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July 17, 2006
"And as all things have been & arose from one by ye mediation of one: so all things have their birth from this one thing by adaptation."
The second Middle East Crisis Open Thread over at the Agonist is probably the best place to go for headlines relevant to that particular clusterfuck.
All beings replicate their DNA the same way, be they prokaryotic or eukaryotic, even including the archaeans.
In two papers that will be concurrently published in the August edition of the journal Nature Structural and Molecular Biology (now available on-line), the researchers report the identification of a helical substructure within a superfamily of proteins, called AAA+, as the molecular “initiator” of DNA replication in a bacteria, Escherichia coli (E. coli), and in a eukaryote, Drosophila melanogaster, the fruit fly. Taken with earlier research that identified AAA+ proteins at the heart of the DNA replication initiator in archaea organisms, these new findings indicate that DNA replication is an ancient event that evolved millions of years ago, prior to when Archae, Bacteria and Eukarya split into separate domains of life.
For the E.coli study, Berger and his team utilized the exceptionally bright and intense x-rays of Beamline 8.3.1 at Berkeley Lab’s Advanced Light Source synchrotron. With the data gathered at this protein crystallography facility, Berger and his team assembled a high-resolution model of the molecular structure of a protein known as DnaA, which is a member of the AAA+ family. While it has long been known that DnaA controls the process of initiating DNA replication in bacteria, the molecular details of its myriad activities have until now been a mystery.
Berger’s team found that when the DnaA protein binds with adenosine triphosphate or ATP, the nucleotide molecule that supplies energy to all components of a cell, the ring-shaped AAA+ proteins assemble into a right-handed spiraling superstructure. This arrangement was unexpected, because in other functional AAA+ complexes, the ring assemblies are closed. In addition, the architecture indicated that the AAA+ superhelix will wrap coils of the DNA double-helix around its exterior, causing the familiar “spiral staircase” of the DNA to deform as a first step in the separation and unwinding of its two gene-carrying strands.
Studies over the past decade have demonstrated that all of the multiple events that initiate DNA replication in a eukaryote are directed by a single complex of proteins called the origin recognition complex (ORC). However, until now, models of the ORC proteins have lacked sufficient detail to identify the structure of the initiator. In their Drosophila study, Nogales and Botchan and their collaborators studied fruit fly ORC using single-particle electron microscopy. Their images revealed for the first time how the ORC when bound to ATP forms a AAA+ helical structure much like the DnaA superhelix found by Berger and his team in their E.coli study.
The idea that all three domains of life share the same DNA replication initiator is new and will require some re-thinking on the part of biologists who study eukaryotes. Re-thinking will also be required for models of DNA replication that predicted initiators would have similar structures to the protein “clamps” and “clamp loaders” already identified as key mechanisms in the DNA replication process.
Said Berger, “Our work shows that there are major structural distinctions between assembled initiator and clamp loader complexes. This not only has important implications for the respective functions of these different mechanisms, it also calls into question some cherished models in the field.”
The two studies by Nogales, Berger, Botchan and their colleagues also show how when nature finds a mechanism that works well, such a mechanism is conserved through evolution.
cat and MPEG-2: there's a first time everything, even for learning something from a LiveJournal comment
Another thing you should know is that VIDEO_TS files, being mpeg2 files, can be stapled together with cat (!) and they'll still play. Like:
cat a.vob b.vob c.vob > finalmovie.mpeg2
Posted by Jon Rubin at July 17, 2006 10:49 PM
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