Sequence, Structure, and Function of DNA-Binding Protein in Deinococcus Wulumuqiensis R12

Abstract Deinococcus wulumuqiensis R12, which was isolated from arid irradiated soil in Xinjiang province of China, belongs to a genus Deinococcus that is well-known for its extreme resistance to ionizing radiation and oxidative stress. The DNA-binding protein Dps has been studied for its great contribution to oxidative resistance. To explore the role of Dps in D. wulumuqiensis R12, the Dps sequence and homologous structure were analyzed. In addition, the dps gene was knocked out and proteomics was used to verify the functions of Dps in D. wulumuqiensis R12. Docking data and DNA binding experiments in vitro showed that the R12 Dps has a better DNA binding ability with the N-terminal than the R1 Dps1. When the dps gene was deleted in D. wulumuqiensis R12, its resistance to H2O2 and UV rays was greatly reduced, and the cell envelope was destroyed by H2O2 treatment. Additionally, the qRT-PCR and proteomics data suggested that when the dps gene was deleted, the catalase gene was significantly down-regulated in cells. And the proteomics data indicated the metabolism, transport and oxidation-reduction processes in D. wulumuqiensis R12 were down-regulated after the deletion of dps gene. Dps protein might play an important role in Deinococcus wulumuqiensis R12.

Download Full-text

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

eLife ◽

10.7554/elife.52542 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 3

Author(s):

Antoine Hocher ◽

Maria Rojec ◽

Jacob B Swadling ◽

Alexander Esin ◽

Tobias Warnecke

Keyword(s):

Dna Binding ◽

Binding Protein ◽

Dna Binding Protein ◽

Coli Strain ◽

Micrococcal Nuclease ◽

Thermoplasma Acidophilum ◽

Chromatin Architecture ◽

Archaeal Histone

Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

Download Full-text

In vitro characterization of a thermolabile herpes simplex virus DNA-binding protein.

Journal of Virology ◽

10.1128/jvi.59.1.31-36.1986 ◽

1986 ◽

Vol 59 (1) ◽

pp. 31-36 ◽

Cited By ~ 6

Author(s):

W T Ruyechan ◽

A Chytil ◽

C M Fisher

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Dna Binding ◽

Binding Protein ◽

Dna Binding Protein ◽

In Vitro Characterization ◽

Simplex Virus

Download Full-text

The Bacterial DNA Binding Protein MatP Involved in Linking the Nucleoid Terminal Domain to the Divisome at Midcell Interacts with Lipid Membranes

mBio ◽

10.1128/mbio.00376-19 ◽

2019 ◽

Vol 10 (3) ◽

Cited By ~ 5

Author(s):

Begoña Monterroso ◽

Silvia Zorrilla ◽

Marta Sobrinos-Sanguino ◽

Miguel Ángel Robles-Ramos ◽

Carlos Alfonso ◽

...

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Lipid Membranes ◽

Binding Protein ◽

Dna Binding Protein ◽

Content Type ◽

E Coli ◽

Daughter Cells ◽

Z Ring

ABSTRACTDivision ring formation at midcell is controlled by various mechanisms inEscherichia coli, one of them being the linkage between the chromosomal Ter macrodomain and the Z-ring mediated by MatP, a DNA binding protein that organizes this macrodomain and contributes to the prevention of premature chromosome segregation. Here we show that, during cell division, just before splitting the daughter cells, MatP seems to localize close to the cytoplasmic membrane, suggesting that this protein might interact with lipids. To test this hypothesis, we investigated MatP interaction with lipidsin vitro. We found that, when encapsulated inside vesicles and microdroplets generated by microfluidics, MatP accumulates at phospholipid bilayers and monolayers matching the lipid composition in theE. coliinner membrane. MatP binding to lipids was independently confirmed using lipid-coated microbeads and biolayer interferometry assays, which suggested that the recognition is mainly hydrophobic. Interaction of MatP with the lipid membranes also occurs in the presence of the DNA sequences specifically targeted by the protein, but there is no evidence of ternary membrane/protein/DNA complexes. We propose that the association of MatP with lipids may modulate its spatiotemporal localization and its recognition of other ligands.IMPORTANCEThe division of anE. colicell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integratedin vivoandin vitroanalysis provides evidence that MatP can interact with lipid membranes reproducing the phospholipid mixture in theE. coliinner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.

Download Full-text