Ribozyme Glyph?

[Chris J. Myers]

Hi,

Circuits from the Cello paper using a ribozyme upstream of the RBS.  The SO term for ribozyme:

http://www.sequenceontology.org/browser/current_release/term/SO:0000374

However, this does not currently have a glyph associated with it or any of its parents as far as I know.  Is this due to:

a) We are using the wrong SO term for this object.

b) This SO term is not in the right place in the SO ontology tree.

c) We need a new glyph for this object.

Thanks,

Chris

[John Sexton]

Hi Chris,

It looks like you already attempted to resolve this, per the last time you raised this issue on the SBOL Visual mailing list. In fact, it looks like you went so far as to request a new SO term, although it looks like that request hasn't moved?

Jake separately started a SBOL Visual mailing list thread and GitHub issue for Hammerhead ribozymes, but those never really gained traction.

I've discussed my thoughts previously in the 2nd half of a post on SEP V007: Stem-Top Glyphs. Currently, I superimpose the cleavage ("X") and stability ("shield") tops on an RNA (wavy) stem (see attached).

The issue is confounded by the fact that self-cleaving ribozyme insulators, like RiboJ and its variants, perform multiple functions related to insulation, RNA cleavage, RNA stability, and being a ribozyme.

-John

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[Chris Myers]

Hi John,

Thanks for digging that up.  I thought I was remembering this had been raised before, but I was not sure if it was just deja vu.

Yeah, the SO term seems stalled.  I will try to figure out who to prod about this.

So, I assume we are still happy with the conclusion from before that we are using the wrong SO term, and the right term just does not exist yet.

Even if this is true though, should SO:0000374 have a glyph associated with it?  Are there times that we would not want it to be rendered as an RNA_stability_element?  A simple solution for now would be to have SO:0000374 as an alternative SO term for RNA_stability_element glpyh.  Would that be wrong?

Thanks,

Chris

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<ribozyme_insulator.png>

[Jacob Beal]

For the longer term, I think the desirable solution is to start building a functional RNA sub-language, similar to the protein sub-language.

At present, however, is there any reason not to simply add SO:0000374 as another grounding term for the current RNA stability element glyph?  That, plus John's superposition, seems like it will cover things sufficiently until we have a chance to build a sub-language that can actually talk about all of these different sorts of functionality.

Thanks,

-Jake

Chris

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[Chris Myers]

Done for VisBOL:

https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/A1_AmtR/1

Cheers,

Chris

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[Jacob Beal]

Before we rush to this solution, I think we should hear some additional voices and make sure that others agree.

I think this is small enough to not need an SEP, but we still shouldn't adjust the spec until we've got more people speaking.

Thanks,

-Jake

Chris

[Chris Myers]

Fair enough on the spec, but I wanted to change VisBOL, since this is really ugly to have these common parts not rendering completely.

Cheers,

Chris

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[John Sexton]

Please forgive my ignorance, but does ribozyme imply self-cleavage? The SO:0000374 (ribozyme) term does not mention RNA cleavage at all, and Wikipedia suggests there are ribozymes that do not catalyze their own self-cleavage. It seems to me like self-cleaving ribozymes could have their own SO term and be a child of SO:0000374 (ribozyme). A self-cleaving ribozyme might also have: has_quality SO:0001977 (Ribonuclease Site). It's unclear to me whether all self-cleaving ribozymes would also warrant: has_quality SO:0001979 (RNA_stability_element).

(On that note, I noticed that there's an SO term for hammerhead_ribozyme (SO:0000380). Seems to me like that should be a child (i.e. the is_a relationship) of SO:0000374 (ribozyme), but it currently is not.)

