The concept of archaea was put forward by carl woese and george fox in 1977, because they are different from other prokaryotes in the phylogenetic tree of 16SrRNA. These two groups of prokaryotes were originally defined as archaea and eubacteria. Woese thinks that they are two fundamentally different organisms, so she renamed them archaea and bacteria, and together with eukaryotes, they formed three domain systems of organisms.
[Editor] Archaea, Bacteria and Eukaryotes
In terms of cell structure and metabolism, archaea is close to other prokaryotes in many aspects. In the two central processes of molecular biology, gene transcription does not obviously show the characteristics of bacteria, but is very close to eukaryotes. For example, the translation of archaea uses eukaryotic initiation and extension factors, and the translation process needs TATA box-binding protein and TFIIB in eukaryotes.
Archaea has some other characteristics. Unlike most bacteria, they have only one cell membrane and no peptidoglycan cell wall. Moreover, the lipids in the cell membranes of most bacteria and eukaryotes are mainly composed of glycerides, while the membrane lipids of archaea are composed of glycerol ethers. These differences may be the adaptation to the ultra-high temperature environment. The composition and formation process of archaea flagella are also different from bacteria.
Image:PhylogeneticTree.jpg Phylogenetic tree based on rRNA sequence shows three distinct branches: bacteria, archaea and eukaryotes) [Edit] Habitat.
Many archaea live in extreme environments. Some people live in extremely high temperatures (usually above 100℃), such as geysers or black chimneys on the seabed. Others live in a very cold environment or in water with high salt, strong acid or strong alkalinity. However, some archaea are neutral and can be found in swamps, wastewater and soil. Many archaea that produce methane live in the digestive tract of animals, such as ruminants, termites or humans. Archaea is usually harmless to other organisms, and the pathogenic archaea is unknown.
[edit] morphology
The diameter of a single archaea cell varies from 0. 1 to 15 microns, and some species form cell clusters or fibers, which can reach 200 microns in length. They can have various shapes, such as spheres, rods, spirals, leaves or squares. They have many metabolic types. It is worth noting that halobacter can make ATP by using light energy, although archaea can't realize photosynthesis by using electronic chain conduction like other organisms that use light energy.
[Editor] Evolution and Classification
According to the phylogenetic tree of rRNA, archaea can be divided into two types, Archaea and Archaea. In addition, these two unidentified species are composed of some environmental samples and the exotic species Nanoarchaeum equitans discovered by Karl Stetter in 2002.
Woese believes that bacteria, archaea and eukaryotes all represent the descendants of a distant ancestor with a simple genetic mechanism. This assumption is embodied in the name archaea (archaea in Greek). Then he officially called these three branches three fields, and each field consisted of several fields. This classification later became very popular, but the idea of distant creatures itself was not generally accepted. Some biologists believe that archaea and eukaryotes originated from specialized bacteria.
The relationship between archaea and eukaryotes is still an important issue. In addition to the similarity mentioned above, many other genetic trees also combine the two. In some trees, eukaryotes are closer to archaea than archaea, but biofilm chemistry has the opposite conclusion. However, genes similar to archaea have been found in some bacteria, such as Huanghua, which complicates these relationships. Some people think that eukaryotes originated from the fusion of archaea and bacteria, which became nucleus and cytoplasm respectively. This explains many genetic similarities, but it is difficult to explain the cell structure.
At present, 22 archaea genomes have been sequenced, and another 15 genomes are being sequenced. [ 1]
[Edit] See
Taxonomy of archaea
[edit] supplement
In 1970s, Dr. carl woese took the lead in studying the evolutionary relationship of prokaryotes. Instead of studying the morphological and biochemical characteristics of bacteria as usual, he determined the genetic relationship of these microorganisms by analyzing the sequence analysis of another nucleic acid-ribonucleic acid (RNA) determined by DNA sequence. As we know, DNA is expressed by directing protein synthesis. protein synthesis determines the genetic characteristics of individual organisms, and it must go through a process of forming corresponding RNA. Protein must be synthesized on a structure called ribosome. Therefore, the most important component in cells is ribonucleoprotein, which is a huge and complex molecule in cells, and its function is to convert DNA information into chemical products. The main component of ribonucleoprotein is RNA, which is very similar to DNA molecules, and the molecules that make up it also have their own sequences.
