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 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 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.

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.

Rapid, Refined, and Robust Method for Expression, Purification, and Characterization of Recombinant Human Amyloid-beta M1-42

2019 ◽  
Author(s):  
Priya Prakash ◽  
Travis Lantz ◽  
Krupal P. Jethava ◽  
Gaurav Chopra
Keyword(s):  
Amyloid Beta ◽  
Western Blots ◽  
Force Microscopy ◽  
E Coli ◽  
Atomic Force ◽  
Set Up ◽  
Short Time

Amyloid plaques found in the brains of Alzheimer’s disease (AD) patients primarily consists of amyloid beta 1-42 (Ab42). Commercially, Ab42 is synthetized using peptide synthesizers. We describe a robust methodology for expression of recombinant human Ab(M1-42) in Rosetta(DE3)pLysS and BL21(DE3)pLysS competent E. coli with refined and rapid analytical purification techniques. The peptide is isolated and purified from the transformed cells using an optimized set-up for reverse-phase HPLC protocol, using commonly available C18 columns, yielding high amounts of peptide (~15-20 mg per 1 L culture) in a short time. The recombinant Ab(M1-42) forms characteristic aggregates similar to synthetic Ab42 aggregates as verified by western blots and atomic force microscopy to warrant future biological use. Our rapid, refined, and robust technique to purify human Ab(M1-42) can be used to synthesize chemical probes for several downstream in vitro and in vivo assays to facilitate AD research.

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