Free DNA Concentration in E. coli Estimated by an Analysis of Competition for DNA Binding Proteins

1994 ◽  
Vol 168 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Douglas F. Stickle ◽  
Karen M. Vossen ◽  
Daniel A. Riley ◽  
Michael G. Fried
Author(s):  
Leise Riber ◽  
Jakob Frimodt-Møller ◽  
Godefroid Charbon ◽  
Anders Løbner-Olesen

2016 ◽  
Vol 18 (16) ◽  
pp. 11184-11192 ◽  
Author(s):  
David Gomez ◽  
Stefan Klumpp

Recognition of specific DNA sequences by DNA-binding proteins (DBPs) takes place by a facilitated diffusion process that depends, among other parameters, on the DBP's sliding length on the DNA and the DNA concentration. In addition, facilitated diffusion is variously impaired by the presence of obstacles with different dynamics on the DNA.


1990 ◽  
Vol 23 (3) ◽  
pp. 205-280 ◽  
Author(s):  
Thomas A. Steitz

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, the E. coli catabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKay et al. 1982; Weber & Steitz, 1987), a cro repressor from phage λ (Anderson et al. 1981), and the DNA-binding proteolytic fragment of λcI repressor protein (Pabo & Lewis, 1982) Although crystallographic studies of the E. coli lac repressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitz et al. 1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure of λcro repressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP, λcro, λcI repressor fragment, 434 repressor fragment (Anderson et al. 1987), 434 cro repressor (Wolberger et al. 1988), E. coli trp repressor (Schevitz et al. 1985), E. coli met repressor (Rafferty et al. 1989)], EcoR I restriction endonuclease (McClarin et al. 1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfull et al. 1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment of E. coli DNA polymerase I (Ollis et al. 1985) and the E. coli Hu protein (Tanaka et al., 1984)].


FEBS Letters ◽  
1997 ◽  
Vol 411 (2-3) ◽  
pp. 313-316 ◽  
Author(s):  
Gordon Webster ◽  
Jochen Genschel ◽  
Ute Curth ◽  
Claus Urbanke ◽  
ChulHee Kang ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Szu-Ning Lin ◽  
Remus T. Dame ◽  
Gijs J. L. Wuite

AbstractArchitectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1107-1107
Author(s):  
Anna Kroeze ◽  
Anne Jan van der Meer ◽  
Arie J Hoogendijk ◽  
Aicha Ait Soussan ◽  
C. Ellen van der Schoot ◽  
...  

Abstract Cell-free DNA (cfDNA) and DNA binding proteins are released in the circulation upon systemic inflammation, the extent of which is proportional to the severity of the systemic inflammation. There is an ongoing debate on the cellular source of cfDNA during systemic inflammatory conditions. During infection, circulating histones and DNA in the form of nucleosomes have been argued to be released by activated neutrophils in the process of NETosis. However, cfDNA has also been attributed to the cell death of other cell types, such as lymphocytes and endothelial cells. The objective of the current study is to investigate the compartmental source of extracellular DNA released into the circulation during a systemic inflammatory response. We determined the plasma levels of nucleosomes as a measure of cfDNA and DNA binding proteins, and of elastase-α1-antitrypsin (EA) complexes as a measure of neutrophil activation in different systemic inflammatory responses. First, we induced a low-grade endotoxemia in eight healthy human subjects by injection of lipopolysaccharide (LPS). In these subjects, nucleosome levels increased to a maximum at 3 hours after LPS injection (mean 529 ± SE 112 AU/ml), after which they returned towards baseline levels. Interestingly, the release of EA showed similar kinetics as that of nucleosomes, reaching a maximal level of 499 ± 58 ng/ml at 3 hours. Furthermore, plasma EA levels positively correlated with nucleosome levels during LPS challenge (r=0,79; p<0.0001), suggesting that during a mild, transient inflammatory response, neutrophils are the predominant source of nucleosomes within the plasma. We next measured nucleosomes and neutrophil activation in twenty patients with severe systemic inflammation caused by sepsis. Surprisingly, sequential measurements in sepsis patients did not show a correlation between plasma EA levels and nucleosome levels (r=0,155; p=0,13), suggestive of a non-neutrophil source of cfDNA. Thus, there might be other potential cellular sources of cfDNA than neutrophils in a severe systemic inflammation. To further investigate the difference of cfDNA release between a mild and a severe systemic inflammation, we used chimeric mice transplanted with bone marrow of the opposite sex. After hematopoietic recovery, mice were challenged with LPS. We were able to follow up on the release of cfDNA from different compartmental sources, that is either the hematopoietic or the non-hematopoietic compartment, by using a specific mouse SRY qPCR as a measure for male DNA, and IL3 qPCR as a measure for total DNA. CfDNA from the hematopoietic compartment was present within the plasma of the mice at 6 and 20 hours after LPS challenge, whereas cfDNA from a parenchymal source could be detected at 20 hours but less at 6 hours after LPS challenge. This suggests that the hematopoietic compartment acts as a source of cfDNA both early and late after LPS challenge, whereas the parenchymal compartment only releases DNA at later stages of severe systemic inflammation. Collectively, our results show that in severe systemic inflammation, circulating cfDNA originates from both hematopoietic cells (e.g. neutrophils and lymphocytes) and parenchymal cells (e.g. endothelial cells). Understanding the kinetics of extracellular DNA may improve knowledge on duration and severity of sepsis and may provide a point of interference during systemic inflammation. Disclosures No relevant conflicts of interest to declare.


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