This brings me to the SO term that Chris proposed. I admittedly don't understand what functions of self-cleaving ribozyme insulators are necessary for insulation (I naively prioritized separation of the promoter-specific 5'UTR sequence from the rest of the mRNA); last I read the RiboJ paper, their evaluation of insulation was practical and did not attempt to tease apart the necessary and sufficient components. All this is to say Chris's SO term might fit better as a child of a hypothetical self-cleaving ribozyme SO term? It might also benefit from incorporating: has_quality SO:0001977 (Ribonuclease Site) (I'll add my thoughts to the SO GitHub issue). So, in order of increasing specificity, the SO tree might go: ribozyme -> self-cleaving ribozyme -> self-cleaving, RNA-stability-standardizing ribozyme insulator?

On a functional RNA sub-language, the jury is still out for me. If it's intuitive and fits naturally with the rest of SBOL Visual, then I could probably be won over. I think I'd need to see it in action first, though.

Regarding a glyph for SO:0000374 (ribozyme), I feel like I've heard talk of using the Aptamer glyph (associated with SO:0000031 (aptamer)), although I don't think that's officially sanctioned.

Chris

Chris

Chris

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<ribozyme_insulator.png>

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[Shyam Bhakta]

John is right; ribozymes are catalytic RNAs in general, extending to the 23S ribosomal and spliceosomal and RNase P RNAs that perform the catalytic activities in their respective complexes.

The parts listed in the ribozyme insulator paper are actually super-parts consisting of a 5′-self-cleaving ribozyme and a small hairpin. The former insulates against 5′ context by cleaving it off as you said; the latter insulates against 3′ context in the CDS by structuring the 5′ UTR adjacent to the RBS so as to not give the CDS much sequence to fold up with. Only these two mechanisms are discussed in the paper, I believe.
1. Honestly, I don't know why the giant 2° structure of the ribozyme doesn't do that second job on its own. Why is a smaller second hairpin needed?
2. If the tiny hairpin is supposed to insulate against 3′ context, why doesn't the structure of the ribozyme intrinsically insulate against the 5′ context, too, by the same mechanism? Sure, it probably would work better by just eliminating the context as it does, but…
3. Lastly, the only function I can imagine as "stability element" is that fact that in general, 5′ and 3′ secondary structure in RNAs protect them against degradation. But that must be an unintentional feature, if a feature at all, as it's not described in the ribozyme insulator paper. By the same logic, intrinsic (ρ-independent) terminators can be classified as stability elements, because without them, mRNAs have substantially shorter half lives – exoRNases pause degradation at the hairpins, whether 3′ like a terminator or 5′ like in the intended use of the ribozyme insulators. But once again, the ribozyme insulator parts are not characterized/intended as stability elements in this capacity.

_________________

When I think of the ribozyme insulators, I imagine the 2° structure, which is exactly what the aptamer glyph shows. To be honest, the aptamer glyph doesn't evoke that the 2° structure it depicts binds anything, as an aptamer should. It can be imagined as an RNA thermometer, or a self-cleaving ribozyme, or an IRES (though technically superimposed with an RBS), or an attenuator element…
I wonder if the definition can be broadened as "structured RNA element".

Shyam Bhakta
Ph.D. Systems, Synthetic, & Physical Biology (2021)
   Rice University, M. Bennett Lab
President, SSPB Graduate Student Assoc.
832-785-9274

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[Chris Myers]

Hi John, Shyam,

Thanks for your very detailed explanations.  They are much appreciated.  To summarize, I have a few questions:

1) Given the current state of SO, Is SO:0000374 (ribozyme) the best SO term for the RiboJ part at this time?  Or is there a more appropriate SO term?

2) What is the best glyph to represent this part?  Is it the RNA stability element, aptamer, or something else?  

3) Given your answers to 1 and 2, if the glyph is not currently assigned to that SO term, do you approve of making this glyph have this SO term as an alternative SO term?

Thanks,

Chris

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[John Sexton]

Hi Chris,

Given the current state of the Sequence Ontology, I would first choose (1) SO:0001977 (Ribonuclease Site) and its associated glyph (2): "X" top, wavy stem.

