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What is the advantage of circular DNA in bacteria?

What is the advantage of circular DNA in bacteria?


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From what I understand, bacteria have circular DNA. What advantages does it have over linear strands like for eukaryotes?

Do there exist bacteria with more than one ring of DNA?


Vibrio cholerae is known to have two circular chromosomes.

Bacteria cell division is a lot simpler and efficient as compared to eukaryotic cell division, partly due in part to the nature of their chromosomes. They don't have to undergo mitosis -- condensation of chromosomes, segregation, spindle fibre formation, attachment et al aren't involved in bacterial cell division.

Circular DNA also circumvents the Hayflick limit (thus allowing it to be "immortal"), which is the number of times a cell population can divide before it stops, presumably due to the shortening of telomeres, the sequences at the end of the chromosomes. Since circular DNA lacks telomeres, it does not get shorter with each replication cycle.

Circular DNA can also facilitate horizontal gene transfer such as Hfr mediated conjugation. Remember, conjugation is analogous to a "rolling-circle" type replication which is of course, only possible on circular pieces of DNA.


To expand a little bit the other answer, I would also add that bacteria can have other (usually circular) DNA segments aside from their main chromosome. These are called plasmids and are double stranded molecules of DNA that can replicate autonomously.

Plasmids often carry genes that allow an organism to survive in certain conditions, for instance they could carry the resistance to an antibiotic, or the gene that encodes for a specific nutrient that may be absent in the environment and so on.

As the other answer says, plasmids can be transferred horizontally between bacteria in a process called bacterial conjugation, and that is made possible by the presence of a specific plasmid, called the F-plasmid in the donor. The F-plasmid encodes, amongst other things, for the F-pilus protein pilin, that allows the formation of the pilus necessary for DNA transfer.

Because of their properties, plasmids are widely used in laboratory as vectors, to transfer genetic material to cells in order to give them specific "abilities" (e.g. you could insert a gene that encodes for a certain receptor normally not expressed by the cells to allow its expression and test its function).

Finally, it is worth remembering that plasmids can also be found in eukaryotes (e.g. in yeast).


George Beadle and Edward Tatum first described the concept that each gene corresponded to an enzyme in a metabolic pathway by exposing the yeast Neurospora crassa to mutagenic conditions (Beadle & Tatum, 1941). Following these procedures, Joshua Lederberg continued these studies with Tatum where they generated two mutants strains in Escherichia coli. These bacteria were auxotrophs, unable to generate some basic nutrients necessary to sustain their growth. The two strains were described as met &minus bio &minus Thr + Leu + Thi + (Strain A) and Met + Bio + thr &minus leu &minus thi &minus (Strain B). Strain A can sufficiently synthesize the amino acids threonine, leucine, and the cofactor thiamine while deficient in producing the cofactor biotin and the amino acid methionine while the converse was true of Strain B. When either of these two strains was plated onto minimal media, no growth occurred. Supplementing minimal media with methionine and biotin permitted Strain A to grow as normal. When the two strains were mixed together and plated on minimal media, there was a growth of bacteria. The two strains were capable of complementing each other in some way as if a sexual exchange of genetic material had occurred (Lederberg & Tatum, 1946).

Bacteria are equipped with all the necessary capacities to replicate DNA. Common bacterial species have bee adapted for use in the lab to carry DNA and propagate it for uses in biotechnology. In addition to chromosomal DNA of the bacterial genome, bacteria also have extrachromosomal DNA called plasmids. These plasmids replicate independently of the bacterial chromosome and can occur in a high copy. These circular pieces of DNA are modified in labs to carry specific pieces of DNA so they can be studied or used for expression into proteins. Plasmids can naturally carry important traits, including antibiotic resistance. Plasmids are relatively small, ranging in size from 1000 bases to 1,000,000 bases long (1kb-1000kb).

Bacterial DNA usually exists as a large circular chromosome (red). Plasmids are extrachromosomal and autonomously replicating pieces of DNA (blue).

