Analysis of sequence databases reveals novel circular RNA genomes belonging to “obelisks”
The latest, reported this week in a preprint, is a new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks,” as they’re called by the Stanford University team that unearthed them, have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world.
It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University, but they could alter the genetic activity of their bacterial hosts, which in turn could affect human genes.
I wish they had expanded the kitchen analogy a bit more. I'm hoping to catch some of y'alls discussion and maybe it'll make more sense. My very poor understanding follows: so in this analogy a...
I wish they had expanded the kitchen analogy a bit more. I'm hoping to catch some of y'alls discussion and maybe it'll make more sense.
My very poor understanding follows: so in this analogy a human gut or mouth dwelling bacteria cell is like a kitchen, with its own goal to make more....kitchens (3D printer that prints 3D printers?). And then viruses are sort of like stray recipe books: they don't have their own tools, ingredients or chefs but they kind of bamboozle existing well running kitchens into making more weird stray recipe books.
But some of the obelisk sequences encoded proteins involved in RNA replication
And then these obelisks guys are much shorter, like sticky notes that say something like "mush rice paste into thin squares...."
Im all kinds of confused and intrigued of course, and would love to see corrections. :)
I'm gonna try to talk about this all in the context of the analogy, but I will mix it a little bit with the idea of crafting because I think it makes more sense. Cells have a kitchen (ribosome)...
Exemplary
I'm gonna try to talk about this all in the context of the analogy, but I will mix it a little bit with the idea of crafting because I think it makes more sense.
Cells have a kitchen (ribosome) that takes the individuals recipes (RNA) from a recipe book (Genomic DNA). The recipes are for tools (proteins) that do many, many tasks a cell needs to continue functioning, such as adding structural support (cytoskeletal proteins), keep an internal state (ion pumps/channels), DNA replication (polymerases), etc. Viruses don't have a kitchen, but they do carry very tiny recipe books with only a few recipes - namely how to make more viruses (replicate the RNA, make a virus shell to hold the RNA, integrate into the host DNA). Viruses will inject their recipes into a host and because the recipes are written in the same language (molecules of RNA), they are transcribed by the host and turned into tools (proteins) that make more viruses.
Some virus-like things, viroids, don't have the shell. They are just little bits of circular recipes (RNA) that are very stable and get constantly translated into tools by the kitchen, namely into tools that replicate more of the recipe. For a long time, people thought that only plants have these, but now it looks like maybe animals have them too but through evolutionary processes they are a bit larger. Bacteria already have tiny recipe books that are like these obelisks and viroids that they use to make specific tools (circular bits of DNA known as plasmids), and these are implicated in antibacterial resistance. Plasmids can be transferred between bacteria, so it's feasible that these obelisks might get transferred the same way.
Hopefully that clears things up. If you have any questions please let me know.
This is super nice thank you! I remember some terminology from highschool exam but have forgotten basically everything since then. The article talked about loops of RNA, circular RNA, RNA...
This is super nice thank you! I remember some terminology from highschool exam but have forgotten basically everything since then.
The article talked about loops of RNA, circular RNA, RNA circles....are they talking about the structure of all RNA, in the way that they refer to the structure of DNA as a helix? Or is it a sub-type of RNA that looks a certain way, eg, not all RNA are circular? What does it mean when RNA instructions are circular - do the transcription process just run forever like a code endless loop then?
RNA will take many different shapes depending on the sequence of the molecule. This is because RNA, like DNA, tends to form connections with specific bases. RNA on its own is highly reactive due...
RNA on its own is highly reactive due to the presence of an extra oxygen (and hence why DNA is a better long term storage for information - deoxyribonucleic acid - it's missing that oxygen atom). It also gets broken down quickly inside of a cell if it's a single, linear strand. Circular RNA is a lot more stable and could help prevent degradation by not allowing enzymes to easily bind to it.
