Elucidating the Role of Electrostatics in Condensed DNA Arrays

ABSTRACT The availability of the complete sequence of the Bacillus subtilis chromosome (F. Kunst et al., Nature 390:249–256, 1997) makes possible the construction of genome-wide DNA arrays and the study of this organism on a global scale. Because we have a long-standing interest in the effects of scoC on late-stage developmental phenomena as they relate toaprE expression, we studied the genome-wide effects of ascoC null mutant with the goal of furthering the understanding of the role of scoC in growth and developmental processes. In the present work we compared the expression patterns of isogenic B. subtilis strains, one of which carries a null mutation in the scoC locus (scoC4). The results obtained indicate thatscoC regulates, either directly or indirectly, the expression of at least 560 genes in the B. subtilisgenome. ScoC appeared to repress as well as activate gene expression. Changes in expression were observed in genes encoding transport and binding proteins, those involved in amino acid, carbohydrate, and nucleotide and/or nucleoside metabolism, and those associated with motility, sporulation, and adaptation to atypical conditions. Changes in gene expression were also observed for transcriptional regulators, along with sigma factors, regulatory phosphatases and kinases, and members of sensor regulator systems. In this report, we discuss some of the phenotypes associated with the scoCmutant in light of the transcriptome changes observed.

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Transcript analysis reveals an extended regulon and the importance of protein–protein co-operativity for the Escherichia coli methionine repressor

Biochemical Journal ◽

10.1042/bj20060021 ◽

2006 ◽

Vol 396 (2) ◽

pp. 227-234 ◽

Cited By ~ 31

Author(s):

Ferenc Marincs ◽

Iain W. Manfield ◽

Jonathan A. Stead ◽

Kenneth J. Mcdowall ◽

Peter G. Stockley

Keyword(s):

Escherichia Coli ◽

Gene Replacement ◽

Dna Arrays ◽

Promoter Regions ◽

Mobility Shift ◽

Metabolic Role ◽

Mobility Shift Assay

We have used DNA arrays to investigate the effects of knocking out the methionine repressor gene, metJ, on the Escherichia coli transcriptome. We assayed the effects in the knockout strain of supplying wild-type or mutant MetJ repressors from an expression plasmid, thus establishing a rapid assay for in vivo effects of mutations characterized previously in vitro. Repression is largely restricted to known genes involved in the biosynthesis and uptake of methionine. However, we identified a number of additional genes that are significantly up-regulated in the absence of repressor. Sequence analysis of the 5′ promoter regions of these genes identified plausible matches to met-box sequences for three of these, and subsequent electrophoretic mobility-shift assay analysis showed that for two such loci their repressor affinity is higher than or comparable with the known metB operator, suggesting that they are directly regulated. This can be rationalized for one of the loci, folE, by the metabolic role of its encoded enzyme; however, the links to the other regulated loci are unclear, suggesting both an extension to the known met regulon and additional complexity to the role of the repressor. The plasmid gene replacement system has been used to examine the importance of protein–protein co-operativity in operator saturation using the structurally characterized mutant repressor, Q44K. In vivo, there are detectable reductions in the levels of regulation observed, demonstrating the importance of balancing protein–protein and protein–DNA affinity.

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Role of Histone-Like Proteins H-NS and StpA in Expression of Virulence Determinants of Uropathogenic Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.01956-05 ◽

2006 ◽

Vol 188 (15) ◽

pp. 5428-5438 ◽

Cited By ~ 78

Author(s):

Claudia M. Müller ◽

Ulrich Dobrindt ◽

Gábor Nagy ◽

Levente Emödy ◽

Bernt Eric Uhlin ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Gene Expression Pattern ◽

Direct Interaction ◽

Virulence Determinants ◽

Dna Arrays ◽

Infectious Dose ◽

E Coli ◽

Huge Impact

ABSTRACT The histone-like protein H-NS is a global regulator in Escherichia coli that has been intensively studied in nonpathogenic strains. However, no comprehensive study on the role of H-NS and its paralogue, StpA, in gene expression in pathogenic E. coli has been carried out so far. Here, we monitored the global effects of H-NS and StpA in a uropathogenic E. coli isolate by using DNA arrays. Expression profiling revealed that more than 500 genes were affected by an hns mutation, whereas no effect of StpA alone was observed. An hns stpA double mutant showed a distinct gene expression pattern that differed in large part from that of the hns single mutant. This suggests a direct interaction between the two paralogues and the existence of distinct regulons of H-NS and an H-NS/StpA heteromeric complex. hns mutation resulted in increased expression of alpha-hemolysin, fimbriae, and iron uptake systems as well as genes involved in stress adaptation. Furthermore, several other putative virulence genes were found to be part of the H-NS regulon. Although the lack of H-NS, either alone or in combination with StpA, has a huge impact on gene expression in pathogenic E. coli strains, its effect on virulence is ambiguous. At a high infection dose, hns mutants trigger more sudden lethality due to their increased acute toxicity in murine urinary tract infection and sepsis models. At a lower infectious dose, however, mutants lacking H-NS are attenuated through their impaired growth rate, which can only partially be compensated for by the higher expression of numerous virulence factors.

