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This article comes from the official account of Wechat: ID:fanpu2019, author: Amanda Heidt

Write article | Amanda Heidt

Compilation | Huang Yan

"where do I come from?"where do I come from", this question and "who am I" and "where am I going" are listed as the three basic philosophical questions. Since the advent of human civilization, people have never given up the exploration of their own sources. For thousands of years, countless writers, scholars and beauties have paid their blood and lives for it-fortunately, this kind of thing only happens in the age of ignorance, and now people only need to pay time and hair. At present, after decades of efforts, scientists have basically answered this question to the stage of "we evolved from primitive eukaryotes", but the origin of eukaryotes is still elusive. So, the question that evolutionists have to answer now is:

"We come from primitive eukaryotes, so where do primitive eukaryotes come from?"

In 2022, L ó pez-Garc í a, a biologist from the University of Paris at Thackeray (University of Paris-Saclay), and his colleagues embarked on a journey to continue exploring the origins of life. To this end, they went to one of the driest places in the world-the shrubby, gravelly plateau of South America's northern Atacama Desert. Visitors are not welcome there, but there may be clues about the origin of complex life. Surrounded by mountains and sand dunes, there is a warm and salty pool. A blanket of cyanobacteria and archaea, like multi-layer steamed bread, layer after layer-for them, it may be a rare oasis in the desert. L ó pez-Garc í a calls it a "primordial forest", meaning a "complex" ecosystem that existed long before the outbreak of species on Earth. Scientists now use these tiny ecosystems to simulate ancient ecosystems, because they must have been born no later than the first appearance of eukaryotes.

The fungus blanket may mimic the conditions under which eukaryotes were produced on early Earth. DIVERSITY, ECOLOGY AND EVOLUTION OF MICROBES (DEEM) / PURIFICACI N / L PEZ-GARC and An each layer of these blankets are supported by different kinds of microbes. The ones that occupy the surface with plenty of light and oxygen are mainly cyanobacteria, which are the earliest photosynthetic oxygen-releasing organisms. Their emergence changed the earth's environment from hypoxia to aerobics, which provided the material basis for aerobic respiration-let's say "Thank you cyanobacteria". Here, cyanobacteria not only feed humans, but also feed on the by-products of cyanobacteria in the lower blanket, where heterotrophic organisms exist in a hypoxic environment. The lower cushion of the bacterial blanket is black and smelly, which is the result of the reduction of sulfate and the production of methane by microorganisms under anoxic environment. It's not easy for everyone here. Each other feeds on metabolic waste-each other feeds each other with shit and urine.

This shit-to-urine relationship is scientifically called "symbiosis" or "nutritional symbiosis". L ó pez-Garc í a says this temporary mutually beneficial symbiosis may stabilize over time and evolve into a permanent relationship-probably what it feels like to have sex until we grow old together. In this environment, individuals of different kinds of microorganisms can be nested together to form a more stable main body. Scientists suspect that this subject is the embryonic form of early complex eukaryotic cells. In the long history, this most primitive "cell" gradually occupied the mainstream niche and thrived into stable eukaryotic cells, while eukaryotic cells with different division of labor joined together in a similar way. it eventually became a variety of macroscopic life. This process is called eukaryotic genesis (eukaryogenesis). The definition of eukaryotic genesis is still controversial, but it generally refers to the evolutionary process of the surge in cellular complexity 10 to 2 billion years ago.

During this period, some iconic characteristics of modern eukaryotic cells, such as nucleus, mitochondria, cytoskeleton, cell membrane, chloroplast and so on, appeared for the first time. These characteristics appear between the first and last common ancestors of all eukaryotic cells. According to the acronym, the former is called FECA (First Eukaryotic Common Ancestor) and the latter is called LECA (Last Eukaryotic Common Ancestor). But many details in the process are still up in the air. What did the earliest eukaryotes look like? What kind of relationship might they establish with other creatures? How do their molecular mechanisms work and evolve? These mysteries remain to be solved. Scientists have not yet reached a consensus on important issues such as "in which branch of life is sprouting" and which microbial participants may have contributed to it.

However, the identification of Asgard archaea in recent years has once again activated the discussion of eukaryotic genesis. The archaea, named after Norse mythology, is "the closest relative of living contemporary eukaryotes", providing evidence for past discussions and introducing new questions. Some researchers believe that this is by far the most exciting development in biology. "people have found so much, and so many predictions are being tested."

