Proposal of RNA world hypothesis
In view of the above paradox, the debate has been endless until two famous experiments led to a new hypothesis in the 1980s.
1982 when studying Tetrahymena thermophilus in the laboratory of T.R. Cech, Department of Chemistry, University of Colorado, USA, it was found that the newly transcribed "precursor ribonucleic acid (rRNA)" can spontaneously catalyze its cleavage and splicing reaction under certain conditions. It excises a nucleotide chain and then connects the two ends of the cutting head to form a mature rRNA molecule. After this reaction, an "insertion sequence, IVS" consisting of 4 13 nucleotides will be released. This process shows that RNA has the catalytic function of enzyme, and IVS plays the catalytic role, which is the self-splicing intron in the premise rRNA. However, once mature RNA is formed, the catalytic activity of IVS is lost, so the self-splicing intron is still not a real catalyst and an authentic enzyme. But it does behave like an enzyme, so Cech and others call it a "ribozyme".
In addition, in 1978, when S.Altman of Yale University purified E.coli ribonuclease P (this enzyme is a tRNA processing enzyme existing in both bacteria and higher eukaryotes, and is a complex of RNA and protein), he found that one of the RNAs is necessary for cell catalytic reaction. In 1983, he cooperated with N.R. Pace to prove that in the cell environment, nuclease P needs both RNA and protein in order to cleave the tRNA precursor at a specific site. However, in vitro, the subunit of RNA alone can cleave tRNA at the correct site, but protein can't. At the beginning of the second year, Altman used a RNA subunit of ribonuclease transcribed from a recombinant DNA template to catalyze the premise of tRNA, and found that it could cause precise mutation of the latter. This experiment ruled out the possibility of protein pollution of the complex, thus clearly proving that the RNA subunit has a real catalytic function.
Later, people obtained dozens of ribozymes from different organisms, including cutting and splicing, which can catalyze both their own reactions and other molecular reactions. At this time, ribozyme has been proved to have the function of catalyst (enzyme) in a complete sense. Cech and Altman also shared the 1989 Nobel Prize in chemistry for this sensational discovery.
In view of the fact that RNA can be used as an information carrier as well as a catalyst, in other words, it can play a role similar to that of DNA and protein, people naturally think that RNA, rather than DNA or protein, is the earliest biomolecular system and genetic material at the origin of life. 1986, W.Gilbert of Harvard University, who won the Nobel Prize for inventing gene sequencing, formally wrote an article on this topic in Nature(3 19:6 18) and put forward the theory of "RNA world" for the first time.
The center of this theory is: in the early days of the origin of life, there was a molecular system composed entirely of RNA molecules, and the information of the system was stored by RNA, and some RNA molecules with catalytic function catalyzed the transmission of information of RNA itself and the self-replication of RNA molecules; Because this system can store and copy information, this system can survive and evolve; Finally, the storage of information is replaced by DNA molecules with more stable structure, and the catalytic function is replaced by protein with stronger catalytic ability, thus forming a modern life system. With the verification of some new experiments and the discovery of new phenomena, the "RNA world" hypothesis still has a high influence in the field of biology, and it is introduced as a confirmed fact in general works and even in some molecular biology textbooks.
In fact, this idea can actually be traced back to the 1960s. At that time, C. Woese of the University of Illinois and L. Orgel of Salk Institute in California, and F. Crick, a British biologist who discovered the double helix structure of DNA, all thought that RNA was the earliest biological intrinsic molecule and predicted that RNA might have catalytic function. Their understanding is based on the ubiquity of RNA in existing organisms: We know that messenger RNA(mRNA), ribosomal RNA(rRNA) and transporter RNA(tRNA) are indispensable in the process of DNA transcription and translation, and finally protein is synthesized. In addition, the discovery that the virus exists in the form of RNA instead of DNA also shows the rationality and possibility of this idea. But at that time, because there was no evidence of RNA catalysis, the idea was dormant for many years until Cech and Altman discovered it. Subsequently, the multifunctional research of RNA was more and more on the experimental platform of biologists, and the discovery of antisense RNA and RNA interference technology (Nobel Prize in Physiology and Medicine in 2006) could not but benefit from this.
Late experiment of RNA catalysis
With the upsurge of RNA research, besides the work of Cech and Altman mentioned above, several other studies are also commendable.
