, and this event primes the DELLA C-terminal domain for interaction with the F-box protein. However, the mechanism of signalling between the N- and C-terminal domains of DELLA proteins is unresolved. In the present study, we used in vivo and in vitro approaches to characterize di- and tri-partite interactions of the DELLA protein RGL1 (REPRESSOR OF GA1-3-LIKE 1) of Arabidopsis thaliana with the gibberellin receptor GID1A (GIBBERELLIC ACID-INSENSITIVE DWARF-1A) and the F-box protein SLY1 (SLEEPY1). Deuterium-exchange MS unequivocally showed that the entire N-terminal domain of RGL1 is disordered prior to interaction with the GID1A; furthermore, association/dissociation kinetics, determined by surface plasmon resonance, predicts a two-state conformational change of the RGL1 N-terminal domain upon interaction with GID1A. Additionally, competition assays with monoclonal antibodies revealed that contacts mediated by the short helix Asp-Glu-Leu-Leu of the hallmark DELLA motif are not essential for the GID1A–RGL1 N-terminal domain interaction. Finally, yeast two- and three-hybrid experiments determined that unabated communication between N- and C-terminal domains of RGL1 is required for recruitment of the F-box protein SLY1.

scholarly journals HPat provides a link between deadenylation and decapping in metazoa

2010 ◽  
Vol 189 (2) ◽  
pp. 289-302 ◽  
Author(s):  
Gabrielle Haas ◽  
Joerg E. Braun ◽  
Cátia Igreja ◽  
Felix Tritschler ◽  
Tadashi Nishihara ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Cellular Mechanism ◽  
Messenger Rnas ◽  
Rich Region ◽  
Mrna Decapping ◽  
Terminal Domain ◽  
Decapping Enzyme ◽  
Proline Rich Region ◽  
Terminal Domains

Decapping of eukaryotic messenger RNAs (mRNAs) occurs after they have undergone deadenylation, but how these processes are coordinated is poorly understood. In this study, we report that Drosophila melanogaster HPat (homologue of Pat1), a conserved decapping activator, interacts with additional decapping factors (e.g., Me31B, the LSm1–7 complex, and the decapping enzyme DCP2) and with components of the CCR4–NOT deadenylase complex. Accordingly, HPat triggers deadenylation and decapping when artificially tethered to an mRNA reporter. These activities reside, unexpectedly, in a proline-rich region. However, this region alone cannot restore decapping in cells depleted of endogenous HPat but also requires the middle (Mid) and the very C-terminal domains of HPat. We further show that the Mid and C-terminal domains mediate HPat recruitment to target mRNAs. Our results reveal an unprecedented role for the proline-rich region and the C-terminal domain of metazoan HPat in mRNA decapping and suggest that HPat is a component of the cellular mechanism that couples decapping to deadenylation in vivo.

scholarly journals Extended and dynamic linker histone-DNA interactions control chromatosome compaction

2020 ◽  
Author(s):  
Sergei Rudnizky ◽  
Hadeel Khamis ◽  
Yuval Ginosar ◽  
Efrat Goren ◽  
Philippa Melamed ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Complex Dynamics ◽  
Linker Histone ◽  
Globular Domain ◽  
Entry And Exit ◽  
Nucleosome Core ◽  
Terminal Domain ◽  
Potential Regulatory Role ◽  
Rapid Binding

AbstractChromatosomes play a fundamental role in chromatin regulation, but a detailed understanding of their structure is lacking, partially due to their complex dynamics. Using single-molecule DNA unzipping with optical tweezers, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as ~ ±140 bp from the dyad. In addition to a symmetrical compaction of the nucleosome core governed by globular domain contacts at the dyad, the C-terminal domain compacts the nucleosome’s entry and exit. These interactions are dynamic, exhibiting rapid binding and dissociation, sensitive to phosphorylation of a specific residue, and crucial to determining the symmetry of the chromatosome’s core. Extensive unzipping of the linker DNA, which mimics its invasion by motor proteins, shifts H1 into an asymmetric, off-dyad configuration and triggers nucleosome decompaction, highlighting the plasticity of the chromatosome structure and its potential regulatory role.

scholarly journals Asymmetric MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

2017 ◽  
Author(s):  
Katarzyna Zawadzka ◽  
Pawel Zawadzki ◽  
Rachel Baker ◽  
Karthik V. Rajasekar ◽  
David J. Sherratt ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Chromosome Segregation ◽  
Active Sites ◽  
Atp Binding ◽  
Dimerization Domain ◽  
Helix Bundle ◽  
Terminal Domain ◽  
Atp Binding And Hydrolysis ◽  
Terminal Domains

AbstractThe Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerization domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head, forming an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerization is preserved during this interaction, MukF directs the formation of dimer of dimers MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate ATPase independently and additively, consistent with them each targeting only one of the two MukB ATPase active sites in the asymmetric complex. We demonstrate that MukF interaction with the MukB neck turns over during cycles of ATP binding and hydrolysis in vivo and that impairment of this interaction leads to MukBEF release from chromosomes.

Analyses of linker histone – chromatin interactions in situThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 427-436 ◽  
Author(s):  
Ingemar Rundquist ◽  
Herbert H. Lindner
Keyword(s):  
Fluorescent Proteins ◽  
Peer Review Process ◽  
Chromatin Condensation ◽  
Human Fibroblasts ◽  
Linker Histone ◽  
Metaphase Chromosomes ◽  
Linker Histones ◽  
Additional Information

Recent studies, using cytometric techniques based on fluorescence microscopy, have provided new information on how linker histones interact with chromatin in vivo or in situ. In particular, the use of green fluorescent proteins (GFPs) has enabled detailed studies of how individual H1 subtypes, and specific motifs in them, interact with chromatin in vivo. Furthermore, the development of cytochemical methods to study the interaction between linker histones and chromatin using DNA-binding fluorochromes as indirect probes for linker histone affinity in situ, in combination with highly sensitive and specific analytical methods, has provided additional information on the interactions between linker histones and chromatin in several cell systems. Such results verified that linker histones have a substantially higher affinity for chromatin in mature chicken erythrocytes than in frog erythrocytes, and they also indicated that the affinity decreased during differentiation of the frog erythrocytes. Furthermore, in cultured human fibroblasts, the linker histones showed a relatively high affinity for chromatin in interphase, whereas it showed a significantly lower affinity in highly condensed metaphase chromosomes. This method also enables the analysis of linker histone affinity for chromatin in H1-depleted fibroblasts reconstituted with purified linker histones. No consistent correlation between linker histone affinity and chromatin condensation has so far been detected.

Sign in / Sign up

Export Citation Format

Share Document