Reverse gyrase

Last updated
Reverse gyrase
Different Classes of Topoisomerases.jpg
Molecular depictions of the different type I and type II topoisomerase classes. Reverse gyrase is indicated by the 'RG' tag under the type IA topoisomerase section of the diagram.
Identifiers
EC no. 5.6.2.2
CAS no. 143180-75-0
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Search
PMC articles
PubMed articles
NCBI proteins

Reverse gyrase is a type I topoisomerase that introduces positive supercoils into DNA, [1] contrary to the typical negative supercoils introduced by the type II topoisomerase DNA gyrase. These positive supercoils can be introduced to DNA that is either negatively supercoiled or fully relaxed. [2] Where DNA gyrase forms a tetramer and is capable of cleaving a double-stranded region of DNA, reverse gyrase can only cleave single stranded DNA. [3] [4] More specifically, reverse gyrase is a member of the type IA topoisomerase class; along with the ability to relax negatively or positively supercoiled DNA [5] (which does not require ATP [6] [7] ), type IA enzymes also tend to have RNA-topoisomerase activities. These RNA topoisomerases help keep longer RNA strands from becoming tangled in what are referred to as "pseudoknots." Due to their ability to interact with RNA, it is thought that this is one of the most ancient class of enzymes found to date. [4]

Contents

Reverse gyrase is an ATP-dependent topoisomerase [8] in terms of its positive supercoiling activity, however, reverse gyrase can also relax DNA strands without introducing positive supercoils through interaction with ADP. [9] The structure of the enzyme includes both a helicase domain, which is responsible for separating nucleic acids, and a topoisomerase domain, which is responsible for the actual introduction of coils into DNA. However, mechanistic studies have shown that these two domains tend to exhibit weak activities separately and can only perform efficient DNA positive supercoiling activity when working in tandem. [10] [11] Other studies have also shown that reverse gyrase enzymes tend to favorably attack regions of single-stranded DNA versus double-stranded DNA, which suggests that this enzyme's critical biological function is to ensure the constant renaturation of melted DNA strands, especially in organisms that grow at high temperatures. [8]

This enzyme has been extensively characterized across several Archaea, with Sulfolobus acidocaldarius reverse gyrase being one of the first to be characterized. [12] Additionally, it has been found that all thermophilic bacteria and archaea contain at least one reverse gyrase enzyme. Some organisms, such as members of the Crenarchaeota phylum, even have two reverse gyrase enzymes: TopR1, which tends to be active in increased temperatures, and TopR2, which shows activity in both low and high temperatures. [4] Other exceptional organisms include Nanoarchaeum equitans, whose reverse gyrase enzyme tends to naturally exist as two separate peptides versus the typical monomeric polypeptide with a topoisomerase IA domain and a helicase domain. [4] [11]

Classification

As seen in the information box above, reverse gyrase is designated under the EC number 5.6.2.2. The first number of this code (5) designates the enzymes identity as an isomerase. [13] While the enzyme itself does have both a topoisomerase and helicase-like domain, as a gyrase, it is primarily classified under the topoisomerase umbrella. Furthermore, the 5.6 number designates this molecule as an isomerase that is capable of changing conformation in cellular molecules. [14] 5.6.2 designates the enzyme further as being capable of altering nucleic acid, or DNA, conformations. [15] Lastly, the full designation of 5.6.2.2 characterizes this enzyme as an ATP-dependent DNA topoisomerase. [16]

Structure

The crystal structure of reverse gyrase has been characterized fully, and a crystal structure has been produced based on the enzyme found in Thermotoga maritima. [12]

Reverse gyrase linear domains and crystal structure. Reverse gyrase structure figure.jpg
Reverse gyrase linear domains and crystal structure.