Through a process called conjugation, bacteria can &ldquosexually&rdquo transfer genetic material to another by passing plasmids through a structure called a conjugation pilus.

Conjugation process between a plasmid bearing donor and a plasmid-less recipient. The donor creates a conjugation pilus to create a cytosolic bridge with the donor where the plasmid is replicated into the recipient through the rolling circle method of replication. The recipient then becomes competent to act as a donor.


Bacterial Transformation

Transformation is the genetic alteration of a cell by the update of DNA from the environment. This process can occur naturally in some types of bacteria, but is typically rare. In a lab, we can subject bacteria to conditions that will cause them to take up DNA from the environment (to become “transformed”). There are several ways to transform bacteria in a lab setting, but one of the most common involves changing the concentration of ions in the bacteria’s surroundings and then heating the cells in a specific way. Bacteria that are able to easily take up DNA from the environment are called “competent”. Making cells competent renders their cell membrane more permeable to DNA. After the new DNA has entered the bacteria, it is used by the cell to make RNA and then protein. The new proteins produced from this DNA are what cause the change in the traits of the cells.

Plasmids

In addition to their DNA genome (which is circular), bacteria can also contain additional smaller circles of DNA called plasmids. A plasmid is a small, circular piece of double-stranded DNA that can be copied by bacterial cells. Plasmids occur naturally in bacteria and they are widely used by scientists as a method of for introducing foreign DNA into these cells because the sequence of DNA within the plasmid can be modified in the lab. Once a plasmid has entered a cell, it is copied by the cell’s DNA replication machinery. When the bacterial cell divides, each new daughter cell receives copies of the plasmid. One original transformed bacteria will divide to form a visible colony made up of one million or more transformed bacteria, which each contain a copy of the plasmid (Figure 3).

Figure 2: Diagram of a bacteria that contains bacterial genomic DNA and three plasmids. Note that the plasmids are not to scale and would typically be much smaller than the bacterial genome. When the bacteria divides, the daughter cells receive a copy of the genomic DNA and of any plasmids present in the cell. Credit: Spaully CC SA 2.5 Plasmid Replication

Figure 3: E. coli growing on a nutrient plate. Each spot is one isolated colony (one distinct circular spot). Each colony is made up of 10’s or 100’s of thousands of cells that grew from a single original bacterial cell. Picture modified from: Madprime “K12 E coli colonies on plate Public Domain.

Selecting for transformed bacteria

In order to transform bacteria using plasmid DNA, biotechnologists must overcome two problems. First, cells that contain plasmid DNA have a disadvantage since cellular resources (such as energy) are being used to replicate the plasmid and to synthesize the proteins that are encoded for by the plasmid’s DNA. If a mixed population of cells with plasmids and cells without plasmids is grown together in the presence of plenty of nutrients, then the cells without the plasmids grow faster because they are not wasting energy on a plasmid that they do not need (Figure 4). Therefore, there is always tremendous pressure on cells to get rid of their plasmids. If they are able to get rid of the plasmid, they will grow faster on a nutrient plate (or in the environment). However, getting rid of the plasmid is exactly what we do not want them to do. To overcome the pressure to get rid of the plasmid, we must provide an advantage to the cells that have and keep the plasmid.

Figure 4: When bacteria with and without a plasmid are grown on an LB nutrient plate (no antibiotic present), the bacteria without the plasmid will grow more quickly because it is not using energy to replicate the plasmid and to make proteins encoded by the plasmid. Photo Credit: Lisa Bartee, 2020, CCBY.

Second, we need to be able to determine which bacteria received the plasmid. In a typical transformation, billions of bacteria are treated to make them competent and then exposed to plasmid DNA. Typically, fewer than 1 in 1000 bacteria will acquire the plasmid (Figure 5). We need a way to get rid of the untransformed bacteria (greater than 99% of the total bacteria present) so that we are left with only the bacteria that were transformed with the plasmid. If we do not get rid of the untransformed bacteria, we will not be able to see the transformed bacteria since they are such a small percentage of the total number.