To answer your last question, these viroids and RNA circular loops aren't being translated in the normal sense that a viral shell might. Their RNA is being copied by a protein known as RNA polymerase, but is let go at certain points (not fully understood how polymerases "decide" to stop, if I remember correctly). Since it's not being degraded as quickly it just keeps bouncing around to different polymerases, and this produces an exponential effect because more viroid molecules are being made. Hopefully you can see this image that highlights the process. You can do a bit more reading on it here, although I warn you that it is heavy on the jargon.
I wish they had expanded the kitchen analogy a bit more. I'm hoping to catch some of y'alls discussion and maybe it'll make more sense.
My very poor understanding follows: so in this analogy a human gut or mouth dwelling bacteria cell is like a kitchen, with its own goal to make more....kitchens (3D printer that prints 3D printers?). And then viruses are sort of like stray recipe books: they don't have their own tools, ingredients or chefs but they kind of bamboozle existing well running kitchens into making more weird stray recipe books.
And then these obelisks guys are much shorter, like sticky notes that say something like "mush rice paste into thin squares...."
Im all kinds of confused and intrigued of course, and would love to see corrections. :)
I'm gonna try to talk about this all in the context of the analogy, but I will mix it a little bit with the idea of crafting because I think it makes more sense.
Cells have a kitchen (ribosome) that takes the individuals recipes (RNA) from a recipe book (Genomic DNA). The recipes are for tools (proteins) that do many, many tasks a cell needs to continue functioning, such as adding structural support (cytoskeletal proteins), keep an internal state (ion pumps/channels), DNA replication (polymerases), etc. Viruses don't have a kitchen, but they do carry very tiny recipe books with only a few recipes - namely how to make more viruses (replicate the RNA, make a virus shell to hold the RNA, integrate into the host DNA). Viruses will inject their recipes into a host and because the recipes are written in the same language (molecules of RNA), they are transcribed by the host and turned into tools (proteins) that make more viruses.
Some virus-like things, viroids, don't have the shell. They are just little bits of circular recipes (RNA) that are very stable and get constantly translated into tools by the kitchen, namely into tools that replicate more of the recipe. For a long time, people thought that only plants have these, but now it looks like maybe animals have them too but through evolutionary processes they are a bit larger. Bacteria already have tiny recipe books that are like these obelisks and viroids that they use to make specific tools (circular bits of DNA known as plasmids), and these are implicated in antibacterial resistance. Plasmids can be transferred between bacteria, so it's feasible that these obelisks might get transferred the same way.
Hopefully that clears things up. If you have any questions please let me know.
This is super nice thank you! I remember some terminology from highschool exam but have forgotten basically everything since then.
The article talked about loops of RNA, circular RNA, RNA circles....are they talking about the structure of all RNA, in the way that they refer to the structure of DNA as a helix? Or is it a sub-type of RNA that looks a certain way, eg, not all RNA are circular? What does it mean when RNA instructions are circular - do the transcription process just run forever like a code endless loop then?
RNA will take many different shapes depending on the sequence of the molecule. This is because RNA, like DNA, tends to form connections with specific bases.
RNA on its own is highly reactive due to the presence of an extra oxygen (and hence why DNA is a better long term storage for information - deoxyribonucleic acid - it's missing that oxygen atom). It also gets broken down quickly inside of a cell if it's a single, linear strand. Circular RNA is a lot more stable and could help prevent degradation by not allowing enzymes to easily bind to it.
To answer your last question, these viroids and RNA circular loops aren't being translated in the normal sense that a viral shell might. Their RNA is being copied by a protein known as RNA polymerase, but is let go at certain points (not fully understood how polymerases "decide" to stop, if I remember correctly). Since it's not being degraded as quickly it just keeps bouncing around to different polymerases, and this produces an exponential effect because more viroid molecules are being made. Hopefully you can see this image that highlights the process. You can do a bit more reading on it here, although I warn you that it is heavy on the jargon.
Pretty cool discovery, though not at all unexpected. Wikipedia rabbit hole for the interested, listing similar self-replicating entities:
https://en.wikipedia.org/wiki/Replicon_(genetics)#Non-cellular_entities