Via superposition, I would further illustrate (2): "shield" top, which, on a wavy stem, is associated with (1) SO:0001979 (RNA_stability_element).

These decisions are rooted in communicating the function of the part over its form, as others have done; outside the RiboJ paper, I haven't seen the RiboJ parts illustrated with the Aptamer glyph.

I also like Shyam's idea of broadening the current Aptamer glyph to mean "structured RNA element" (I'm not sure if there's an immediately appropriate SO term for that, though). I could further envision and child glyph for self-cleaving ribozymes that shows a cleavage "X" in the Aptamer (some ideas attached). I think such a glyph would most appropriately match a hypothetical self-cleaving ribozyme SO term, which currently doesn't exist in the SO.

-John

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[Chris Myers]

Hi John,

Thanks for your feedback.  I’m not sure though I completely understand.  Are you saying this:

1) We should add a new glyph that RNA cleavage site and RNA stability element and use that glyph for RiboJ?

2) If that is the case, then could we not use the ribozyme SO term for this new glyph?

This would allow me to keep the SO term that I’m currently using and have it associated with your new proposed glyph. 

For the time being, I can associate the ribozyme SO term with either the RNA cleavage site OR RNA stability element glyph depending on which you think is better stop gap for now.

In the meantime, could you perhaps write a SEP proposing your ribozyme glyph idea?

Thanks,

Chris

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<self_cleaving_ribozyme_2.png><self_cleaving_ribozyme_3.png><self_cleaving_ribozyme_1.png>

[Shyam Bhakta]

Hey Chris,

I agree with everything John said.

old 1–2: Our ribonuclease site glyph, x~~, and SO:0001977 (ribonuclease site) are currently the best description for RiboJ and other self-cleaving ribozymes.
Though the rationale for the cleavage is "insulation" from 5′ sequence, I prefer the functional description, since "insulation" is a rather vague term, and requires further description of "insulation from what" in order to be meaningful at all. Thus the insulator glyph isn't ideal.

And though I saw in an example for RNA stability element SO:0001979 that "3′ hairpins" are listed as an example, and so by extension 5′ hairpins as in RiboJ would technically count, too, in accordance with the RNA protection phenomenon I mentioned earlier, this nucleolytic protection property is not the primary use of RiboJ etc, and neither is the 3′ insulation of the RBS conferred by the synthetic small hairpin. However, if someone just happens to be using a self-cleaving ribozyme's secondary structure itself as an RNA stability element primarily, sure, it would seem correct to use the RNA stability element glyph.

old 3/new 1. I do think an SO term for "self-cleaving ribozyme" should be assigned to the ribonuclease site glyph, but that the preferred glyph should be a new one we eventually design, to differentiate it from a simple RNase target site cut by an RNase enzyme in trans, which is by far the most common example of "RNase site" in biology (self-cleaving ribozymes are relatively very rare).

new 2. (The following assumes a broader SO term shouldn't be applied to a more specific glyph, which may not be the case.) I think it would be incorrect to use the generic ribozyme SO term for a new RiboJ/self-cleaving ribozyme glyph or the current RNase site glyph, because neither imply inherent catalycity. The inherent catalycity of RiboJ that makes it a ribozyme is a rare, specific case. The current SO term for ribozymes should apply to many more kinds of enzymatic RNAs, as previously mentioned.

I actually don't see a need for the SO ribozyme term to necessarily correspond to any glyph well; it's too generic of a term. So, if we had to choose between assigning the ribozyme SO term to "RNA cleavage site" or "RNA stability element", I can't really say either fits, because as before, most cases are not ribozymes, but the former sometimes is mediated by a ribozyme's catalyticity (in the case of RiboJ) and the latter is never mediated by a ribozyme's catalycity to my knowledge (just secondary structure).

Hope this helps!
And I am curious whether SO terms are to be applicable to every glyph that can possibly describe them, or only glyphs that necessarily describe them.

