scholarly journals Kinetic Pathways of Topology Simplification by Type-II Topoisomerases in Knotted Supercoiled DNA

2018 ◽  
Author(s):  
Riccardo Ziraldo ◽  
Andreas Hanke ◽  
Stephen D. Levene
Keyword(s):  
Atp Hydrolysis ◽  
Probability Distributions ◽  
Bacterial Cells ◽  
Type Ii ◽  
Dna Molecules ◽  
Equilibrium Dynamics ◽  
Topological States ◽  
Topological State ◽  
Strand Passage ◽  
Topology Simplification

ABSTRACTThe topological state of covalently closed, double-stranded DNA is defined by the knot type K and the linking-number difference ΔLk relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both K and ΔLk by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a puzzle how small enzymes are able to preferentially select strand passages that result in topology simplification in much larger DNA molecules. Using numerical simulations, we consider the non-equilibrium dynamics of transitions between topological states (K, ΔLk) in DNA induced by type-II topoisomerases. For a biological process that delivers DNA molecules in a given topological state (K,ΔLk) at a constant rate we fully characterize the pathways of topology simplification by type-II topoisomerases in terms of stationary probability distributions and probability currents on the network of topological states (K,ΔLk). In particular, we observe that type-II topoisomerase activity is significantly enhanced in DNA molecules that maintain a supercoiled state with constant torsional tension. This is relevant for bacterial cells in which torsional tension is maintained by enzyme-dependent homeostatic mechanisms such as DNA-gyrase activity.

scholarly journals DNA-Topology Simplification by Topoisomerases

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3375
Author(s):  
Andreas Hanke ◽  
Riccardo Ziraldo ◽  
Stephen D. Levene
Keyword(s):  
Dna Sequences ◽  
Atp Hydrolysis ◽  
Dna Topology ◽  
Type Ii ◽  
Independent Manner ◽  
Sequence Recognition ◽  
Dna Strands ◽  
Topological States ◽  
Topology Simplification ◽  
Non Equilibrium

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.

The role of ATP in the reactions of type II DNA topoisomerases

2010 ◽  
Vol 38 (2) ◽  
pp. 438-442 ◽  
Author(s):  
Andrew D. Bates ◽  
Anthony Maxwell
Keyword(s):  
Atp Hydrolysis ◽  
Dna Gyrase ◽  
Dna Topology ◽  
Type Ii ◽  
Free Energies ◽  
Dna Topoisomerases ◽  
Type Ii Dna Topoisomerases ◽  
Topology Simplification ◽  
Hydrolysis Of

Type II DNA topoisomerases catalyse changes in DNA topology in reactions coupled to the hydrolysis of ATP. In the case of DNA gyrase, which can introduce supercoils into DNA, the requirement for free energy is clear. However, the non-supercoiling type II enzymes carry out reactions that are apparently energetically favourable, so their requirement for ATP hydrolysis is not so obvious. It has been shown that many of these enzymes (the type IIA family) can simplify the topology of their DNA substrates to a level beyond that expected at equilibrium. Although this seems to explain their usage of ATP, we show that the free energies involved in topology simplification are very small (<0.2% of that available from ATP) and we argue that topology simplification may simply be an evolutionary relic.

Realizing topological states in type-II Dirac semimetal PdTe2: an angle-resolved photoemission and quantum oscillations study

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Jadupati Nag ◽  
Anshu Kataria ◽  
Ravi Prakash Singh ◽  
Soma Banik ◽  
Aftab Alam ◽  
...  
Keyword(s):  
Type Ii ◽  
Quantum Oscillations ◽  
Dirac Semimetal ◽  
Topological States

scholarly journals IMMUNOLOGICAL PROPERTIES OF A TYPICAL (S-PRODUCING) AND A DEGRADED (NON-S-PRODUCING) STRAIN OF TYPE II PNEUMOCOCCUS WITH SPECIAL REFERENCE TO PROTECTIVE ANTIBODIES

1927 ◽  
Vol 46 (1) ◽  
pp. 101-111 ◽  
Author(s):  
Emidio L. Gaspari ◽  
William L. Fleming ◽  
James M. Neill
Keyword(s):  
Special Reference ◽  
Bacterial Cells ◽  
Type Ii ◽  
Passive Protection ◽  
Specific Antibodies ◽  
Immunological Properties ◽  
Antigenic Properties ◽  
Protective Antibodies ◽  
Specialized Function

The loss of the specialized function of S production by Type II pneumococcus was accompanied by a loss of the antigenic properties involved in both active and passive protection of mice. Absorption of Type II serum with S-producing pneumococci removed all the protective antibodies, as well as the type-specific agglutinins and S precipitins. The same absorption treatment of the serum by non-S-producing pneumococci failed entirely to remove the type-specific antibodies and did not affect the protective value of the serum. Absorption with bacteria-free culture fluids containing the reactive carbohydrate removed the protective antibodies as completely as absorption with the whole bacterial cells of type-specific strains. The results taken as a whole indicate that the antibodies involved in the usual protection of mice against Type II pneumococci are closely related, if not identical, to the specific anticarbohydrate precipitin.

