scholarly journals New Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2018 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Histone H1 ◽  
Dna Supercoiling ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Genetic Events ◽  
Current Report ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes, (2) well-established axioms about sign, shapes and handedness of DNA supercoils, as well as (3) the fact that alterations of DNA supercoils are affiliated with every single steps of cellular genetic events, we analyze effects of DNA supercoils on eukaryotic chromosomal structures in systematical and comprehensive manners in the current report, and present new theory and models of eukaryotic chromosomal structures from the DNA supercoiling perspective. It is our hope that our current presentation of new supercoiling theory and models could provoke future new efforts to unravel exquisite eukaryotic chromosomal architectures in an all-inclusive manner.

scholarly journals Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2019 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Histone H1 ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Negative Supercoils ◽  
Current Report ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated physical driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes, (2) well-accepted six axioms about signs, shapes and handedness of DNA supercoils, and (3) our three new prepositions about correlations between DNA supercoils and chromosomal structures, we formulate new theories and models of eukaryotic chromosomal structures in the current report. It is our conclusion that all levels of chromosomal structures in eukaryotic cells are governed mainly by negative supercoils that are present in their naked linker DNA regions.

scholarly journals Supercoiling Theory and Model of Chromosomal Structures in Eukaryotic Cells

2018 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Driving Forces ◽  
Three Dimensional ◽  
Histone H1 ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Negative Supercoils ◽  
Theory And Model

About six billion base pairs of DNA reside highly orderly in each human cell’s nucleus through their manifestation as twenty-three pairs of chromosomes. Delicate patterns of spatial organizations of DNA macromolecules in these eukaryotic chromosomes as well as their associated physical driving forces have, however, not been fully understood thus far. On the basis of (1) our four recent discoveries about supercoiling properties of histone H1, nucleosomes, linker DNA and polynucleosomes and (2) well-established axioms about signs, shapes and handedness of DNA supercoils, we formulate new theories and models of eukaryotic chromosomal structures. It is our conclusion that three-dimensional structures of eukaryotic chromosomes and their sublevel architectures are govern mainly by negative supercoils that are present in their naked linker DNA regions.

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

scholarly journals Supercoiling DNA locates mismatches

2017 ◽  
Author(s):  
Andrew Dittmore ◽  
Sumitabha Brahmachari ◽  
Yasuhara Takagi ◽  
John F. Marko ◽  
Keir C. Neuman
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Dna Supercoiling ◽  
Magnetic Tweezers ◽  
Relative Probability ◽  
Base Pairs ◽  
Damage Sensing ◽  
Mismatched Base Pair ◽  
Monovalent Salt

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

scholarly journals Regulation of the higher-order structure of chromatin by histones H1 and H5.

1981 ◽  
Vol 90 (2) ◽  
pp. 279-288 ◽  
Author(s):  
J Allan ◽  
G J Cowling ◽  
N Harborne ◽  
P Cattini ◽  
R Craigie ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Single Species ◽  
Histone H1 ◽  
Higher Order ◽  
Linker Histone ◽  
Micrococcal Nuclease ◽  
Order Structure ◽  
Chicken Erythrocyte ◽  
Base Pairs ◽  
Native Chicken

Chicken erythrocyte chromatins containing a single species of linker histone, H1 or H5, have been prepared, using reassembly techniques developed previously. The reconstituted complexes possess the conformation of native chicken erythrocyte chromatin, as judged by chemical and structural criteria; saturation is reached when two molecules of linker histone are bound per nucleosome, as in native erythrocyte chromatin, which the resulting material resembles in its appearance in the electron microscope and quantitatively in its linear condensation factor relative to free DNA. The periodicity of micrococcal nuclease-sensitive sites in the linker regions associated with histone H1 or H5 is 10.4 base pairs, suggesting that the spatial organization of the linker region in the higher-order structure of chromatin is similar to that in isolated nucleosomes. The susceptible sites are cut at differing frequencies, as previously found for the nucleosome cores, leading to a characteristic distribution of intensities in the digests. The scission frequency of sites in the linker DNA depends additionally on the identity of the linker histone, suggesting that the higher-order structure is subject to secondary modulation by the associated histones.

scholarly journals Mechanotransduction in Prokaryotes: A Possible Mechanism of Spaceflight Adaptation

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Patricia Fajardo-Cavazos ◽  
Wayne L. Nicholson
Keyword(s):  
Gene Expression ◽  
Mechanical Stress ◽  
Dna Supercoiling ◽  
Eukaryotic Cells ◽  
Current Evidence ◽  
Mechanical Signals ◽  
Bacterial Nucleoid ◽  
Sense And Respond ◽  
Eukaryotic Organisms ◽  
Review Current