Active Site

Reverse gyrases have helicase and topoisomerase domains. The active site, where nucleotides are bound by the enzyme, is characterized by Asp78, Phe75, Gln83, Lys106, Asp203, and Thr107 residues. [12] It is hypothesized that the H1 and H2 subdomains also contain nucleotide-binding abilities, and the DNA strand is able to be grabbed by these subdomains and are subsequently fed up through the topoisomerase domain of the enzyme to complete positive supercoiling. [12]

Latch Domain

The latch domain appears to be variable across species, with domain size ranging from as small as 10 amino acids to as large as 120 amino acids. [12] The latch is thought to function as a control mechanism to prevent the topoisomerase domain from creating negative supercoils and relaxing the DNA, and instead allows the enzyme to create positive supercoils in an ATP-dependent manner during the strand passage step of the helicase domain. [5] [17]

Zinc Fingers

The reverse gyrase enzyme contains a zinc finger domain, where two zinc ions help to coordinate enzymatic function. The first zinc ion is kept in place by interactions with four cysteine residues. [12] The second zinc ion is not always found in reverse gyrase enzymes. However, when present, both ions are found near the binding site for nucleic acids. It is thought that these zinc fingers play a role in initial binding of DNA and strand passage, but their exact mechanisms of action appear to vary between organisms. [12]

Thermophile significance

Organisms that live under standard temperature and pressure conditions, or mesophiles (living in temperature ranges between 20 °C and 40 °C), tend to have negative supercoiling in their DNA strands. This helps to condense the genetic material so that it fits within the host cells (or in the case of eukaryotes, within the cell's nuclear region). Negative supercoiling, also referred to as underwinding, results in the counterclockwise twisting of the DNA strand. Negative supercoiling leaves the DNA strands available for various cellular processes, like genome replication and transcription, as DNA typically needs to be underwound in order to be denatured and accessed by the proper enzymes. [2]

On the other hand, thermophiles (organisms that can live in temperatures ranging from 40 °C up to as high as 122 °C [18] ) are thought to maintain several positive supercoils in their DNA in order to assist with maintaining structural integrity of the DNA under the denaturing capabilities of these high temperatures. Positive supercoiling, which is referred to as overwinding, results in the clockwise twisting of the strand. As previously discovered, one of the biggest benefits to maintaining positive supercoils in DNA strands is preventing separation of the strands in high temperatures. [2]

While positive supercoiling is certainly more common in thermophiles, positive supercoiling has been found in mesophilic organisms. For example, telomeres and condensins can both utilize positive supercoiling as a means for contributing to chromosomal structure. [19] Furthermore, the reverse gyrase enzyme is not exclusive to thermophiles. Some reverse gyrase enzymes even function outside of thermophilic temperature ranges, suggesting that there may be some organisms at mesophilic temperatures that utilize this enzyme. [4]

Supercoiling mechanism

Visual depiction of the proposed mechanism of action of the reverse gyrase enzyme with ATP hydrolysis. Reverse Gyrase Mechanism.jpg
Visual depiction of the proposed mechanism of action of the reverse gyrase enzyme with ATP hydrolysis.

It is suspected that the helicase and topoisomerase domains of the reverse gyrase enzyme work together to promote positive supercoiling in DNA. However, the exact mechanisms of action appear to differ between organisms. For example, Sulfolobus solfataricus and Thermotoga maritima experience opposite phenomena in terms of helicase activity: Sulfolobus solfataricus helicase's ability to hydrolyze ATP appears to be activated by the topoisomerase, whereas Thermotoga maritima ATP hydrolysis ability via the helicase appears to be reduced by the topoisomerase domain. [12]

