Interesting results about the evolutionary systematics of prokaryotes or “multiple origin”
Phylogenetic systematics is trying to determine the kinship of various organisms and their evolutionary proximity. If not so long ago, this was judged by the appearance of organisms (morphology, to be more precise), then now they have definitely passed judgment by comparing the genomes of these organisms.
But the DNA of an organism consists of many nucleotides and it is very difficult to take them all into account to determine the similarity of organisms. In addition, DNA is constantly evolving. Therefore, biologists began to rely on ribosomal ribonucleic acid (rRNA), because these molecules are found in all cellular life forms, their functions are associated with the most important translation process for the organism, the primary structure as a whole is characterized by high conservatism.
A feature of rRNA is believed to be outside the scope of selection, therefore these molecules evolve as a result of spontaneous mutations occurring at a constant rate, and the accumulation of such mutations depends only on time. Thus, a measure of the evolutionary distance between organisms is the number of nucleotide substitutions in the molecules of the rRNA being compared.
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It is known that 3 types of rRNA are present in the ribosomes of prokaryotes and eukaryotes. The information capacity of large molecules is larger, but they are harder to analyze. Therefore, the analysis of medium-sized rRNA molecules turned out to be the most convenient: 16S (~ 1600 nucleotides). Systematics is based on the calculation of the similarity coefficients of compared organisms. It is on the basis of the analysis of rRNA that modern taxonomy identifies three domains of bacteria, archaea and eukaryotes, as well as systematics, bacteria and archaea of the X edition of Bergi are based on this.
This is the current state of affairs in this area. I tried to create a basis for a slightly different, if you want alternative, systematics. Why? The conservativeness of rRNA, however, is not large enough; only some of its parts are conservative. And since there are enough variable parts of rRNA, we have to make assumptions and assume where there were breaks and insertions of individual fragments during mutation. A so-called. alignment is now done with a very large error.
As a result, I came to the conclusion that when comparing genomic sequences, it is necessary to compare such areas that have not undergone mutations at all, and which are absolutely identical in different organisms.
Look what came out of it.
Are there DNA segments that are not mutated at all for a long time?
But are there such areas that were not subjected to mutations at all, and absolutely identical in different organisms? It turns out there is. A number of proteins (their DNA code) are absolutely the same for many species belonging to the same genus, or even family. But even more conservative transport RNA (tRNA). In the chromosome of a bacterium, as a rule, there are all 20 types of tRNA, each of which is responsible for transporting a particular amino acid to the place of protein synthesis. And on the basis of them it is possible to trace the evolutionary connection not only of individual families, but also entire classes and even types.
In this study, I was based on only one tRNA that transports alanine (Ala tRNA). Therefore, conclusions about the evolutionary relationship do not claim to the final result. To do this, compare the results for other tRNAs. Nevertheless, the study done allows us to outline a number of provisions on the proximity of certain genera of bacteria. Then it will be shown that close evolutionary relationships cannot be spoken in terms of a phylogenetic tree. This is due to the fact that there is horizontal transfer and conjugation in bacteria, and other approaches are required.
Genome analysis
The genus Yersinia (Plague Wand) will be in the center of our attention, but as a result of the study, others such as Shewanella, Pseudomonas, Vibrio, Erythrobacter, Pseudoalteromonas, Photobacterium and a number of others (a total of 109 loci) were considered
tRNA in bacteria, as a rule, has a constant length of 76 nucleotides, while the anticodon is located at the positions 34,35,36. Alanine in DNA is encoded by four codons: GCT, GCC, GCA, GCG. Therefore, 4 types of Ala tRNA are potentially possible, with AGC, GGC, TGC, CGC anticodons.
But the overwhelming majority of the bacteria in question in the genome has only 2 species of Ala tRNA_GCA and Ala tRNA_GCC. There are, of course, exceptions.
For analysis, sequenced DNA genomes were used that are available in the NCBI database. All identical unmutated tRNAs were tagged with a unique identifier (Id). With the help of a computer program written for analysis, in a semi-automatic mode with manual verification, a list of various types of Ala tRNA was compiled, and their location in one or another sequenced locus.
results
All the considered strains of the genus Yersinia (9 pcs.) Have the same Ala tRNA_GCA with Id = 00046 and Ala tRNA_GCC with Id = 00043 in the genome. Based on this fact, it can be concluded that indeed these strains have a strong evolutionary connection, and therefore they all belong to the genus Yersinia.
