Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3′-dATP

2015 ◽  
Vol 469 (3) ◽  
pp. 367-374 ◽  
Author(s):  
Martina Müller ◽  
Tobias Deimling ◽  
Karl-Peter Hopfner ◽  
Gregor Witte
Keyword(s):  
Structural Analysis ◽  
Thermotoga Maritima ◽  
Bacterial Species ◽  
Protein A ◽  
Dna Integrity

Structures of Thermotoga maritima DNA-integrity-scanning protein A (DisA) in different reaction states describe the diadenylate cyclase (DAC) reaction and the possibility of its inhibition. We conclude that the mechanisms of cyclic-di-AMP (c-di-AMP) synthesis and its inhibition are conserved among different DAC enzymes and bacterial species.

scholarly journals Genome-Wide Identification of Resveratrol Intrinsic Resistance Determinants in Staphylococcus aureus

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 82
Author(s):  
Liping Liu ◽  
Hanne Ingmer ◽  
Martin Vestergaard
Keyword(s):  
Staphylococcus Aureus ◽  
Stress Response ◽  
Inhibitory Activity ◽  
Bacterial Species ◽  
Dna Integrity ◽  
Intrinsic Resistance ◽  
Potential Health ◽  
Cellular Effects ◽  
Development Of Resistance ◽  
Wide Range

Resveratrol has been extensively studied due to its potential health benefits in multiple diseases, for example, cancer, obesity and cardiovascular diseases. Besides these properties, resveratrol displays inhibitory activity against a wide range of bacterial species; however, the cellular effects of resveratrol in bacteria remain incompletely understood, especially in the human pathogen, Staphylococcus aureus. In this study, we aimed to identify intrinsic resistance genes that aid S. aureus in tolerating the activity of resveratrol. We screened the Nebraska Transposon Mutant Library, consisting of 1920 mutants with inactivation of non-essential genes in S. aureus JE2, for increased susceptibly to resveratrol. On agar plates containing 0.5× the minimum inhibitory concentration (MIC), 17 transposon mutants failed to grow. Of these, four mutants showed a two-fold reduction in MIC, being the clpP protease mutant and three mutants with deficiencies in the electron transport chain (menD, hemB, aroC). The remaining 13 mutants did not show a reduction in MIC, but were confirmed by spot-assays to have increased susceptibility to resveratrol. Several genes were associated with DNA damage repair (recJ, xerC and xseA). Treatment of S. aureus JE2 with sub-inhibitory concentrations of resveratrol did not affect the expression of recJ, xerC and xseA, but increased expression of the SOS–stress response genes lexA and recA, suggesting that resveratrol interferes with DNA integrity in S. aureus. Expression of error-prone DNA polymerases are part of the SOS–stress response and we could show that sub-inhibitory concentrations of resveratrol increased overall mutation frequency as measured by formation of rifampicin resistant mutants. Our data show that DNA repair systems are important determinants aiding S. aureus to overcome the inhibitory activity of resveratrol. Activation of the SOS response by resveratrol could potentially facilitate the development of resistance towards conventional antibiotics in S. aureus.

scholarly journals Structural Analysis of Redox-sensing Transcriptional Repressor Rex from Thermotoga maritima

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Young Woo Park ◽  
Young Yoon Jang ◽  
Hyun Kyu Joo ◽  
Jae Young Lee
Keyword(s):  
Structural Analysis ◽  
Thermotoga Maritima ◽  
Transcriptional Repressor ◽  
Redox Sensing

scholarly journals Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA

2013 ◽  
Vol 42 (5) ◽  
pp. 3478-3491 ◽  
Author(s):  
Wei Wang ◽  
Jingjin Ding ◽  
Ying Zhang ◽  
Yonglin Hu ◽  
Da-Cheng Wang
Keyword(s):  
Helicobacter Pylori ◽  
Bacterial Species ◽  
Complex Structure ◽  
Protein A ◽  
Binding Mode ◽  
Binding Assays ◽  
Mobility Shift ◽  
Single Stranded Dna ◽  
Exogenous Dna ◽  
Ssdna Binding

Abstract Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.

scholarly journals Structural Analysis of Human Replication Protein A

1995 ◽  
Vol 270 (9) ◽  
pp. 4534-4543 ◽  
Author(s):  
Xavier V. Gomes ◽  
Marc S. Wold
Keyword(s):  
Structural Analysis ◽  
Protein A ◽  
Replication Protein A ◽  
Replication Protein

scholarly journals Expression, Purification and Structural Analysis of Human IL-18 Binding Protein: A Potent Therapeutic Molecule for Allergy