In 1992, American biologist Noller et al. treated the large subunit of Escherichia coli 50S with high concentration protease K, strong ion detergent SDS and phenol to remove various ribosomal proteins bound to 23SrRNA. The results show that the obtained 23SrRNA still has peptidyl transferase activity and can catalyze the synthesis of peptide chains. At the same time, Cech's laboratory also found that the formation and breaking of the bond between amino acids and tRNA is only catalyzed by rRNA; In 1995, M. Illangasekare of the University of Colorado and others found that RNA (neither rRNA nor aminoacyl -trna synthetase) can catalyze the transfer of aminoacyl groups, and the reaction speed is at least 105 times higher after screening; Also in 1995, team Szostak of Harvard University discovered ribozymes that can participate in the synthesis of C-N bonds through "in vitro evolution system" (Nature, 374:777). In 1998, David Bater's team at MIT discovered a monomer-pyrimidine nucleotide that can catalyze RNA synthesis (Natuer, 395:223). Their further research also found that ribozyme can synthesize a third RNA based on 1 RNA template. Therefore, RNA can synthesize a third RNA based on 1 RNA template, that is, RNA can copy RNA and transmit genetic information, although the length of the synthesized third RNA is only 14 nucleotides (Science, 200 1 292: 13 19).
The above research results greatly enrich the chemical content of RNA, and provide strong evidence for the theory of RNA world, indicating that early life activities may be mainly realized by RNA catalysis. "RNA world" is a very important period in the early life, during which there may be no protein and DNA at all.
Another explanation of RNA world
The virus was mentioned earlier, so let's start with the virus. The virus is a cell-free organism with a core-capsid structure consisting of a nucleic acid molecule (DNA or RNA) and a protein shell. Although its evolutionary position is controversial at present. However, what attracts people's attention is that the existence of viruses with RNA as their genetic material, especially viroids (consisting of only one infectious RNA molecule), also proves the functional particularity of RNA molecules? How did the virus originate? What does it have to do with the origin of other species? If we simply discuss the evolution of the virus itself, can we think that there are virus-like, then RNA virus and finally DNA virus? This problem has puzzled evolutionary biologists for a long time.
For a long time, there has been a hypothesis that viruses come from cells, and the genes of viruses come from cell genes. Viruses are formed when small fragments of cell genes escape from the cell genome and are wrapped in protein. Of course, based on the boarding nature of the virus, scientists have reason to think that the virus is so simple that it cannot complete various life activities without cells.
However, Patrick Fortel, a French biologist who has been studying the mechanism of DNA replication for a long time, doesn't think so. In the study of DNA replication, he found that the DNA replication enzymes and replication mechanisms of viruses are different from those of bacteria and eukaryotes. If the virus originated from a cell, it should be similar to the replication of cellular DNA.
In contrast, Fortress believes that viruses are the center of species evolution, and the DNA of other species comes from viruses. He believes that RNA should be the earliest carrier of genetic information, and during this period, a single-celled organism with RNA as its genome (considered as the fourth undiscovered new species except prokaryotes, eukaryotes and eukaryotes) was formed. Because of the instability of RNA, the RNA of these cells is easy to form small fragments, which are wrapped by protein to form the original virus. These viruses infect cells and are resisted by cells, which produce protein to degrade RNA and decompose foreign RNA. This is the origin of the degradation mechanism of exogenous RNA(RNAi) cells. Viruses are also evolving. They constantly modify their genomes, from single-stranded to double-stranded, and from RNA to DNA, so they are more stable and resistant to degradation by the host. Then these viruses live in the host. Because DNA is more stable than RNA, it replaces the host RNA and becomes the only genetic material in the cell. So cell DNA comes from viral DNA, and the nucleus comes from virus.
This hypothesis has been questioned by many people, who think that such a complex life system could not exist before the appearance of DNA, so the predecessor of Patrick's fortress hypothesis is untenable. However, Patrick Fortel said that these people's views are contrary to Darwin's theory of evolution, because evolution is a reflection from RNA to DNA.
Indeed, from an evolutionary point of view, it seems that there should be RNA before DNA. In addition to the hypothesis of "laying hens paradox" and "RNA world" mentioned above, it is also true from the point of view of pure chemistry: 1)RNA molecule is relatively simple with only one chain, while DNA molecule is very complex with two chains. According to the law of evolution, simple molecules always appear first; 2) Compared with deoxyribose on DNA molecules, the C2 position of ribose in RNA molecules has hydroxyl groups, and the chemical properties of the former are very active, which makes the RNA chain unstable. According to the evolutionary direction from unstable to more stable, RNA appeared first.
