Interactions between N- and C-Terminal Domains of the <i>Saccharomyces cerevisiae</i> High-Mobility Group Protein HMO1 Are Required for DNA Bending

Bauerle, Kevin T.; Kamau, Edwin; Grove, Anne

doi:10.1021/bi0522798

Cited by 34 publications

(58 citation statements)

References 39 publications

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“…Box A, which has only limited similarity to consensus HMG domains, functions as a dimerization domain; it has a low affinity for DNA but exhibits some structural specificity, including preferred binding to four-way junction DNA, whereas canonical box B has a higher affinity for DNA but a lower structural specificity (130,132). The HMO1 box A domain contributes to DNA bending; in contrast, the box B domain contributes most of the DNA binding affinity but fails to bend linear DNA (133). There is no high-resolution structural information available for HMO1; however, a structure-based model predicts that both box A and box B domains adopt the HMG fold (Fig.…”

Section: Hmo1 Domain Organizationmentioning

confidence: 99%

Yeast HMO1: Linker Histone Reinvented

Panday

Grove

2017

Microbiol Mol Biol Rev

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SUMMARY Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or “fragile” nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.

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Section: Hmo1 Domain Organizationmentioning

confidence: 99%

Yeast HMO1: Linker Histone Reinvented

Panday

Grove

2017

Microbiol Mol Biol Rev

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“…21,22) In contrast to these findings, a mutation in box A of Hmo1 (T30R) identified in the genetic screen abolished the DNA binding activity of Hmo1 both in vivo and in vitro (Fig. 3(B) and (C)).…”

Section: Box a Is Essential For Binding Of Hmo1 To Dna Both In Vitro mentioning

confidence: 74%

“…For example, while box A has only a slight contribution to the DNA binding activity of Hmo1 compared with that of box B, it is responsible for structure-specific DNA binding of the protein, albeit less significantly. 21) Furthermore, box A may interact with the carboxy-terminal tail of Hmo1 to bend DNA, 22) or with box A itself to form dimer or oligomer. 32) However, the significance of these properties of box A in vivo has not been verified.…”

Section: Discussionmentioning

confidence: 99%

“…The fact that mutations affecting the DNA binding ability of Hmo1 were located at or close to the first α-helix of box B is consistent with the previously held notion that box B is responsible for most of the DNA binding activity of Hmo1. 21,22) On the other hand, two large α-helices were also predicted within box A of Hmo1 (Supplemental Fig. 5, amino acids 7-41 (1st) and 45-63 (2nd)).…”

Section: Box a Is Essential For Binding Of Hmo1 To Dna Both In Vitro mentioning

confidence: 99%

“…Previous in vitro studies suggested that box B is responsible for most of the DNA binding activity of Hmo1, whereas the contribution of box A to this activity is very limited. 21,22) It was reported recently that the integrity of box A is required for the function of Hmo1 in the RNA polymerase I transcription in vivo, whereas the requirement of box A in the transcription of RPG (such as RPS23A) by RNA polymerase II is unclear. 23) In contrast to these previous studies, the box A mutations identified in the genetic screen performed here impaired the ability of Hmo1 to bind to DNA.…”

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confidence: 99%

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Both HMG boxes in Hmo1 are essential for DNA binding in vitro and in vivo

Higashino

Shiwa

Yoshikawa

et al. 2015

Bioscience, Biotechnology, and Biochemistry

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Hmo1, a member of the high mobility group B family proteins in Saccharomyces cerevisiae, associates with the promoters of ribosomal protein genes (RPGs) to direct accurate transcriptional initiation. Here, to identify factors involved in the binding of Hmo1 to its targets and the mechanism of Hmo1-dependent transcriptional initiation, we developed a novel reporter system using the promoter of the RPG RPS5. A genetic screen did not identify any factors that influence Hmo1 binding, but did identify a number of mutations in Hmo1 that impair its DNA binding activity in vivo and in vitro. These results suggest that Hmo1 binds to its target promoters autonomously without any aid of additional factors. Furthermore, characterization of Hmo1 mutants showed that the box A domain plays a pivotal role in DNA binding and may be required for the recognition of structural properties of target promoters that occur in native chromatin.

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DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity

et al. 2014

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DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.

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Interactions between N- and C-Terminal Domains of the Saccharomyces cerevisiae High-Mobility Group Protein HMO1 Are Required for DNA Bending

Cited by 34 publications

References 39 publications

Yeast HMO1: Linker Histone Reinvented

Yeast HMO1: Linker Histone Reinvented

Both HMG boxes in Hmo1 are essential for DNA binding in vitro and in vivo

DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity

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