What is the RNA world?

The Central Dogma and the Modern Genetic World

Soon after the discovery of the double-helical structure of DNA in 1953 by James Watson
and Francis Crick, Crick proposed an idea regarding information flow in cells that he called the “central dogma of molecular biology.” Crick correctly predicted that in all cells, information flows from DNA to RNA to protein. DNA was known to be the genetic material, the “library” of genetic information, and it had been clear for some time that the enzymes that actually did the work of facilitating chemical reactions were invariably protein molecules. The discovery of three classes of RNA during the 1960s seemed to provide the link between the DNA instructions and the protein products.

In the modern genetic world, cells contain three classes of RNA that act as helpers in the synthesis of proteins from information stored in DNA, a process called translation. A messenger RNA (mRNA) is transcribed from a segment of DNA (a gene) that contains information about how to build a particular protein and carries that information to the cellular site of protein synthesis, the ribosome. Ribosomal RNA (rRNA) interacting with many proteins make up the ribosome, whose major job is to coordinate and facilitate the protein-building procedure. Transfer RNA (tRNA) acts as decoding molecules, reading the mRNA information and correlating it with a specific amino acid. As the ribosome integrates the functions of all three types of RNA, polypeptides are built one amino acid at a time. These polypeptides, either singly or in aggregations, can then function as enzymes, ultimately determining the capabilities and properties of the cell in which they act.

While universally accepted, the central dogma led many scientists to question how this complex, integrated system came about. It seemed to be a classic “chicken and egg” dilemma: proteins could not be built without instructions from DNA, but DNA could not replicate and maintain itself without help from protein enzymes. The two seemed inextricably mutually dependent on each other. An understanding of the origins of the modern genetic system seemed far away.

The Discovery of Ribozymes

In 1983, a discovery was made that seemed so radical it was initially rejected by most of the scientific community. Molecular biologists Thomas Cech and Sidney Altman, working independently and in different systems, announced the discovery of RNA molecules that possessed catalytic activity. This meant that RNA itself could function as an enzyme, obliterating the idea that only proteins could function catalytically.

Cech had been working with the protozoan Tetrahymena. In most organisms except bacteria, the coding portions of DNA genes (exons) are interrupted by noncoding sequences (introns), which are transcribed into mRNA but must be removed before translation. Protein enzymes called nucleases are usually responsible for cutting out the introns and joining together the exons in a process called splicing. The molecule with which Cech was working was an rRNA molecule that contained introns but could apparently remove them and rejoin the coding regions without any help. It was a self-splicing RNA molecule, which clearly indicated its enzymatic capability. Altman was working with the enzyme ribonuclease (RNase) P in bacteria, which is responsible for cutting mature tRNA molecules out of an immature RNA segment. RNase P thus also acts as a nuclease. It was known for some time that RNase P contains both a protein and an RNA constituent, but Altman was ultimately able to show that it was the RNA rather than the protein that actually catalyzed the reaction.

The importance of these findings cannot be overstated, and Cech and Altman ultimately shared the 1989 Nobel Prize in Chemistry for the discovery of these RNA enzymes, or ribozymes (joining the terms “ribonucleic acid” and “enzymes”). Subsequently, many ribozymes have been found in various organisms, from bacteria to humans. Some of them are able to catalyze different types of reactions, and new ones are periodically reported. Ribozymes have thus proven to be more than a mere curiosity, playing an integral role in the molecular machinery of many organisms.

At around the same time as these important discoveries, still other functions of RNA were being identified. While perhaps not as dramatic as the ribozymes, antisense RNAs, small nuclear RNAs, and a variety of others further proved the versatility of RNA. While understanding the roles of ribozymes and other unconventional RNAs is important to the understanding of genetic functioning in present-day organisms, these discoveries were more intriguing to many scientists interested in the origin and evolution of life. In a sense, the existence of ribozymes was a violation of the central dogma, which implied that information was ultimately utilized solely in the form of proteins. While the central dogma was not in danger of becoming obsolete, a clue had been found that might possibly allow a resolution, at least in theory, to questions about whether the DNA or the protein came first. The exciting answer: perhaps neither.

The RNA World Theory and the Origin of Life

Given that RNA is able to store genetic information (as it certainly does when it functions as mRNA) and the new discovery that it could function as an enzyme, there was no longer any need to invoke the presence of either DNA or protein as necessities in the first living system. The first living molecule would have to be able to replicate itself without any help, and just such an “RNA replicase” has been proposed as the molecule that eventually led to life as it is now known. Like the self-splicing intron of Tetrahymena, this theoretical ribozyme could have worked on itself, catalyzing its own replication. This RNA would therefore have functioned as both the genetic material and the replication enzyme, allowing it to make copies of itself without the need for DNA or proteins. Biologist Walter Gilbert
coined the term “RNA world” for this interesting theoretical period dominated by RNA. Modern catalytic RNAs can be thought of as molecular fossils that remain from this period and provide clues about its nature.