In fact, Fortress's hypothesis is reasonable, and today's RNA interference technology is undoubtedly an excellent proof of this hypothesis. But there are some questions: 1) Does a cell-like system with RNA as its genome exist? 2) This hypothesis provides an external motive force for the transformation from RNA to DNA (resisting the degradation of the host). What is its internal mechanism? That is, why did single-stranded RNA become double-stranded DNA? 3) 3) How can RNA be transformed into DNA?
We don't know the answer to the first question. For the second point, on the one hand, we can think that the relative stability of DNA molecule mentioned above makes nature choose it and abandon RNA, on the other hand, it can be explained by the experimental results of Bell and others at Scripps Institute in California. On the basis of synthetic experiments, they found that RNA exists in the form of partial double strands in modern organisms, and nature chose the double helix structure of RNA. Because it has both high bonding strength and good flexibility, it can better perform the duties of life (Science,1999,83: 699). Once the ribose in RNA molecules is replaced by more stable deoxyribose, it will naturally evolve into double-stranded DNA, which is determined by the internal mechanism of chemistry.
There is no convincing evidence as to how the early life with RNA as the genetic material transferred the ability of carrying genetic information to the present DNA and the catalytic function to protein. Especially in the aspect of function, because it depends on the arrangement of three-dimensional space, the function cannot be effectively transferred from DNA to RNA through base pairing, especially from RNA to DNA (in some viruses), which leads to the unclear mechanism of function transfer between biomolecules. In 2006, Gerald F. Joyce of Scripps Institute in the United States synthesized the corresponding DNA sequence for the first time on the basis of R3C RNA (a ribozyme consisting of 57 nucleic acids). Of course, this synthetic DNA sequence has no catalytic activity. Then, through an accelerated evolution process in vitro, the researchers successfully found the DNA sequence with the same activity as the original ribozyme in the test tube, which proved that the genetic information system based on nucleic acid can be transmitted in a linear way, and the function can also be carried out between the two systems in the same way on the basis of a certain number of mutations (chemistry &: Biology, 2006, 13:329). The third problem has also been solved.
Say a few more words about Gerald F. Joyce 1978 graduated from the university of Chicago, 1984 received the doctor's degree from UCSD, 1985- 1988 worked as a doctoral student at Salk Institute, and 1989 became a professor of molecular biology at Scripps Institute. His research fields include RNA biochemistry and the development of new RNA and DNA polymerases through in vitro evolution technology. He is very interested in early biochemistry and thinks that nucleic acid is a gene molecule that can be amplified and mutated in test tubes. Using the dual properties of nucleic acid as catalyst and gene molecule, his laboratory designed and invented the direct evolution technology of RNA molecules in vitro. The highest evolution speed of nucleic acid polymerase in test tubes can reach 100 generations per day, which is much faster than that in nature. They used this in vitro evolution system to explore the catalytic potential of RNA, focusing on those RNA polymerases that have the ability to catalyze self-replication. Using this artificial evolution system and selective mutation theory, Josie revealed that the new RNA polymerase may have played an important role in the formation of early life, and showed us how to evolve from an inanimate chemical substance to a living substance. It is because of his outstanding contribution in this field that he won the highest award of the International Association for the Origin of Life in 2005-the Yuri Award.
Several research papers in Science magazine are used to explain the RNA world and the origin of life.
Ribosome is a molecular factory that translates all the genetic information in life into protein. The structural diagram of a large ribosome subunit with atomic resolution obtained for the first time shows some unexpected details, which strengthens the support for the "RNA world" model of the origin of life on earth.
Scientists Peter B. Moore and Thomas A. Steitz, who have been engaged in ribosome research for a long time at Yale University, and their colleagues reported the complete atomic structure of a large ribosome subunit with a resolution of 2.4 angstrom from Haloarcula marismortui. This subunit consists of two ribosomal RNA(rRNA) molecules and 3 1 protein. These researchers found that rRNA domains interlock like the components of a three-dimensional jigsaw puzzle in ribosomes, thus forming a single entity. With the globular proteins around the ribosome, some protein strangely extend into the ribosome. However, active sites)-on ribosomes-those places that catalyze the formation of protein peptide chains-only include rRNA. Ribosomal proteins themselves do not seem to participate in the reaction of transforming genetic information into protein, and their functions may be similar to clay or mortar, sticking together the key "bricks" of rRNA.
