The Role of Surface-Exposed Lysines in Wrapping DNA about the Bacterial Histone-Like Protein HU

Grove, Anne; Saavedra, Tatiana C.

doi:10.1021/bi016095e

Cited by 34 publications

(42 citation statements)

References 35 publications

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“…The presence of histone H1-like repeats is the reason these proteins are described as "histone-like" (10). Figure 1A shows the residues critical for the interaction of Hlps with DNA and their conservation in HupB (34,(36)(37)(38). The tetrapeptide repeats (AKKA) similar to eukaryotic histone H1 are also marked (Fig.…”

Section: Resultsmentioning

confidence: 99%

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

et al. 2014

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e HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen Mycobacterium tuberculosis, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of M. tuberculosis H 37 Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined in vitro and the residues modified by the STPKs are identified for both in vivo and the in vitro proteins through mass spectrometry. Of the identified phosphosites, Thr 65 and Thr 74 in the DNA-embracing ␤-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg 55 is also identified as an important residue for N-HupB-DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore, hupB is shown to be maximally expressed during the stationary phase in M. tuberculosis H 37 Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.

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Section: Resultsmentioning

confidence: 99%

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

et al. 2014

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“…Bph2 has a role in virulence gene expression and shares limited (likely convergent) sequence similarity with histone H1 [33]. The dinoflagellate and bacterial HLPs also contain an N-terminal extension in comparison to HU proteins.…”

Section: Resultsmentioning

confidence: 99%

Insights into a dinoflagellate genome through expressed sequence tag analysis

et al. 2005

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Background: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

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“…The co-crystal structure of an HUαβ protein with DNA indicated that K3 is in contact with the DNA backbone in a nucleoprotein complex but is in a salt bridge with D26 in the absence of DNA (31–33). Replacing K3 with an alanine in HUαβ protein led to the disruption of the salt bridge and is expected to lead to significant reduction in DNA binding affinity (32). Arginine-61 of HUαβ has been shown to be in close proximity to proline-63, an amino acid residue that was demonstrated to be important for the binding of HUαβ to DNA (34).…”

Section: Resultsmentioning

confidence: 99%

Escherichia coli HU protein has a role in the repair of abasic sites in DNA

Kow

Imhoff

Weiss

et al. 2007

Nucleic Acids Research

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HU is one of the most abundant DNA binding proteins in Escherichia coli. We find that it binds strongly to DNA containing an abasic (AP) site or tetrahydrofuran (THF) (apparent Kd ≈50 nM). It also possesses an AP lyase activity that cleaves at a deoxyribose but not at a THF residue. The binding and cleavage of an AP site was observed only with the HUαβ heterodimer. Site-specific mutations at K3 and R61 residues led to a change in substrate binding and cleavage. Both K3A(α)K3A(β) and R61A(α)R61A(β) mutant HU showed significant reduction in binding to DNA containing AP site; however, only R61A(α)R61A(β) mutant protein exhibited significant loss in AP lyase activity. Both K3A(α)K3A(β) and R61K(α)R61K(β) showed slight reduction in AP lyase activities. The function of HU protein as an AP lyase was confirmed by the ability of hupA or hupB mutations to further reduce the viability of an E. coli dut(Ts) xth mutant, which generates lethal AP sites at 37°C; the hupA and hupB derivatives, respectively, had a 6-fold and a 150-fold lower survival at 37°C than did the parental strain. These data suggest, therefore, that HU protein plays a significant role in the repair of AP sites in E. coli.

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The Role of Surface-Exposed Lysines in Wrapping DNA about the Bacterial Histone-Like Protein HU

Cited by 34 publications

References 35 publications

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

Insights into a dinoflagellate genome through expressed sequence tag analysis

Escherichia coli HU protein has a role in the repair of abasic sites in DNA

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