{"id":5448,"date":"2019-10-31T12:08:31","date_gmt":"2019-10-31T19:08:31","guid":{"rendered":"http:\/\/www.wou.edu\/chemistry\/?page_id=5448"},"modified":"2020-07-15T09:18:30","modified_gmt":"2020-07-15T16:18:30","slug":"chapter-9-dna-replication-and-repair-2","status":"publish","type":"page","link":"https:\/\/wou.edu\/chemistry\/courses\/online-chemistry-textbooks\/ch450-and-ch451-biochemistry-defining-life-at-the-molecular-level\/chapter-9-dna-replication-and-repair-2\/","title":{"rendered":"Chapter 9: DNA Replication"},"content":{"rendered":"
The elucidation of the structure of the double helix by James Watson and Francis Crick in 1953 provided a hint as to how DNA is copied during the process of DNA replication<\/strong><\/em>. Separating the strands of the double helix would provide two templates for the synthesis of new complementary strands, but exactly how new DNA molecules were constructed was still unclear. In one model, semiconservative replication<\/strong>,<\/em> the two strands of the double helix separate during DNA replication, and each strand serves as a template from which the new complementary strand is copied. After replication in this model, each double-stranded DNA includes one parental or \u201cold\u201d strand and one daughter or \u201cnew\u201d strand. There were two competing models also suggested: conservative<\/em><\/strong> and dispersive<\/em><\/strong>, which are shown in Figure 9.1.<\/span><\/p>\n Figure 9.1 Three Models of DNA replication.<\/strong> In the conservative model,<\/em><\/strong> parental DNA strands (blue) remained associated in one DNA molecule while new daughter strands (red) remained associated in newly formed DNA molecules. In the semiconservative model,<\/em><\/strong> parental strands separated and directed the synthesis of a daughter strand, with each resulting DNA molecule being a hybrid of a parental strand and a daughter strand. In the dispersive model<\/em><\/strong>, all resulting DNA strands have regions of double-stranded parental DNA and regions of double-stranded daughter DNA.<\/span><\/p>\n Figure by<\/span> Parker, N., et.al. (2019) Openstax<\/em><\/a><\/span><\/p>\n Matthew Meselson and Franklin Stahl devised an experiment in 1958 to test which of these models correctly represents DNA replication (Figure 9.2). They grew the bacterium, Escherichia coli<\/em>\u00a0<\/em>for several generations in a medium containing a \u201cheavy\u201d isotope of nitrogen (15<\/sup>N) that was incorporated into nitrogenous bases and, eventually, into the DNA. This labeled the parental DNA. The E. coli <\/em>culture was then shifted into a medium containing 14<\/sup>N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was separated by ultracentrifugation, during which the DNA formed bands according to its density. DNA grown in 15<\/sup>N would be expected to form a band at a higher density position than that grown in 14<\/sup>N. Meselson and Stahl noted that after one generation of growth in 14<\/sup>N, the single band observed was intermediate in position in between DNA of cells grown exclusively in 15<\/sup>N or 14<\/sup>N. This suggested either a semiconservative or dispersive mode of replication. Some cells were allowed to grow for one more generation in 14<\/sup>N and spun again. The DNA harvested from cells grown for two generations in 14<\/sup>N formed two bands: one DNA band was at the intermediate position between 15<\/sup>N and 14<\/sup>N, and the other corresponded to the band of 14<\/sup>N DNA. These results could only be explained if DNA replicates in a semiconservative manner. Therefore, the other two models were ruled out. As a result of this experiment, we now know that during DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or \u201cold\u201d strand. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.<\/span><\/p>\n Figure 9.2 Meselson and Stahl experimented with E. coli<\/em>\u00a0grown first in heavy nitrogen (15<\/sup>N) then in 14<\/sup>N.