Immunity by incompatibility – hope in chiral life

[AlexSorokin]

I think it is really hard to predict when it happens, but I am quite sure that all building blocks can be synthesized very soon (see also https://doi.org/10.1002/cbic.202200537), because it is a self-accelerating process which already started. The real problem is to assemble the minimal artificial cell, which is able to replicate (not nesessary designed as a replicator). 

[Duda Jarek]

Fully synthetic cells are already created and working (e.g. https://en.wikipedia.org/wiki/Artificial_cell ,  https://www.nist.gov/news-events/news/2021/03/scientists-create-simple-synthetic-cell-grows-and-divides-normally ) - for simple microbes it is just a matter of putting what's needed into phospholipid bag ... and there are financial motivations: to cheaply synthesize mirror chemicals e.g. for drugs.

It is quite likely there will be first mirror microbes in a decade - it is now time to prepare for that: understand the dangers (e.g. taking over ecological niches while being toxic), try to prevent them ...

[AlexSorokin]

These JCVI-syn3.0 bacteria (that are able to replicate) are not truly synthetic. They are obtained by genome transplantation into already existing cell (top-down approach). Bottom-up approach (using phospholipid bags filled with synthetic compounds) is still in its infancy.

[Duda Jarek]

‘Unprecedented risk’ to life on Earth: Scientists call for halt on ‘mirror life’ microbe research
"Experts warn that mirror bacteria, constructed from mirror images of molecules found in nature, could put humans, animals and plants at risk of lethal infections"

299 page "Technical Report on Mirror Bacteria Feasibility and Risks.pdf": Technical Report on Mirror Bacteria: Feasibility and Risks

[exchemist]

10 hours ago, Duda Jarek said:

‘Unprecedented risk’ to life on Earth: Scientists call for halt on ‘mirror life’ microbe research
"Experts warn that mirror bacteria, constructed from mirror images of molecules found in nature, could put humans, animals and plants at risk of lethal infections"

299 page "Technical Report on Mirror Bacteria Feasibility and Risks.pdf": Technical Report on Mirror Bacteria: Feasibility and Risks

How would this work? Surely these bacteria would be unable to utilise biochemical molecules from normal organisms, because they would have the wrong handedness? 

[CharonY]

2 hours ago, exchemist said:

How would this work? Surely these bacteria would be unable to utilise biochemical molecules from normal organisms, because they would have the wrong handedness? 

The first issue is that we remain unable to synthesize life with "proper" chirality. Not sure why folks should panic about doing something with it. I think a lot of folks are skipping over the technical and conceptional barriers that still exist.

[Duda Jarek]

I am starting reading the report above and e.g. "Mirror-image enzymes have recently been used to construct kilobase-length mirror RNA and DNA, and research is progressing toward building a mirror ribosome" suggests mirror bacteria could be made in a few years, and there are financial incentives - they are needed for mass production of especially mirror proteins, which could find lots of applications especially in medicine.

From the other side, I remember some articles that bacteria could easily adapt to consumption of mirror sugars - such mirror bacteria escaping the lab, not having natural enemies, could find ecological niches, evolve ... often being toxic if consumed - could turn out extremely dangerous for Earth ecosystem.

Anyway, mirror life is both great possibilities, but also dangers - needs wide discussion before it is too late ... I am repeating since 2007, glad it has finally reached the mainstream.

[CharonY]

No, you can make bacteria use and create some uncommon molecules. That part is easy for the most part. Bacteria already produce metabolites with different chirality and use enzymes like racemases to convert them into a form they want. Many enzymatic reactions can produce molecules with different chirality, it is not like antimatter or something drastically toxic, as you seem to  imagine.

The worry, I presume that folks have is that entirely new organisms would compete with existing one in changing the distribution of stereoisomeres in the world. But again, there is there is a huge jump from producing a few unusual molecules to create synthetic life (mirror or not). The latter is still quite far out of reach.

[Duda Jarek]

But for mass production of larger mirror proteins you need mirror ribosomes (they work on), preferably in mirror at least bacteria ... 2022: https://www.science.org/content/article/mirror-image-protein-factories-one-day-make-durable-drugs-body-cant-break

Being able to synthesize mirror RNA and ribosomes, getting the rest is relatively simple ... then there are lots of successes for building artificial cells: https://en.wikipedia.org/wiki/Artificial_cell

If such mirror organisms find some ecological niches (and evolve) due unprepared natural enemies, remind the thalidomide story ... now imagine consuming entire mirror organisms - there could be thousands of new interactions evolution did not prepared us for - some of them might be toxic.

