Escherichia colicAMP Receptor Protein−DNA Complexes. 1. Energetic Contributions of Half-Sites and Flanking Sequences in DNA Recognition†

Biochemistry ◽  
1998 ◽  
Vol 37 (15) ◽  
pp. 5194-5200 ◽  
Author(s):  
Erica A. Pyles ◽  
Anita J. Chin ◽  
J. Ching Lee
Keyword(s):  
Dna Recognition ◽  
Receptor Protein ◽  
Dna Complexes ◽  
Flanking Sequences

scholarly journals Structural basis for DNA recognition by the transcription regulator MetR

2016 ◽  
Vol 72 (6) ◽  
pp. 417-426 ◽  
Author(s):  
Avinash S. Punekar ◽  
Jonathan Porter ◽  
Stephen B. Carr ◽  
Simon E. V. Phillips
Keyword(s):  
Molecular Level ◽  
Dna Recognition ◽  
Data Driven ◽  
Structural Basis ◽  
Methionine Biosynthesis ◽  
Dna Complexes ◽  
Winged Helix ◽  
Target Dna ◽  
Operator Sequence ◽  
Dna Complex

MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of themetgenes and specifically recognizes the interrupted palindromic sequence 5′-TGAA-N5-TTCA-3′. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix–turn–helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD–DNA complex with the crystal structures of other LTTR-DBD–DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription ofmetgenes.

Linkage of Multiequilibria in DNA Recognition by the D53HEscherichia colicAMP Receptor Protein†

Biochemistry ◽  
2002 ◽  
Vol 41 (50) ◽  
pp. 14935-14943 ◽  
Author(s):  
Shwu-Hwa Lin ◽  
J. Ching. Lee
Keyword(s):  
Dna Recognition ◽  
Receptor Protein

Toward an Understanding of the Drug−DNA Recognition Mechanism. Hydrogen-Bond Strength in Netropsin−DNA Complexes

1996 ◽  
Vol 100 (27) ◽  
pp. 11480-11487 ◽  
Author(s):  
Carlos Alemán ◽  
M. Cristina Vega ◽  
Lydia Tabernero ◽  
Jordi Bella
Keyword(s):  
Hydrogen Bond ◽  
Bond Strength ◽  
Dna Recognition ◽  
Dna Complexes ◽  
Recognition Mechanism ◽  
Hydrogen Bond Strength ◽  
Dna Recognition Mechanism

scholarly journals Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xue Huang ◽  
Wei Sun ◽  
Zhi Cheng ◽  
Minxuan Chen ◽  
Xueyan Li ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Dna Recognition ◽  
Structural Basis ◽  
Seed Region ◽  
Dna Complexes ◽  
Metal Ion Catalysis ◽  
Type V ◽  
Cas Proteins

Abstract To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we report structures of Cas12i2–crRNA–DNA complexes and a Cas12i2–crRNA complex. We reveal the mechanism of DNA recognition and cleavage by Cas12i2, and activation of the RuvC catalytic pocket induced by a conformational change of the Helical-II domain. The seed region (nucleotides 1–8) is dispensable for RuvC activation, but the duplex of the central spacer (nucleotides 9–15) is required. We captured the catalytic state of Cas12i2, with both metal ions and the ssDNA substrate bound in the RuvC catalytic pocket. Together, our studies provide significant insights into the DNA cleavage mechanism by RuvC-containing Cas proteins.

scholarly journals Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes

Structure ◽  
2006 ◽  
Vol 14 (3) ◽  
pp. 555-565 ◽  
Author(s):  
Jason S. Lamoureux ◽  
J.N. Mark Glover
Keyword(s):  
Structural Analysis ◽  
Dna Recognition ◽  
Dna Complexes

Interplay between Site-Specific Mutations and Cyclic Nucleotides in Modulating DNA Recognition byEscherichia coliCyclic AMP Receptor Protein†,‡