Now the genus Yersinia belongs to the family Enterobacteriaceae. But on the basis of the analysis performed, within the framework of the similarity in Ala tRNA, this connection is poorly founded .
If you look at the classic members of the Enterobacteriaceae family, such as Escherichia, Salmonella, Shigella, Citrobacter, Cronobacter, Klebsiella, Pectobacterium, then all of them have completely different Ala tRNA. Namely, they have Ala tRNA_GCA with Id = 00011 and Ala tRNA_GCC with Id = 00012. On this basis, we can consider the listed genera of the family Enterobacteriaceae to be classical representatives.
And only with the genus Photorhabdus, along the same line Ala tRNA_GCA with Id = 00046, Yersinia has a connection. Therefore, the genus Yersinia has features from different families . We will call this kind of transition between different families .
So, if the genus Yersinia connects to the Enterobacteriaceae family only one non-mutated Ala tRNA_GCA configuration with Id = 00046 (and that partially), then the question arises with which family the Yersinia genus is associated with another configuration of the non-mutated Ala tRNA_GCC Id = 00043?
It turns out the most direct link along this line is the genus Shewanella (family: Shewanellaceae, order: Alteromonadales, class: gamma proteobacteria). At the same time, the line Ala tRNA_GCS uniting them with Id = 00043 is the key in evolutionary terms, since it is also present in the genera Pseudomonas and Vibrio. All these connections are closer than it follows from the modern classification, where these genera are combined only at the class level.
In turn, some members of the Shewanella genus have the same Ala tRNA_GCA with Id = 00047 and Ala tRNA_GCC with Id = 00043. Having already found out that Yersinia and Shewanella have a connection along one line (Id = 00043), it is interesting with whom the genus Shewanella is connected along a different line (Id = 00047). It turns out that this line is also quite key in evolutionary terms. It branches further and Ala tRNA_GCA with Id = 00047 also has representatives of the genera Vibrio, Thiomicrospira, Saccharophagus.
We can also trace these connections further (see figure). But now it is clear that in order to systematize these evolutionary connections, it is necessary to somewhat change the approach to their description.
in higher resolution
findings
It should be emphasized once again that all conclusions made in the work are based on the analysis of only tRNA Ala, and of course for the recognition of the results we need to check for other types of tRNA. However, even now we can draw some conclusions and describe how to change the approaches to taxonomy taxonomy.
Sufficient complexity is the determination of which species is more evolutionarily ancient, and which is younger. But if we proceed from the hypothesis that the biological world has evolved from the simple to the complex, then we have at least one indisputable fact. If a bacterium has two chromosomes, then it seems obvious that it is evolutionarily more young than having one.
Therefore, in our study, it is safe to say that the genus Vibrio is younger than Shewanella or Yersinia. And then, since Vibrio and Shewanella are united by identical Ala tRNAGCA with Id = 00047, then, with a high probability, the genus Vibrio originated from Shewanella and thus one chromosome occurred. After that, other members of the genus Vibrio descended from the genus Colwellia, and so the second chromosome occurred. As a result of combining these chromosomes in one organism, we can talk about the genus Vibrio, which is descended along one line from Shewanella, and along the other from Colwellia.
Thus, we should not talk about the descent from one ancestor, but about at least two or even more.
With single chromosomal bacteria, it is more difficult to determine the direction of evolution (who is younger and who is more ancient). But based on the two-chromosome species, it can be said, since there is a Vibrio species with Ala tRNA_GCA with Id = 00049 and Ala tRNA_GCC with Id = 00043; and there are Vibrio species with Ala tRNA_GCA with Id = 00047, then Ala tRNA_GCA with Id = 00047 and Ala tRNA_GCC with Id = 00043 existed initially. And they were contained in Shewanella, and therefore it must be recognized as the most ancient organism, and should be based on the systematics of the organisms considered here.
Then we can conclude that Yersinia originated from Shewanella in a single line. From Yersinia, in turn, Photorhabdus, from which the whole family Enterobacteriaceae. But this is only one line. On the other hand, we have already mentioned what kind of childbirth originated from Shewanella.
The multi-species origin greatly confuses the evolutionary picture, but nothing can be done about it - such is the complexity of speciation, and we only need to reflect them most accurately in conditions when not all species are known.
upd. Oh yes. I completely forgot, then they began to say - well, why should programmers fool any biology. So I actually wanted to make programmers interested in this topic, since it is they who are able to write algorithms for bio-computation. I simply do not have the strength to conduct a more complete analysis. Suddenly, someone interested in you, please write in a personal.