Shyam Bhakta
Ph.D. Systems, Synthetic, & Physical Biology (2021)
   Rice University, M. Bennett Lab
President, SSPB Graduate Student Assoc.
832-785-9274

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[Chris Myers]

Hi Shyam,

I agree with everything John said.

old 1–2: Our ribonuclease site glyph, x~~, and SO:0001977 (ribonuclease site) are currently the best description for RiboJ and other self-cleaving ribozymes.
Though the rationale for the cleavage is "insulation" from 5′ sequence, I prefer the functional description, since "insulation" is a rather vague term, and requires further description of "insulation from what" in order to be meaningful at all. Thus the insulator glyph isn't ideal.

And though I saw in an example for RNA stability element SO:0001979 that "3′ hairpins" are listed as an example, and so by extension 5′ hairpins as in RiboJ would technically count, too, in accordance with the RNA protection phenomenon I mentioned earlier, this nucleolytic protection property is not the primary use of RiboJ etc, and neither is the 3′ insulation of the RBS conferred by the synthetic small hairpin. However, if someone just happens to be using a self-cleaving ribozyme's secondary structure itself as an RNA stability element primarily, sure, it would seem correct to use the RNA stability element glyph.

Ok, I’ve updated our Cello library, please see:

https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/A1_AmtR/1

old 3/new 1. I do think an SO term for "self-cleaving ribozyme" should be assigned to the ribonuclease site glyph, but that the preferred glyph should be a new one we eventually design, to differentiate it from a simple RNase target site cut by an RNase enzyme in trans, which is by far the most common example of "RNase site" in biology (self-cleaving ribozymes are relatively very rare).

Sounds good.  We should make a request to SO for this.

new 2. (The following assumes a broader SO term shouldn't be applied to a more specific glyph, which may not be the case.) I think it would be incorrect to use the generic ribozyme SO term for a new RiboJ/self-cleaving ribozyme glyph or the current RNase site glyph, because neither imply inherent catalycity. The inherent catalycity of RiboJ that makes it a ribozyme is a rare, specific case. The current SO term for ribozymes should apply to many more kinds of enzymatic RNAs, as previously mentioned.

I actually don't see a need for the SO ribozyme term to necessarily correspond to any glyph well; it's too generic of a term. So, if we had to choose between assigning the ribozyme SO term to "RNA cleavage site" or "RNA stability element", I can't really say either fits, because as before, most cases are not ribozymes, but the former sometimes is mediated by a ribozyme's catalyticity (in the case of RiboJ) and the latter is never mediated by a ribozyme's catalycity to my knowledge (just secondary structure).

Ok, makes sense.  We will not assign it a glyph for now.

Hope this helps!
And I am curious whether SO terms are to be applicable to every glyph that can possibly describe them, or only glyphs that necessarily describe them.

Not sure the question.  For auto rendering, there must be a single glyph for each SO term.  There is no way to know which glyph is the most appropriate when going from SO to glyph unless there is only one glyph per SO.

Cheers,

Chris

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[John Sexton]

Hi Chris and Shyam,

On developing an SEP, it's not clear to me yet what would be included. I'm happy to start a separate GitHub thread to flush that out, though, if we feel there are still unresolved issues (e.g. changing what the Aptamer glyph is associated with, discussing a new self-cleaving ribozyme glyph, etc.).

Other responses below inline.

-John

On Thu, Jun 6, 2019 at 6:43 PM Chris Myers <my...@ece.utah.edu> wrote:

Hi Shyam,

I agree with everything John said.

old 1–2: Our ribonuclease site glyph, x~~, and SO:0001977 (ribonuclease site) are currently the best description for RiboJ and other self-cleaving ribozymes.
Though the rationale for the cleavage is "insulation" from 5′ sequence, I prefer the functional description, since "insulation" is a rather vague term, and requires further description of "insulation from what" in order to be meaningful at all. Thus the insulator glyph isn't ideal.

