Genome complexity: transcription mechanism (Introduction)

by David Turell , Tuesday, September 15, 2015, 16:45 (3358 days ago) @ David Turell

How the molecules work together:-http://phys.org/news/2015-09-chemists-physicists-rna-polymerase-real.html-"RNA polymerase II (pol II) plays the key role of transcribing genetic code from DNA into segments of RNA, which pass those instructions on to the molecular machinery that assemble proteins. In order to do this, pol II needs the help of other molecules to form a multi-protein assembly called the preinitiation complex (PIC), which can pry apart the DNA's double-stranded helix and begin the process. As the PIC attaches to a section of DNA, it unwinds the helix and separates the two strands, forming a sort of "bubble" for the enzyme to sneak in and commence its work.-***-"The project was made possible by what Block, the senior author, describes as a "tour de force" of biochemistry from study co-author Kenji Murakami, a former postdoc in Roger Kornberg's lab at Stanford School of Medicine, to build a PIC. Working at Stanford with Kornberg, Murakami, now at the University of Pennsylvania, expressed and assembled 32 different proteins from yeast into the exact molecular machine that is required in higher organisms.-"'What he built is fully functional, and together, we got it to work in my lab at the single-molecule level, which is the first time it has even been attempted with an assembly this complex," Block said. "Even without everything else we learned during this work, this is a significant technical breakthrough."-"Next, they loaded the handmade PIC and a section of template DNA into a custom-built apparatus called an optical trap, in which two powerful lasers essentially hold on to either end of the genetic material. As the PIC initiated pol II activity and began to transcribe the template DNA, it either pulled or pushed the strands of DNA, and this motion affected the light scattered from a third laser in the apparatus. This tiny change in light scattering allowed the researchers to measure the motions of the PIC all the way down to the nanometer level.-***-"The sensitivity of their apparatus allowed the researchers not only to measure the size of the bubble created by the PIC but also to observe the activity of a separate transcription factor, called TFIIH, that serves as the molecular motor to help push the PIC along at the start. -"The researchers were pleased to see the motor in action, as it hadn't been documented before, but it was the size of the transcription bubble - the loop of DNA created to allow the gene to be converted to DNA - that was particularly exciting. Although scientists had seen a similar bubble in bacteria, the version they observed in higher organisms was enormous, at over 10 times larger."-Comment: Note that bacteria have a comparable mechanism. We should assume that cells in a multicellular animal work automatically, and I feel the same is true in bacteria, since the same mechanisms are at work.