Our understanding of the mechanisms of microgravity perception and response in prokaryotes (Bacteria and Archaea) lag behind those which have been elucidated in eukaryotic organisms. In this hypothesis paper, we: (i) review how eukaryotic cells sense and respond to microgravity using various pathways responsive to unloading of mechanical stress; (ii) we observe that prokaryotic cells possess many structures analogous to mechanosensitive structures in eukaryotes; (iii) we review current evidence indicating that prokaryotes also possess active mechanosensing and mechanotransduction mechanisms; and (iv) we propose a complete mechanotransduction model including mechanisms by which mechanical signals may be transduced to the gene expression apparatus through alterations in bacterial nucleoid architecture, DNA supercoiling, and epigenetic pathways.

scholarly journals Interaction of the Escherichia coli HU Protein with Various Topological Forms of DNA

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1724
Author(s):  
Li Huang ◽  
Zhenfeng Zhang ◽  
Roger McMacken
Keyword(s):  
Dna Supercoiling ◽  
Cellular Level ◽  
Base Pairs ◽  
Supercoiled Dna ◽  
Linear Dna ◽  
Hu Protein ◽  
Binding Preference ◽  
Mass Ratios ◽  
Superhelical Density

E. coli histone-like protein HU has been shown to interact with different topological forms of DNA. Using radiolabeled HU, we examine the effects of DNA supercoiling on HU–DNA interactions. We show that HU binds preferentially to negatively supercoiled DNA and that the affinity of HU for DNA increases with increases in the negative superhelical density of DNA. Binding of HU to DNA is most sensitively influenced by DNA supercoiling within a narrow but physiologically relevant range of superhelicity (σ = −0.06–0). Under stoichiometric binding conditions, the affinity of HU for negatively supercoiled DNA (σ = −0.06) is more than 10 times higher than that for relaxed DNA at physiologically relevant HU/DNA mass ratios (e.g., 1:10). This binding preference, however, becomes negligible at HU/DNA mass ratios higher than 1:2. At saturation, HU binds both negatively supercoiled and relaxed DNA with similar stoichiometries, i.e., 5–6 base pairs per HU dimer. In our chemical crosslinking studies, we demonstrate that HU molecules bound to negatively supercoiled DNA are more readily crosslinked than those bound to linear DNA. At in vivo HU/DNA ratios, HU appears to exist predominantly in a tetrameric form on negatively supercoiled DNA and in a dimeric form on linear DNA. Using a DNA ligase-mediated nick closure assay, we show that approximately 20 HU dimers are required to constrain one negative supercoil on relaxed DNA. Although fewer HU dimers may be needed to constrain one negative supercoil on negatively supercoiled DNA, our results and estimates of the cellular level of HU argue against a major role for HU in constraining supercoils in vivo. We discuss our data within the context of the dynamic distribution of the HU protein in cells, where temporal and local changes of DNA supercoiling are known to take place.

scholarly journals Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches

2019 ◽  
Author(s):  
Parth Rakesh Desai ◽  
Sumitabha Brahmachari ◽  
John F. Marko ◽  
Siddhartha Das ◽  
Keir C. Neuman
Keyword(s):  
Salt Concentration ◽  
Mechanical Response ◽  
Dna Supercoiling ◽  
Coarse Grained ◽  
Base Pairs ◽  
Mismatched Dna ◽  
Double Stranded Dna ◽  
Theoretical Predictions ◽  
Statistical Mechanical

ABSTRACTDamaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (> 2 pN) and high salt concentration (> 0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.

scholarly journals Mechanistic Analyses of Supercoiling Behaviors of DNA in Nucleosomes and Chromatins

2019 ◽  
Author(s):  
Hao Zhang ◽  
Tianhu Li
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Histone H1 ◽  
Molecular Pathways ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core ◽  
Histone Octamers ◽  
Dynamic Structures ◽  
Current Report

AbstractBesides those in 146-base pair nucleosome core particle DNA, supercoils have been known to be present in 10-base pair arm DNA segments and naked linker DNA segments. The interacting patterns among histone octamers, histone H1, 10-base pair arm DNA segments and linker DNA have, however, not yet been elucidated. In the current report, we examine correlations among constituents of nucleosomes from the mechanistic perspectives and present molecular pathways for elucidating supercoiling behaviors of their component DNA sequences. It is our hope that our new analyses could serve as incentives to further clarify correlations between histones and DNA in the dynamic structures of chromatins in the future.

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