How might this initial RNA have come into being in the first place? Biologist Aleksandr Oparin
predicted in the late 1930s that if simple gases thought to be present in Earth’s early atmosphere were subjected to the right conditions (energy in the form of lightning, for example), more complex organic molecules would be formed. His theory was first tested in 1953 and was resoundingly confirmed. A mixture of methane, ammonia, water vapor, and hydrogen gas was energized with high-voltage electricity, and the products were impressive: several amino acids and aldehydes, among other organic molecules. Subsequent experiments have been able to produce ribonucleotide bases. It seems reasonable, then, that nucleotides could have been present on the early Earth and that their random linkage could lead to the formation of an RNA chain.

After a while, RNA molecules would have found a way to synthesize proteins, which by their very nature are able to act as more efficient and diverse enzymes than ribozymes. Why are proteins better enzymes than ribozymes? Since RNA contains only four bases, which are fundamentally similar in their chemical properties, the range of different configurations and functional capabilities is somewhat limited. Proteins, on the other hand, can be constructed from a pool of at least twenty different amino acids, whose functional groups differ widely in terms of their chemical makeup and potential reactivity. It is logical to suppose, therefore, that proteins eventually took over most of the roles of RNA enzymes because they were simply better suited to doing so. Several of the original, efficient ribozymes would have been retained, and those are the ones that still can be observed.

How could a world composed strictly of RNAs, however, be able to begin protein synthesis? While it seems like a tall order, scientists have envisioned an early version of the ribosome that was composed exclusively of RNA. Biologist Harry Noller reported in the early 1990s that the activity of the modern ribosome that is responsible for catalyzing the formation of peptide bonds between amino acids is in fact carried out by rRNA. This so-called peptidyl-transferase activity had always been attributed to one of the ribosomal proteins, and rRNA had been envisioned as playing a primarily structural role. Noller’s discovery that the large ribosomal RNA is actually a ribozyme allows scientists to picture a ribosome working in roughly the same way that modern ones do, without containing any proteins. As proteins began to be synthesized from the information in the template RNAs, they slowly began to assume some of the RNA roles and probably incorporated themselves into the ribosome to allow it to function more efficiently.

The transition to the modern world would not be complete without the introduction of DNA as the major form of the genetic material. RNA, while well suited to diverse roles, is actually a much less suitable genetic material than DNA for a complex organism, even one only as complex as a bacterium. This is because the slight chemical differences between the sugars contained in the nucleotides of RNA and DNA cause the RNA to be more reactive and much less chemically stable, which is good for a ribozyme but bad if the genetic material is to last for any reasonable amount of time. Once DNA came into existence, therefore, it is likely that the relatively complex organisms of the time quickly adopted it as their genetic material; shortly thereafter, it became double-stranded, which facilitated its replication immensely. This left RNA, the originator of it all, relegated to the status it now enjoys; molecular fossils exist that uncover its former glory, but it functions mainly as a helper in protein synthesis.

This still leaves the question of how DNA evolved from RNA. At least two protein enzymes were probably necessary to allow this process to begin. The first, ribonucleoside diphosphate reductase, converts RNA nucleotides to DNA nucleotides by reducing the hydroxyl group located on the 2′ carbon of ribose. Perhaps more important, the enzyme reverse transcriptase would have been necessary to transcribe RNA genomes into corresponding DNA versions. Examples of both of these enzymes exist in the modern world.

Some concluding observations are in order to summarize the evidence that RNA, and not DNA, was very likely the first living molecule. No enzymatic activity has ever been attributed to DNA; in fact, the 2′ hydroxyl group that RNA possesses and DNA lacks is vital to RNA’s ability to function as a ribozyme. Furthermore, ribose is synthesized much more easily than deoxyribose under laboratory conditions. All modern cells synthesize DNA nucleotides from RNA precursors, and many other players in the cellular machinery are RNA-related. Important examples include adenosine triphosphate (ATP), the universal cellular energy carrier, and a host of coenzymes such as nicotinamide adenine dinucleotide (NAD), derived from B vitamins and vital for energy metabolism.

Impact and Applications

The discovery of ribozymes and the other interesting classes of RNA has dramatically altered the understanding of genetic processes at the molecular level and has provided compelling evidence in support of exciting new theories regarding the origin of life and cellular evolution. The RNA world theory, first advanced as a radical and unsupported hypothesis in the early 1970s, has gained widespread acceptance by scientists. It is the solution to the evolutionary paradox that has plagued scientists since the discovery and understanding of the central dogma: Which came first, DNA or proteins? Since they are inextricably dependent on each other in the modern world, the idea of the RNA world proposes that, rather than one giving rise to the other, they are both descended from RNA, that most ancient of genetic and catalytic molecules.