<\/span><\/strong> DNA grown in 15<\/sup>N (blue band) was heavier than DNA grown in 14<\/sup>N (red band), and sedimented to a lower level on ultracentrifugation. After one round of replication, the DNA sedimented halfway between the 15<\/sup>N and 14<\/sup>N levels (purple band), ruling out the conservative model of replication. After a second round of replication, the dispersive model of replication was ruled out. These data supported the semiconservative replication model.<\/span><\/p>\n Figure by<\/span> Parker, N., et.al. (2019) Openstax<\/em><\/a><\/span><\/p>\n DNA replication has been well studied in bacteria primarily because of the small size of the genome and the mutants that are available. E. coli <\/em>has 4.6 million base pairs (Mbp) in a single circular chromosome and all of it is replicated in approximately 42 minutes, starting from a single origin of replication<\/strong><\/em> and proceeding around the circle bidirectionally (i.e., in both directions) (Figure 9.3). This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs with few errors. E. coli <\/em>has a single origin of replication<\/em><\/strong>, called oriC<\/em>, on its one chromosome. The origin of replication is approximately 245 base pairs long and is rich in adenine-thymine (AT) sequences.<\/span><\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n<\/div>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n Figure 9.3 Prokaryotic DNA Replication<\/strong>. Replication of DNA in prokaryotes begins at a single origin of replication, shown in the figure to the left, and proceeds in a bidirectional manner around the circular chromosome until replication is complete. The bidirectional nature of replication creates two replication forks that are actively mediating the replication process. The right hand figure shows a dynamic model of this process. The red and blue dots represent the incorporation of daughter strand nucleotides during the process of replication.<\/span><\/p>\n Figures from:<\/span> Daniel Yuen at David Tribe Derivatives<\/a> and Catherinea228<\/a><\/p>\n The open regions of DNA that are actively undergoing replication are called replication forks<\/em><\/strong>. All the proteins involved in DNA replication aggregate at the replication forks<\/em><\/strong> to form a replication complex called a replisome <\/em><\/strong>(Table 9.1 and Figure 9.4). <\/em><\/strong>DNA replication in the model organism\u00a0E. coli<\/em>\u00a0has been extensively studied, providing a foundation for understanding the diverse mechanisms of genome duplication employed by all organisms. In\u00a0E. coli<\/em>, DNA replication is initiated at\u00a0oriC<\/em> (Figure 9.3).\u00a0oriC<\/em>\u00a0is \u2018melted\u2019 by the action of the DnaA initiator protein<\/em><\/strong> to expose two template ssDNA strands that act as platforms for loading the replicative DnaB helicase<\/em><\/strong>. One full DnaB hexamer is loaded onto each ssDNA strand with the aid of the helicase loader, DnaC<\/em><\/strong>. Additional exposed ssDNA is quickly coated by the ssDNA-binding protein (SSB)<\/em><\/strong>, which protects DNA and blocks additional DnaB helicase loading. Each DnaB hexamer recruits primase (DnaG),<\/em><\/strong> which synthesizes RNA primers used to initiate DNA synthesis, along with the subunits that comprise the replicative DNA polymerase III holoenzyme (PolIII HE)<\/em><\/strong>. These proteins form the core replisomes that copy the\u00a0E. coli<\/em>\u00a0genome. Once assembled, replisomes replicate bi-directionally away from\u00a0oriC<\/em>\u00a0until, ideally, they undergo programmed disassembly at the termination region, where they encounter\u00a0ter<\/em>\u00a0sites bound by Tus proteins<\/em><\/strong> that create \u2018replication fork traps’. After completion of DNA replication, the newly synthesized genomes are separated and segregated to daughter cells.<\/span><\/p>\n Table 9.1 Enzymes involved in DNA Replication in the prokaryote, E. coli<\/strong><\/span><\/p>\n Figure 9.4 General Overview of a DNA Replication Fork.