DNA replication in prokaryotes

The overall process of DNA replication in prokaryotes and eukaryotes is compared in Figure 1-2-1. 

The mechanism of replication in eukaryotes is believed to be very similar to this. However, the details have not yet been completely worked out. The steps and proteins involved in DNA replication in prokaryotes are compared with those used in eukaryotes in Table 1-2-2. 

Postreplicational mismatch repair has been found to correct errors in base substitution occurring during DNA replication in prokaryotes.48 This lowers the error rate for the polymerase from 1 in 106 to 107 to the observed range of values of 1 in 108 to 1010 in E. coli. How does the repair system know in this case which base in a mispair is the incorrect one The answer appears to be that the parent strand is tagged by methylation. A small proportion, some 0.2%, of the cytosine residues are methylated at the 5 position, and a similar proportion of the adenine residues are methylated at the 6 position. As methylation is a postreplicative event, the daughter strand is temporarily undermethylated after replication. 

The flow of genetic information involves biosyntheses of DNA, RNA, and proteins, known as replication, transcription, and translation, respectively. DNA replication in prokaryotes (Nossal, 1983) and eukaryotes (Campbell, 1985) are very similar, though eukaryotic replication is more complex (DePamphilis, 1996). A... 

Fig 11.14 Single bubble for DNA Replication in Prokaryotic Chromosomes Requirements for DNA Synthesis... 

DNA SYNTHESIS IN EUKARYOTES Although the principles of DNA replication in prokaryotes and eukaryotes have a great deal in common (e.g., semiconservative replication and bidirectional replicons), they also have significant differences. Not surprisingly, these differences appear to be related to the size and complexity of eukaryotic genomes. 

Another important difference between DNA replication in prokaryotes and in eukaryotes is that prokaryotic DNA is not complexed to histones, as is eukaryotic DNA. Histone biosynthesis occurs at the same time and at the same rate as DNA biosynthesis. In eukaryotic replication, histones are associated with DNA as it is formed. An important aspect of DNA replication in eukaryotes, specifically affecting humans, is described in the Biochemical Connections box on pages 282 and 283. 

EXAMPLE 8.7 One way in which difference 1 in Example 8.6 is addressed is that, in contrast to the single initiation site for DNA replication in prokaryotes, there are multiple initiation sites, between 3 x 10 and 3 x 10 base pairs apart, on eukaryotic chromosomes. Therefore, even though replication fork movement is slower in eukaryotes than in prokaryotes (about 50 nucleotides s ), the presence of multiple sites of initiation allows chromosome replication to occur on a time scale of 10 h whereas it would take -500 h if there were only a single initiation site. 

The enzymology of DNA replication in prokaryotes 227 TABLE 18.1 The subunit structure of DNA polymerase III holoenzyme of E. coli... 

The process of eukaryotic DNA replication closely follows that of prokaryotic DNA synthesis. Some differences, such as the multiple origins of replication in eukaryotic cells versus single origins of replication in prokaryotes, have already been discussed. Eukaryotic single-stranded DNA-binding proteins and ATP-dependent DNA helicases have been identified, whose functions are analogous to those of the prokaryotic enzymes previously discussed. In contrast, RNA primers are removed by RNase H. 

Many important details have emerged concerning the mechanisms of DNA replication in both bacteria (Prokaryotes) and higher cells (Eukaryotes). These mechanisms are vital in understanding how a cell duplicates its genetic material (DNA), and how this duplication is related to cell division. For these reasons, cells have evolved elaborate mechanisms to ensure that the process of duplication (DNA replication) is error free. This level of control is so important that cells will actually cease cell division if errors become too frequent and wait until the DNA is repaired. 

Related topics DNA replication in bacteria (F3) Transcription in DNA replication in eukaryotes (F4) prokaryotes (G2) RNA structure (Gl) Transcription in eukaryotes an overview (G5)... 