[AlexSorokin]

Finally, the discussion about risks of mirror life truly goes mainstream. 

https://www.science.org/doi/10.1126/science.ads9158

 

https://purl.stanford.edu/cv716pj4036

[Duda Jarek]

Indeed, and looks the discussion has started in this thread in 2007: 17 years ago ... for ANS it took me ~8, I have more waiting 15 - science needs patience

I have created "Chiral life concept" Wikipedia article in 2007 ( https://en.wikipedia.org/w/index.php?title=Mirror_life&action=history&dir=prev ), but it was quickly deleted as SciFi ... then I have recreated it in 2017.

My original motivation here was becoming incompatible with pathogens as in the title - previous idea was by changing codon language: replace tRNA and rewrite DNA - I wonder if it could work? Probably there would be lots of issues with gene regulation ...

[exchemist]

8 hours ago, CharonY said:

The first issue is that we remain unable to synthesize life with "proper" chirality. Not sure why folks should panic about doing something with it. I think a lot of folks are skipping over the technical and conceptional barriers that still exist.

That was certainly how it seemed to me. We are nowhere close to creating organisms from scratch. 

But my real interest is in whether a hypothetical bacterium or virus employing molecules of opposite chirality to that present in terrestrial life could interact effectively with it. My understanding is that the wrong chirality in, say, sugars renders them useless because they can't be metabolised by organisms.  

[Duda Jarek]

Synthesis of artificial cells is already being made - nice summary graphics from 2022 https://pubs.acs.org/doi/10.1021/acsnano.2c06104

While it is much more difficult for higher organisms, bacteria often can use L-sugars (and quickly evolve) - e.g. from https://asu.elsevierpure.com/en/publications/bacterial-utilization-of-l-sugars-and-d-amino-acids

"In our laboratory, we have investigated several anaerobic bacterial strains, and have found that some of these bacteria are capable of using D-amino acids and L-sugars. Strain BK1 is capable of growth on D-arginine, but its growth characteristics on L-arginine are approximately twice as high. Another alkaliphilic strain SCA^T (= ATCC BAA-1084^T = JCM 12857^T = DSM 17722^T = CIP 107910^T) was found to be capable of growth on L-ribose and L-arabinose. It is interesting that this strain was incapable of growth on D-arabinose, which suggests the involvement of some alternative mechanism of enzyme activity"

However, it might require special enzymes, e.g. from: https://pmc.ncbi.nlm.nih.gov/articles/PMC3504760/

"An l-glucose-utilizing bacterium, Paracoccus sp. 43P, was isolated from soil by enrichment cultivation in a minimal medium containing l-glucose as the sole carbon source. In cell-free extracts from this bacterium, NAD⁺-dependent l-glucose dehydrogenase was detected as having sole activity toward l-glucose. This enzyme, LgdA, was purified, and the lgdA gene was found to be located in a cluster of putative inositol catabolic genes. LgdA showed similar dehydrogenase activity toward scyllo- and myo-inositols. l-Gluconate dehydrogenase activity was also detected in cell-free extracts, which represents the reaction product of LgdA activity toward l-glucose. Enzyme purification and gene cloning revealed that the corresponding gene resides in a nine-gene cluster, the lgn cluster, which may participate in aldonate incorporation and assimilation. Kinetic and reaction product analysis of each gene product in the cluster indicated that they sequentially metabolize l-gluconate to glycolytic intermediates, d-glyceraldehyde-3-phosphate, and pyruvate through reactions of C-5 epimerization by dehydrogenase/reductase, dehydration, phosphorylation, and aldolase reaction, using a pathway similar to l-galactonate catabolism in Escherichia coli. Gene disruption studies indicated that the identified genes are responsible for l-glucose catabolism."

From the report: "Mirror bacteria could evade many aspects of human immunity and potentially cause life-threatening infection

Most immunological mechanisms rely on precise stereospecific interactions between host and pathogen macromolecules. The mirror-image macromolecules of mirror bacteria would likely not properly bind to host receptors, enzymes, or other host effectors, as they would have the “wrong” chirality. This could grant mirror bacteria a degree of intrinsic immune evasion well beyond any known natural pathogen.