Because ribosomes are so important to the biological expression function, they will not change easily, because any change in ribosome sequence may make ribosomes unable to perform their duties of building a new protein for cells, and then this individual cannot exist. Therefore, we can say that ribosomes are very conservative, and they have remained as stable as possible for hundreds of millions of years, and have not changed, even if they change, they are very slow and cautious. This slow molecular evolution rate makes the sequence of ribonucleoprotein RNA become the material to decipher the mystery of bacterial evolution. By comparing the RNA sequences of ribonucleoprotein in various bacteria, animals and plants, Uss ranked the genetic relationship of these organisms according to their similarity.
When Uss and his colleagues studied the RNA sequences in bacterial ribonucleoprosomes, they found that not all microorganisms were relatives. They found that Escherichia coli, which we thought was all bacteria, had nothing to do with methane-producing microorganisms. Their RNA sequence is no less different from that of ordinary bacteria than that of fish or flowers. Methane-producing microorganisms are different in the microbial world, because they will be killed by oxygen and produce some enzymes that cannot be found in other organisms, so they call this methane-producing microorganism the third kind of organism. Later, it was found that some microorganisms have RNA sequences similar to methanogens, which can grow in salt or in hot springs near boiling. And we know that there was no oxygen in the atmosphere of the early earth, but it contained a lot of ammonia and methane, which might be very hot. Animals and plants can't survive under such conditions, but they are very suitable for these microorganisms. Under this abnormal earth condition, only these strange creatures can survive, evolve and dominate the early earth, and these microorganisms are probably the oldest life on the earth.
Therefore, Uss named this kind of third organism archaea, which became one of the three kinds of organisms that kept pace with bacterial domain and eukaryotic domain. At first, they were not so bold, but were called archaea. Later, they thought that the term might mislead people into thinking that it was the same general bacteria and could not show their uniqueness, so they simply removed the suffix "bacteria". This is the origin of the word archaea.
[edit] supplement
Discovery of archaea
People's interest in archaea didn't begin in 1970' s. Some peculiar living habits of archaea and its potential biotechnology development prospects have attracted many people's attention for a long time. Archaea is often found living in various extreme natural environments, such as submarine high-pressure thermal overflow, hot springs, saline-alkali lakes and so on. In fact, on our planet, archaea represents the limit of life and determines the scope of the biosphere. For example, an archaea called Firemouth can grow at temperatures as high as 1 13℃. This is the highest biological growth temperature found so far. In recent years, using molecular biology methods, it has been found that archaea is also widely distributed in various natural environments, and archaea lives in soil, seawater and swamps.
At present, archaea that can be cultured in the laboratory mainly includes methanogenic bacteria, extremely thermophilic bacteria and extremely halophilic bacteria. Methanogenic bacteria live in an environment rich in organic matter and strictly oxygen-free, such as swamps, rice fields and ruminant stomach of ruminants. Participate in the carbon cycle on the earth and be responsible for methane biosynthesis; Extremely halophilic bacteria live on the surface of salt lakes, salt pans and salt products, and can grow in salt-saturated environment, but they cannot grow when the salt concentration is lower than 10%. Extremely thermophilic bacteria are usually distributed in hot spots of land or water containing sulfur or sulfide, such as sulfur-containing hot springs, swamps and submarine thermal overflows. Most extremely thermophilic bacteria are strictly anaerobic and completely sulfur-converted when gaining energy.
Although their living habits are quite different, all groups of archaea have the same cytological and biochemical characteristics, which is different from other organisms. For example, the cell membrane of archaea contains lipids linked by branched hydrocarbon chains and D-type phosphoglycerol through ether bonds, while the cell membranes of bacteria and eukaryotes contain lipids linked by unbranched fatty acids and L-type phosphoglycerol through ester bonds. The main component of bacterial cell wall is peptidoglycan, while archaea cell wall does not contain peptidoglycan.
Interestingly, although similar to bacteria, archaea chromosome DNA is closed-loop, and genes are also organized into operons (operons are the basic structural units of gene expression and regulation in prokaryotes, and genes related to biological activities often coordinate the opening and closing of gene expression in the form of operons). Archaea has obvious eukaryotic characteristics in DNA replication, transcription and translation. Non-formylated methylthio tRNA is used as initial tRNA, promoter, transcription factor, etc.
The results of comparative biochemistry show that archaea and bacteria are essentially different, which is consistent with the alienation of their phylogenetic relationship.