In addition, three enzymes involved in DNA replication, including DNA primases, prokaryotic DNA topoisomerase I and some hexameric DNA helicases, are also classic zinc-ribbon proteins. In bacteriophage DNA primases, mutations of the zinc-binding residues abrogate the synthesis of RNA primers for lagging strand DNA synthesis. Strikingly, each subunit of the mini-chromosomal maintenance (MCM) protein, a heterohexameric helicase that initiates DNA replication in S. cerevisiae, contains an independently folded zinc-ribbon domain that appears to stabilize the dodecameric structure (a dimer of hexamers) of this replication complex. ... 

DNA SYNTHESIS IN PROKARYOTES DNA replication in E. coli has proven to be a complex process that consists of several basic steps. Each step requires certain enzyme activities. 

The biological significance of DNA methylation in prokaryotes is now fairly clear, but its importance in eukaryotes has not yet been defined. What is known, however, is that methylation at a particular site is a heritable phenomenon. That is, when eukaryotic DNA replicates, a maintenance methylase ensures that all of the sites that were methylated in parental DNA are methylated in daughter DNA. The process is shown in Figure 25.3a. 

Eukaryotic cell cycle - The processes by which cells divide and DNA is replicated (see here) are somewhat more complicated in eukaryotes than in prokaryotes. DNA replication in bacteria is an almost continuous process, at least during exponential growth. The somatic cells of eukaryotes, on the other hand, typically divide much less frequently, and some, in certain types of mature tissue, do not divide at all. Eukaryotic cells that are dividing in growing tissues exhibit a well-defined cell cycle, which is almost always separated into several distinct phases, as shown in Figure 28.14, Figure 28.15, and Figure 28.16. 

The general features of DNA replication in eukaryotes are similar to those in prokaryotes. Table 10.5 summarizes the differences. As with prokaryotes, DNA replication in eukaryotes is semiconservative. There is a leading strand with continuous synthesis in the 5 3 direction and a lagging strand with discontinuous synthesis in the 5 3 direction. An RNA primer is formed hy a specihc enzyme in eukaryotic DNA replication, as is the case with prokaryotes, hut in this case the primase activity is associated with Pol a. The structures... 

Replication in eukaryotes follows the same general outline as replication in prokaryotes, with the most important difference being the presence of histone proteins complexed to eukaryotic DNA. 

Recall How does DNA replication in eukaryotes differ from the process in prokaryotes ... 

It is faster in prokaryotes. The DNA is smaller, and the lack of compartmen-talization within the cell facilitates the process. DNA replication in eukaryotes is linked to the cell cycle, and prokaryotic cells proliferate more quickly than those of eukaryotes. 

DNA replication in eukaryotes is fundamentally similar to that in prokaryotes. It is catalyzed by DNA polymerases which synthesize new DNA strands in a 5 —>3 direction. Synthesis of leading strand eukaryotic DNA is continuous while synthesis of lagging strand DNA entails the production of Okazaki fragments. However, there are a number of differences between prokaryotic and eukaryotic DNA replication. 

Termination and telomere The binding of the replication termination protein (Tus protein) to the terminus region (x locus) in prokaryotic chromosome impedes the progression of the replication fork and terminates DNA replication. In eukaryotes, the linear chromosomes terminate with telomeres by the action of telomerase. 

The replicon model used to describe the regulation of DNA synthesis in prokaryote cells has influenced many concepts of the same process in eukaryote cells. Since the basis of this discussion will center around the limitations of the replicon model as applied to eukaryotes, several terms will be emphasized here. The term "replication unit used here refers to any stretch of DNA in a eukaryote chromosome which is replicated by the efforts of one growing point. The growing point is defined as any one site on a parental, double-standard DNA molecule where enzymatic activity results in the replication of both strands of parental DNA. 

Table 71.1 Summary and comparison of DNA replication in eukaryotes and prokaryotes (see Chapters 63 and 64). Numbers refer to Fig. 64.1.

Mammalian plasmid-based vectors, in addition to a prokaryotic replicon and a selection marker to permit DNA replication in E. coli, commonly have a eukaryotic replicon and a eukaryotic selection marker. The replicon usually comes from viruses such as Simian virus 40 (SV40), bovine papilloma virus (BPV) or Epstein Barr virus (EPV). The commonly used promoters are the SV40 early promoter (including its upstream enhancer... 

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