Functions of alternative replication protein A in initiation and elongation.

Replication protein A (RPA) is a single-stranded DNA-binding complex that is essential for DNA replication, repair, and recombination in eukaryotic cells. In addition to this canonical complex, we have recently characterized an alternative replication protein A complex (aRPA) that is unique to primates. aRPA is composed of three subunits: RPA1 and RPA3, also present in canonical RPA, and a primate-specific subunit RPA4, homologous to canonical RPA2. aRPA has biochemical properties similar to those of the canonical RPA complex but does not support DNA replication. We describe studies that aimed to identify what properties of aRPA prevent it from functioning in DNA replication. We show aRPA has weakened interaction with DNA polymerase alpha (pol alpha) and that aRPA is not able to efficiently stimulate DNA synthesis by pol alpha on aRPA-coated DNA. Additionally, we show that aRPA is unable to support de novo priming by pol alpha. Because pol alpha activity is essential for both initiation and Okazaki strand synthesis, we conclude that the inability of aRPA to support pol alpha loading causes aRPA to be defective in DNA replication. We also show that aRPA stimulates synthesis by DNA polymerase alpha in the presence of PCNA and RFC. This indicates that aRPA can support extension of DNA strands by DNA polymerase partial differential. This finding along with the previous observation that aRPA supports early steps of nucleotide excision repair and recombination indicates that aRPA can support DNA repair synthesis that requires polymerase delta, PCNA, and RFC and support a role for aRPA in DNA repair.

Small ncRNA binding protein, PIWI: A potential molecular bridge between blood brain barrier and neuropathological conditions.

The blood brain barrier (BBB) is a neuroprotective layer that maintains the homeostasis of central nervous system and provides an appropriate environment for neurons to execute their functions. The fundamental role of the dynamic semi-permeable BBB is selective and stringent transport of molecules from circulating blood and surrounding extracellular matrix across brain. Disruption of BBB has critical implications that can lead to various neuropathological disorders (NPDs) namely multiple sclerosis, Alzheimer's disease, epilepsy, traumatic brain injuries and neuropsychiatric disorders, etc. Therapeutic management of NPDs is still a daunting challenge in the field of neuromedicine and there is a great need for identifying novel drug targets and biomarkers. Recently, noncoding RNAs (ncRNA) have emerged as promising prognostic markers in NPDs. Piwi interacting RNAs (piRNA), a family of short noncoding RNAs which in association with PIWI-like proteins have shown to regulate neuronal function and memory formation. In addition, piRNAs are differentially expressed in Alzheimer's brain tissues and studies also revealed the association of denovo mutations in PIWI genes with autism. Moreover, the role of PIWI-like proteins in neuronal long-term potentiation and neurite outgrowth is now evident, confirming their importance in normal physiology of the brain. Notably, we have reported the significance of PIWI-like proteins in the maintenance of Blood Retinal Barrier (BRB) and its potential role in diseases like diabetic retinopathy through modulation of tight junction proteins. Further studies in hydra and cancer cells confirmed the important function of PIWI-like proteins in the organization of tight junctions. Interestingly, we also observed that loss of PIWI-like proteins affected the activity of Ephrin receptors which have an established functional link to tight junction assembly. Collectively, the evidences profoundly support the novel concept that piRNAs/PIWI-like proteins may have a potential role on the governance of BBB by altering the tight junctions through Ephrin effectors, commotion of which could be the preceding event to various NPDs. Here, we propose PIWI-like proteins and associated piRNAs as potential restorative drug targets for combating neuropathological conditions.

The binding of topoisomerase I to T antigen enhances the synthesis of RNA-DNA primers during simian virus 40 DNA replication.

Topoisomerase I (topo I) is required for the proper initiation of simian virus 40 (SV40) DNA replication. This enzyme binds to SV40 large T antigen at two places, close to the N-terminal end and near the C-terminal end of the helicase domain. We have recently demonstrated that the binding of topo I to the C-terminal site is necessary for the stimulation of DNA synthesis by topo I and for the formation of normal amounts of completed daughter molecules. In this study, we investigated the mechanism by which this stimulation occurs. Contrary to our expectation that the binding of topo I to this region of T antigen provides the proper unwound DNA substrate for initiation to occur, we demonstrate that binding of topo I stimulates polymerase alpha/primase (pol/prim) to synthesize larger amounts of primers consisting of short RNA and about 30 nucleotides of DNA. Topo I binding also stimulates the production of large molecular weight DNA by pol/prim. Mutant T antigens that fail to bind topo I normally do not participate in the synthesis of expected amounts of primers or large molecular weight DNAs indicating that the association of topo I with the C-terminal binding site on T antigen is required for these activities. It is also shown that topo I has the ability to bind to human RPA directly, suggesting that the stimulation of pol/prim activity may be mediated in part through RPA in the DNA synthesis initiation complex.

Assembly of the replication initiation complex on SV40 origin DNA.

The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association with the origin. The order in which these various proteins bind to the DNA was investigated by performing binding assays using biotinylated origin DNA. We demonstrate that in the presence of all four proteins, pol/prim was essential to stabilize the initiation complex from the disruptive effects of topo I. At the optimal concentration of pol/prim, topo I and RPA bound efficiently to the complex, although pol/prim itself was not detected in significant amounts. At higher concentrations less topo I was recruited, suggesting that DNA polymerase is an important modulator of the binding of topo I. Topo I, in turn, appeared to be involved in recruiting RPA. RPA, in contrast, seemed to have little or no effect on the recruitment of the other proteins to the origin. These and other data suggested that pol/prim is the first cellular protein to interact with the double-hexameric T antigen bound to the origin. This is likely followed by topo I and then RPA, or perhaps by a complex of topo I and RPA. Stoichiometric analysis of the topo I and T antigen present in the complex suggested that two molecules of topo I are recruited per double hexamer. Finally, we demonstrate that DNA has a role in recruiting topo I to the origin.

The cap region of topoisomerase I binds to sites near both ends of simian virus 40 T antigen.

Two independent binding sites on simian virus 40 (SV40) T antigen for topoisomerase I (topo I) were identified. One was mapped to the N-terminal domain (residues 83 to 160) by a combination of enzyme-linked immunosorbent assays (ELISAs) and glutathione S-transferase (GST) pull-down assays performed with various T antigen deletion mutants. The second was mapped to the C-terminal domain (residues 602 to 708). The region in human topo I that binds to both sites in T antigen was identified by ELISAs, GST pull-down assays, and double-hexamer binding assays with topo I deletion mutants. This region corresponds to a distinct domain on topo I known as the cap region that maps from residues 175 to 433. By combining these data with information about the structure of T-antigen double hexamers associated with origin DNA, we propose that the cap region of topo I associates specifically with both ends of the double hexamer bound to the SV40 origin to initiate DNA replication.