Learning the ABCs one at a time: structure and mechanism of ABC transporters

2019 ◽  
Vol 47 (1) ◽  
pp. 23-36 ◽  
Author(s):  
Robert C. Ford ◽  
Konstantinos Beis
Keyword(s):  
Abc Transporters ◽  
Atp Hydrolysis ◽  
Atp Binding ◽  
Bacterial Cells ◽  
The Novel ◽  
Mechanism Model ◽  
Binding Domains ◽  
Atp Binding And Hydrolysis ◽  
Alternating Access

Abstract ATP-binding cassette (ABC) transporters are essential proteins that are found across all kingdoms of life. ABC transporters harness the energy of ATP hydrolysis to drive the import of nutrients inside bacterial cells or the export of toxic compounds or essential lipids across bacteria and eukaryotic membranes. Typically, ABC transporters consist of transmembrane domains (TMDs) and nucleotide-binding domains (NBDs) to bind their substrate and ATP, respectively. The TMDs dictate what ligands can be recognised, whereas the NBDs are the power engine of the ABC transporter, carrying out ATP binding and hydrolysis. It has been proposed that they utilise the alternating access mechanism, inward- to outward-facing conformation, to transport their substrates. Here, we will review the recent progress on the structure determination of eukaryotic and bacterial ABC transporters as well as the novel mechanisms that have also been proposed, that fall out of the alternating access mechanism model.

scholarly journals Analysis of the Interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 Complexes with DNA Using a Reversible DNA End-blocking System

2005 ◽  
Vol 280 (23) ◽  
pp. 22245-22257 ◽  
Author(s):  
Marc L. Mendillo ◽  
Dan J. Mazur ◽  
Richard D. Kolodner
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Atp Hydrolysis ◽  
Ternary Complexes ◽  
Lac Repressor ◽  
Dna Molecules ◽  
Direct Dissociation ◽  
Total Internal Reflectance ◽  
Dna Ends ◽  
Internal Reflectance ◽  
Operator Interaction

The Lac repressor-operator interaction was used as a reversible DNA end-blocking system in conjunction with an IAsys biosensor instrument (Thermo Affinity Sensors), which detects total internal reflectance and allows monitoring of binding and dissociation in real time, in order to develop a system for studying the ability of mismatch repair proteins to move along the DNA. The MSH2-MSH6 complex bound to a mispaired base was found to be converted by ATP binding to a form that showed rapid sliding along the DNA and dissociation via the DNA ends and also showed slow, direct dissociation from the DNA. In contrast, the MSH2-MSH6 complex bound to a base pair containing DNA only showed direct dissociation from the DNA. The MLH1-PMS1 complex formed both mispair-dependent and mispair-independent ternary complexes with the MSH2-MSH6 complex on DNA. The mispair-independent ternary complexes were formed most efficiently on DNA molecules with free ends under conditions where ATP hydrolysis did not occur, and only exhibited direct dissociation from the DNA. The mispair-dependent ternary complexes were formed in the highest yield on DNA molecules with blocked ends, required ATP and magnesium for formation, and showed both dissociation via the DNA ends and direct dissociation from the DNA.

scholarly journals Mechanism of topology simplification by type II DNA topoisomerases

2001 ◽  
Vol 98 (6) ◽  
pp. 3045-3049 ◽  
Author(s):  
A. V. Vologodskii ◽  
W. Zhang ◽  
V. V. Rybenkov ◽  
A. A. Podtelezhnikov ◽  
D. Subramanian ◽  
...  
Keyword(s):  
Type Ii ◽  
Dna Topoisomerases ◽  
Type Ii Dna Topoisomerases ◽  
Topology Simplification

scholarly journals Mutation of a key residue in the type II secretion system ATPase uncouples ATP hydrolysis from protein translocation

2007 ◽  
Vol 65 (2) ◽  
pp. 401-412 ◽  
Author(s):  
Sheng-Jie Shiue ◽  
I-Ling Chien ◽  
Nei-Li Chan ◽  
Wei-Ming Leu ◽  
Nien-Tai Hu
Keyword(s):  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Secretion System ◽  
Type Ii Secretion ◽  
Type Ii ◽  
Type Ii Secretion System

The Interplay between DNA Topology and Accessory Factors in Site-Specific Recombination in Bacteria and their Bacteriophages

2016 ◽  
Vol 99 (4) ◽  
pp. 420-437 ◽  
Author(s):  
Charles J. Dorman ◽  
Marina M. Bogue
Keyword(s):  
Dna Sequences ◽  
Dna Topology ◽  
Life Cycles ◽  
Physiological Status ◽  
Bacterial Cells ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Topological State ◽  
Accessory Factors ◽  
Recombination Reactions

Site-specific recombination is employed widely in bacteria and bacteriophage as a basis for genetic switching events that control phenotypic variation. It plays a vital role in the life cycles of phages and in the replication cycles of chromosomes and plasmids in bacteria. Site-specific recombinases drive these processes using very short segments of identical (or nearly identical) DNA sequences. In some cases, the efficiencies of the recombination reactions are modulated by the topological state of the participating DNA sequences and by the availability of accessory proteins that shape the DNA. These dependencies link the molecular machines that conduct the recombination reactions to the physiological state of the cell. This is because the topological state of bacterial DNA varies constantly during the growth cycle and so does the availability of the accessory factors. In addition, some accessory factors are under allosteric control by metabolic products or second messengers that report the physiological status of the cell. The interplay between DNA topology, accessory factors and site-specific recombination provides a powerful illustration of the connectedness and integration of molecular events in bacterial cells and in viruses that parasitise bacterial cells.

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