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RNA --"DNA's Messenger, or the Origin of Life on Earth?" (Weekend Feature)




Scientists today generally agree that DNA is the result of life on Earth, rather than its origin. But many molecular biologists are embracing the intruiging possibility, and strong evidence that the first life on Earth involved chemical multitasking by another key life molecule, ribonucleic acid or RNA. Molecular subunits of RNA have been found in alien carbonaceous chondrite meteorites, or could have formed through chemical reactions in the early Earth's oceans or primordial atmosphere leading to the exciting new theory that RNA is our earliest molecular ancestor. 

Many biologists still view RNA as a messenger to shutlle inforamtion from DNA to the cell's protein manufacturing centers, ribosomes. Like DNA, RNA is a string of four different kinds of nucleotide building blocks, except that RNA has a single chain rather than DNA's iconic double helix that uses a different sugar in its molecular architecture, and substitutes uracil instead of thymine.  However, unlike DNA, RNA is capable of carrying both genetic information and getting metabolic work done making it the "origin of life" molecule capabable of both reproducing itself and carrying the code to guide the needed copying.

Some bacterial cells can swim, morph into new forms and even become dangerously virulent - all without initial involvement of DNA. In 2009, Yale University researchers discovered how bacteria accomplish this amazing feat - and in doing so provided a glimpse of what the earliest forms of life on Earth may have looked like.

To initiate many important functions, bacteria sometimes depend entirely upon ancient forms of RNA, once viewed simply as the chemical intermediary between DNA's instruction manual and the creation of proteins, said Ronald Breaker, the Henry Ford II Professor of Molecular, Cellular and Developmental Biology at Yale and senior author of the study.




Proteins carry out almost all of life's cellular functions today, but many scientists like Breaker believe this was not always the case and have found many examples in which RNA plays a surprisingly large role in regulating cellular activity. The Yale study illustrates that - in bacteria, at least - proteins are not always necessary to spur a host of fundamental cellular changes, a process Breaker believes was common on Earth some 4 billion years ago, well before DNA existed.




"How could RNA trigger changes in ancient cells without all the proteins present in modern cells? Well, in this case, no proteins, no problem," said Breaker, who is also a Howard Hughes Medical Institute investigator.

Breaker's lab solved a decades-old mystery by describing how tiny circular RNA molecules called cyclic di-GMP are able to turn genes on and off. This process determines whether the bacterium swims or stays stationary, and whether it remains solitary or joins with other bacteria to form organic masses called biofilms. For example, in Vibrio cholerae, the bacterium that causes cholera, cyclic di-GMP turns off production of a protein the bacterium needs to attach to human intestines.

The tiny RNA molecule, comprised of only two nucleotides, activates a larger RNA structure called a riboswitch. Breaker's lab discovered riboswitches in bacteria six years ago and has since shown that they can regulate a surprising amount of biological activity. Riboswitches, located within single strands of messenger RNA that transmit a copy of DNA's genetic instructions, can independently "decide'' which genes in the cell to activate, an ability once thought to rest exclusively with proteins.

Breaker had chemically created riboswitches in his own lab and - given their efficiency at regulating gene expressions - predicted such RNA structures would be found in nature. Since 2002, almost 20 classes of riboswitches, including the one described in today's paper, have been discovered, mostly hidden in non-gene-coding regions on DNA.

"We predicted that there would be an ancient 'RNA city' out there in the jungle, and we went out and found it,'' Breaker said.

Bacterial use of RNA to trigger major changes without the involvement of proteins resolves one of the questions about the origin of life: If proteins are needed to carry out life's functions and DNA is needed to make proteins, how did DNA arise?

The answer is what Breaker and other researchers call the RNA World. They believe that billions of years ago, single strands of nucleotides that comprise RNA were the first forms of life and carried out some of the complicated cellular functions now done by proteins. The riboswitches are highly conserved in bacteria, illustrating their importance and ancient ancestry, Breaker said.

Understanding how these RNA mechanisms work could lead to medical treatments as well, Breaker noted. For instance, a molecule that mimics cyclic di-GMP could be used to disable or disarm bacterial infections such as cholera, he said.

The Daily Galaxy via Yale University and The Stardust Revolution, by Jacob Berkowitz

Image Credits: Universitat Pampeu Fabra (RNA) and wallpapers.free-review.net (meteorites)



Thermodynamics of origin of life: Why is there life?

(Why does life originate and exist now? It is the main question!
How does life originate? It is the second question!)
The transition between the animate and inanimate matter is a slow. It was predestined by the action of "thermodynamic principle of the substance stability" ( http://www.mdpi.org/ijms/papers/i7030098.pdf ) which describes the forward and backward linkages at the transmission of information between structural hierarchies during the chemical and biological evolution. http://gladyshevevolution.wordpress.com/article/thermodynamic-theory-of-evolution-of-169m15f5ytneq-3/
See: Thermodynamics and the emergence of life.
The phenomena of life can be explained on the basis of quasi-equilibrium hierarchical thermodynamics of dynamic systems which stands at the solid foundation of thermodynamics of JW Gibbs. Theory can be constructed without using the concept of dissipative structures of I. Prigogine and his ideas about negentropy.
http://www.youtube.com/watch?v=CYr1G5TZO50 http://gladyshevevolution.wordpress.com/article/science-evolution-and-reality-169m15f5ytneq-12/
From the point of view of thermodynamics, the phenomenon of life is defined as: "Life is the process the existence of the constantly renewed polyhierarchical structures during cycles of transformation of labile chemical substances in the presence of liquid water on the planet."
Georgi Gladyshev
Professor of Physical Chemistry

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