The immune system could be compromised in three key ways. First, the innate immune response relies upon initial detection of conserved microbial biomolecules, such as bacterial lipopolysaccharides and peptidoglycans, by host pattern recognition receptors. Because these molecules are almost exclusively chiral, immune recognition of mirror bacteria could be substantially impaired. Second, many innate immune mechanisms of pathogen control could be directly compromised; for example, phagocytosis, antimicrobial enzymes, and several complement system pathways rely on stereospecific protein interactions. Finally, mirror proteins would resist degradation and other stereospecific mechanisms necessary for antigen processing and presentation by innate immune cells, which would impair the activation of adaptive T and B immune cells and antibody production. "

Edited Saturday at 12:23 PM by Duda Jarek

[CharonY]

None of the examples in the review are true living and entirely synthetic cells. Also, how would these theoretical organism infect if their molecules don't interact with tge host? Host pathogen interaction goes both ways.

[Duda Jarek]

Regarding time estimates, the report says: "We estimate that if substantial resources were invested in a concerted effort, the creation of a mirror bacterium might still be 10 years away; and if research continues on its current trajectory, mirror bacteria might be created in the next 15 to 30 years."

Regarding dangers, basically mirror bacteria could be able to adapt to our e.g. sugars, especially thanks to very fast evolution, and immune system of standard life could be nearly defenseless - from the report: "In addition to functioning as a dangerous “accidental pathogen” to a wide range of natural-chirality species, mirror bacteria could persist within and potentially colonize external environments. Unlike their natural chirality counterparts, mirror bacteria would be completely resistant to all bacteriophages, partially evasive of and largely indigestible to predators, and largely resistant to antimicrobial compounds released by competing microbial species. These potentially decisive competitive advantages could allow sufficiently robust mirror bacteria to successfully invade many ecological niches despite lacking specific adaptations for them. Because predators would not be able to digest most mirror macromolecules, a growing mirror bacterial population would not be controlled by any commensurate increase in predation, which could allow populations to reach high abundance."

It is hard to find better sources than this report now - I am slowly reading. It is around the Build-a-Cell community, but I got disclaimer "This Science paper does not represent any official position of the Build-a-Cell community", also with "Mirror Biology Dialogues Fund": https://www.mbdialogues.org/ and information about open discussion this Thursday.

Edited Saturday at 01:22 PM by Duda Jarek

[exchemist]

12 hours ago, CharonY said:

No, you can make bacteria use and create some uncommon molecules. That part is easy for the most part. Bacteria already produce metabolites with different chirality and use enzymes like racemases to convert them into a form they want. Many enzymatic reactions can produce molecules with different chirality, it is not like antimatter or something drastically toxic, as you seem to  imagine.

The worry, I presume that folks have is that entirely new organisms would compete with existing one in changing the distribution of stereoisomeres in the world. But again, there is there is a huge jump from producing a few unusual molecules to create synthetic life (mirror or not). The latter is still quite far out of reach.

Ah, racemases. I didn’t know about those. So there are biological ways to convert one stereoisomer into another. That answers my question.

[CharonY]

Isomerases in general, I probably should have said. I worked with racemases and it was the first thing that came to mind.

[Duda Jarek]

Below Table of Contents of https://purl.stanford.edu/cv716pj4036 itself allows to imagine our situation in ~20 years, when such synthesis should be relatively simple ... and deadly - how to prevent it?

