Cure for Aging Can Be Created Using Directed Evolution


Project description:

Accumulating evidence suggests that microbiota plays an important role in modulating lifespan. This makes possible to use symbiotic bacteria as “living drugs”, which live in the host organism and promote its longevity. We propose to create bacteria, which dramatically extend lifespan of its host. Such bacteria have to produce not one, but a set of longevity-promoting substances with optimal concentrations and dynamics of secretion. To obtain such bacteria we propose to use directed evolution, a process that mimics Darwinian selection on a laboratory scale. This approach has never been applied to drug development before. Directed evolution enables simultaneous modulation of a number of bacterial metabolic pathways andsubsequent selection of the most effective longevity-promoting variants. Experiments will be conducted on a model system consisting of C.elegans and its intestinal symbiont E.coli. Due to highly conserved aging pathways, obtained bacteria may be further used to develop longevity-promoting human drug.

Bacteria E.coli serve as the food source for C.elegans, but at particular stages of the nematode life course they can also exist as intestinal symbionts. Moreover, it was shown that E.coli influence physiology and lifespan of C.elegans. It was revealed that several mutations in E.coli genome increase or vice versa reduce the nematode lifespan.

Symbiont 1

The relationship between C.elegans and E.coli at different stages of the life course of the nematode

Left picture – During development, bacteria mainly serve as a source of food for C.elegans

Center picture – In adult worms some bacteria are not digested and become symbionts

Right picture – As the worm ages, bacteria proliferating within the lumen of the gut become detrimental to the host (Cabriero and Gems, 2013)

The project aims to create E.coli strains that are able to extend the lifespan of C.elegans. For this purpose we propose to employ directed evolution – a process that mimics Darwinian selection on a laboratory scale. At first, phenotypic diversity of E.coli is generated using global transcription machinery engineering (gTME) approach. The gTME randomly alters key proteins regulating the global transcriptome and generates a new type of diversity at the transcriptional level. Then a set of bacterial strains with reprogrammed transcriptome (a bacterial library) is created and E.coli strains which demonstrate the highest ability to extend C.elegans lifespan are selected. We propose to perform not less than 2 cycles of gTME.

For gTME we propose to alter genes of transcription initiation factors σ, which regulate expression of hundreds of genes. At the first cycle of gTME the gene which encodes the main sigma factor σ70 (RpoD) is subjected to random mutagenesis. At the second cycle of gTME the gene of sigma factor σ38 (RpoS), which regulates expression of stationary phase genes, is targeted for mutation.

The selected bacteria are studied to identify transcriptome, proteome and metabolome modifications which result in longevity-promoting phenotype.

Research goal:

Creation of symbiotic bacteria, which are able to increase the lifespan of the host, and study of biological mechanisms underlying these longevity-promoting interactions.

Symbiont 2Research plan

I stage – Creation of bacterial strains which extend the lifespan of C.elegans

(duration – 1,5 years)

1) Construction of library of E.coli strains with reprogrammed transcriptome

– Random mutagenesis of σ-factor gene using error-prone PCR.

– Cloning of obtained sequences into plasmids and transformation into E.coli.

2) Selection of E.coli strains which demonstrate the highest ability to extend C.elegans lifespan

C.elegans are raised on one of the bacterial mutant strains and analyzed for their lifetime. 1500-2000 strains from mutant library are screened.

– Selection of E.coli strains which demonstrate the highest ability to extend C.elegans lifespan.

2nd cycle of gTME using the gene of another σ-factor – iteration of experiments 1)-2)

II Stage – Study of E.coli strains which extend the lifespan of C.elegans

(duration – 1 year)

– Analysis of transcriptome, proteome and metabolome of E.coli strains which promote longevity of C.elegans.

– Identification of E.coli genes and biological pathways which affect the lifespan of C.elegans.

Expected results:

  • Development of longevity-promoting “living drug” based on symbiotic bacteria.
  • Demonstration of the possibility of directed evolution to create symbiotic bacteria with such a complex phenotype as ability to extend the host lifespan.
  • Identification of new genes and biological pathways of coli which affect C.elegans longevity.

13 Comments

Filed under Biology of Aging

13 responses to “Cure for Aging Can Be Created Using Directed Evolution

  1. Marcus V

    What makes you think that directed evolution has not been applied to drug development? Enter “Directed evolution” and “drug development” into Google Scholar, and you’ll get several thousand publication hits.

