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The quirks of evolution: the discovery of an organism living without oxygen



The flora and fauna of our planet is incredibly rich in a wide variety of organisms, each of which has its own unique characteristics. Nevertheless, despite the infinite number of differences, there are always some common evolutionary rules for everyone. One such rule is the need for oxygen. Of course, mushrooms, amoeba, or ciliates over time have lost the ability to breathe, but these are only exceptions that confirm the rule. It was previously believed that aerobic respiration is inherent in all species of animals, but this is not entirely true. Scientists from Tel Aviv University (Israel) made an amazing discovery - the parasite Henneguya salminicolathat lives in the muscle tissue of salmon, which does not need oxygen. What information was obtained during the study of the new species and what differences were found in its gene information? We learn about this from the report of scientists. Go.

Study basis


Any feature of any living organism can be associated with its environment and the conditions in which its evolution took place. Aerobic respiration is the intersection point of many eukaryotic species, however there are several unicellular lines that have lost this ability due to their habitat in a hypoxic environment.

If we consider the organisms of aerobic creatures in terms of cells, but the most important is mitochondria. This two-membered spherical or ellipsoidal organelle with a diameter of the order of 1 μm is a kind of power plant, carrying out the oxidation of organic compounds. As a result of this, energy is generated, which is then used to generate electric potential, thermogenesis and synthesis of adenosine triphosphate (ATP, an energy source for biochemical processes).

If there is no oxygen in the habitat, and the body has evolved so as to do without it, then the mitochondria partially or completely lose their genome, turning into mitochondria-like organelles (MROs, mitochondria-related organelles ).

Researchers note that the issue of the presence of these MROs in animals has long spawned controversy in the scientific community. Some considered this impossible, while others were convinced of the opposite, but did not have material evidence of their theories. However, with the opening of Henneguya salminicola, the debate will not be so fierce.


Image No. 1: phylogenetic relationships of eukaryotes derived from the supermatrix from 9490 amino acid positions for 78 species. Species that have lost aerobic respiration are marked in bold and with an asterisk.

One of the main differences between MRO and conventional mitochondria is the absence in the first cristae * , which are replaced by hydrogenosomes * and mitosomes * .
Krista * - folds of the inner membrane of mitochondria.
Hydrogenosomes * - a closed membrane organelle of some unicellular anaerobic (not using oxygen) organisms, such as ciliates, trichomonads and fungi.
Mitosomes * - organelles of some unicellular anaerobic (not using oxygen) organisms. Most likely, mitosomes are involved in the synthesis of Fe – S (iron-sulfur) clusters, however, data on these organelles are still scarce.
In the study we are examining today, scientists demonstrated that the myxosoic parasite ( Cnidaria ) during evolution lost both its mitochondrial genome and aerobic metabolic pathways, replacing them with a new type of anaerobic MRO.

The main experimental in this study were made by Myxozoa (miksozoya) - class type of parasitic invertebrate Cnidaria ( Cnidaria ). Myxozoa mitochondria have very different genome structures, with large multi-part ring mitochondrial chromosomes and unusually high rates of evolution. Two closely related species were selected for analysis - Henneguya salminicola and Myxobolus squamaliswhich both parasitize in salmonids.

Research results


Before the actual analysis, transcriptomes and genomes of both species were collected. Phylogenetic analyzes based on 78 genes encoding a nuclear ribosomal protein in taxa representing eukaryotic diversity have confirmed that organisms that have been sequenced are closely related myxozoa.

Evaluation of the assembly quality of the genome showed that H. salminicola has a more complete assembly with higher coverage and more predictable protein sequences than M. squamalis (table No. 1).


Table No. 1: assessment of the quality of the assembly of the genome of the studied and representative species.

Targeted searches in the genomes identified 75/78 genes of nuclear ribosomal proteins, suggesting that the completeness is> 90% for both species. However, estimates of genome completeness using the basic eukaryotic gene mapping (CEGMA) method yielded only 53.6% of the main eukaryotic genes for H. salminicola and 37.5% for M. squamalis .

Scientists have suggested that it was the high rate of evolution that reduced the ability to detect many common eukaryotic genes.

Analysis of the mitochondrial (hereinafter mt ) genome showed striking differences between the two species under consideration. The circular mt genome was successfully restored for M. squamalis, consisting of one chromosome, which according to the phylogenetic analysis was mixozoal. As in other myxozoic species, tRNAs were absent in the mt genome of M. squamalis , and the rate of their evolution was quite high.

The situation with H. salminicola was the opposite, since it was not possible to identify the mt sequence, despite the even higher quality of this assembly compared to M. squamalis .

