Since the first deciphering of the genetic code in the 1960s, our genes have been like an open book, containing a blueprint for life that has become increasingly clear to scientists. By analyzing the base sequences on chromosomes, we can identify genes and understand how genetic variations affect health status. This fundamental law of life applies universally to all living organisms, from the smallest bacteria to complex humans.
However, a recent study has revealed that bacteria may not follow this traditional rule, as they are able to create genes that are free and fleeting. This discovery suggests that similar gene structures may exist outside of our genome.
The relevant research results were published online in the journal Science, with the title “De novo gene synthesis by an antiviral reverse transcriptase”.
A few months ago, when this paper first appeared as a preprint, the scientific community’s reaction had already become news. Some scientists refer to this discovery as ‘extraterrestrial biology’, ‘surprising’, and ‘shocking’. The first author of the study, Stephen Tang, a doctoral student in Sternberg’s laboratory, said, “As this mechanism gradually became known, we also went through a journey from confusion to shock.”
Our Related Proteins
| Cat.No. | Product Name | Source | Species | Tag |
| Cas9 -121S | Recombinant CRISPR Cas9 protein | E. coli | Non | |
| CAS9-22S | Recombinant Full Length Streptococcus pyogenes serotype M1 type II CRISPR RNA-guided endonuclease Cas9 Protein, GFP-tagged | E. coli | Streptococcus pyogenes serotype M1 | C-GFP |
| neo-5599K | Recombinant Klebsiella pneumoniae neo Protein (Met1-Phe264) | E.coli | Klebsiella pneumoniae | Non |
| Neo1-611M | Active Recombinant Mouse Neo1 Protein, Fc Chimera | Mammalian cells | Mouse | Fc |
| NEO1-3002R | Recombinant Rhesus monkey NEO1 Protein, His-tagged | Mammalian Cell | Rhesus Macaque | His |
| NEO1A-9492Z | Recombinant Zebrafish NEO1A | Mammalian Cell | Zebrafish | His |
For a long time, the war between bacteria and viruses has been ongoing, with viruses attempting to inject their genetic material into bacteria, while bacteria have evolved sophisticated defense mechanisms such as CRISPR to resist invasion. The defense strategies of many bacteria have not been fully explored yet, but they may contain new gene editing tools.
The bacterial defense system studied by Sternberg and Tang appears exceptionally unique: it involves an RNA fragment of unknown function and a reverse transcriptase – an enzyme that can synthesize DNA using RNA as a template. Tang pointed out that the defense mechanism of most bacteria is to directly destroy viral DNA, so “we are confused about this way of protecting our genome through DNA synthesis.”
To explore the workings of this unique defense mechanism, Tang developed a new technique for identifying DNA fragments generated by reverse transcriptase.
The Sternberg team discovered that this defense system encodes a novel immune pathway, where reverse transcriptase performs rolling reverse transcription on non-coding RNA to generate new genes. The template hopping of reverse transcriptase on non-coding RNA leads to the production of a series of tandem repeats of cDNA, which transform into double-stranded cDNA after viral infection.
Of particular significance is that this DNA product encodes an almost infinitely long open reading frame (ORF) gene, whose expression can inhibit cell growth and thus limit the spread of the virus. Sternberg metaphorically said, “It’s like you want to copy a book, but the photocopier keeps copying the same page.”
At first, Sternberg and his team suspected that there might be problems with the experiment, or that the reverse transcriptase had made an error and the generated DNA had no practical significance.
However, further in-depth analysis revealed that these DNA molecules constitute fully functional, freely floating, and short-lived genes. They found that the protein encoded by this gene is a core component of bacterial antiviral defense mechanisms. Viral infection triggers the production of the protein (named Neo), which prevents further replication of the virus and invasion of surrounding bacterial cells.
Sternberg speculates that if similar extrachromosomal genes also exist in higher organisms, “this would be a groundbreaking discovery. There may be some genes or DNA sequences that are not fixed on the 23 pairs of chromosomes in humans. They may only be generated in specific environments, developmental stages, or genetic backgrounds, but provide coding information that is crucial for our physiological functions.”
At present, the Sternberg laboratory is using Tang’s technology to search for genes produced by reverse transcriptase outside the human chromosome. There are thousands of genes encoding reverse transcriptase in the human genome, and the functions of many of these genes remain a mystery. Sternberg said, “This is a huge untapped field that may reveal even more fascinating biological phenomena.”
Although CRISPR-based gene editing technology has entered the clinical trial stage, and even a gene therapy for sickle cell disease was approved last year, CRISPR technology is not perfect. The new method of combining CRISPR with reverse transcriptase is giving gene editors greater control.
Tang explained, “Reverse transcriptase makes it possible for you to write new information at the site of CRISPR cleavage, which CRISPR itself cannot achieve. However, we are still using the reverse transcriptase discovered decades ago.”
The reverse transcriptase that generates Neo possesses certain special properties, which may make it an ideal choice for laboratory gene editing and the development of novel gene therapies. There are still more unsolved reverse transcriptases hidden inside bacteria, waiting for scientists to explore. Sternberg emphasized, “We believe that bacteria may be the treasure trove of reverse transcriptase, and once we understand their working mechanisms, they can become the cornerstone driving the development of new technologies.”
Related Products and Services
Protein Expression and Purification Services
Reference
Stephen Tang et al. De novo gene synthesis by an antiviral reverse transcriptase. Science, 2024, doi:10.1126/science.adq0876.