2:15 PM - 2:35 PM
[BBG01-02] Illuminating the extra-genomic genetic elements
★Invited Papers
Keywords:RNA virus, viroid, genetic elements
Cells contain various obligate parasitic genetic elements. These extragenomic genetic elements, such as viruses, plasmids, viroids, and prions, significantly impact the function and evolution of host cells. Therefore, illuminating the diversity of these extragenomic genetic elements is crucial for understanding the functions and evolution of cells. However, recognition of these elements is difficult due to their small size, unique molecular properties, and inability to be cultured independently. Even in the well-studied viruses and plasmids, many previously overlooked lineages have been identified in recent years. Also, recent reports have begun to unveil new viroid-like elements. These facts mark the research field as one of the frontiers in exploring Earth's biosphere.
RNA viruses, which store their genetic information in RNA, form the realm Riboviria. Over 100,000 RNA virus species have been discovered, and they are classified into two kingdoms based on their self-replicating enzyme types: reverse transcriptase (RT) and RNA-directed RNA polymerase (RdRP). The RNA-seq technology has significantly increased the number of reported RNA viruses. However, detecting novel RNA viruses in RNA-seq data has been challenging due to the need for homology with known RNA viruses. To address this, we developed the FLDS method, enabling the detection of RNA viruses without relying on homology. This method was applied to various biological samples, including hot spring samples. Here, we identified an RNA virus genome named Hot spring RNA virus (HsRV) that did not show homology to known sequences and whose self-replicating enzyme is predicted to have an intermediate structure between RT and RdRP. This indicates the potential existence of a previously overlooked third kingdom of RNA viruses. Our findings suggested that there are methodological limitations in widely used RNA-seq technology for understanding the comprehensive diversity of RNA viruses. In addition, our data mentioned that RNA viruses can survive in high-temperature environments above 70°C. This discovery is crucial for unraveling the co-evolutionary history of RNA viruses and cells.
Viroids are known as an extra-genomic genetic element that infects plants. Their genomes are small (several hundred nucleotides) circular RNA that do not encode any protein. Recent analyses using large-scale RNA-seq data have suggested the presence of unknown viroid-like circular RNA elements, making these small circular RNAs a hot topic for discoveries of new extra-genomic genetic elements. We hypothesized that our FLDS method could capture small circular RNAs undetectable by standard RNA-seq and surveyed small circular RNA from FLDS data. This led to the discovery of a circular RNA approximately 280 nucleotides long from a filamentous fungus. The element named MoVd1 did not show homology to known sequences. Several experiments suggested that MoVd1 is a novel extragenomic genetic element. However, the search for MoVd1-like sequences in large-scale RNA-seq data yielded only one hit, indicating that short RNAs might be missed during RNA-seq library construction or discarded during assembly, highlighting the challenges in comprehensively capturing extragenomic genetic elements.
These findings imply that cells consist of a variety of extragenomic genetic elements. The reason for their existence is still not fully understood. However, it is speculated that, like in the case of plasmids, cells may ensure epigenetic diversity and adapt to changing environments through interactions with these elements. With ongoing improvements in sequencing data volume and analytical techniques, the discovery of diverse, previously unreported extragenomic genetic elements is expected to continue, and these studies will be exciting.
RNA viruses, which store their genetic information in RNA, form the realm Riboviria. Over 100,000 RNA virus species have been discovered, and they are classified into two kingdoms based on their self-replicating enzyme types: reverse transcriptase (RT) and RNA-directed RNA polymerase (RdRP). The RNA-seq technology has significantly increased the number of reported RNA viruses. However, detecting novel RNA viruses in RNA-seq data has been challenging due to the need for homology with known RNA viruses. To address this, we developed the FLDS method, enabling the detection of RNA viruses without relying on homology. This method was applied to various biological samples, including hot spring samples. Here, we identified an RNA virus genome named Hot spring RNA virus (HsRV) that did not show homology to known sequences and whose self-replicating enzyme is predicted to have an intermediate structure between RT and RdRP. This indicates the potential existence of a previously overlooked third kingdom of RNA viruses. Our findings suggested that there are methodological limitations in widely used RNA-seq technology for understanding the comprehensive diversity of RNA viruses. In addition, our data mentioned that RNA viruses can survive in high-temperature environments above 70°C. This discovery is crucial for unraveling the co-evolutionary history of RNA viruses and cells.
Viroids are known as an extra-genomic genetic element that infects plants. Their genomes are small (several hundred nucleotides) circular RNA that do not encode any protein. Recent analyses using large-scale RNA-seq data have suggested the presence of unknown viroid-like circular RNA elements, making these small circular RNAs a hot topic for discoveries of new extra-genomic genetic elements. We hypothesized that our FLDS method could capture small circular RNAs undetectable by standard RNA-seq and surveyed small circular RNA from FLDS data. This led to the discovery of a circular RNA approximately 280 nucleotides long from a filamentous fungus. The element named MoVd1 did not show homology to known sequences. Several experiments suggested that MoVd1 is a novel extragenomic genetic element. However, the search for MoVd1-like sequences in large-scale RNA-seq data yielded only one hit, indicating that short RNAs might be missed during RNA-seq library construction or discarded during assembly, highlighting the challenges in comprehensively capturing extragenomic genetic elements.
These findings imply that cells consist of a variety of extragenomic genetic elements. The reason for their existence is still not fully understood. However, it is speculated that, like in the case of plasmids, cells may ensure epigenetic diversity and adapt to changing environments through interactions with these elements. With ongoing improvements in sequencing data volume and analytical techniques, the discovery of diverse, previously unreported extragenomic genetic elements is expected to continue, and these studies will be exciting.