In 2013, Anja Spang, who received a doctorate in evolutionary microbiology from the Nordic shrine Asgard, is looking for a post-doctoral position. ). His PhD project focused on a group of archaea called Thaumarchaeota (now renamed Nitrososphaerota). (the translator renotes: does it look like you can find a job on this subject? During his PhD, Anja discovered that the genomes of these and other archaea contain genes that encode "eukaryotic signature proteins (ESP)". They are called eukaryotic characteristic proteins because they are characteristic proteins in eukaryotic cells, which means they should not be present in archaea-but they just do. With this doubt in mind, Anja Spang joined Professor Thijs Ettema's research group at Uppsala University (Uppsala University) in Sweden and began his deep-sea exploration. The translator, who graduated from Uppsala University in Sweden, said when he saw this paragraph: eat melons to your own home. Jpg. )

Loki's Castle Castle in the mid-Atlantic consists of five active hot spring vents. (Image Credit: Centre for Geobiology BY R.B. Pedersen) more than 2300 meters below the surface of the North Atlantic Ocean between Norway and Greenland, there is a pile of undersea sediments called "Loki Castle" from which the Ettema team intends to extract the genome. The initial sample was less than a teaspoon of undersea mud, but during the analysis, the software used to annotate and analyze genetic material returned strange results-which is good, according to scientific experience. the good thing about the unexpected and unsatisfactory result is that it is likely to be true. The software marked the homologous genes of the gene encoding actin (actin). Actin, which is used to maintain cell morphology in eukaryotic cells, is a typical eukaryotic characteristic protein, which obviously should not be present in archaea. So the homologous genes of the software markers come from a new group.

In 2015, the Ettema team wrote in the journal Nature that the gene was named Lokiarchaeota, and the "Loki" in it paid homage to Loki in Nordic mythology. Over the next few years, the team gradually enriched this group and named it the "Asgard superphylum". In addition to Loki, it also included groups named after Thor, Odin, Heimdahl and other Nordic gods-all of whom lived in the Asgard shrine, and the most important thing was to keep the family together.

Since then, the researchers have found other eukaryotic characteristic proteins in the above-mentioned "family", such as protein homologues involved in various physiological processes, from ubiquitin signaling to gamete fusion. Eukaryotic characteristic proteins are very common in this family, indicating that these microbes may be the closest living prokaryotes to modern eukaryotes. And modern eukaryotes may have inherited their molecular mechanisms from archaea. Traditionally, eukaryotes are thought to have evolved from ancient bacteria or so-called prokaryotes. But now that view is about to be subverted. Most scientists now believe that the common ancestor of living eukaryotes is the ancestor of the Asgard supersystem, or another similar group of archaea (archaea).

In 2019, researchers successfully cultivated creatures of the Asgard supersystem for the first time, and were able to study the family more deeply. They found that one cultured species is small and grows slowly, dividing only once every two to three weeks, while other microbes can double in minutes or hours. They named the former "Candidatus Prometheoarchaeum syntrophicum" (apparently from Prometheus), while Candidatus Prometheoarchaeum syntrophicum lived closely with another group of archaea called "Methanogenium". The former obtains nitrogen and energy by digesting amino acids and peptides, which produces hydrogen, which is absorbed and utilized by the latter. This process can reduce the hydrogen content in the microenvironment, thereby relieving cell pressure. Scientists who study the Asgard supersystem believe that this symbiotic relationship may be a model of eukaryotic occurrence.

Researchers first identified Asgard Archaea from metagenomic data in 2015, which is considered to be the closest living prokaryote to modern eukaryotes. A few years later, the first Asgard Archaea Candidatus Prometheoarchaeum syntrophicum was cultivated, revealing its unique biological aspects. HIROYUKI IMACHI, MASARU K. NOBU, AND JAMSTECAnja Spang said that this symbiotic relationship was also detected at the genetic level of other archaea, but the relationship between Candidatus Prometheoarchaeum syntrophicum and Methanogenium provided solid evidence. Years later, Anja, who has successfully landed and set up his own team at the Royal Dutch Institute of Oceanography (Royal Netherlands Institute for Sea Research), recalled: "when I first learned that a paper describing the symbiotic relationship between this creature and its nutrients had finally been published, I was very happy. This proves that this kind of experimental work is meaningful for the metabolic prediction of the Asgard supersystem."