<\/strong> At the origin of replication, topoisomerase II relaxes the supercoiled chromosome. Two replication forks are formed by the opening of the double-stranded DNA at the origin, and helicase separates the DNA strands, which are coated by single-stranded binding proteins to keep the strands separated. DNA replication occurs in both directions. An RNA primer complementary to the parental strand is synthesized by RNA primase and is elongated by DNA polymerase III through the addition of nucleotides to the 3\u2032-OH end. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments. RNA primers within the lagging strand are removed by the exonuclease activity of DNA polymerase I, and the Okazaki fragments are joined by DNA ligase.<\/span><\/p>\n Figure by<\/span> Parker, N., et.al. (2019) Openstax<\/em><\/a><\/span><\/p>\n As noted above, the replication of the bacterial chromosome is initiated at ori<\/em>C <\/em>where the initiator protein, DnaA, binds to start the <\/span>assembly of the enzymatic replisome machine. The early stages of this process involve the assembly of a primosome<\/em><\/strong>, that functions to unwind the two strands of DNA at the replication forks and add RNA primers to the DNA templates that will be used by the DNA Polymerase enzymes to begin replication. Subsequent to the remodelling of the replication origin induced by DnaA, the assembly of the bacterial loader-dependent primosome occurs in discrete steps and involves at least four different proteins (initiator protein, helicase, helicase loader protein, and primase) that act in a coordinated and sequential manner (Table 9.1).<\/span><\/p>\n The oriC<\/em> region of prokaryotes contains highly conserved sequence motifs that include an AT-rich box domain that serves as the recognition sequence for the binding of the DnaA initiator protein. Initial binding of DnaA to oriC\u00a0<\/em>promotes the melting of the DNA double helix and the recruitment of multiple DnaA subunits that form a helical oligomer along the newly opened single stranded DNA (ssDNA) (Figure 9.5). The DnaA protein contains four major domains. Domains III and IV are integral to binding the ssDNA, while domain I is involved with protein-protein interactions. Domain II forms a flexible linker between the protein interaction domain and the DNA binding domains.<\/span><\/p>\n Figure 9.5 Assembly of a Primosome.<\/strong> DNA melting at\u00a0oriC<\/em>\u00a0and loading of the DnaB6<\/sub>\u2013(DnaC)6<\/sub>\u00a0helicase\u2013loader complex onto the DNA bubble. Lower schematic: ATP-bound DnaA (the initiator protein) binds to DnaA-boxes via Domain IV, thereby promoting dsDNA to wrap around the DnaA filament, causing torsional strain\u00a0to the dsDNA. Meantime, Domain III of DnaA binds to one of the two ssDNA strands of DNA unwiding element and stretches the strand. These interactions cause the AT-rich DNA unwinding element to melt, forming a bubble. At the same time, binding of DnaC (the helicase loader) traps DnaB (the helicase) in an open lockwasher conformation, to enable its loading onto ssDNA. DnaC interacts with DnaA at the end of the filament and serves as an adaptor to load one DnaB\u2013DnaC complex. It is not known if closing of DnaB around ssDNA to form a hexameric ring occurs before or concomitantly with dissociation of DnaC. Domain I of DnaA interacts with the\u00a0N-terminal domain of DnaB, helping to load another DnaB\u2013DnaC on the complementary strand. Upper insets: The helical filament of DnaA formed by Domains III (light orange) and IV (pale green) of\u00a0Aquifex aeolicus<\/em> DnaA (PDB: 3R8F) and Domain IV of\u00a0E. coli<\/em>\u00a0DnaA (pale green) bound to dsDNA (PDB: 1J1V). The ssDNA binds in the middle of the DnaA filament via interactions with the\u00a0AAA+\u2009Domain III of DnaA.