Biochemistry ◽  
2004 ◽  
Vol 43 (28) ◽  
pp. 8901-8910 ◽  
Author(s):  
Jiayin Dai ◽  
Shwu-Hwa Lin ◽  
Carly Kemmis ◽  
Anita J. Chin ◽  
J. Ching Lee
Keyword(s):  
Cyclic Nucleotides ◽  
Dna Recognition ◽  
Receptor Protein ◽  
Site Specific

scholarly journals Cellular Transcription Factors Enhance Herpes Simplex Virus Type 1 oriS-Dependent DNA Replication

1998 ◽  
Vol 72 (5) ◽  
pp. 3635-3645 ◽  
Author(s):  
Anh Tuan Nguyen-Huynh ◽  
Priscilla A. Schaffer
Keyword(s):  
Dna Replication ◽  
Binding Sites ◽  
Cellular Proteins ◽  
Consensus Binding Site ◽  
Mobility Shift ◽  
Dna Complexes ◽  
Flanking Sequences ◽  
Gel Mobility Shift ◽  
Simplex Virus

ABSTRACT The herpes simplex virus type 1 (HSV-1) origin of DNA replication, oriS, contains three binding sites for the viral origin binding protein (OBP) flanked by transcriptional regulatory elements of the immediate-early genes encoding ICP4 and ICP22/47. To assess the role of flanking sequences in oriS function, plasmids containing oriS and either wild-type or mutant flanking sequences were tested in transient DNA replication assays. Although the ICP4 and ICP22/47 regulatory regions were shown to enhance oriS function, most individual elements in these regions, including the VP16-responsive TAATGARAT elements, were found to be dispensable for oriS function. In contrast, two oriS core-adjacent regulatory (Oscar) elements, OscarL and OscarR, at the base of the oriS palindrome were shown to enhance oriS function significantly and additively. Specifically, mutational disruption of either element reduced oriS-dependent DNA replication by 60 to 70%, and disruption of both elements reduced replication by 90%. The properties of protein-DNA complexes formed in gel mobility shift assays using uninfected and HSV-1-infected Vero cell nuclear extracts demonstrated that both OscarL and OscarR are binding sites for cellular proteins. Whereas OscarR does not correspond to the consensus binding site of any known transcription factor, OscarL contains a consensus binding site for the transcription factor Sp1. Gel mobility shift and supershift experiments using antibodies directed against members of the Sp1 family of transcription factors demonstrated the presence of Sp1 and Sp3, but not Sp2 or Sp4, in the protein-DNA complexes formed at OscarL. The abilities of OscarL and OscarR to bind their respective cellular proteins correlated directly with the efficiency of oriS-dependent DNA replication. Cooperative interactions between the Oscar-binding factors and proteins binding to adjacent OBP binding sites were not observed. Notably, Oscar element mutations that impaired oriS-dependent DNA replication had no detectable effect on either basal or induced levels of transcription from the ICP4 and ICP22/47 promoters, as determined by RNase protection assays. The Oscar elements thus appear to provide binding sites for cellular proteins that facilitate oriS-dependent DNA replication but have no effect on transcription of oriS-flanking genes.

Escherichia colicAMP Receptor Protein−DNA Complexes. 2. Structural Asymmetry of DNA Bending†

Biochemistry ◽  
1998 ◽  
Vol 37 (15) ◽  
pp. 5201-5210 ◽  
Author(s):  
Erica A. Pyles ◽  
J. Ching Lee
Keyword(s):  
Dna Bending ◽  
Receptor Protein ◽  
Dna Complexes ◽  
Structural Asymmetry

scholarly journals The specificity of DNA recognition by the RAGE receptor

2014 ◽  
Vol 211 (5) ◽  
pp. 749-750 ◽  
Author(s):  
Laure Yatime ◽  
Gregers Rom Andersen
Keyword(s):  
Advanced Glycation End Products ◽  
Diffraction Data ◽  
Dna Recognition ◽  
Experimental Medicine ◽  
Immune Recognition ◽  
Toll Like Receptor ◽  
Advanced Glycation ◽  
Dna Complexes ◽  
Glycation End Products ◽  
End Products