When bound to the DNA, reverse gyrase induces a change in structure via a left-handed wrapping, which more or less functions as an unwinding. [20] Specifically, the reverse gyrase found in S. solfataricus (a Crenarchaeota TopR2 reverse gyrase) initiates an unwinding of approximately 20 base pairs upon binding to a DNA structure. [4] Upon initial binding to the DNA, the helicase domain is in an open conformation, while the topoisomerase IA domain is in a closed conformation. [5] After the binding of ATP to the reverse gyrase structure, the helicase domain closes, and the topoisomerase IA domain opens. This triggers a rewinding of 10 of the 20 base pairs in the unwound bubble, and the topoisomerase IA domain can introduce positive supercoiling during strand passage. [5] As the strand passage occurs, reverse gyrase's topoisomerase IA domain is able to increase the linking number (how many times a strand of DNA is wrapped around the other strand) of the DNA strand as they are renatured. [9] Following ATP hydrolysis-induced rewinding, the reverse gyrase enzyme domains return to their original state (open helicase domain and closed topoisomerase IA domain) and the reverse gyrase is released, ready to bind to a new region of DNA and repeat the process. [4] [5] [9]

Regardless of the differences in interactions between the topoisomerase and helicase domains, in general, reverse gyrase enzymes all undergo conformational changes when nucleotides are bound to the active site. [12]

Related Research Articles

<span class="mw-page-title-main">DNA replication</span> Biological process

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritance. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. The cell possesses the distinctive property of division, which makes replication of DNA essential.

DNA topoisomerases are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA. Topological issues in DNA arise due to the intertwined nature of its double-helical structure, which, for example, can lead to overwinding of the DNA duplex during DNA replication and transcription. If left unchanged, this torsion would eventually stop the DNA or RNA polymerases involved in these processes from continuing along the DNA helix. A second topological challenge results from the linking or tangling of DNA during replication. Left unresolved, links between replicated DNA will impede cell division. The DNA topoisomerases prevent and correct these types of topological problems. They do this by binding to DNA and cutting the sugar-phosphate backbone of either one or both of the DNA strands. This transient break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed. Since the overall chemical composition and connectivity of the DNA do not change, the DNA substrate and product are chemical isomers, differing only in their topology.

DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.

<span class="mw-page-title-main">Helicase</span> Class of enzymes to unpack an organisms genes

Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two hybridized nucleic acid strands, using energy from ATP hydrolysis. There are many helicases, representing the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases.

dnaB helicase

DnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. Initially when DnaB binds to dnaA, it is associated with dnaC, a negative regulator. After DnaC dissociates, DnaB binds dnaG.

A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upwards. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are often within the domain Archaea, although some bacteria are also able to tolerate extreme temperatures. Some of these bacteria are able to live at temperatures greater than 100 °C, deep in the ocean where high pressures increase the boiling point of water. Many hyperthermophiles are also able to withstand other environmental extremes, such as high acidity or high radiation levels. Hyperthermophiles are a subset of extremophiles. Their existence may support the possibility of extraterrestrial life, showing that life can thrive in environmental extremes.

<span class="mw-page-title-main">Nucleoid</span> Region within a prokaryotic cell containing genetic material

The nucleoid is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies and a cell may contain multiple copies of it.

DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase and is a subclass of Type II topoisomerases that reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase or by helicase in front of the progressing replication fork. The enzyme causes negative supercoiling of the DNA or relaxes positive supercoils. It does so by looping the template so as to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break, changing the linking number by two in each enzymatic step. This process occurs in bacteria, whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each other to form supercoils. Gyrase is also found in eukaryotic plastids: it has been found in the apicoplast of the malarial parasite Plasmodium falciparum and in chloroplasts of several plants. Bacterial DNA gyrase is the target of many antibiotics, including nalidixic acid, novobiocin, albicidin and ciprofloxacin.

Topoisomerase IV is one of two Type II topoisomerases in bacteria, the other being DNA gyrase. Like gyrase, topoisomerase IV is able to pass one double-strand of DNA through another double-strand of DNA, thereby changing the linking number of DNA by two in each enzymatic step. Both share a hetero-4-mer structure formed by a symmetric homodimer of A/B heterodimers, usually named ParC and ParE.

A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. Nicks allow DNA strands to untwist during replication, and are also thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands.