Further, to determine the presence / absence of DNA in myxozoic mitochondria, scientists stained the living multicellular developing stages of M. squamalis and H. salminicola using DAPI (4 ', 6-diamidino-2-phenylindole fluorescent dye).


Image 2: Microscopic images showing the absence of mitochondria in H. salminicola. M. squamalis

cells showed characteristic eukaryotic staining of both nuclei and mitochondria ( 2A ), while H. salminicola showed only nuclear staining ( 2B ). Microscopic results confirmed that the mt genome is missing in H. salminicola . However, mitochondria-like two-membrane organelles with cristae were also detected in H. salminicola ( 2C ) and even in M. squamalis

. Accordingly, genes involved in the organization of cristae have also been found in the genome of both species, in particular DNAJC11 and MTX1.

The totality of these data confirms that the examined species present MRO without the mitochondria genome, but there are cristae.

Researchers recall that in animals, most of the proteome * mitochondria is encoded in the nucleus.
Proteome * - a set of proteins that are expressed by a genome, cell, tissue or organism at a specific time.
With this in mind , 51 genes were identified in H. salminicola and 57 genes in M. squamalis involved in key metabolic pathways of mitochondria (e.g., metabolism of amino acids, carbohydrates or nucleotides).


Image 3: Comparison between pathways present in typical aerobic mitochondria ( A ) and H. salminicola MRO ( B ).

This suggests that the MRO of H. salminicola still performs a variety of metabolic functions similar to mitochondria of M. squamalis .

In contrast, almost all nuclear-encoded proteins involved in replication and translation of the mt genome were absent in the genome of H. salminicola. Using the database 118 of such nuclear encoded genes of Drosophila (fruit fly), able to determine from 41 to 58 homologous genes mt in M. squamalis , but only six of these genes have been found in H. salminicola .

It is worth noting that the gamma-1 DNA polymerase of the mt gene in the species H. salminicola is a pseudogen because it contains three point mutations that create premature stop codons * .
Stop codon * - a unit of the genetic code encoding the cessation of translation (synthesis of the polypeptide chain).
In addition, this gene is not expressed in H. salminicola and is not present in the H. salminicola transcriptome assembly , whereas homologous contigs * were identified in all other Myxozoic transcriptomes * .
Kontig * is a group of several series-connected DNA sections.
The presence of a pseudogenic copy of this polymerase is evidence of several previously expressed theories and observations. Firstly, this confirms the theory that H. salminicola lost its mt DNA because it does not have a mechanism for its replication. Secondly, this proves that the absence of protein homologs in this species is the result of pseudogenization, and not an assembly error.

Naturally, the loss of the mitochondrial genome has a direct effect on the respiratory format of the body, as animal mitochondria encode important proteins of the electron transfer chain. To check if mt genome loss meant loss of aerobic respiration in H. salminicola, scientists began searching for homologues of the known Drosophila nuclear genes, which usually encode ∼100 proteins from mt electron transport chain complexes .

A search revealed only seven of these proteins in H. salminicola , while the other Myxozoic was about 18-25. In particular, all gene complexes (I, III, and IV) that were detected in other Myxozoic species are absent in H. salminicola ( 3B ) or presented as pseudogenes.

Since complex IV interacts with O 2 molecules , this may mean that H. salminicola may be incapable of standard cellular aerobic respiration.

In addition to complexes I, III, and IV, which are responsible for the passage of protons into the mitochondrial intermembrane space, complex V responsible for ATP synthesis was also not detected in H. salminicola .

For a more detailed acquaintance with the nuances of the study, I recommend that you look into the report of scientists and additional materials to it.

Epilogue


In this study, the first data was collected regarding the genetic characteristics of a creature capable of, apparently, living without the need for aerobic respiration. What was previously considered an integral part of the animal world was not so important for some of its representatives.

The authors of this discovery note that usually evolution proceeds from simple to complex, but in the case of H. salminicola the opposite situation is observed. Life in an oxygen-free environment forced this organism to lose the more unnecessary genes responsible for aerobic respiration, which made it a simpler organism.

Of course, it remains unclear exactly how the evolution of the parasitic organism of the species H. salminicola proceeded.what exactly circumstances forced him to lose his mitochondria and actually abandon oxygen and why exactly such a variant of changes occurred. Scientists intend to consider these issues in their future research.

Be that as it may, this discovery is truly unique, as it once again confirms that nature still has something to surprise us with. Generally accepted laws and norms that were previously considered unshakable are violated in some rare cases. On the one hand, this is surprising; on the other, it is quite expected. After all, what else can you expect from evolution, which from a chaotic primary broth created such a complex and beautiful flora and fauna that surrounds us every day.

Thank you for your attention, stay curious and have a great weekend everyone, guys! :)

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