Figure 5: Only a few bacteria in a transformation (typically less than 1%) will actually take up the plasmid and become transformed. We need a way to get rid of the bacteria that have not taken up the plasmid so that we are left with only transformed bacteria. Photo Credit: Lisa Bartee, 2020, CCBY.

Antibiotic resistance genes provide a means of finding the bacteria that acquired the plasmid DNA in the midst of all those bacteria that did not. Antibiotics are chemicals that inhibit the growth of or kill bacteria. If the plasmid contains a gene for resistance to an antibiotic, then after transformation, bacteria grown on a nutrient plate containing the antibiotic will not be inhibited or killed by it. This means that bacteria that took up the plasmid during transformation can be distinguished from bacteria that did not by growing the bacteria on a nutrient plate containing the antibiotic (Figure 6). Only the bacteria that were transformed with the plasmid will survive the killing effect of the antibiotic and grow to form visible colonies on the plate. Remember that a colony is formed from more than one million genetically identical bacterial cells. This means that the only colonies growing on a nutrient + antibiotic plate after a transformation are the bacteria that acquired and kept the plasmid. Using an antibiotic in the nutrient plate and an antibiotic resistance gene in the plasmid accomplishes our two goals of giving an advantage to cells that have a plasmid so the plasmid is retained and of having a marker so we know our cells contain new DNA. Resistance to an antibiotic is known as a selectable marker because we can select for cells that contain it.

Figure 6: When bacteria with and without a plasmid are grown on an LB nutrient plate containing antibiotic, the bacteria without the plasmid will all be killed by the antibiotic. Only bacteria containing the antibiotic will be able to grow. Photo Credits: Lisa Bartee, 2020, CCBY. Gabriel Van Helsing, CCSA 3.0, Skull and Crossbones.

This is what it using an antibiotic to select transformed cells that contain a plasmid would look like:

For Our Lab:

The plasmid that we will be using is called pGLO (available from Bio-Rad). This plasmid contains several important pieces:

  • Ori – an origin of replication, which allows the plasmid to be copied when the bacteria divide.
  • GFP (green fluorescent protein) gene – the GFP protein gives a green glow in the presence of UV light.
  • bla gene – the enzyme beta-lactamase is produced from this gene. This enzyme breaks down some antibiotics such as ampicillin when they are present in the environment before they can kill the bacteria.
  • araC gene – the AraC protein produced by this gene turns on the GFP gene when arabinose is present in the environment.

Bacteria that are transformed with this plasmid will have two new traits: they will fluoresce green under UV light and they will be resistant to the antibiotic ampicillin.

The basic steps in the process of bacterial transformation are:

  • Mix actively growing bacteria with the plasmid DNA you want to insert in a tube containing CaCl2 (calcium chloride) solution.
  • “Heat shock” the bacteria by rapidly heating and then cooling them. This process causes the plasmid to enter the bacteria.
  • Transfer the bacteria to an LB nutrient plate (containing nutrients) so that they can recover and express their newly acquired genes.

After the bacterial transformation procedure has been carried out, cells that contain the plasmid are selected for by growing the bacteria on LB nutrient plates that contain ampicillin. The ampicillin kills any cell that did not get transformed with the plasmid. This means that the only bacteria which can grow to form visible colonies on a plate containing LB nutrients and ampicillin are transformed cells. These cells will produce GFP at very low levels and will appear whitish when viewed under UV light.

Arabinose is a type of sugar that can be added to the plates when they are poured. Although arabinose is a sugar, it is not being used as a nutrient source in this experiment. When transformed bacteria are grown on plates containing LB nutrients + ampicillin + arabinose, the arabinose interacts with the araC protein (which is produced from the araC gene). The interaction of arabinose + araC protein stimulates transcription of the GFP gene. This results in a brilliant green glow when the bacteria are viewed under a UV light source.