And though I saw in an example for RNA stability element SO:0001979 that "3′ hairpins" are listed as an example, and so by extension 5′ hairpins as in RiboJ would technically count, too, in accordance with the RNA protection phenomenon I mentioned earlier, this nucleolytic protection property is not the primary use of RiboJ etc, and neither is the 3′ insulation of the RBS conferred by the synthetic small hairpin. However, if someone just happens to be using a self-cleaving ribozyme's secondary structure itself as an RNA stability element primarily, sure, it would seem correct to use the RNA stability element glyph.

Ok, I’ve updated our Cello library, please see:

https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/A1_AmtR/1

This looks to me like the most appropriate way to represent RiboJ currently.  👍

 

old 3/new 1. I do think an SO term for "self-cleaving ribozyme" should be assigned to the ribonuclease site glyph, but that the preferred glyph should be a new one we eventually design, to differentiate it from a simple RNase target site cut by an RNase enzyme in trans, which is by far the most common example of "RNase site" in biology (self-cleaving ribozymes are relatively very rare).

Sounds good.  We should make a request to SO for this.

I've submitted a request for a "self_cleaving_ribozyme" SO term via GitHub: https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470.

Chris, do you still believe your "Ribozyme_stability_element" term should be requested?

 

new 2. (The following assumes a broader SO term shouldn't be applied to a more specific glyph, which may not be the case.) I think it would be incorrect to use the generic ribozyme SO term for a new RiboJ/self-cleaving ribozyme glyph or the current RNase site glyph, because neither imply inherent catalycity. The inherent catalycity of RiboJ that makes it a ribozyme is a rare, specific case. The current SO term for ribozymes should apply to many more kinds of enzymatic RNAs, as previously mentioned.

I actually don't see a need for the SO ribozyme term to necessarily correspond to any glyph well; it's too generic of a term. So, if we had to choose between assigning the ribozyme SO term to "RNA cleavage site" or "RNA stability element", I can't really say either fits, because as before, most cases are not ribozymes, but the former sometimes is mediated by a ribozyme's catalyticity (in the case of RiboJ) and the latter is never mediated by a ribozyme's catalycity to my knowledge (just secondary structure).

Ok, makes sense.  We will not assign it a glyph for now.

I also don't think a specific self-cleaving ribozyme glyph or our wavy-stem X-top glyph should be associated with the general SO:0000374 (ribozyme) term.

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[Chris Myers]

Hi,

I will close the SO term request for ribozyme stability element, if people think it is no longer needed. Let me know.

I’m also not sure what the SEP would be.  I thought there was a proposal about putting the X into the stability element top. 

Cheers,

Chris

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[Jacob Beal]

If I've understood the conversation correctly, it sounds like things don't need an SEP at all right now.

The cleavage site description, however, might be given an example of RiboJ to capture the conclusion of this discussion? https://github.com/SynBioDex/SBOL-visual/blob/master/Glyphs/cleavage-site/README.md

Thanks,

-Jake

Chris

Chris

Chris

Chris

Chris

Chris

Chris

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<self_cleaving_ribozyme_2.png><self_cleaving_ribozyme_3.png><self_cleaving_ribozyme_1.png>

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[Chris Myers]

John, Shyam,

I will leave this update to one of you, since you know the biology better than I.

Thanks,

Chris

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[John Sexton]

I'm pleased to report that our request for a "self_cleaving_ribozyme" sequence ontology (SO) term has been approved and a new term has been added: http://www.sequenceontology.org/browser/current_release/term/SO:0002231.

Chris, your ribozyme stability element request hasn't moved, and honestly I don't think we need it anymore, so I would cancel/close it.

-John

Chris

Chris

Chris

Chris

Chris

Chris

Chris

Chris

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<ribozyme_insulator.png>

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[Chris Myers]

Hi,

Ok, I’ve closed it.  Wonder why they are so slow in their response.

Cheers,

Chris

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[Bryan Bartley]

Personnel turnover was the story I got, after it took 2.5 years for my request to get approved....

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