A recent paper by Sirois et al. in The Journal of Experimental Medicine reports that the receptor for advanced glycation end-products (RAGE) promotes uptake of DNA into endosomes and lowers the immune recognition threshold for the activation of Toll-like receptor 9. Two crystal structures suggested that the DNA phosphate-deoxyribose backbone is recognized by RAGE through well-defined interactions. However, the electron densities for the DNA molecules are weak enough that the presented modeling of DNA is questionable, and models only containing RAGE account for the observed diffraction data just as well as the RAGE–DNA complexes presented by the authors.

Multiple Integration Events into Several Putative Oncogenes Was Required To Cause Leukemogenesis in Two Primate Recipients of RCR Contaminated Stem-Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2102-2102
Author(s):  
Martin A. Pule ◽  
Alexandra Rousseau ◽  
Elizabeth Kang ◽  
Takahiro Ueda ◽  
Christof von Kalle ◽  
...  
Keyword(s):  
Malignant Transformation ◽  
Expression Profile ◽  
Peripheral Blood ◽  
Insertional Mutagenesis ◽  
Integration Site ◽  
Retroviral Vectors ◽  
Receptor Protein ◽  
Thymic Tissue ◽  
Integration Sites ◽  
Flanking Sequences

Abstract Integrating vectors are essential for stem-cell and T cell gene-therapy approaches to enable passage of the transgene to subsequent progeny, and retroviral vectors have been the commonly utilized for clinical applications. However, insertional events can potentially cause malignant transformation of transduced cells. In 1991, adult rhesus macaques received CD34+ cells transduced with a NEO expressing retroviral vector which was inadvertently contaminated with ampho-pseudotyped replication competent retrovirus(RCR). Three primates (88053, 15445 and 88049) developed a rapidly progressive lymphoid neoplasm 6–7 months after transplantation characterized by diffuse lymphadenompathy, hepatosplenomegaly and a large thymic mass. Immunohistochemistry of the neoplasm revealed a CD8+ CD2+ alphabeta TCR+ phenotype strongly positive for RCR. The neoplasm was preceeded by increasing amphotropic envelope detectable in peripheral blood by PCR which was ultimately detectable in 100% of peripheral blood leukocytes. Tissue is available for study from primates 15445 and 88049. Genomic Southern blotting revealed multiple integrants, more in 15445 than in 88049. Using a simplified technique (FLEA-PCR) for generating libraries of Integrant-Host-Junctions (IHJ), we studied leukemia samples from these two (primates 15545 and 88049). So far we have characterized 52 different flanking sequences from primate 15545 of which we could match 43 genomic loci. We have isolated 39 different flanking sequences from primate 88049 of which we could match 29 genomic loci. Of the characterized integration sites from 15445 the following potential oncogenes could be affected: DKK3, CUTL1, RUNX1, RUNX3, TCF7L2, FOXP1, MTIF2, GAB1, CST7, CABIN1 and RHOH. Of the characterized integration sites from 88049 the following potential oncogenes could be affected: LY86, JARID2, TNIK(TRAF2 and NCK interacting kinase), SMT3H2, PTK2B, MSF, FBXL10 and RAPH1. Both primate leukemia samples contain an integration site just 5 to the gene for Neuronal acetylcholine receptor protein (CHRNA9). RNA derived from leukemic bone marrow from both animals and involved thymic tissue from one was subjected to microarray analysis and compared to that of control tissue using the Affymetrix human genome U133 plus 2 array. The gene expression profile was similar among diseased tissues, and efforts to correlate the expression profile with genes potentially dysregulated by integration events is ongoing. Together with some subjects of the recent X-SCID study, these macaques represent the only cases of leukemogenesis caused by vector induced insertional mutagenesis in primates. Our findings confirm the assumption that with an inert transgene (NEO, RCR), multiple integrations effecting different oncogenes are required to result in malignant transformation of transduced cells.

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