<span class="mw-page-title-main">Replisome</span> Molecular complex

The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthesized. The Total result is formation of two new double stranded DNA sequences that are exact copies of the original double stranded DNA sequence.

<span class="mw-page-title-main">DNA supercoil</span> Amount of twist in a particular DNA strand

DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled". The amount of a strand’s supercoiling affects a number of biological processes, such as compacting DNA and regulating access to the genetic code. Certain enzymes, such as topoisomerases, change the amount of DNA supercoiling to facilitate functions such as DNA replication and transcription. The amount of supercoiling in a given strand is described by a mathematical formula that compares it to a reference state known as "relaxed B-form" DNA.

<span class="mw-page-title-main">DNA unwinding element</span> Initiation site for the opening of the DNA double helix

A DNA unwinding element is the initiation site for the opening of the double helix structure of the DNA at the origin of replication for DNA synthesis. It is A-T rich and denatures easily due to its low helical stability, which allows the single-strand region to be recognized by origin recognition complex.

<span class="mw-page-title-main">Type I topoisomerase</span>

In molecular biology Type I topoisomerases are enzymes that cut one of the two strands of double-stranded DNA, relax the strand, and reanneal the strand. They are further subdivided into two structurally and mechanistically distinct topoisomerases: type IA and type IB.

<span class="mw-page-title-main">Type II topoisomerase</span>

Type II topoisomerases are topoisomerases that cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP, unlike Type I topoisomerase. In this process, these enzymes change the linking number of circular DNA by ±2. Topoisomerases are ubiquitous enzymes, found in all living organisms.

<span class="mw-page-title-main">Aminocoumarin</span>

Aminocoumarin is a class of antibiotics that act by an inhibition of the DNA gyrase enzyme involved in the cell division in bacteria. They are derived from Streptomyces species, whose best-known representative – Streptomyces coelicolor – was completely sequenced in 2002. The aminocoumarin antibiotics include:

In enzymology, glutamate racemase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Circular chromosome</span> Type of chromosome

A circular chromosome is a chromosome in bacteria, archaea, mitochondria, and chloroplasts, in the form of a molecule of circular DNA, unlike the linear chromosome of most eukaryotes.

Saccharolobus solfataricus is a species of thermophilic archaeon. It was transferred from the genus Sulfolobus to the new genus Saccharolobus with the description of Saccharolobus caldissimus in 2018.

<span class="mw-page-title-main">Cruciform DNA</span>

Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. The formation of cruciform DNA requires the presence of palindromes called inverted repeat sequences. These inverted repeats contain a sequence of DNA in one strand that is repeated in the opposite direction on the other strand. As a result, inverted repeats are self-complementary and can give rise to structures such as hairpins and cruciforms. Cruciform DNA structures require at least a six nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling.

