Recently, with the funding of the National Natural Science Foundation of China and the High Technology Development Program of the Ministry of Science and Technology (863) and the National Major Basic Research and Development Program (973), the research team led by Professor Xu Anlong of CUHK discovered the "molecular living fossils" of RAGtranspostes 600 million years ago, providing the most powerful evidence for "the transposon origin hypothesis of human antibody rearrangement mechanism". The research results were recently published in the international biological journal Cell.
In 1979, the team of Japanese-American scientist Susumu Tonegawa discovered the mechanism of human antibody V(D)J rearrangement and creatively proposed the transposon origin hypothesis of the rearrangement mechanism, and in 1987 he won the Nobel Prize in Medicine and Physiology for "Antibody Rearrangement Mechanism". His "transposon origin hypothesis of the human antibody rearrangement mechanism" has inspired generations of scholars to explore the rearrangement mechanism and its origin. Over the past four decades, although many significant advances have been made in the study of the mechanism of rearrangement, especially the function and regulation of the core enzyme-antibody rearrangement activator (RAG1/RAG2), the hypothesis itself has never been confirmed and has become a classic puzzle that has plagued the immunological community.
The body's immune system is divided into two parts: innate innate immunity and acquired modifiable adaptive immunity, antibody rearrangement mechanism is adaptive immunity, the most critical mechanism of acquired response to countless pathogenic attacks (such as the role of vaccines is based on this mechanism), it is so important, the search for the origin of antibody rearrangement mechanism has been a hot topic in immunological research, thus inspiring generations of immunologists to work for it. After Tonegawa discovered the "antibody rearrangement mechanism" in 1979, a series of studies by immunologists found that the key enzymes that mediate the mechanism of antibody rearrangement are: recombinant activation genes RAG1 and RAG2, but the RAG gene encodes the body's own protein, not transposase, so scientists naturally ask: "How does the RAG gene enter the human and other vertebrate genomes and integrate into the adaptive immune system mediated V(D)J rearrangement?" The question thus became one of the key puzzles in the provenance of recognized adaptive immunity.
In order to solve the puzzle, Professor Xu Anlong and his team have shifted their research from the past disease-related immune research to a very basic scientific problem of the origin of the human immune system since returning from studying in the United States 20 years ago. His team first chose Wenchang fish, a living fossil of animal evolution research, as the core research object, because Wenchang fish is the most critical species to uncover the origin of our vertebrates, and it is found in Qingdao, Xiamen, Zhanjiang and other coastal areas in China, providing a long-term reliable resource advantage for the study.
The evolutionary status of the Chinese Bai's Wenchang fish (amphioxus). Wenchang fish, together with urochordate and vertebrate, form the phylum Chordata. It is generally believed that only vertebrates have evolved adaptive immune systems and antibody rearrangement mechanisms. As the oldest surviving chordate, the Wenchang fish, which is thought to be a "living fossil" that can represent the ancestral state of vertebrates, has not yet evolved the relevant mechanism of adaptive immunity.
After more than a decade of research, his team conducted deep informatics analysis of multiple high-quality Wenchang fish genome sketches and found that Wenchang fish retained a large number of ancient transposon superfamily that had long been extinct in vertebrates. One of the DNA transposon families happened to encode the protein RAG1/2 and had a TIR at the end of the antibody gene recombinant signal sequence RSS, which they named ProtoRAG, meaning transposon encoding the prototype RAG. Through systematic and in-depth functional and mechanism studies, they found that The Wenchang fish ProtoRAG is the RAG transposon that people have been searching for for a long time to determine the mechanism of antibody rearrangement, and it can also be considered that the transposon is the "molecular living fossil" left by the RAG transposon 600 million years ago.
Functional comparison of the original RAG protein of Wenchang fish with the vertebrate RAG protein. In vertebrates, the RAG1/2 protein complex is responsible for rearranging fragments of the V(D)J gene from adversaries. But in Wenchang fish, the original RAG protein exists as a transposase for ProtoRAG transposons, which is only responsible for mediating its own transfer and replication in the genome.
This discovery provides the strongest and most direct evidence for the transposon origin hypothesis of human antibody rearrangement, and the discovery of this transposon also provides a new gene editing idea and technology for the future design of new immune antibodies and immune genes using the rearrangement mechanism. From the perspective of immunology, the discovery pushes the origin of adaptive immunity from vertebrates to invertebrate Wenchang fish, thereby advancing 100 million years, and will rewrite the current immunology textbook view on the origin of adaptive immunity.
comments
Reviewer1 Review:
Since 1979, it has been thought that the origins of VDJ recombination might lie in a transposable element. The discovery of RAG1/2 and their ability to mediate transposition led to the specific model that a RAG1/2 transposon was the element in question. However, the analysis of many genome sequences failed to turn up a RAG1/2 transposon, leading some in the field to doubt this model and to propose alternatives. Here, Huang et al. provide powerful evidence for the existence of a RAG transposon (ProtoRAG) with all of the key features predicted for such an element: convergently oriented RAG ORFs, flanking TIRs that resemble the heptamer of the RSS, and 5 bp target site duplications. Excitingly, the elements turn up in the genome of amphioxus, the best extant candidate as the last common chordate ancestor. Also exciting is evidence that these elements have fairly recently (last few million years) been active in the amphioxus genome, and that the bbRAG1L and bbRAG2L proteins encoded by one amphioxus transposon are active in DNA cutting (and perhaps transposition; see comment 1 below). This raises the possibility that these transposons are still active in amphioxus today, although as the authors note, it would appear that their activity is kept quite low. These findings are likely to have a major impact on the current model for RAG and VDJ evolution, and also provide important tools for studying the functional properties of RAG1 and RAG2 early in their evolution.