The divergent eukaryotic hypothesis these early observations led to a great deal of research-and irrigation. In the years that followed, preprints of hundreds of papers on the Asgard supersystem and eukaryotic genesis emerged on bioRxiv.

The most direct impact of the above findings is that eukaryotes and archaea are divided into the same domain, thus reducing the three-domain life tree model composed of eukaryotes, prokaryotes and archaea to a two-domain model. (translator's note: "domain" is the largest unit in biological taxonomy. There are several realms in a domain, followed by the familiar genera and species of the phylum. For example, humans belong to the eukaryotic domain, the animal kingdom, the phylum Chordata, mammals, primates, Homo sapiens, Homo sapiens, Homo sapiens. )

It was once thought that both bacteria and archaea were prokaryotes, but with the continuous study of planned biology, people found that archaea were more and more different from other prokaryotes, so archaea were classified as archaea independently. In the traditional three-domain model, eukaryotes and archaea have common ancestors, but they belong to different branches. In recent years, studies in the field of systems biology have shown that complex eukaryotic cells come from archaea. This allows eukaryotes and archaea to be divided into the same domain. The two-domain system was debated before the Asgard supersystem was discovered, but the Asgard supersystem provides more evidence for it. The dual-domain hypothesis also supports the theory that eukaryotes come from archaea rather than the so-called prokaryotes.

01. Are there cells or mitochondria first? Many scientists believe that the first eukaryotes evolved from the cooperation between archaea and bacteria. In this process, bacteria enter the archaea in some way and become organelles such as nuclei and mitochondria-a decisive sign of eukaryotes. The details of the process remain unclear, but the clues are most likely to come from the mitochondria. "there is DNA in the mitochondria, and these DNA can be traced back to α-amoeba (alphaproteobacteria)." "even if we don't know the exact route of this process, it's a real hammer," said Laura Eme, an evolutionary microbiologist at the French National Centre for Scientific Research (France's National Centre for Scientific Research, CNRS).

α-amoeba is a class of Proteobacteria. Its internal differences are great, and there are few similarities, commonly known as "bulk class". Most of the α-amoeba are gram-negative, and the typical members are plant symbiotic bacteria such as rhizobium, Wolbakite and intracellular parasites such as Rickettsia. Some people think that α-amoeba is on the way of transforming into organelles, while the current organelles are α-amoeba which have been "organized" in the cells.

Even if gossip has a real hammer, onlookers have to pick up the details-and so do scientists. There have always been different and even opposing hypotheses about the process of α-amoeba coming ashore in the cell. How does alpha-amoeba get into the cell? Scientists have been smacking for a long time, but they don't understand: the endocytosis process requires a lot of energy. for such a luxurious physiological function, is it that the mitochondria provide energy for this process before the cells evolve the endocytosis function? or do you have endocytosis function before you can swallow mitochondria into the cell? So scientists divided into two groups: "first mitochondria" and "first endocytosis", and launched a war of words in academic journals. In any case, endocytosis has not been observed in prokaryotes for a long time.

Until recently, researchers found a "endocytosis" in a bacterium. "many people think that prokaryotes could not be swallowed, so the ancestors of mitochondria could not have been swallowed into cells," Laura Eme commented. "but now, at least we know that prokaryotes can be endocytosis."

This is where the torment of biology and chemistry is-unlike concise formula chemistry such as mathematics and physics, chemistry and biology are always full of exceptions. For example, the description of "Beijing Man" in mathematics and physics may be "Beijing Man begins with ID number 110." whether this statement is correct or not, there is at least a clear criterion for judgment. On the other hand, chemistry and biology are closer to "the people who like to drink Fermented Bean Drink are Beijingers, but we have found that some people are really born in Beijing but do not like Fermented Bean Drink, so we define them as' Beijingers in a broad sense'. The traditionally defined Beijingers are called 'classic Beijingers'. Now we have 'super Beijingers', which can be divided into 'classic Beijingers' and 'broad Beijingers who are not classic Beijingers'. Then we found that some people also like to drink Fermented Bean Drink but are not Beijingers, so we call it 'quasi-Beijingers'.... "

In addition, another phagocytic mechanism was found in the preliminary observation of the Asgard supersystem. When scientists first cultured Candidatus Prometheoarchaeum syntrophicum, they noticed elongated protrusions on the surface of the cell body-an extension of the membrane structure known as vesicles. With the help of the actin homologues described above, these bubbles may be able to surround an external entity and fuse together, thus wrapping the external objects inside. As a result, the problem of phagocytosis is "getting less and less important". In other words, α-amoeba is likely to be swallowed into prokaryotes to become mitochondria.

