Eukaryotic DNA primase. Abortive synthesis of oligoadenylates

A mitochondrial DNA primase from the trypanosomatid Crithidia fasciculata

We have purified to near homogeneity a DNA primase from a mitochondrial fraction of the trypanosomatid Crithidia fasciculata. The enzyme is a single polypeptide chain of 28 kDa. Using a poly(dT) template and ATP as a substrate, the enzyme makes oligonucleotides of which the vast majority are about 10 nucleotides in size or smaller. With a single-stranded M13 DNA template and the four rNTPs as substrates, the enzyme makes heterogeneous oligonucleotides in the same size range. These oligonucleotides efficiently prime the synthesis of DNA by the Klenow DNA polymerase. Immunolocalization with antibodies against the purified enzyme confirms that the primase is mitochondrial. Furthermore, the enzyme localizes to specific regions of the cell's single mitochondrion, above and below the condensed kinetoplast DNA. The primase does not co-localize with the mitochondrial topoisomerase II and DNA polymerase beta, both of which are associated with two protein complexes positioned on opposite sides of the kinetoplast disc. These localization studies have significant implications for the mechanism of kinetoplast DNA replication.

Highly selective affinity labeling of DNA polymerase alpha-primase from human placenta by reactive analogs of ATP

Highly selective affinity labeling of a DNA-polymerase alpha-primase complex from human placenta by o-formylphenyl esters of ATP, ADP and AMP was performed in a two-step procedure in which a substrate analog attached to the active center was elongated by radioactive ATP. If the covalent attachment is performed in the presence of poly(dT) template, the ATP esters modify selectively the delta subunit of the complex. If poly(dT) is added after the covalent binding of the reagent, both delta and gamma subunits become labeled. With the o-formylphenyl ester of AMP the delta-subunit is modified. The ADP ester modifies both the delta and gamma subunit in the presence and absence of template. It is shown that formylphenyl ester of ATP is not the substrate in the reaction of elongation catalyzed by primase. The data obtained suggest the binding site of initiating substrate to be located in the region of contact of the two subunits of primase. The role of the template in the formation of the active site is discussed.

Evolutionary role of abortive transcript as a primer for DNA replication

Abortive cycling features transcription initiation by RNA polymerase in both prokaryote and eukaryote. It is known that T7 RNA polymerase produces abortive transcripts up to eight ribonucleotides in length depending on the initial sequence of the DNA message. On the other hand, T7 RNA polymerase initiates DNA replication from the T7 primary origin by synthesizing primers. And the shortest primer from the phi l.lB promoter in the primary origin also seems to be eight ribonucleotides in length. Therefore, it is likely that the longest abortive transcript serves as the shortest primer for T7 DNA replication from the primary origin. Considering that promoters often exist in DNA replication origins for example, E. coli oriC and many eukaryotic origins, the early DNA replication system appears to have taken advantage of the abortive cycling of RNA-dependent RNA polymerase that already existed before the emergence of DNA world. The evolutionary primitive RNA polymerase could do both transcription and priming of DNA replication. Accordingly, abortive cycling would play an important role in evolution at the emergence of DNA world. The priming activity of the primitive RNA polymerase would be taken over by primase later, which seems to be a specialized RNA polymerase for abortive cycling.

Eukaryotic DNA primase appears to act as oligomer in DNA-polymerase-alpha--primase complex

Human placenta and calf thymus DNA-polymerase-alpha-primases were analyzed using native gradient-polyacrylamide-gel electrophoresis followed by overlay assays of polymerase and primase activities. The human enzyme contained three catalytically active native forms of 330, 440 and 560 kDa and the bovine enzyme five forms of 330, 440, 500, 590 and 660 kDa. Of the various DNA polymerase forms, only the largest (560 kDa for human DNA polymerase and 590 kDa and 660 kDa for bovine DNA polymerase) contained primase activity. Titration of human DNA-polymerase-alpha-primase with DNA-polymerase-free primase caused the conversion of the 440-kDa to the 560-kDa form. The data favour the idea that primase binds to DNA polymerase alpha as an oligomer of 3 primases/polymerase core. In addition, the ability of primase to utilize oligoriboadenylates containing (prA)n or pp(prA)n was investigated. The primase elongated pp(prA)2-7 up to nanoadenylates or decaadenylates, but did not add 9 or 10 mononucleotides to a preexistent primer. In contrast to pp(prA)n less than 10, (prA)n less than 10 were rather poor primers for the primase. Both pp(prA)8,9 and (prA)n greater than 10 were elongated by primase, producing characteristic multimeric oligonucleotides. The possible connection of the structure of the DNA-polymerase-alpha-primase complex with the catalytical properties of primase is discussed.