Since 1979, it has been believed that the VDJ rearrangement may have originated from a transpose element. The discovery of the RAG1/2 protein and its ability to mediate transposing has led to the hypothesis that "RAG transposons" are looking for that transposon element. However, analysis of many genomic sequences did not find the so-called RAGtransposon, which led to doubts about whether this RAGtransposon model really holds, and some even began to consider new alternative models. In this study, Huang Shengfeng et al. present strong evidence that ProtoRAG has all the key features that a RAG transposon should have... (Omitted). Excitingly, the element they found (ProtoRAG) is a genome from the Wenchang fish, which is the best living representative of the ancestors of the chordate. Equally exciting is the fact that the elements found by the authors still retain transpose activity! (Omitted)... These findings could have a significant impact on existing MODELS OF RAG/VDJ evolution, while also providing an important tool for in-depth study of the early evolution of RAG.
Reviewer2 Reviews:
The supporting data for the proposal that ProtoRAG represents a molecular "living fossil" of the RAG transposon are extensive and convincing.
The study presents the assertion that ProtoRAG is a molecular "living fossil" of the RAG transposon and gives broad and convincing evidence.
Reviewer3 Reviews:
As such this paper is of substantial interest to the field and worthy of serious consideration. Because the work goes far beyond a simple sequence gazing exercise, and includes a variety of molecular analyses that come together to form a compelling story.
This paper is extremely valuable and worthy of serious scrutiny in the field of immunology. The work is not a simple sequence search analysis, it synthesizes multiple molecular function studies and ultimately converges to form a compelling story.
Reviewer4 Rating:
Overall, this is one of the more substantial CELL manuscripts that I have reviewed in the last few years and I think the study will have a strong and sustained impact on the general scientific community due to the importance of V(D)J recombination as a milestone event in the evolution of adaptive immunity.
Overall, this is the most substantive cell article I've reviewed in years. Since the VDJ rearrangement is a milestone in the evolution of adaptive immunity, I think this article will have an important impact on the academic community as a whole.
The media said that China Science Daily - "Scientists find 'molecular living fossils' 600 million years ago":
Today, the reporter learned from Sun Yat-sen University that the team of Professor Xu Anlong of the university found the "molecular living fossil" of RAGtransposons 600 million years ago, providing the most powerful evidence for the "transposon origin hypothesis of human antibody rearrangement mechanism". The relevant research was recently published in Cell.
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After more than a decade of research, the team conducted deep informatics analysis of several high-quality Wenchang fish genome sketches and found that Wenchang fish retained a large number of ancient transposon superfamily that had long been extinct in vertebrates. One of the DNA transposon families happened to encode the protein RAG1/2 and had a reverse repeat sequence TIR at the end of the antibody gene recombinant signal sequence RSS, which they named ProtoRAG, meaning the protoRAG transposon. Through the study of the function and mechanism of the system, they found that the Wenchang fish ProtoRAG is the RAG metastase that people have been searching for for a long time to determine the mechanism of antibody rearrangement, and it can also be considered that the transposon is a "molecular living fossil" left by the RAGtranspot 600 million years ago.
People's Daily — "China's immunologists discovered immunization "molecular living fossils" 600 million years ago":
This finding provides the strongest and most direct evidence for the "transposon origin hypothesis of human antibody rearrangement", and provides a new idea for the future design of new antibodies or immune molecules using the rearrangement mechanism. From the broader perspective of immunology, the discovery pushes the origin of adaptive immunity forward by vertebrates to invertebrates to invertebrate Wenchang fish, thereby pushing forward 100 million years.
It is reported that this research result has been published in the top international biology journal "Cell", which has been called "a milestone in immunological research" by foreign experts.
Nanfang Daily — "CUHK Scientists Solve the World Immunology Puzzle":
This discovery provides the strongest and most direct evidence for the "transposon origin hypothesis of human antibody rearrangement", which has multiple scientific significance: from the perspective of immunological research, the results push the origin of adaptive immunity from vertebrates to invertebrates to invertebrate Wenchang fish, pushing forward the time from 500 million years to 600 million years, rewriting the textbook view. At the same time, to provide new ideas for future DNA research, the Discovery ProtoRAG is an ancient transposon, which was previously considered "junk DNA" and "selfish DNA", but now it seems that it actually plays an important and positive role; it provides a new idea for the design of new immune antibodies and immune genes for future rearrangement mechanisms.
Yangcheng Evening News — "Pushing the Origins of Adaptive Immunity Forward 100 Million Years":
With the financial support of the National Natural Science Foundation of China and the High Technology Development Program of the Ministry of Science and Technology (863) and the National Major Basic Research and Development Program (973), the research team led by Professor Xu Anlong discovered the "molecular living fossil" of rag (recombinant activating enzyme) transposons 600 million years ago after more than ten years of research on the living fossil of animal evolution, Wenchang fish, which provides the most powerful evidence for the "transposon origin hypothesis of human antibody rearrangement mechanism". The research results were published in the international biological journal "cell", which has aroused widespread concern in the academic community.
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