02. How did the nucleus appear? But when it comes to the nucleus, things are not so clear. It is generally believed that the most typical feature that distinguishes eukaryotes from prokaryotes is that they have nuclei. Speculation about nuclear formation ranges from "bacteria that host amoebas" to "remnants of ancient giant viruses". In the 1990s, L ó pez-Garc í a proposed the "vegetative symbiosis hypothesis" for the origin of eukaryotes, assuming that there is a symbiotic relationship between two bacteria and one archaea.

After the Asgard supersystem was discovered, L ó pez-Garc í an and her colleagues updated this hypothesis a few years ago. Instead of using archaea as the original host, they put forward the concept of "progenitor bacteria". In their hypothesis, the "progenitor" is a hydrogen-producing archaea similar to the organisms in the Asgard supersystem, as well as the original nucleus. The host that accepts such a "nucleus" is most likely to be the ancestor of a class of δ-amoebos, that is, mitochondria and alpha-amoeba. Most genes in modern eukaryotes actually come from bacteria rather than archaea, and the fact that the lipids that make up eukaryotic cell membranes are closer in structure and composition to bacteria than archaea (a phenomenon known as "lipid separation" (lipid divide)) supports their hypothesis. Their hypothesis is so far the only one that can explain both the origin of the nucleus and the phenomenon of lipid separation.

Michelle Leger is a postdoctoral student in the field of evolutionary microbiology at the Institute of Evolutionary Biology in Barcelona (Institute of Evolutionary Biology in Barcelona). His main work is to trace the genomes of existing archaea to support or oppose various hypotheses. As for the "vegetative symbiosis hypothesis" put forward by L ó pez-Garc í an and others, Leger said that there is a clear genome signal of α-amoeba in mitochondria, but he has not found a similar signal of δ-amoeba in the nucleus.

Leger also believes that the current evidence does support the claim that the origin of the nucleus is archaea. Although the genes of archaea account for only a small part of the current nuclear genome, many of these genes are highly conserved. For example, the genes responsible for DNA replication and transcription are largely from archaea. Therefore, Leger believes that "these hypotheses make sense, but we still don't know which other organisms are involved in these evolutionary processes."

Many researchers say that although the number of bacteria and archaea that have been sequenced is increasing rapidly, providing new clues to the relationship between such organisms and early eukaryogenesis, it is a pity that many questions in this field may never be perfectly answered.

Eukaryotes have been around for too long, and too many genes have been exchanged and transferred between too many species. Scientists can't put everything together, but they're still trying. At present, the research methods widely used in academic circles include assemblage, molecular biology, fossil research and so on.

The next good place for irrigation will be the functional study of the genome and proteome of modern eukaryotes. The study of function can suggest the behavior of individual genes and proteins in early ancestors. A few years ago, there was only one Asgard superline genome, but now there are hundreds of such groups, and researchers are discovering the details of them. " Now we know exactly which genes in eukaryotes are inherited from Asgard archaea, and there's a lot of novelty here, "Laura Eme said." but what we don't know is what these genes have done and are doing in the Asgard superline-and that's the trick.

Remember that Archaea has a suspected homologous gene that encodes eukaryotic actin gene? In 2020, researchers synthesized such homologous genes in the Asgard superline genome. They injected these homologues into rabbit cells and found that they could bind to eukaryotic actin and perform similar functions, such as assisting calcium transmembrane. This suggests that calcium-controlled actin cytoskeletons may exist in archaea before the emergence of eukaryotes.

