20 Biochemical Society Transactions (2011) Volume 39, part 1 The archaeal PCNA proteins Miao Pan * †, Lori M. Kelman‡ and Zvi Kelman * † 1 ∗ Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, U.S.A., †Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, U.S.A., and ‡Program in Biotechnology, Montgomery College, 20200 Observation Drive, Germantown, MD 20876, U.S.A. Abstract PCNA (proliferating-cell nuclear antigen) is a ring-shaped protein that encircles duplex DNA and plays an essential role in many DNA metabolic processes. The PCNA protein interacts with a large number of cellular factors and modulates their enzymatic activities. In the present paper, we summarize the structures, functions and interactions of the archaeal PCNA proteins. Introduction PCNA (proliferating-cell nuclear antigen) was originally identified in humans as an antigen in patients with systemic lupus erythaematosus and as a protein that was synthesized during the S-phase of the cell cycle. The presence of the protein in the nucleus of dividing cells led to the name PCNA. Subsequent studies demonstrated that genes that encode PCNA are present in all eukarya and that the proteins are essential for cell viability. It was also found that the protein plays diverse roles in many aspects of DNA metabolic processes by interacting and modulating the activities of a large number of enzymes [1,2]. When genome sequences became available, it was found that all archaeal species sequenced contain at least one gene encoding a homologue of the eukaryotic PCNA. All PCNA proteins studied were shown to form ring- shaped structures that encircle duplex DNA and slide bi- directionally along it. This ability to slide on DNA leads to the term ‘DNA sliding clamp’ commonly used to de- scribe the protein. The first described, and to date best understood, function for PCNA is its role in chromosomal DNA replication as the processivity factor for the replica- tive DNA polymerases. Following primer synthesis by primase, PCNA is assembled around the primer, and, upon binding to the polymerase, tethers it to the template, resulting in processive DNA synthesis. To date, all activities described for the PCNA proteins require them to encircle the duplex; no biochemical function for PCNA off DNA has been reported. However, the PCNA proteins form stable rings in solution that cannot assemble independently around the duplex. RFC (replication factor C) complex was shown to function as the clamp loader in archaea and eukarya. RFC is capable of assembling PCNA around the DNA (reviewed in [3,4]). Following primer synthesis by primase, RFC recognizes the primer terminus and uses Key words: archaeon, DNA interaction, DNA sliding clamp, proliferating-cell nuclear antigen (PCNA), proliferating-cell nuclear antigen-interacting protein box (PIP-box), replication factor C (RFC). Abbreviations used: Fen1, flap endonuclease 1; PCNA, proliferating-cell nuclear antigen; PIP-box, PCNA-interacting protein box; RFC, replication factor C; UDG, uracil-DNA glycosylase. 1 To whom correspondence should be addressed (email zkelman@umd.edu). the energy from ATP hydrolysis to open the PCNA ring and assemble it around the primer. Although the mechanism of clamp opening by RFC is not yet understood, molecular dynamics simulation suggested a lateral opening and right- handed spiral of the ring which matches the right-handed spiral of RFC, resulting in clamp opening [5]. However, as PCNA participates in other cellular functions besides replication (see below), it is possible that other proteins or complexes, not yet identified, are also capable of loading PCNA on to DNA. The number of Okazaki fragments synthesized during the replication of the chromosome is larger than the number of PCNA molecules within the cell. Therefore PCNA has to be unloaded from the DNA so that it can be used on subsequent Okazaki fragments. It was shown that the eukaryotic RFC could also unload the PCNA from duplex DNA [6]. It is likely that the archaeal RFC has a similar function. In the present paper, we provide a summary of the current knowledge on the archaeal PCNA. For studies on the eukaryotic PCNA, the reader is referred to reviews on the subject [1,7]. The archaeal PCNA proteins All sequenced archaeal genomes contain at least one homologue of the eukaryotic PCNA protein. However, the number of homologues differs between members of the different archaeal kingdoms. Whereas the genomes of organisms belonging to the Euryarchaeota and Thaumarchae- ota kingdoms contain a single homologue of PCNA [8– 10], those belonging to the Crenarchaeota branch contain three homologues each [11,12]. Whereas the single PCNA in Euryarchaeota forms a homotrimer similar to the eukaryotic PCNA, the crenarchaeote proteins are active as heterotrimers [11,12]. To date, the genomes of only two archaeal species contain two genes encoding PCNA. One is the crenarchaeote Pyrobaculum aerophilum, and the other is the euryarchaote Thermococcus kodakaraensis. It is not yet clear, however, whether both PCNA proteins are essential for viability, whether both are active, or whether their activity is C  The Authors Journal compilation C  2011 Biochemical Society Biochem. Soc. Trans. (2011) 39, 20–24; doi:10.1042/BST0390020 Biochemical Society Transactions www.biochemsoctrans.org