But the DNA of an organism consists of many nucleotides and it is very difficult to take them all into account to determine the similarity of organisms. In addition, DNA is constantly evolving. Therefore, biologists began to rely on ribosomal ribonucleic acid (rRNA), because these molecules are found in all cellular life forms, their functions are associated with the most important translation process for the organism, the primary structure as a whole is characterized by high conservatism.
A feature of rRNA is believed to be outside the scope of selection, therefore these molecules evolve as a result of spontaneous mutations occurring at a constant rate, and the accumulation of such mutations depends only on time. Thus, a measure of the evolutionary distance between organisms is the number of nucleotide substitutions in the molecules of the rRNA being compared.
')
It is known that 3 types of rRNA are present in the ribosomes of prokaryotes and eukaryotes. The information capacity of large molecules is larger, but they are harder to analyze. Therefore, the analysis of medium-sized rRNA molecules turned out to be the most convenient: 16S (~ 1600 nucleotides). Systematics is based on the calculation of the similarity coefficients of compared organisms. It is on the basis of the analysis of rRNA that modern taxonomy identifies three domains of bacteria, archaea and eukaryotes, as well as systematics, bacteria and archaea of the X edition of Bergi are based on this.
This is the current state of affairs in this area. I tried to create a basis for a slightly different, if you want alternative, systematics. Why? The conservativeness of rRNA, however, is not large enough; only some of its parts are conservative. And since there are enough variable parts of rRNA, we have to make assumptions and assume where there were breaks and insertions of individual fragments during mutation. A so-called. alignment is now done with a very large error.
As a result, I came to the conclusion that when comparing genomic sequences, it is necessary to compare such areas that have not undergone mutations at all, and which are absolutely identical in different organisms.
Look what came out of it.
Are there DNA segments that are not mutated at all for a long time?
But are there such areas that were not subjected to mutations at all, and absolutely identical in different organisms? It turns out there is. A number of proteins (their DNA code) are absolutely the same for many species belonging to the same genus, or even family. But even more conservative transport RNA (tRNA). In the chromosome of a bacterium, as a rule, there are all 20 types of tRNA, each of which is responsible for transporting a particular amino acid to the place of protein synthesis. And on the basis of them it is possible to trace the evolutionary connection not only of individual families, but also entire classes and even types.
In this study, I was based on only one tRNA that transports alanine (Ala tRNA). Therefore, conclusions about the evolutionary relationship do not claim to the final result. To do this, compare the results for other tRNAs. Nevertheless, the study done allows us to outline a number of provisions on the proximity of certain genera of bacteria. Then it will be shown that close evolutionary relationships cannot be spoken in terms of a phylogenetic tree. This is due to the fact that there is horizontal transfer and conjugation in bacteria, and other approaches are required.
Genome analysis
The genus Yersinia (Plague Wand) will be in the center of our attention, but as a result of the study, others such as Shewanella, Pseudomonas, Vibrio, Erythrobacter, Pseudoalteromonas, Photobacterium and a number of others (a total of 109 loci) were considered
tRNA in bacteria, as a rule, has a constant length of 76 nucleotides, while the anticodon is located at the positions 34,35,36. Alanine in DNA is encoded by four codons: GCT, GCC, GCA, GCG. Therefore, 4 types of Ala tRNA are potentially possible, with AGC, GGC, TGC, CGC anticodons.
But the overwhelming majority of the bacteria in question in the genome has only 2 species of Ala tRNA_GCA and Ala tRNA_GCC. There are, of course, exceptions.
For analysis, sequenced DNA genomes were used that are available in the NCBI database. All identical unmutated tRNAs were tagged with a unique identifier (Id). With the help of a computer program written for analysis, in a semi-automatic mode with manual verification, a list of various types of Ala tRNA was compiled, and their location in one or another sequenced locus.
results
All the considered strains of the genus Yersinia (9 pcs.) Have the same Ala tRNA_GCA with Id = 00046 and Ala tRNA_GCC with Id = 00043 in the genome. Based on this fact, it can be concluded that indeed these strains have a strong evolutionary connection, and therefore they all belong to the genus Yersinia.
Now the genus Yersinia belongs to the family Enterobacteriaceae. But on the basis of the analysis performed, within the framework of the similarity in Ala tRNA, this connection is poorly founded .