Unfortunately, the RNA world model is not without its problems. In the mid- to late 1990s, several studies on the stability of ribose, the sugar portion of ribonucleotides, showed that it breaks down relatively easily, even in neutral solutions. A study of the decay rate of ribonucleotides at different temperatures also caused some concern for the RNA world theory. Most current scenarios see life arising in relatively hot conditions, at least near boiling, and the instability of ribonucleotides at these temperatures would not allow for the development of any significant RNA molecules. Ribonucleotides are much more stable at 0 degrees Celsius (32 degrees Fahrenheit), but evidence for a low-temperature environment for the origin of life is limited. Consequently, some evolutionists are suggesting that the first biological entities might have relied on something other than RNA, and that the RNA world was a later development. Therefore, although the RNA world seems like a plausible model, another model is now needed to establish the precursor to the RNA world.

Apart from origin-of-life concerns, the discoveries that led to the RNA world theory are beginning to have a more practical impact in the fields of industrial genetic engineering and medical gene therapy. The unique ability of ribozymes to find particular sequences and initiate cutting and pasting at desired locations makes them powerful tools. Impressive uses have already been found for these tools in theoretical molecular biology and in the genetic engineering of plants and bacteria. Most important to humans, however, are the implications for curing or treating genetically related disease using this powerful RNA-based technology.

Gene therapy, in general, is based on the idea that any faulty, disease-causing gene can be replaced by a genetically engineered working replacement. While theoretically a somewhat simple idea, in practice it is technically very challenging. Retroviruses
may be used to insert DNA into particular target cells, but the results are often not as expected; the new genes are difficult to control or may have adverse side effects. Molecular biologist Bruce Sullenger pioneered a new approach to gene therapy that seeks to correct the genetic defect at the RNA level. A ribozyme can be engineered to seek out and replace damaged sequences before they are translated into defective proteins. Sullenger has shown that this so-called trans-splicing technique can work in nonhuman systems, and in 1996 he began trials to test his procedure in humans.

Many human diseases could be corrected using gene-therapy technology of this kind, from inherited defects such as sickle-cell disease to degenerative genetic problems such as cancer. Even pathogen-induced conditions such as acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), could be amenable to this approach. It is ironic and gratifying that an understanding of the ancient RNA world holds promise for helping scientists to solve some of the major problems in the modern world of DNA-based life.

Key Terms




ribosomal RNA (rRNA)


:

a type of RNA that forms a major part of the structure of the ribosome





ribosome


:

an organelle that functions in protein synthesis, containing a large and a small subunit composed of proteins and ribosomal RNA molecules




ribozyme

:

an RNA molecule that can function catalytically as an enzyme





Bibliography

Atkins, John F., Raymond F. Gesteland, and Thomas R. Cech, eds. RNA Worlds: From Life's Origins to Diversity in Gene Regulation. Cold Spring Harbor: Cold Spring Harbor, 2011. Print.

Bernhardt, Harold S. "The RNA World Hypothesis: The Worst Theory of the Early Evolution of Life (except for All the Others)." Biology Direct 7.23 (2012):1–10. Web. 14 Aug. 2014.

de Duve, Christian. “The Beginnings of Life on Earth.” American Scientist Sept./Oct. 1995: 428–37. Print.

Elliott, David, and Michael Ladomery. Molecular Biology of RNA. New York: Oxford UP, 2011. Print.

Hart, Stephen. “RNA’s Revising Machinery.” BioScience 46.5 (1996): 318–21. Print.

Hazen, Robert M. Genesis: The Scientific Quest for Life’s Origin. Washington: Henry, 2005. Print.

Horgan, John. “The World according to RNA.” Scientific American Jan. 1996: 27–30. Print.

Luisi, Pier Luigi. The Emergence of Life: From Chemical Origins to Synthetic Biology. New York: Cambridge UP, 2006. Print.

Miller, Stanley L. From the Primitive Atmosphere to the Prebiotic Soup to the Pre-RNA World. Washington: Natl. Aeronautics and Space Administration, 1996. Print.

Rauchfuss, Horst. Chemical Evolution and the Origin of Life. Trans. Terence N. Mitchell. Berlin: Springer, 2008. Print.

Szostak, Jack W. "The Eightfold Path to Non-Enzymatic RNA Replication." Journal of Systems Chemistry 3.2 (2012): 1–14. Web. 14 Aug. 2014.

Watson, James D., et al. Molecular Biology of the Gene. 7th ed. San Francisco: Benjamin, 2014. Print.

Yang, Lin, John E. Froberg, and Jeannie T. Lee. "Long Noncoding RNAs: Fresh Perspectives into the RNA World." Trends in Biochemical Sciences 39.1 (2014): 35–43. Print.