Samples in our experiment

In our lab, we will compare transformed (+pGLO) and non-transformed (-pGLO) bacteria grown on several different types of plate. Here are the key points to remember:


Debunking the error myth

The power of SMRT sequencing data lies both in its long read lengths and in the random nature of the error process (Figure 2). It is true that individual reads contain a higher number of errors: approximately 11% to 14% or Q12 to Q15, compared with Q30 to Q35 from Illumina and other technologies. However, given sufficient depth (8x or more, say), SMRT sequencing provides a highly accurate statistically averaged consensus perspective of the genome, as it is highly unlikely that the same error will be randomly observed multiple times. Notoriously, other platforms have been found to suffer from systematic errors that need to be resolved by complementary methods before the final sequence is produced [16].

A sequencing context breakdown of the empirical insertion error rate of the two platforms on NA12878 whole genome data. In this figure we show all contexts of size 8 that start with AAAAA. The empirical insertion quality score (y-axis) is PHRED scaled. Despite the higher error rate (approximately Q12) of the PacBio RS instrument, the error is independent of the sequencing context. Other platforms are known to have different error rates for different sequencing contexts. Illumina's HiSeq platform, shown here, has a lower error rate (approximately Q45 across eight independent runs), but contexts such as AAAAAAAA and AAAAACAG have extremely different error rates (Q30 versus Q55). This context-specific error rate creates bias that is not easily clarified by greater sequencing depth. Empirical insertion error rates were measured using the Genome Analysis Toolkit (GATK) - Base Quality Score Recalibration tool.

Another approach that benefits from the stochastic nature of the SMRT error profile is the use of circular consensus reads, where a sequencing read produces multiple observations of the same base in order to generate high-accuracy consensus sequence from single molecules [17]. This strategy trades read length for accuracy, which can be effective in some cases (targeted re-sequencing, small genomes) but is not necessary if one can achieve some redundancy in the sequencing data (8x is recommended). With this redundancy, it is preferable to benefit from the improved mapping of longer inserts than opt for circular consensus reads, because the longer reads will be able to span more repeats and high accuracy will still be achieved from their consensus.


DNA Topoisomerases: Biochemistry and Molecular Biology

Karl Drlica , Barry Kreiswirth , in Advances in Pharmacology , 1994

A Maintenance of Fixed Supercoiling Levels

Intact circular DNA extracted from bacterial cells has a linking deficit that is, the DNA has fewer duplex turns than would be found in a nicked or linear molecule of the same length. This linking deficit causes the DNA to be under negative superhelical tension, so a linking deficit observed with extracted DNA is often called “negative supercoiling.” Tension is also present inside cells, but at only half the level found with extracted DNA (for references, see Drlica, 1992 ). Unidentified factors constrain the remainder of the linking deficit and prevent intracellular nicks in the DNA from totally eliminating it. Since many activities of DNA are sensitive to levels of supercoiling (for examples, see Drlica, 1984 Pruss and Drlica, 1989 ), understanding how these levels are established and perturbed is of general interest.

Four topoisomerases have been identified in Escherichia coli: topoisomerase I ( Wang, 1971 ), gyrase [topoisomerase II ( Gellert et al., 1976a )], topoisomerase III ( Dean et al., 1983 ), and topoisomerase IV ( Kato et al., 1990 ). Only gyrase introduces negative supercoils in vitro. It appears to be the primary source of negative supercoiling in vivo, since inhibitors of gyrase block the introduction of negative supercoils into bacteriophage λ DNA during superinfection of a lysogen ( Gellert et al., 1976b ). These inhibitors, particularly the coumarins, also cause a loss of supercoils from both the chromosome and plasmids ( Drlica and Snyder, 1978 Kano et al., 1981 Manes et al., 1983 ). In vitro, gyrase, as well as topoisomerases I and III, relaxes DNA. Defects in topoisomerase I (the product of topA) lead to elevated levels of supercoiling consequently, topoisomerase I normally prevents excess supercoiling from being maintained. Deletion of topA blocks growth of E. coli, and this led to the recovery of compensatory mutations. Many of these map in the gyrase genes (gyrA and gyrB) and reduce supercoiling below normal levels ( DiNardo et al., 1982 Pruss et al., 1982 Richardson et al., 1984 Raji et al., 1985 ). These mutational studies emphasize the importance of supercoiling in cell growth and establish that vigorous growth occurs within a ± 15% range of supercoiling. There is little evidence that topoisomerase III or IV normally participates in the control of supercoiling.