This 16 page work was published as an article in Science (2000,289: 905-920). In addition, in the second article published as a companion (Science, 289:920-930), they pointed out that the above structure means that ribosomes are actually ribozymes, that is, RNA molecules that can catalyze their own chemical reactions. This large ribosomal subunit includes a tunnel from its contact point with the small ribosomal subunit to its back. This tunnel is the main outlet of the ribosome factory "assembly line". After adding more amino acids, it will continuously emit polypeptide chains. At the bottom of a deep crack at the entrance of the tunnel is the active site of peptide chain formation, where researchers carefully observed the catalytic performance of the whole RNA domain.
Where and how do these sites on ribosomes obtain catalytic ability? In the same issue of Science, an article by Gregory W. Muth, who works in the Department of Molecular Biophysics and Biochemistry of Yale University, was also published (Science, 289:947). According to Gregory W. Muth, a halophilic bacteria researcher, and his colleagues' corresponding work on the active part of ribosomes in Escherichia coli, it seems that a single nucleotide base on rRNA is reserved by all living species and has just the right acid-base properties. The independence and leading role of RNA in these ribosomes may further support the view that life on earth originated from RNA, because RNA is a molecule that can not only store genetic information, but also catalyze reactions to propagate other molecules.
According to the above three results, Thomas R. Cech, who first discovered ribozyme, expressed his views and discussed the possibility of these discoveries and the RNA world (Science, 289:879).
Speaking of which, it's time to go back to the article about "riboswitch" mentioned at the beginning. Some bacteria can swim around, change into new forms, and sometimes even become highly toxic, all without the participation of DNA. In view of many discoveries of functional diversity of RNA, people will naturally think that it is at work. So, how does RNA regulate genes? Ronald Breaker (also from Yale University, but affiliated with Howard Hughes Medical Institute) and his colleagues found that an RNA molecule named cyclic di-GMP, which consists of only two nucleosides, can activate a larger RNA structure-ribose switch. Ribose switch can regulate a large number of biological activities. They are located on the single strand of messenger RNA, transmitting the genetic instructions of DNA, and can independently decide which genes to activate in cells, which was once considered as protein's unique ability. Blake's laboratory has made riboswitches by chemical methods. Since 2002, about 20 kinds of natural riboswitches have been discovered, most of which are hidden in the non-gene coding region of DNA. This study helps to explain the problems related to the origin of life. That is to say, billions of years ago, single-stranded nucleoside containing RNA may be the primitive form of life, which performed some complex cellular functions currently performed by protein. Breaker believes that riboswitches are highly preserved in bacteria, indicating their importance and ancient lineage (Science, 2008, 32 1: 4 1 1).
Let's talk about the RNA world hypothesis
In the Origin of Life, the theory of RNA first can be accepted by more scholars in the scientific community, thanks to the discovery of the functional diversity of RNA mentioned above. However, there are still many problems to prove that RNA is the earliest genetic material. The biggest problem is that it is very difficult to synthesize RNA under simulated original conditions. Joyce also thinks that this is the weakest link in the "RNA world" hypothesis (Science,1989,246:1248).
Experiments before biosynthesis show that on the primitive earth, when gas molecules such as water vapor, CO2 and N2 meet lightning or solar ultraviolet radiation, a large amount of hydrocyanic acid and formaldehyde can be generated, and they further react to obtain bases. However, there is no obvious evolutionary reason for selecting these bases and ribose from a large number of isomers and products with similar structures, and designated binding patterns and perfect sequence structures can also be formed.
This even makes people suspect that a "hand of God" is secretly controlling all this. Christian Renede Duve, the winner of the Nobel Prize in Physiology and Medicine from 65438 to 0974, thought that the "RNA world" was too complicated and inconceivable. In the book Blueprint of a Cell written by 199 1, De Dewey put forward an older view: life originated from some primitive metabolism. He believes that the chemical reactions that occurred randomly on the earth in the early days may have produced a large number of peptides, and there are many other organic molecules around; Many of these compounds are naturally catalyzed, and once formed, the original chemical reaction can be selectively controlled; Then the concentration of some substances will increase first, and then start to catalyze further reactions in turn; Numerous networks connecting catalysts and reaction products will reduce side reactions, thus providing a non-genetic natural selection model, and these selected catalysts are the original ancestors of some enzymes in today's organisms. De Dewey's systematic hypothesis is actually consistent with asymmetric autocatalysis and Wachtershauser's chemoautotrophic theory mentioned in my previous blog post, and the latter two can even be said to provide experimental evidence for De Dewey's "cell blueprint" hypothesis. However, by his own admission, these key steps have not been proved in the laboratory.