    • In all of those cases bacteria are used as drug producing factories. Directed evolution is applied to maximize the drug production properties of the bacteria, but they are merely production plant, not the drug itself. Here we propose a completely different idea – using the symbioic organism, its evolution to improve the wellbeing of the host.

  2. designscheap

    As Marcus said, I don’t see the difference. Seems like you are splitting hairs here or aren’t explaining the difference clearly. Maria in your reply you said “In all those cases bacteria are used as drug producing factories….Here we propose a completely different idea – using the symbiotic organism, its evolution to improve the well being of the host.”

    But early in the article it says: “We propose to create bacteria, which dramatically extend lifespan of its host. Such bacteria have to produce not one, but a set of longevity-promoting substances with optimal concentrations and dynamics of secretion.”

    The symbiotic relationship doesn’t change the fact that it’s the compounds / substances that the bacteria produce that cause the change you are trying to bring about.

    • Of course, the therapeutic effect will be reached by the impact of bacteria’s life (everything they secrete) on the surrounding tissue. Our point is not to dissect those substances that the bacteria will be producing, but rather having it do what it’s doing over a long period of time, because it’s the regulatory function of the bacteria that is what we are looking for. We don’t want to know the substances, because the regime, the timing of the substance release is crucial. It’s only the bacteria can “decide” when and how much of subtance A it needs to produce, we can’t make this decision, because we don’t know what’s happening inside the organism. Bacteria, on the other hand, do know that, because they are excellent sencors, that is the quality we would like to use and enhance using directed evolution so that the evolved symbiont make the host live for as long and as healthy as possible.

  3. This is a very clever expansion upon existing techniques to restore normal function and address individual diseases with readily available microbes. Besides directly attacking age-related decline, it aims to engineer and introduce rare and/or new microbiome residents with heretofore inaccessible therapeutic features.

  4. The benefits of this project are going to be significant enough, but there is an implication here similar to the motivation for the search for life on other planets if such bacteria are proven to be possible but have not appeared in the same way as harmful ones..

    Bacteria that do harm and use animals to procreate by excreting infectious material proliferate, but there seems to be no evidence of any that do good to the extent of increasing lifespan. A bacterium that produced no adverse symptoms and in addition extended lifespan should proliferate as it will have longer in which to do it. It would pass undetected because of the lack of symptoms, and there would be no active suppression of its procreation like burning bodies or imposing quarantine regulations.

    There are plenty of examples of people whose lifespan has been shortened as a result of infection, but none as far as we know whose lifespan has been extended. This gives us some more understanding of the nature of the universe we are in, just as would the discovery of the remains of life on Mars that is different to life on Earth.

    As far as I know there has never been anyone with a substantially increased healthy lifespan, such as 200 years. All people get frail even if they live to be between 100 and 120. There have been hoards of people with substantially reduced lifespans as a result of bacteria, even instant death such as plague. It is also possible the people who have received “a little sniffle” have adverse effects at the ends of their lives that knock years off.

    Maybe an additional approach would be to find super-centenarians whose relations have lived ordinary natural lifespans and see if their biomes contain any unusual bacteria. In this instance their long lifespan could be attributed not to their genes by these acquired bacteria.

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  8. Reblogged this on The Longevity Letter and commented:
    We share our bodies with millions of microorganisms, creatures which were recently shown to modulate our lifespan. Today I’m sharing with you an article by Maria Konovalenko on creating bacteria as living drugs, which may dramatically extend our healthy years!

  9. The only good Microbiome, is a dead microbe/flora/jungle.. As far as Life extension/immortality is concerned… As shown of the Site wherein ageing now ends… Respect to the Wonder Woman of Transhumanism.. Maria Konovalenko Esquiress… http://adamandevewordresearch.blogspot.com/

  10. James Clark

    As already noted by Longevity letter. This isn’t that far fetched of an idea as Natural selection has already allowed a great deal of symbiotic bacterial strains to populate our bodies for our benefit and the benefit of the bacteria. Maria this is a brilliant idea and I wish you the best of luck with it.
    Synopsis is a very interesting aspect of Natural selection and should in my personal view be looked into in a deeper sense there’s much we can learn from the most basic biological concepts and how they relate to many other aspects of the world around us.

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