Gyrase and topoisomerase I tend to maintain supercoiling within a fixed range through their substrate specificity. Gyrase is more active on relaxed than on supercoiled substrates ( Sugino and Cozzarelli, 1980 ) topoisomerase I clearly favors highly negatively supercoiled DNA as a substrate in vitro, and it does not completely relax DNA ( Wang, 1971 ). In vivo, topoisomerase I is not a major source of relaxing activity once supercoiling drops below normal levels: In one study the presence of this enzyme had no detectable effect on the rate of DNA relaxation induced by inhibitors of gyrase that probably stimulate gyrase to relax DNA ( Pruss et al., 1986 ) in another study topoisomerase I produced slow and only partial relaxation ( Bliska and Cozzarelli, 1987 ).

The topoisomerases correct for perturbations of helical pitch that alter superhelical tension. For example, decreasing temperature increases the number of duplex turns in DNA, which should increase superhelical tension. The topoisomerases appear to relax this excess tension, since DNA exhibits fewer supercoils when extracted from cells grown at lower temperatures ( Goldstein and Drlica, 1984 ). In another example treatment of cells with the intercalating dye chloroquine unwinds DNA this should decrease superhelical tension. Gyrase then appears to introduce supercoils ( Esposito and Sinden, 1987 ). Subsequent removal of chloroquine has the opposite effect, eliciting rapid relaxation.

Other examples of corrective action by the topoisomerases are associated with activities of DNA involving strand separation. Some striking cases have emerged from the study of transcriptional effects on supercoiling. In a topA mutant transcription of the tet gene on pBR322 caused plasmic DNA supercoiling to become highly negative ( Pruss and Drlica, 1986 ). This, coupled with the observation that inhibition of gyrase can generate positive supercoils in pBR322 ( Lockshon and Morris, 1983 ), led to the idea that translocation of transcription complexes along DNA generates negative superhelical tension behind the complex and positive tension (or relaxation of negative tension) ahead of it ( Liu and Wang, 1987 ). Topoisomerase I would correct for excess negative tension, while gyrase would correct for relaxation (or the introduction of positive supercoils). Thus, an imbalance between the two enzymes leads to transcription-induced changes in net linking deficit: Negative supercoils accumulate in the absence of topoisomerase I ( Pruss and Drlica, 1986 ) and positive supercoils accumulate in the presence of an inhibitor of gyrase ( Wu et al., 1988 ). Under normal circumstances transcription could at least transiently generate local supercoiling that deviates significantly from average values the magnitude of transcriptional perturbation of supercoiling would depend on how effectively the topoisomerases respond to correct it. With plasmids local perturbations have been observed in vivo ( Rahmouni and Wells, 1989, 1992 ).

Another level of maintenance involves expression from the genes encoding gyrase and topoisomerase I. The coumarin inhibitors of gyrase cause DNA relaxation ( Drlica and Snyder, 1978 ), and associated with relaxation is an increase in expression of both gyrA and gyrB ( Menzel and Gellert, 1983 ) as well as a decrease in expression of topA ( Tse-Dinh, 1985 ). Cases have also been found in which the quinolones can increase supercoiling ( Manes et al., 1983 Pruss et al., 1986 Franco and Drlica, 1989 ) under these conditions topA expression increases ( Tse-Dinh and Beran, 1988 ). Thus, there is homeostatic regulation of supercoiling and topoisomerase gene expression.