Chapter 2: Pathways to Mirror Life 26
2.1 Advances in chemistry permit the synthesis of mirror biomolecules with diverse applications 28
2.2 Progress in synthetic biology could allow the assembly of a mirror bacterium from non-living mirror components 33
2.3 A natural-chirality bacterium might be converted into a mirror bacterium in a stepwise fashion 41
2.4 Other approaches to creating mirror bacteria are plausible 50
2.5 The feasibility of mirror life will increase as related technologies advance 51
Chapter 3: Engineering, Biosafety, and Biosecurity of Mirror Bacteria 54
3.1 The creation of any mirror bacterium could enable the generation of diverse mirror bacterial strains and species and their modification by routine genetic engineering 55
3.2 Biocontainment approaches might reduce accident risk, but they would face challenges 60
3.3 Creating robustly biosecure mirror bacteria is not feasible 62
Chapter 4: Risks to Human Health 65
4.1 Innate immune detection of mirror bacteria could be significantly impaired 67
4.2 Mirror bacteria would likely be resistant to most innate immune responses 72
4.3 Adaptive immunity to mirror bacteria would likely be impaired 81
4.4 Mirror bacteria could plausibly pass barrier surfaces and translocate into the bloodstream and tissues 91
4.5 Mirror bacteria could plausibly replicate in blood and cause lethal systemic infection 98
Chapter 5: Medical Countermeasures 107
5.1 New antimirror compounds could be developed to target mirror bacteria, but most existing antibiotics would not function 108
5.2 Conjugate vaccines could plausibly be developed against mirror bacteria 113
5.3 The efficacy of other countermeasures against mirror bacterial infection is unclear 116
Chapter 6: Animal Infection 119
6.1 Vertebrate susceptibility to mirror bacterial infection would likely be similar to that of humans 120
6.2 Many invertebrates would likely be susceptible to mirror bacteria 123
Chapter 7: Plant Infection 134
7.1 Mirror bacteria are likely to evade plant innate immunity 135
7.2 Mirror bacteria could plausibly establish chronic local infections within leaves and roots 138
7.3 The extent to which mirror bacteria could spread through and colonize plant vascular tissue is unclear 145
7.4 Countermeasures for agricultural plants 151
Chapter 8: Environmental Survival and Spread 156
8.1 Mirror bacteria would be inherently resistant to many biological controls 157
8.2 Mirror bacteria could colonize natural environments outside of multicellular hosts 165
8.3 Invasive mirror bacteria could rapidly disperse through the environment 175
8.4 Invasive mirror bacteria could rapidly evolve and diversify 178
8.5 Invasive mirror bacteria could cause irreversible ecological harm 181
8.6 Countermeasures to invasive mirror bacteria might lessen but would not halt the ecological damage 187

[KJW]

4 hours ago, Duda Jarek said:

4.1 Innate immune detection of mirror bacteria could be significantly impaired 67

It's my understanding that the innate immune system is designed to detect foreign bodies. It seems unlikely to me that it would limit itself to the "correct enantiomer"

 

 

4 hours ago, Duda Jarek said:

4.2 Mirror bacteria would likely be resistant to most innate immune responses 72

It's my understanding that a particularly important way that the immune system kills pathogens is to use "bleach" on them, and "bleach" does not stereochemically discriminate.

 

 

4 hours ago, Duda Jarek said:

4.3 Adaptive immunity to mirror bacteria would likely be impaired 81

It seems to me that this is based on the incorrect assumption that an antibody consisting of natural enantiomer components will only bind to antigens consisting of natural enantiomer components. For example, while it is generally true that a receptor that binds to a particular enantiomer of a given compound will not bind to the opposite enantiomer of that compound, it doesn't mean that there isn't a different receptor, composed of the same chirality building blocks, that can bind to that opposite enantiomer. Thus, even when presented with a mirror antigen, the immune system ought to be able to find an antibody that binds to the antigen.

 

 

Edited Monday at 09:33 AM by KJW

[Duda Jarek]

This is entire Chapter 4: Risks to Human Health of https://purl.stanford.edu/cv716pj4036, maybe take a look there.

For example for macrophages looks like nearly nothing would work:

[CharonY]

I skimmed over parts the report and do not find it very convincing as a whole. Chapter 2 does a lot of handwaving and the main message is basically that with new tech, at some point mirror life might be possible. Given the challenges with actual synthetic life (as opposed to introducing synthetic elements into existing life) it has too many unknowns to call. We might all have died from antibiotic resistant infections before it comes to that.

I found it also odd that they spent so much time on the immune system, and only little regarding the survival and proliferation of these hypothetical mirror organisms. The latter is way more relevant than the former. If they cannot establish a replication niche, the immune system would not need to do anything in the first place. There again, they waffle a lot and seem to suggest that the mirror organisms would not be fully mirrored, but instead be also designed to use more common nutrients. At this point the suggestion is apparently less about mirror organisms per se, but more about partially engineered organism. I.e. able to use abundant stereoisomers but have modified surfaces for immune evasion, for example. Where they are accurate, they determine specific mechanisms that could be escaped due to incompatibility, though they kind of go light on the mechanisms that "regular" pathogens already have access to. As a whole it seems that the main argument really is just about a pathogen with a tougher surface to recognize, though again, they do not talk much about the decoration that current bacteria are able to do.