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Ion Competition in Condensed DNA Arrays in the Attractive Regime

Biophysical Journal ◽

10.1016/j.bpj.2013.07.004 ◽

2013 ◽

Vol 105 (4) ◽

pp. 984-992 ◽

Cited By ~ 16

Author(s):

Xiangyun Qiu ◽

John Giannini ◽

Steven C. Howell ◽

Qi Xia ◽

Fuyou Ke ◽

...

Keyword(s):

Dna Arrays ◽

Ion Competition ◽

Condensed Dna

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Role of Amino Acid Insertions on Intermolecular Forces Between Arginine Peptide Condensed DNA Helices: Implications for Protamine-DNA Packaging in Sperm

Biophysical Journal ◽

10.1016/j.bpj.2011.11.437 ◽

2012 ◽

Vol 102 (3) ◽

pp. 75a

Author(s):

Jason E. DeRouchey ◽

Donald Rau

Keyword(s):

Amino Acid ◽

Intermolecular Forces ◽

Dna Packaging ◽

Condensed Dna

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The Role of Neutrophil Extracellular Traps in Cancer

Frontiers in Oncology ◽

10.3389/fonc.2021.714357 ◽

2021 ◽

Vol 11 ◽

Author(s):

Bo-Zong Shao ◽

Yi Yao ◽

Jin-Ping Li ◽

Ning-Li Chai ◽

En-Qiang Linghu

Keyword(s):

Malignant Tumors ◽

Current Knowledge ◽

Neutrophil Extracellular Traps ◽

Innate And Adaptive Immunity ◽

Extracellular Traps ◽

Pathological Conditions ◽

Microbial Infections ◽

Dna Strands ◽

Condensed Dna

Neutrophils are vital components of innate and adaptive immunity. It is widely acknowledged that in various pathological conditions, neutrophils are activated and release condensed DNA strands, triggering the formation of neutrophil extracellular traps (NETs). NETs have been shown to be effective in fighting against microbial infections and modulating the pathogenesis and progression of diseases, including malignant tumors. This review describes the current knowledge on the biological characteristics of NETs. Additionally, the mechanisms of NETs in cancer are discussed, including the involvement of signaling pathways and the crosstalk between other cancer-related mechanisms, including inflammasomes and autophagy. Finally, based on previous and current studies, the roles of NET formation and the potential therapeutic targets and strategies related to NETs in several well-studied types of cancers, including breast, lung, colorectal, pancreatic, blood, neurological, and cutaneous cancers, are separately reviewed and discussed.

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Genomic Applications for Transfusion Support

Blood ◽

10.1182/blood.v128.22.sci-23.sci-23 ◽

2016 ◽

Vol 128 (22) ◽

pp. SCI-23-SCI-23

Author(s):

Stella Chou

Keyword(s):

Conflicts Of Interest ◽

Blood Group Antigens ◽

Dna Arrays ◽

Transfusion Therapy ◽

The Past ◽

Whole Exome ◽

Platelet Antigen ◽

Antigen Determination ◽

Highly Correlated

Abstract Red blood cell (RBC) and platelet antigen determination by DNA methods (genotyping) has become an important part of the practice of transfusion medicine over the past decade.The results are reliable and highly correlated with serologic phenotyping results, and are superior in some situations. Application of RBC genotyping to provide more precise transfusion therapy for various patient populations will be discussed, with a particular emphasis on those requiring chronic RBC therapy or with complex serologic reactivity. Current DNA arrays can test for a large number of blood group antigens, but routine typing of the ABO and Rh systems is not currently feasible due to the large number of genetic mutations. Patients with sickle cell disease (SCD) are one of the most challenging populations to safely transfuse, in part due to high rates of alloimmunization against Rh antigens despite prophylactic matching for D, C, and E antigens. Genotyping of the RH loci has revealed that RHD and RHCE variants are prevalent in African Blacks. Nearly 90% of patients with SCD have at least one altered RH gene and contributes to Rh alloimmunization in patients with SCD. The role of RH variation and alloimmunization in SCD will be reviewed, and the feasibility and approach to genetic RBC matching of patients and donors will be discussed. The use of targeted DNA arrays, whole exome sequencing, or whole genome sequencing to identify common and variant RH alleles will be addressed, including limitations of each method. Disclosures No relevant conflicts of interest to declare.

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