DNA in Bacteria (With Diagram)

The DNA of bacteria, e.g. E. coli, is a covalently closed circular molecule. It forms the bacterial chromosome, though this chromosome is much simpler in structure and in level of organization than the eukaryotic chromosomes of plants and animals. Also, each bacterial cell normally has a single chromosome containing a single circular DNA molecule.

In E.coli, the DNA molecule is 1,300 μm long when fully stretched containing some 4,700 x 10 3 base-pairs which encode about 4,000 genes. In order to pack this long DNA molecule into a cell measuring only about 1 μm x 3 μm, the molecule has to be highly folded and supercoiled.

The prokaryotic chromosome — which is also called a nucleoid — consists of a number of loops which are held together by several proteins. For example, E. coli nucleoid has 45 (40-50) loops which radiate from a central protein core. Each loop is supercoiled (Fig. 9.8A). The supercoiled state of the loops of DNA can be removed by treatment with DNase which causes a single-stranded break (nick).

A single nick results in the uncoiling of a single loop without affecting the supercoiling of other loops (Fig. 9.8B). This shows that each loop is isolated from the other, although the ds-DNA molecule runs through all the loops. The association with proteins in the nucleoid core prevents unwinding of other loops. The E. coli chromosome needs some 45 nicks to remove all the supercoiled loops, thereby producing a closed circular ring.

A circular DNA molecule without any supercoiling is said to be in a relaxed state. In this state, the standard right-handed DNA-double helix contains about 10 nucleotide pairs per turn of the helix. If now one of the two strands is nicked and rotated through 360° to unwind one complete turn of the helix and the cut-ends are resealed, the circular DNA molecule may respond in either of the two following ways—It may produce a region of unpaired bases, called a bubble or, alternatively it may twist in a direction opposite to that of unwinding to produce a negatively supercoiled circular DNA molecule.

The three states of circular DNA — relaxed, with bubble and negatively supercoiled — are diagrammatically shown in Fig. 9.9:

Negative supercoiling of ds-DNA is produced by a class of enzymes known as topoisomerases. The single stranded nick is generated by topoisomerase I producing a break or gap in the phosphodiester bond of the DNA strand. The intact complementary strand is passed through the gap and the nick is then resealed. Another class of topoisomerases, topoisomerase II, is also known as DNA- gyrase.

These enzymes induce double-stranded break in the phosphodiester bonds of both strands. This class of enzymes plays a vital role in DNA replication. By inducing breaks in both strands, the enzyme helps to pass an intact double-stranded DNA molecule or a part to pass through another.

Thus, when a circular DNA molecule replicates, the two daughter molecules may be interlocked like two rings of a chain. DNA gyrase can separate the two molecules by inducing a double-cut in one and allowing the other to pass through the gap which is then resealed.

DNA gyrase has a more important function in normal DNA replication. With the advancement of the replication fork a positive supercoiling develops in the un-replicated portion of the ds-DNA helix. To compensate the tension, DNA gyrase introduces negative supercoiling by nicking.


Q20: a) Bacteria have small circular DNA outside the genomic DNA. What is it called? Does it have any significance for bacteria?c) How difference in composition and thickness of glycocalyx varies among bacteria?d) What is the role of mesosome and fimbriae in bacteria?​

These smaller DNA are called plasmids. . Decades after their first use, plasmids are still crucial laboratory tools in biotechnology: Scientists can force bacteria to keep them. Virtually all plasmids that are used to deliver DNA contain genes for antibiotic resistance. . Only those cells that contain the plasmid will survive, grow and reproduce.

c) Structure of endothelial glycocalyx and its activation of vascular muscle relaxation via nitric oxide (NO) in response to increased shear force3,6

d) Fimbriae are thin filamentous appendages that extend from the cell, often in the tens or hundreds. They are composed of pilin proteins and are used by the cell to attach to surfaces. They can be particularly important for pathogenic bacteria, which use them to attach to host tissues.