2008 ◽  
Vol 57 (4) ◽  
pp. 367-376 ◽  
Author(s):  
Takeshi Kimura ◽  
Zenichiro Kato ◽  
Hidenori Ohnishi ◽  
Hidehito Tochio ◽  
Masahiro Shirakawa ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Binding Protein ◽  
Protein A

scholarly journals Characterization of GTPase Activity of TrmE, a Member of a Novel GTPase Superfamily, from Thermotoga maritima

2000 ◽  
Vol 182 (24) ◽  
pp. 7078-7082 ◽  
Author(s):  
Kunitoshi Yamanaka ◽  
Jihwan Hwang ◽  
Masayori Inouye
Keyword(s):  
Thermotoga Maritima ◽  
Binding Protein ◽  
Protein A ◽  
Hydrolysis Rate ◽  
Gtpase Activity ◽  
Gtp Binding Protein ◽  
Gene Encoding ◽  
Gtp Hydrolysis ◽  
Gtp Binding

ABSTRACT A gene encoding a putative GTP-binding protein, a TrmE homologue that is highly conserved in both prokaryotes and eukaryotes, was cloned from Thermotoga maritima, a hyperthermophilic bacterium.T. maritima TrmE was overexpressed in Escherichia coli and purified. TrmE has a GTPase activity but no ATPase activity. The GTPase activity can be competed with GTP, GDP, and dGTP but not with GMP, ATP, CTP, or UTP. Km andk cat at 70°C were 833 μM and 9.3 min−1, respectively. Our results indicate that TrmE is a GTP-binding protein with a very high intrinsic GTP hydrolysis rate. We also propose that TrmE homologues constitute a novel subfamily of the GTPase superfamily.

scholarly journals c-di-AMP, a likely master regulator of bacterial K+ homeostasis machinery, activates a K+ exporter

2021 ◽  
Vol 118 (14) ◽  
pp. e2020653118
Author(s):  
Tatiana B. Cereija ◽  
João P. L. Guerra ◽  
João M. P. Jorge ◽  
João H. Morais-Cabral
Keyword(s):  
Bacterial Species ◽  
Structural Data ◽  
Regulatory Function ◽  
Dna Integrity ◽  
Master Regulator ◽  
Quantitative Evidence ◽  
Physiological Properties ◽  
The Impact

bis-(3′,5′)-cyclic diadenosine monophosphate (c-di-AMP) is a second messenger with roles in virulence, cell wall and biofilm formation, and surveillance of DNA integrity in many bacterial species, including pathogens. Strikingly, it has also been proposed to coordinate the activity of the components of K+ homeostasis machinery, inhibiting K+ import, and activating K+ export. However, there is a lack of quantitative evidence supporting the direct functional impact of c-di-AMP on K+ transporters. To gain a detailed understanding of the role of c-di-AMP on the activity of a component of the K+ homeostasis machinery in B. subtilis, we have characterized the impact of c-di-AMP on the functional, biochemical, and physiological properties of KhtTU, a K+/H+ antiporter composed of the membrane protein KhtU and the cytosolic protein KhtT. We have confirmed c-di-AMP binding to KhtT and determined the crystal structure of this complex. We have characterized in vitro the functional properties of KhtTU and KhtU alone and quantified the impact of c-di-AMP and of pH on their activity, demonstrating that c-di-AMP activates KhtTU and that pH increases its sensitivity to this nucleotide. Based on our functional and structural data, we were able to propose a mechanism for the activation of KhtTU by c-di-AMP. In addition, we have analyzed the impact of KhtTU in its native bacterium, providing a physiological context for the regulatory function of c-di-AMP and pH. Overall, we provide unique information that supports the proposal that c-di-AMP is a master regulator of K+ homeostasis machinery.

scholarly journals Structural Analysis of Replication Protein A Recruitment of the DNA Damage Response Protein SMARCAL1

Biochemistry ◽  
2014 ◽  
Vol 53 (18) ◽  
pp. 3052-3061 ◽  
Author(s):  
Michael D. Feldkamp ◽  
Aaron C. Mason ◽  
Brandt F. Eichman ◽  
Walter J. Chazin
Keyword(s):  
Dna Damage ◽  
Structural Analysis ◽  
Dna Damage Response ◽  
Protein A ◽  
Replication Protein A ◽  
Replication Protein ◽  
Damage Response
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