Again, too handwavy and not enough contextualization with current pathogen strategies. Combine that with the fact that they also have to make excuses how the mirror bacteria are going to survive in the first place, it does seem a bit sensationalized. They certainly do not make a stronger argument than other discussions on e.g. gain of function research, especially as they have to point out to hypotheticals to highlight potential dangers. To be fair, the keep mentioning parts that are unclear but then just conclude it could be bad, which, again is not terribly convincing.

 

[Duda Jarek]

For me Chapter 2 is quite detailed, bottom-up, top-down and other approaches. If reaching first synthetic cell, what seems a matter of a decade, mirror one would just need to use enantiomers - and their synthesis is quickly developing, especially that there are financial motivations, like mass production of mirror proteins, DNA/RNA ... and there could be some malicious players, like nihilist terrorists, or AGI wanting to get rid of humans ...

Chapter 4 is indeed extremely detailed, and difficult without immunology background, but basic scenario is such mirror bacteria getting into the bloodstream, and freely multiply being nearly invisible for immune system - reaching sepsis or different problems.

Anyway, I agree this is still early (10-30 years away) - good time to discuss, understand, try to find protections if possible.

[CharonY]

49 minutes ago, Duda Jarek said:

If reaching first synthetic cell, what seems a matter of a decade, mirror one would just need to use enantiomers - and their synthesis is quickly developing, especially that there are financial motivations, like mass production of mirror proteins, DNA/RNA ... and there could be some malicious players, like nihilist terrorists, or AGI wanting to get rid of humans ...

That is a big if. We have been just a few years away from synthetic life for a few decades now. And you have to read carefully, they say it is at least a decade away. My contention is that we are looking at a much longer timeline, we first need to be able create synthetic life, before being to create a mirror of that.

So far, in biology we have not seen a clear path to that. In contrast, simplified approaches which are conceptionally old, such as replacing DNA have repeatedly been sold as artificial life, which is really just overhyping things for laypersons (and the easily excited).

Also, I think you have still a fundamental misunderstanding of mirror molecules. Just because of their reverse chirality, molecules do not suddenly become more toxic. Many building blocks, such as amino acids exist in both orientations naturally, it is just that organisms exclusively use one for protein formation (and convert the other form before usage). For example, bacteria, D-amino acids may serve a role in stress related signaling.

So the only thing that does not exist in nature are D-proteins synthesized from D-amino acids. But in labs, those have been produced for decades for structural investigations. Again, the issue is not the presence of those mirror-molecules, especially as they also exist in nature. What the authors argue is more of a biohazrd risk which, in my opinion and with our current knowledge is overstated. It is not unlike the worries folks had (and still have) regarding biowarfare agents, which, theoretically, could be easily produced with modern biotech capabilities. And while those are far more realistic, they have not really been realized (we apparently are much better at spreading disease the "natural" way with the help of anti vaccination efforts).

 

[Duda Jarek]

> We have been just a few years away from synthetic life for a few decades now

There is continuous progress (timeline from 2019 https://elifesciences.org/articles/45379 ), synthetic cells are created since 2010 ... where do you think will be the main difficulty for complete synthesis of natural minimal cell?

I completely agree interactions between both chiralities are very complex, recommend in the report: "Table 1.1: Achiral organic molecules that can be utilized by wild-type or mutant E. coli K-12", "Table 1.2: Utilization of ʟ- and ᴅ-amino acids by E. coli", "Table 1.3: Utilization of the enantiomers of common monosaccharides by E. coli".

And reminded thalidomide example - toxicity from basically random interactions, there would be a huge number of them e.g. from necrosis of mirror bacteria in human bloodstream - there is a large chance for various toxicities.

[CharonY]

Gibson et al. 2010 described a cell with an artificially synthesized genome injected into an existing only. However even that one was based on the existing one, just pruned down and reinserted. This essentially was feasible with different and more inconvenient methods since the 2000s. The challenge is, as mentioned earlier, that to our current knowldge we do not know how we can prune down cells to its essential co ponents to live and replicate. Most work still focuses on DNA, not because it is so essentisl, but more because it is easier to msnipulate.