Using pulse-field gel electrophoresis, the A. tumefaciens genome was analyzed, where one linear chromosome and one circular chromosome were identified [1]. The size of the linear chromosome is 2100 Kb, which is smaller than the 3000 Kb circular chromosome [1]. The Agrobacterium species have a close 16s rRNA sequence relationship with Brucella species, which have members known to have two circular chromosomes [1].

B. melitensis is a Gram-negative coccobacillus bacterium, which has two circular chromosomes [5]. The two chromosome sizes are 2117 Kb and 1178 Kb [5]. Other Brucella species with two circular chromosomes include B. suis biovar 1, B. suis biovar 2, B. suis biovar 4, B. abortus and B. ovis [9].


Supercoiling of Bacterial DNA | Microbiology

DNA molecules exist in two states, relaxed and supercoiled. A relaxed state of DNA molecule is one in which the exact number of turns of the helix can be predicted by calculating the number of base pairs, whereas when the relaxed DNA molecules is highly twisted to accommodate itself in a little space the state is called supercoiled.

The example of Escherichia coli makes clear why relaxed DNA molecule enters into the supercoiled state. The DNA of E. coli in its relaxed state becomes more than 1 mm in length, about 400 times longer than the E. coli cell itself. How can so much DNA be packed into such a little space of E. coli cell? Nature has solved this problem by imposing a kind of ‘high order’ structure on the DNA molecule.

In this structure the double-stranded helical DNA is further highly twisted employing the process called supercoiling, and is easily packed within E. coli cell. The supercoiled DNA molecule remains under torsion almost similar to the added tension to a rubber band that occurs when it is twisted.

DNA molecule supercoils in either a positive or negative direction it is the negative supercoiling that predominantly operates in all non-hyperthermophilic organisms in nature. In negative supercoiling, the DNA molecule is twisted about its axis in the opposite direction from that of the right-handed double helix.

DNA molecule can be alternately supercoiled and relaxed. It is because the supercoiling is necessary for packaging the DNA into the bacterial cell and relaxing is necessary for the replication of DNA. Fig. 5.35 shows how supercoiling takes place in a relaxed covalently closed circular dsDNA molecule, and it also shows how a supercoiled DNA molecule becomes relaxed one.

Supercoiling in bacterial and most archaeal DNA is carried out with the help of an enzyme called DNA gyrase, which is a type of enzyme called a topoisomerase, particularly a topoisomerase II.

The process completes via several steps:

(i) One strand of circular relaxed DNA is laid over the other,

(ii) Laiding one part over the other results in contact between the helix in two places, and DNA gyrase (topoisomerase II) makes a double-strand break (nick) in the region of contact at one place, and(3) the broken (nicked) double-strand is resealed on the opposite side of the intact strand resulting in supercoiling in DNA molecule.

Supercoiling in DNA molecule removed by the action of another enzyme called topoisomerase I. This enzyme introduces a single-strand break (nick) in the supercoiled DNA and causes the rotation of one single- strand of the double-strand DNA around the other resulting in the return of supercoiled state of DNA to the relaxed state.

However to prevent the entire bacterial DNA from becoming relaxed every time a break (nick) is made, the DNA contains supercoiled domains (Fig. 5.36). Actually, the double-stranded bacterial DNA is arranged not in one supercoil but in several supercoiled domains.

In E. coli over 50 supercoiled domains are reported to exist, each of which is thought to be stabilized by binding to specific proteins. However, a nick in one strand of double-stranded DNA in one of these domains does not allow DNA to relax in other domains.


Watch the video: Μαθήματα Βιολογίας - Η αντιγραφή του DNA (February 2023).