Dichotomy and three-domain theory
How many life forms are there on the earth? When Aristotle established biology class, he divided biology into animals and plants by dichotomy. The birth of the microscope made people discover bacteria invisible to the naked eye. The most fundamental difference in cell structure between bacteria and animals and plants is that there are nuclei in animal and plant cells, which mainly store genetic material DNA, while bacteria have no nuclei and DNA is free in cytoplasm. Because the difference between animals and plants is smaller than that between them and bacteria, E. Chatton put forward a new biological dichotomy rule in 1937, that is, organisms are divided into nucleated eukaryotes and seedless prokaryotes. Animals and plants belong to eukaryotes, and bacteria belong to prokaryotes.
After Darwin published the Origin of Species in 1859, biologists began to establish a classification system based on evolutionary relationship rather than phenotypic similarity, which is called phylogenetic classification system. However, due to the lack of fossil records, this classification method has not been effectively applied to the classification of prokaryotes for a long time. From 65438 to 0970, with the development of molecular biology, Wuss finally made a major breakthrough in this field.
In the long process of evolution, the sequence of information molecules (nucleic acid and protein) in every biological cell is constantly changing. The generation of many information molecular sequence changes is random in time, and the evolution rate is relatively constant, that is, it has clock characteristics. Therefore, the genetic relationship between species can be quantitatively described by the sequence difference of a clock characteristic gene or its product (such as protein). These genes or their products become molecular timers to record biological evolution. Obviously, this kind of molecular timer for recording the development of biological system should be widely distributed in all living things. Based on this consideration, Wuss chose a molecule called small subunit ribosomal nucleic acid (SSU rRNA) as a molecular timer. This molecule is an integral part of the ribosome of the intracellular protein synthesis machine, and protein synthesis is an important aspect of almost all biological activities. Therefore, it is appropriate to use SSU rRNA as a molecular timer.
After comparing the similarity of SSU rRNA sequences between different prokaryotes and eukaryotes, Wuss found that methanococcus, which was originally considered as bacteria, represented a different life form from eukaryotes and bacteria. Considering that the living environment of methanococcus may be similar to the natural environment on earth when life was born, Wuss called this creature archaea. On this basis, Wuss proposed in 1977 that organisms can be divided into three groups, namely eukaryotes, eubacteria and archaea. Based on the results of SSU rRNA analysis, a pan-system phylogenetic tree was born.
Further research shows that the first bifurcation on the evolutionary tree produced a branch of eubacteria and a branch of archaea/eukaryote, and the bifurcation of archaea and eukaryote occurred later. In other words, archaea is closer to eukaryotes than eubacteria.
On this basis, 1990, Wuss put forward a three-domain classification theory: organisms are divided into three domains: eukaryotes, eubacteria and archaea, and domains are defined as taxonomic units above the upper limit. In order to highlight the difference between archaea and eubacteria, Wuss renamed archaea archaea. Eubacteria changed its name to bacteria. Three-domain theory gives archaea the same taxonomic status as eukaryotes and bacteria.
Wuss's three-domain theory has been opposed by some people since its birth, especially those outside the field of microbiology. Opponents insist that the distinction between prokaryotes and eukaryotes is the most fundamental and evolutionary classification rule in biology; Compared with eukaryotes with rich phenotypes, the difference between archaea and bacteria is far from great enough to need to change the dichotomy rule. However, in the nearly 20 years before the genome sequencing of Methanococcus jejuni was completed, the phylogenetic studies with various molecular timers have repeatedly proved that archaea is a unique life form.
The first genomic evidence of the three-domain theory
Despite the above knowledge of archaea, people were surprised when they first faced the whole genome sequence of Methanococcus jejuni. Methanococcus jejunum has 1738 genes, 56% of which have never been seen before! In contrast, only about 20% of the genomes of Haemophilus influenzae and Mycoplasma genitalium are unknown. So people finally realized at the genome level that archaea is a brand-new life form.
More interestingly, genes whose functions are more or less known account for 44% of the total genome of Methanococcus jejuni, which seems to outline the evolutionary relationship between archaea and other two types of organisms: archaea is similar to bacteria in productivity, cell division and metabolism, but similar to eukaryotes in transcription, translation and replication. In other words, an eccentric microorganism living at the bottom of the ocean has genes similar to those of human beings (not bacteria in human digestive tract) in genetic information transmission! While admiring the wonder of life, many people began to cheer for the final establishment of the three-domain theory. In 1996, the weekly magazine Science of the United States regarded the sequencing of the genome of Methanococcus jejuni as one of the major scientific breakthroughs, claiming that this achievement almost ended the debate around the three-domain theory.
