Ribotyping

Reciprocally, the growth on single C source significantly decreases the bacterial diversity. For example, in the rhizosphere soil of potato, a dramatic reduction in the number of ribotypes was found by temperature gradient gel electrophoresis (TGGE) after 48 h of incubation with single C source substrate in Biolog microplate wells (I46). 

O Neill, G. L. Brazier, J. S. Magee, J. T. Duerden, B. I. A comparison of PCR ribotyping and pyrolysis mass spectrometry for typing clinical isolates of Clostridium difficile. Anaerobe 1996, 2, 211-215. 

Bacterial Ribotyping Kit complete kit of products for analysis of complex microbial communities. 

In 1981 I proposed the first model of postchemical evolution with the ribotype theory on the origin of life, and with the concept of ribotype, a term that indicates all RNAs and ribonucleoproteins of any organic system (Barbieri, 1981). Since ribonucleoproteins are advanced compounds, the name rihosoids was introduced to indicate all molecules made of RNA, or RNA and peptides, and the ribotype was also defined as the collective of all rihosoids of an organic system. 

Let us now come to the second part of postchemical evolution, the stage that was destined to lead to the origin of the first cells. It is in this stage that we must look for an answer to the problem that the replication paradigm has been unable to solve how did primitive systems manage to increase their complexity without being destroyed by error catastrophes The ribotype answer is based on three points. 

This then is the solution of the ribotype theory in order to avoid the error catastrophes in the journey toward exact replication, it was necessary to have high molecular weight protoribosomes, and the production of these ribosomes for an indefinite number of generations was possible, before exact replication, because ribosoids could achieve it with processes of self-assembly and quasi-replication. The development of high-molecular-weight protoribosomes took place during postchemical evolution, simply because all necessary conditions existed in that period, and the development could be realised with processes that were both natural and primitive. 

The 1981 paper, furthermore, pointed out that the ribotype is not only independent from genotype and phenotype, but has a logical and a historical priority over them. According to the ribotype theory,... 

At this point, however, we cannot ignore the fact that the evolution of protein synthesis started before the origin of the first cells, in systems which could not have cell walls, cytoskeleton filaments or sodium pumps, for the very good reason that all these structures require well-developed proteins. How could precellular systems have high potassium concentrations, and low sodium levels, without any of the molecular mechanisms that cells employ to this end The most plausible answer is that those concentrations did not have to be produced in prebiotic systems because they already existed in the environment of the primitive seas. The ribotype world, in short, was also a potassium world. 

As for the first living cells (the first common ancestor) we know even less, but again we are not completely in the dark. The evidence that we do have tells us that they came from the ribotype world, and therefore their genomes were made almost completely of RNAs. This means that during the transition from first to last common ancestor, the cells substituted RNA with DNA in their genes, probably by using enzymes that were very similar to reverse transcriptases. Traces of this substitution, in fact, seem to have survived, because many modern enzymes that produce DNA (the DNA polymerases) are still capable of functioning as reverse transcriptases (Poole et al., 1998). 

One of the main bacterial features is the fact that DNA transcription is immediately followed by translation, to the extent that in most cases protein synthesis starts on primary transcripts that are still attached to DNA. The result is that there is neither the time nor the space for a modification of the transcripts. In the ribotype world, on the other hand, the first nucleic acids were mostly random molecules, and the first systems were necessarily full of statistical RNAs. It is likely therefore that some kind of screening had to be made before protein synthesis, which means that primitive translation was taking place some time after primitive transcription. A system that contains both useful and useless RNAs is more primitive than a system in which all RNAs are useful, and so it is likely that in the common ancestor transcription was separated from translation. 

In 1981, the Journal of Theoretical Biology published The ribotype theory on the origin of life , a paper which proposed two novel ideas ... 

The origin-of-life scenario was instrumental for the new theory of the cell, because it led to the the conclusion that the ribotype had an evolutionary priority over genotype and phenotype. More precisely, the scenario described a precellular ribotype world (not to be confused with the RNA world) where some ribosoids could act as templates (ribogenotype), others as enzymes (ribophenotype), and others as polymerising ribosoids (ribotype) that were responsible for the growth and the quasi-replication of the ribonucleoprotein systems. 

The ribotype cannot be given up because there is no DNA and no protein that can do the job of protein synthesis. Proteins and DNAs are two independent worlds, and only an organic code can build a bridge between them. The genetic code is that bridge, and that code... 

Barbieri, M. 1981. The ribotype theory of the origin of life. Journal of Theoretical Biology, 91,545-601. 

Mange, D. and Sipper, M. 1998. Von Neumann s quintessential message genotype + ribotype = phenotype. Artificial Life, 4,225-227. 

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