If you look at the classic members of the Enterobacteriaceae family, such as Escherichia, Salmonella, Shigella, Citrobacter, Cronobacter, Klebsiella, Pectobacterium, then all of them have completely different Ala tRNA. Namely, they have Ala tRNA_GCA with Id = 00011 and Ala tRNA_GCC with Id = 00012. On this basis, we can consider the listed genera of the family Enterobacteriaceae to be classical representatives.
And only with the genus Photorhabdus, along the same line Ala tRNA_GCA with Id = 00046, Yersinia has a connection. Therefore, the genus Yersinia has features from different families . We will call this kind of transition between different families .
So, if the genus Yersinia connects to the Enterobacteriaceae family only one non-mutated Ala tRNA_GCA configuration with Id = 00046 (and that partially), then the question arises with which family the Yersinia genus is associated with another configuration of the non-mutated Ala tRNA_GCC Id = 00043?
It turns out the most direct link along this line is the genus Shewanella (family: Shewanellaceae, order: Alteromonadales, class: gamma proteobacteria). At the same time, the line Ala tRNA_GCS uniting them with Id = 00043 is the key in evolutionary terms, since it is also present in the genera Pseudomonas and Vibrio. All these connections are closer than it follows from the modern classification, where these genera are combined only at the class level.
In turn, some members of the Shewanella genus have the same Ala tRNA_GCA with Id = 00047 and Ala tRNA_GCC with Id = 00043. Having already found out that Yersinia and Shewanella have a connection along one line (Id = 00043), it is interesting with whom the genus Shewanella is connected along a different line (Id = 00047). It turns out that this line is also quite key in evolutionary terms. It branches further and Ala tRNA_GCA with Id = 00047 also has representatives of the genera Vibrio, Thiomicrospira, Saccharophagus.
We can also trace these connections further (see figure). But now it is clear that in order to systematize these evolutionary connections, it is necessary to somewhat change the approach to their description.
in higher resolution
findings
It should be emphasized once again that all conclusions made in the work are based on the analysis of only tRNA Ala, and of course for the recognition of the results we need to check for other types of tRNA. However, even now we can draw some conclusions and describe how to change the approaches to taxonomy taxonomy.
Sufficient complexity is the determination of which species is more evolutionarily ancient, and which is younger. But if we proceed from the hypothesis that the biological world has evolved from the simple to the complex, then we have at least one indisputable fact. If a bacterium has two chromosomes, then it seems obvious that it is evolutionarily more young than having one.
Therefore, in our study, it is safe to say that the genus Vibrio is younger than Shewanella or Yersinia. And then, since Vibrio and Shewanella are united by identical Ala tRNAGCA with Id = 00047, then, with a high probability, the genus Vibrio originated from Shewanella and thus one chromosome occurred. After that, other members of the genus Vibrio descended from the genus Colwellia, and so the second chromosome occurred. As a result of combining these chromosomes in one organism, we can talk about the genus Vibrio, which is descended along one line from Shewanella, and along the other from Colwellia.
Thus, we should not talk about the descent from one ancestor, but about at least two or even more.
With single chromosomal bacteria, it is more difficult to determine the direction of evolution (who is younger and who is more ancient). But based on the two-chromosome species, it can be said, since there is a Vibrio species with Ala tRNA_GCA with Id = 00049 and Ala tRNA_GCC with Id = 00043; and there are Vibrio species with Ala tRNA_GCA with Id = 00047, then Ala tRNA_GCA with Id = 00047 and Ala tRNA_GCC with Id = 00043 existed initially. And they were contained in Shewanella, and therefore it must be recognized as the most ancient organism, and should be based on the systematics of the organisms considered here.
Then we can conclude that Yersinia originated from Shewanella in a single line. From Yersinia, in turn, Photorhabdus, from which the whole family Enterobacteriaceae. But this is only one line. On the other hand, we have already mentioned what kind of childbirth originated from Shewanella.
The multi-species origin greatly confuses the evolutionary picture, but nothing can be done about it - such is the complexity of speciation, and we only need to reflect them most accurately in conditions when not all species are known.
upd. Oh yes. I completely forgot, then they began to say - well, why should programmers fool any biology. So I actually wanted to make programmers interested in this topic, since it is they who are able to write algorithms for bio-computation. I simply do not have the strength to conduct a more complete analysis. Suddenly, someone interested in you, please write in a personal.
Source: https://habr.com/ru/post/146331/
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