References

  1. ↑ Kikuchi A, Asai K (21 June 1984). "Reverse gyrase--a topoisomerase which introduces positive superhelical turns into DNA". Nature. 309 (5970): 677–681. Bibcode:1984Natur.309..677K. doi:10.1038/309677a0. PMID   6328327. S2CID   4242694.
  2. 1 2 3 Fogg JM, Catanese DJ, Randall GL, Swick MC, Zechiedrich L (2009). Benham CJ, Harvey S, Olson WK, Sumners WL, Swigon D (eds.). "Differences Between Positively and Negatively Supercoiled DNA that Topoisomerases May Distinguish". The IMA Volumes in Mathematics and Its Applications. 150: 73–121. doi:10.1007/978-1-4419-0670-0_5. ISBN   978-1-4419-0669-4.
  3. ↑ Jaxel C, Nadal M, Mirambeau G, Forterre P, Takahashi M, Duguet M (October 1989). "Reverse gyrase binding to DNA alters the double helix structure and produces single-strand cleavage in the absence of ATP". The EMBO Journal. 8 (10): 3135–3139. doi:10.1002/j.1460-2075.1989.tb08466.x. PMC   401394 . PMID   2555155.
  4. 1 2 3 4 5 6 7 Garnier F, Couturier M, Débat H, Nadal M (25 May 2021). "Archaea: A Gold Mine for Topoisomerase Diversity". Frontiers in Microbiology. 12: 661411. doi: 10.3389/fmicb.2021.661411 . PMC   8185306 . PMID   34113328.
  5. 1 2 3 4 5 Yang X, Garnier F, Débat H, Strick TR, Nadal M (May 2020). "Direct observation of helicase-topoisomerase coupling within reverse gyrase". Proceedings of the National Academy of Sciences of the United States of America. 117 (20): 10856–10864. Bibcode:2020PNAS..11710856Y. doi: 10.1073/pnas.1921848117 . PMC   7245102 . PMID   32371489.
  6. ↑ "EC 5.6.2.1". IUBMB Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology.
  7. ↑ Gellert M (1981). "DNA topoisomerases". Annual Review of Biochemistry. 50: 879–910. doi:10.1146/annurev.bi.50.070181.004311. PMID   6267993.
  8. 1 2 Shibata T, Nakasu S, Yasui K, Kikuchi A (August 1987). "Intrinsic DNA-dependent ATPase activity of reverse gyrase". The Journal of Biological Chemistry. 262 (22): 10419–10421. doi: 10.1016/S0021-9258(18)60974-3 . PMID   3038879.
  9. 1 2 3 Hsieh TS, Plank JL (March 2006). "Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate". The Journal of Biological Chemistry. 281 (9): 5640–5647. doi: 10.1074/jbc.M513252200 . PMID   16407212.
  10. ↑ Déclais AC, Marsault J, Confalonieri F, de La Tour CB, Duguet M (June 2000). "Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling". The Journal of Biological Chemistry. 275 (26): 19498–19504. doi: 10.1074/jbc.M910091199 . PMID   10748189.
  11. 1 2 Capp C, Qian Y, Sage H, Huber H, Hsieh TS (December 2010). "Separate and combined biochemical activities of the subunits of a naturally split reverse gyrase". The Journal of Biological Chemistry. 285 (51): 39637–39645. doi: 10.1074/jbc.M110.173989 . PMC   3000944 . PMID   20929866.
  12. 1 2 3 4 5 6 7 8 9 Lulchev P, Klostermeier D (July 2014). "Reverse gyrase--recent advances and current mechanistic understanding of positive DNA supercoiling". Nucleic Acids Research. 42 (13): 8200–8213. doi:10.1093/nar/gku589. PMC   4117796 . PMID   25013168.
  13. ↑ "EC 5. Isomerases". IUBMB Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology.
  14. ↑ "EC 5.6". IUBMB Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology.
  15. ↑ "EC 5.6.2 Enzymes altering nucleic acid conformation". IUBMB Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology.
  16. ↑ "5.6.2.2". IUBMB Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology.
  17. ↑ Rodríguez AC, Stock D (February 2002). "Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA". The EMBO Journal. 21 (3): 418–426. doi:10.1093/emboj/21.3.418. PMC   125824 . PMID   11823434.
  18. ↑ Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, et al. (August 2008). "Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation". Proceedings of the National Academy of Sciences of the United States of America. 105 (31): 10949–10954. doi: 10.1073/pnas.0712334105 . PMC   2490668 . PMID   18664583.
  19. ↑ Valenti A, Perugino G, Rossi M, Ciaramella M (January 2011). "Positive supercoiling in thermophiles and mesophiles: of the good and evil". Biochemical Society Transactions. 39 (1): 58–63. doi:10.1042/BST0390058. PMID   21265747.
  20. ↑ Confalonieri F, Elie C, Nadal M, de La Tour C, Forterre P, Duguet M (May 1993). "Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide". Proceedings of the National Academy of Sciences of the United States of America. 90 (10): 4753–4757. Bibcode:1993PNAS...90.4753C. doi: 10.1073/pnas.90.10.4753 . PMC   46591 . PMID   8389456.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.