Abstract
The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.
Highlights
Replication, transcription and translation are fundamental events occurring in all living organisms
It has been reported that beta clamps and Proliferating Cell Nuclear Antigen (PCNA) share no sequence homology at all beta clamp proteins and PCNA are highly conserved in bacteria and in archaea/eukaryotes, respectively [2, 3, 9]
From the second iteration of the PSI blast, a number of bacterial beta clamps were found as homologues of P. furiosus PCNA
Summary
Replication, transcription and translation are fundamental events occurring in all living organisms. Two replication proteins, DNA sliding clamps and clamp loader share structural homology in the different domains of life. The existing body of information reveals that bacterial beta clamps and eukaryotic PCNA share structural homology. It has been reported that beta clamps and PCNA share no sequence homology at all beta clamp proteins and PCNA are highly conserved in bacteria and in archaea/eukaryotes, respectively [2, 3, 9]. We analyzed sequence homology between bacterial beta clamp and archaeal/eukaryotic PCNA To understand their evolution, sliding clamp sequences from representative bacteria, archaea and eukarya were retrieved and a phylogenetic tree was drawn for each domain of life. They reveal gene duplication and horizontal gene transfer events
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