In addition to cultivating archaea to study function, people also study "small microfossils" directly. The so-called small microfossils are the microscopic imprints of early cells in rocks. Susannah Porter, a paleontologist at the University of California, University of California, Santa Barbara, believes that fossil research may also reveal ways in which eukaryotes occur. When macrogenomic sequencing appeared, fossils seemed out of favor, she said, but many phylogenetic trees relied on a method called a "molecular clock", in which fossils were used to anchor analysis time. In addition, fossils themselves may be useful to help scientists determine when certain external features first appear. The specimens that Porter is studying can determine the sequence of events in the evolution of early eukaryotes. "We do have fossils from the past 2 billion to 1 billion years, and they haven't been put to the best use. Maybe we can use these characteristics of fossils to piece together the origin of eukaryotes." In a word, although genomics and molecular biology have developed to a certain height, traditional fossil evidence still plays an important role in the field of microbial evolution and eukaryotic genesis.

750 million-year-old microfossil Valeria lophostriataCOURTESY OF SUSSANAH PORTER

In order to avoid "standing alone", scientists are also looking for other evidence to support fossil evidence. For example, Berend Snel, a computational biologist at the University of Utrecht (Utrecht University) in the Netherlands, recently used a method called "gene repetition". This method assumes that the length of each branch on the phylogenetic tree (phylogenetic tree) is related to its development time. However, this method is so controversial that Snel himself has to admit that it may be flawed. But Snel also said that evolution is a continuous process, when and only when people connect the small fragments of this long process, the real and complete evolutionary map will be shown to people.

Michelle Leger agrees that at this stage, human understanding of eukaryotic occurrence is like an infant's understanding of the world. "part of the nature of these deep evolutionary problems is that we will never know and will never have a clear evidence to prove our hypothesis, but that does not prevent us from continuing to refine our ideas.

Alternative hypothesis: viruses are the ancestors. Much of what is said about the origin of the nucleus is speculative. There is a hypothesis that the nucleus of modern eukaryotes may come from the cooperative relationship between the prokaryotic host and the virus.

At the beginning of the 21st century, Masaharu Takemura, a molecular biologist at the School of Medicine of Nagoya University (Nagoya University School of Medicine in Japan) in Japan, noticed that the DNA polymerase of a group of viruses (poxvirus) was very similar to that found in eukaryotes, and that poxvirus replicated in host cells by creating "independent compartments". At the same time, Philip Bell, head of research and development at biotech company MicroBioGen, is also confused about the difference between eukaryotes and bacteria. For example, eukaryotic chromosomes are linear, while bacterial chromosomes are circular. Many characteristics of the nucleus do not support the origin of bacteria. Both researchers published their own papers before 2001. And after learning about the Asgard supersystem and its research results, the two research groups updated their virus origin hypothesis.

Since then, researchers have identified giant viruses that were first discovered in 2003. These viruses are much larger than most viruses, have a large enough genome, and contain genes associated with various metabolic processes. Now, Masaharu Takemura, Philip Bell and others think that this giant virus may be the original nucleus. Giant viruses replicate in complex compartments that look very similar to modern nuclei. They are all large, contain both intima and adventitia, and all carry genes that encode the proteins that host cells need to operate.

However, the idea that the nucleus may come from a virus has been hard to sell. It lacks structural evidence and is not supported by available data. However, Valerie De Anda, a microbiologist who studies the metabolism of early prokaryotes, is not deterred by the current lack of evidence to support the "virus hypothesis". She and her colleagues are currently looking for mRNA-capped genes involved in transcription and translation. They believe that these genes came from the "ancestor of the first eukaryote nucleus" a long time ago.

Valerie De Anda can't help being annoyed when it comes to the fact that his theory is not widely accepted by the scientific community. This reminds her of an ancient Chinese poem taught by her teacher when she was at school:

In the grass since childhood.

Now I gradually feel that Artemisia annua L.

People didn't know Ling Yunmu at that time.

Wait until Lingyunshi Road is high.

reference

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[6] Chaikeeratisak, Vorrapon et al. "Assembly of a nucleus-like structure during viral replication in bacteria." Science (New York, N.Y.) Vol. 355 Person.6321 (2017). Doi:10.1126/science.aal2130

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This article is authorized to be compiled from: https://www.the-scientist.com/ features / the-long-and-winding-road-to-eukaryotic-cells-70556?_ga=2.200353838.1403010427.1666753497-1684915652.1666340439

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