New Challenges to the Phylogenetic Tree of Wu Si
Just when the suspense of archaea seems to be about to disappear, the new discoveries that followed make people fall into confusion again. Various complete microbial genome sequences have appeared in the database that people can consult with a click of the mouse. Among the published 18 biological genome sequences, archaea accounts for 4. Using a more sensitive method to analyze these genomes (including the genome of M. jejuni), we got a surprising result: only 30% (not more than half of the previous estimate) of the genes in the genome of M. jejuni encode functions that are unknown at present, which is similar to the bacterial genome. So the mystery and uniqueness of archaea have been reduced a lot.
What is even more unfavorable to the three-domain theory is that 44% of the gene product (protein) of Methanococcus jejuni with putative function has the characteristics of bacterial protein, and only 13% resembles eukaryotic protein. The genome of another archaea, methanobacterium thermophilum, has a similar situation. Therefore, the difference between archaea and bacteria is far less than that between archaea and eukaryote, which is not enough to convince the opponents of the three-domain theory.
It is even more difficult to understand that using different genes in the same organism to map the phylogeny of this species often leads to different results. Recently, the genome sequence of a bacterium (Aquifex aeolicus) that can grow near the boiling point has been determined. The phylogenetic study of several genes of this strain shows that if protein FtsY, which is involved in the regulation of cell division, is used as a molecular timer, this strain is similar to the soil bacterium Bacillus subtilis located in the branch of Phylogenetic Tree in Wu Si. If an enzyme involved in tryptophan synthesis is taken as the standard, the bacteria should belong to archaea; However, when comparing the enzymes that synthesize cytidine triphosphate (one of the basic structural units of DNA) with those of other organisms, it is found that archaea no longer forms independent groups. It seems that different genes are telling different evolutionary stories. So, can archaea be a unique and unified life form?
After the genome sequencing of Saccharomyces cerevisiae belonging to eukaryotes was completed, the three-domain theory encountered a greater crisis. Among the yeast nuclear genes, the genes related to bacteria are twice as many as those related to archaea. Some people also analyzed 34 protein families existing in all three life forms, and found that 17 families originated from bacteria, and only 8 families showed the genetic relationship between archaea and eukaryotes.
If Wu Si's phylogenetic tree is correct, the difference between archaea and eukaryote is later than that between them and bacteria, how can we explain these results?
According to the popular endogenous hypothesis in the study of cell evolution, the production of eukaryotic organelles (mitochondria and chloroplasts) originated from the endogenous relationship between bacteria and prokaryotes in the early stage of evolution. In this relationship, eukaryotic cells provide a stable microenvironment, while endosymbionts (bacteria) provide energy. Over time, endosymbionts evolved into organelles. Some genes of bacteria in eukaryotic nuclei may come from mitochondria. These genes usually encode protein molecules, and these protein molecules are transported back to mitochondria. However, it is now found that protein encoded by many nuclear genes of bacteria plays a role in cytoplasm rather than mitochondria. So where did these genes come from? Obviously, the endogenous hypothesis is not enough to save Wu Si's phylogenetic tree.
However, Wu Si's evolutionary tree will not fall down easily, and there are still many hypotheses to support it. Recently, a new version of the hypothesis of "horizontal gene transfer" has been proposed. According to this hypothesis, the heterozygous composition of genome is caused by gene transfer between different lineages during evolution. One organism can obtain the genes of another organism that may be far away by swallowing. Wuss speculated that before ancestors evolved into three lineages of bacteria, archaea and eukaryotes, they lived in a "commune" where genes could be exchanged with each other, and creatures from this "prehistoric commune" may have obtained different genetic inheritance. All these make it difficult to distinguish the branches of the evolutionary tree. But Wuss thinks that the phylogenetic tree based on SSU rRNA is correct on the whole, and there are three life forms.
The controversy continues.
The publication of the genome sequence of Methanococcus jejuni three years ago seems to indicate the end of a debate about how many life forms there are on earth that has lasted for more than 20 years. Archaea seems to be considered as the third life form. Now, only three years later, even the most optimistic people can't predict the fate of the evolutionary tree of Worcester. In this continuous debate, although the taxonomic status of archaea is questioned, the uniqueness of archaea as a life form is still affirmed to varying degrees.
At present, the research on archaea is heating up all over the world, not only because the unknown biological processes and functions contained in archaea far exceed those of the other two organisms, but also because archaea has immeasurable prospects for biotechnology development. Archaea surprises people again and again. It is certain that this unique biological group will continue to show people the infinite mystery of life in the years to come.