<\/span><\/p>\n Figure from:<\/span> Xu, Z-Q. and Dixon, N.E. (2018) <\/a>Curr<\/a> Op Struct Biol 53:159-168<\/a><\/p>\n In the E.coli <\/em><\/span>system, the helicase loader protein, DnaC, complexed with ATP, binds to hexameric helicase DnaB and forms a DnaB\u2013DnaC complex, which has been con\ufb01rmed by cryo-electronmicroscope (cryo-EM) studies. The loader protein delivers the helicase on to the melted DNA single strands of the DnaA\u2013ori<\/span>C nucleoprotein complex at the origin of replication. In vivo<\/span><\/em>, this delivery is associated with the initiator protein, DnaA, whose amino-terminal domain (NTD) is thought to have a role in loading the helicase and helicase loader complex onto the ori<\/span>C <\/em>by interacting with helicase, DnaB. After the loader protein dissociates from the helicase ring, the NTD of the helicase interacts with the carboxy-terminal domain (CTD) of the primase and forms a functional primosome.<\/em><\/strong> Within the primosome, the helicase (DnaB) acts to unwind the double stranded helix and the primase (DnaG) synthesizes RNA primers on both the leading and lagging DNA strands.<\/span><\/p>\n Helicases<\/b><\/em> are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands such as DNA and RNA, using energy from\u00a0ATP\u00a0hydrolysis. 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.\u00a0The\u00a0human genome\u00a0codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases.\u00a0Many cellular processes, such as\u00a0DNA replication,\u00a0transcription,\u00a0translation,\u00a0recombination,\u00a0DNA repair, and\u00a0ribosome biogenesis\u00a0involve the separation of nucleic acid strands that necessitates the use of helicases. In E. coli<\/em>, the DnaB Helicase (Figure 9.5) is responsible for unwinding the two parent DNA strands to unwind and separating them from one another to form a “Y”-shaped replication fork. The replication forks are the actual site of DNA copying. During replication within the fork, helix destabilizing proteins, called single stranded binding proteins (SSB)<\/em><\/strong>, bind to the single-stranded regions preventing the strands from rejoining.<\/span><\/p>\n DNA polymerase enzymes<\/strong><\/em> are required for the assembly of the daughter strands along each of the template DNA strands. All DNA polymerases require a DNA template and a primer that is used to begin the replication process. The primer is a short strand of RNA that is placed on the DNA template by the primase enzyme. Recall also that DNA contains two antiparallel strands and that DNA polymerases can only add new nucleotides in the 5′ to 3′ direction when synthesizing the daughter strands of DNA. Since both strands of DNA are replicated simultaneously by the same replisome, the leading strand,<\/em><\/strong>where the daughter strand of DNA is moving in the 5′ to 3′ direction, is replicated continuously and flows in the same direction as replisome movement. The lagging strand,<\/em><\/strong> that lies in the antiparallel dirction, has to be synthesized in the opposite direction of replisome movement and is created using short bursts of DNA polymerase activity leading to the formation of Okazaki Fragments <\/strong><\/em>along the template strand. <\/strong><\/em>Thus, the lagging strand<\/strong><\/em> must continually be primed with short RNA sequences to maintain the formation of the Okazaki Fragments<\/em><\/strong>. The RNA primer sequences must then be replaced by DNA and gaps in the backbone of the DNA must also be repaired.<\/span><\/p>\n E. coli<\/em> has a total of five
<\/p>\n
\n
<\/p>\n
\nThink about It<\/span><\/em><\/strong><\/span><\/h4>\n
\n
Back to the Top<\/em><\/strong><\/span><\/a><\/h4>\n
\n<\/div>\n9.2 DNA Replication in Prokaryotes<\/strong><\/span><\/h2>\n
<\/p>\n
<\/p>\n
\nReplication Overview<\/em><\/strong><\/span><\/h4>\n
<\/a><\/p>\n
<\/a><\/p>\nBack to the Top<\/em><\/strong><\/span><\/a><\/h4>\n
\nPrimosome Assembly<\/em><\/strong><\/span><\/h4>\n
<\/a><\/p>\n
\nBack to the Top<\/em><\/strong><\/span><\/a><\/h4>\n
\nDNA Polymerases<\/em><\/strong><\/span><\/h4>\n