scholarly journals Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA

2021 ◽  
Author(s):  
D. Czernecki ◽  
F. Bonhomme ◽  
P.A. Kaminski ◽  
M. Delarue
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Crystal Structures ◽  
Biophysical Properties ◽  
Bacterial Dna ◽  
E Coli ◽  
Synthetic Organisms ◽  
Conserved Gene

AbstractCyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in Siphoviridae phage genomes, and show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes – datZ, mazZ and purZ – was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.

scholarly journals Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dariusz Czernecki ◽  
Frédéric Bonhomme ◽  
Pierre-Alexandre Kaminski ◽  
Marc Delarue
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Biophysical Properties ◽  
Bacterial Dna ◽  
Related Phage ◽  
E Coli ◽  
Adenylosuccinate Synthetase ◽  
Synthetic Organisms ◽  
Conserved Gene

AbstractCyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes – datZ, mazZ and purZ – was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.

scholarly journals High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

2020 ◽  
Vol 76 (2) ◽  
pp. 94-102 ◽  
Author(s):  
Maria A. Schumacher ◽  
Tomoo Ohashi ◽  
Lauren Corbin ◽  
Harold P. Erickson
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Cell Division ◽  
High Resolution ◽  
Crystal Structures ◽  
Bacterial Cell ◽  
Model System ◽  
E Coli ◽  
Z Ring ◽  
Main Model

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

scholarly journals Water spines and networks in G-quadruplex structures

2020 ◽  
Author(s):  
Kevin Li ◽  
Liliya Yatsunyk ◽  
Stephen Neidle
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Water Molecule ◽  
Crystal Structures ◽  
Water Molecules ◽  
Nmr Structures ◽  
Loop Conformations ◽  
G Quadruplex ◽  
Guanine Base ◽  
Loop Regions

Abstract Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.

scholarly journals Ndd, the Bacteriophage T4 Protein That Disrupts theEscherichia coli Nucleoid, Has a DNA Binding Activity

1998 ◽  
Vol 180 (19) ◽  
pp. 5227-5230 ◽  
Author(s):  
Jean-Yves Bouet ◽  
Henry M. Krisch ◽  
Jean-Michel Louarn
Keyword(s):  
Dna Binding ◽  
Bacteriophage T4 ◽  
Binding Activity ◽  
Bacterial Dna ◽  
E Coli ◽  
Dna Binding Activity ◽  
Double Stranded Dna ◽  
Rapid Destruction ◽  
Chromosomal Sequences

ABSTRACT Early in a bacteriophage T4 infection, the phage nddgene causes the rapid destruction of the structure of theEscherichia coli nucleoid. Even at very low levels, the Ndd protein is extremely toxic to cells. In uninfected E. coli, overexpression of the cloned ndd gene induces disruption of the nucleoid that is indistinguishable from that observed after T4 infection. A preliminary characterization of this protein indicates that it has a double-stranded DNA binding activity with a preference for bacterial DNA rather than phage T4 DNA. The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid.

scholarly journals High-resolution crystal structures of the solubilized domain of porcine cytochromeb5

2015 ◽  
Vol 71 (7) ◽  
pp. 1572-1581 ◽  
Author(s):  
Yu Hirano ◽  
Shigenobu Kimura ◽  
Taro Tamada
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
High Resolution ◽  
Crystal Structures ◽  
Axial Ligand ◽  
Amino Acid Residues ◽  
Hydrogen Bond Network ◽  
Porcine Liver ◽  
Crystal Forms ◽  
Bond Network

Mammalian microsomal cytochromeb5has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochromeb5from porcine liver were determined at sub-angstrom resolution (0.76–0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

High-resolution electron microscopy of nanostructured materials

1995 ◽  
Vol 53 ◽  
pp. 172-173
Author(s):  
M. José-Yacamán
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Grain Boundaries ◽  
Nanostructured Materials ◽  
High Resolution Electron Microscopy ◽  
Hrem Image ◽  
Small Particles ◽  
Resolution Electron ◽  
Nanophase Materials

Electron microscopy is a fundamental tool in materials characterization. In the case of nanostructured materials we are looking for features with a size in the nanometer range. Therefore often the conventional TEM techniques are not enough for characterization of nanophases. High Resolution Electron Microscopy (HREM), is a key technique in order to characterize those materials with a resolution of ~ 1.7A. High resolution studies of metallic nanostructured materials has been also reported in the literature. It is concluded that boundaries in nanophase materials are similar in structure to the regular grain boundaries. That work therefore did not confirm the early hipothesis on the field that grain boundaries in nanostructured materials have a special behavior. We will show in this paper that by a combination of HREM image processing, and image calculations, it is possible to prove that small particles and coalesced grains have a significant surface roughness, as well as large internal strain.

High-resolution transmission electron microscopic study of highly oxygen doped silicon layer

1989 ◽  
Vol 47 ◽  
pp. 692-693
Author(s):  
H. Takaoka ◽  
M. Tomita ◽  
T. Hayashi
Keyword(s):  
High Resolution ◽  
Oxygen Concentration ◽  
Silicon Layer ◽  
Detailed Structure ◽  
Electron Microscopic ◽  
Cross Sectional ◽  
Transmission Electron ◽  
Doped Silicon ◽  
Argon Ion

High resolution transmission electron microscopy (HRTEM) is the effective technique for characterization of detailed structure of semiconductor materials. Oxygen is one of the important impurities in semiconductors. Detailed structure of highly oxygen doped silicon has not clearly investigated yet. This report describes detailed structure of highly oxygen doped silicon observed by HRTEM. Both samples prepared by Molecular beam epitaxy (MBE) and ion implantation were observed to investigate effects of oxygen concentration and doping methods to the crystal structure.The observed oxygen doped samples were prepared by MBE method in oxygen environment on (111) substrates. Oxygen concentration was about 1021 atoms/cm3. Another sample was silicon of (100) orientation implanted with oxygen ions at an energy of 180 keV. Oxygen concentration of this sample was about 1020 atoms/cm3 Cross-sectional specimens of (011) orientation were prepared by argon ion thinning and were observed by TEM at an accelerating voltage of 400 kV.

HRTEM simulation of interfacial structure in amorphous multilayers

1989 ◽  
Vol 47 ◽  
pp. 466-467
Author(s):  
Margaret L. Sattler ◽  
Michael A. O'Keefe
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Cross Section ◽  
High Resolution Electron Microscopy ◽  
Interfacial Structure ◽  
Multilayer Sample ◽  
Resolution Electron ◽  
Multilayered Materials ◽  
Simulated Images

Multilayered materials have been fabricated with such high perfection that individual layers having two atoms deep are possible. Characterization of the interfaces between these multilayers is achieved by high resolution electron microscopy and Figure 1a shows the cross-section of one type of multilayer. The production of such an image with atomically smooth interfaces depends upon certain factors which are not always reliable. For example, diffusion at the interface may produce complex interlayers which are important to the properties of the multilayers but which are difficult to observe. Similarly, anomalous conditions of imaging or of fabrication may occur which produce images having similar traits as the diffusion case above, e.g., imaging on a tilted/bent multilayer sample (Figure 1b) or deposition upon an unaligned substrate (Figure 1c). It is the purpose of this study to simulate the image of the perfect multilayer interface and to compare with simulated images having these anomalies.

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