DNA Replication Proteins 

Various DNA replication systems from bacteria, plasmids, bacteriophage, viruses, and eukaryotic cells have been studied to elucidate the mechanism of DNA replication. It emerged that most of them can complete the reaction with a limited number of enzymes called replication proteins (or factors)  (Table 1). The primary experiments were identification, as conditional mutants for bacterial growth and DNA synthesis, of the dna genes from Escherichia coli that encode replication proteins (1, 2).

About a dozen dna genes were identified and grouped as quick- or slow-stop mutants, which indicate whether the gene products are involved in the elongation or initiation stages, respectively. Development of in vitro DNA replication systems with E. coli crude lysates for single-stranded DNA phage and the E. coli chromosomal origin made it possible to identify and purify replication proteins by complementation of the missing activity caused by these mutations. In addition, some replication proteins were identified as proteins harboring known enzymatic activities required for replication, such as DNA Ligase, single-stranded DNA binding protein, ribonuclease H, topoisomerase I, and DNA gyrase. DNA gyrase subunits were also identified as drug-sensitivity gene products. 

Table 1. Essential Replication Proteins from Prokaryotes and Eukaryotes

Some proteins that have roles in other cellular processes function as replication proteins at specific stages in DNA replication; eg, RNA polymerase is necessary to activate several replication origins or to synthesize primer RNA; a heat-shock protein, grpE, is required to initiate lambda phage DNA replication, and thioredoxin is involved in T7 phage DNA polymerase.

Replication of T4 phage DNA is dependent primarily on its own encoded proteins, and a search for its replication proteins was carried out by the conditional mutant technique. As a result, seven replication proteins essential for the DNA synthesis, and many proteins with related functions, were identified.

Reconstitution of these replication reactions revealed that the replication factors do not react with a template DNA individually, but as a multimeric protein complex. Furthermore, the configurations and functions of the complex alter successively, from pre-initiation to elongation stages. For example, an assembly of DNA helicase and primase (and the assembly factors in some cases), called the primosome, is formed at the replication origins (or the assembly sites); subsequently, the addition of two DNA polymerase subunits and their accessory proteins in this complex generates a replisome, a super-protein complex that synthesizes leading and lagging DNA strands coordinately at a replication fork (2).

Due to the difficulty of applying genetics to most eukaryotes, the identification of eukaryotic replication proteins was started by a search of activities known to be involved in replication, such as DNA polymerases, topoisomerases, and DNA ligases. In contrast, a unicellular eukaryote, the yeast Saccharomyces cerevisiae, is exceptionally adaptable for genetic analysis, and many genes necessary for the cell cycle to progress have been identified. However, it was difficult to identify their biochemical activities and distinguish their requirement in DNA replication, due to the absence of any in vitro replication systems. The first breakthrough in studies of eukaryotic replication proteins occurred with the development the SV40 virus in vitro DNA replication system using human cell lysates (for a review, see (3)). Replication of this virus largely relies on the replication functions of the cell, so fractionation could identify the required proteins; this has isolated several replication proteins also involved in cellular chromosomal DNA replication. Furthermore, because these replication proteins are highly conserved throughout eukaryotes, several yeast replication genes were identified by homology searches (Table 1). Using previously and newly identified replication proteins, the process of SV40 DNA replication was totally reconstituted, and the functions of the proteins in DNA replication have been well elucidated (4). The replication reaction can be roughly divided into four stages: pre-initiation, initiation, elongation, and segregation (maturation), and specific sets of replication proteins are required to process these stages. The SV40 replication system primarily reproduced the cellular replication reaction from elongation to maturation but, in contrast, insufficient information about cellular initiation proteins was obtained from this viral system. One characteristic feature of eukaryotic DNA elongation obtained from the analysis is the involvement of multiple DNA polymerases in one replication fork.

Another breakthrough was the discovery of the origin recognition complex (ORC) from yeast (5) and licensing factor (MCM) from Xenopus (6). ORC specifically binds to the yeast replication origin sequence in an ATP-dependent manner and is a strong candidate for the initiator protein. MCM is a key player in the licensing reaction, and yeast MCM forms a pre-replicative complex at the origin, together with ORC. Through studies on their functions, the understanding of yeast chromosomal DNA replication has progressed drastically. Furthermore, these proteins are also highly conserved among eukaryotes, implying the existence of a common mechanism to initiate eukaryotic chromosomal DNA replication.

Another specific feature of eukaryotic replication proteins is that the replication process is tightly linked with several eukaryote-specific processes, such as cell-cycle control and chromatin assembly, so the boundary between replication and these processes is ambiguous. Therefore, cyclin-dependent kinases, licensing factors, and chromatin assembly factors are part of replication factors in eukaryotes and, indeed, some of them form assemblies with major replication proteins at replication foci during S phase.

References

1. T. A. Baker and A. Kornberg (1992) DNA Replication, 2nd ed., W. H. Freeman, New York, pp. 478-483.

2. K. J. Marians (1992) Ann. Rev. Biochem. 61, 673–719. 

3. B. Stillman (1989) Ann. Rev. Cell Biol. 5, 197–245. 

4. S. Waga and B. Stillman (1994) Nature 359, 207–212. 

5. S. P. Bell and B. Stillman (1992) Nature 357, 128–134. 

6. Y. Kubota et al. (1995) Cell 81, 601–609.