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Room For Improvement

How much can we improve on Nature? Fixing defective proteins and pathways is one thing, but in those cases we’re trying to get back to what the function should be (and what it is in healthy organisms). But what about “better than healthy”? That’s a tricky area to enter, because (for one thing) billions of years of evolutionary pressure have given us few opportunities for obvious improvements – and it also means that some of the ones that look obvious might not be such a good idea (see “Chesterton’s fence” for general thoughts on this in human affairs). At the extreme end of things, this is what unnerves people – and should – about using a technique like CRISPR to not only fix disease-causing mutations, but to enhance otherwise normal embryos in some way that we find valuable.

But let’s take a look at something less controversial: fixing plants. Photosynthesis has had plenty of time to evolve, although when you look at one of the key enzymes (RuBisCO), you wonder. It is, by enzyme standards, amazingly slow and inefficient. Its turnover is pitiful, and a good part of the time it grabs an oxygen instead of a carbon dioxide, because it’s too damn sloppy to be able to tell them apart. When that happens, RuBisCO does something completely inappropriate with it, producing 2-phosphoglycolate, which is not just useless but actively toxic. The photorespiration pathway exists just to clear out the 2-PG that keeps getting blindly pumped out from photosynthesis.

I have made the case for the prosecution there, but in RuBisCO’s defense, no one has ever been able to engineer anything better. And many have tried. Evolution has, in fact, had plenty of time to do just that, and it’s possible that what we’re seeing, as brutal and bumbling as it may look, is the most elegant solution available (at least in that particular part of the landscape, short of wholesale re-engineering – and if you’re thinking about that, it’s worth noting that no such alternate carbon-dioxide-fixer photosynthetic pathway seems to ever have emerged, either). It’s very likely that the ability to distinguish carbon dioxide from oxygen and the ability to actually turn over the enzymatic reaction are working against each other, and that what we see is the best compromise that a billion years could come up with.

But outside of the enzyme’s structure, there is apparently room for improvement. Evolution has already hit on the C4 pathway versus the older C3 version, improving RuBisCO function by giving it an environment that’s lower in oxygen in the first place. The problem there is that you need extra enzymatic steps to work C4, which costs you extra ATP, so while C4 plants win out at higher temperatures or under stress, C3 plants will outcompete them under other conditions. But what about fixing that photorespiration pathway? That’s what this new paper from Illinois shows. They’ve engineered in glycolate-handing enzymes in the pathway from bacteria and/or algae in an attempt to tune things up, and after many constructs, promoters, and combinations, they appear to have something.

They now have field-tested plants (tobacco as a test case, since it has easy genetics, is robust, and produces large amounts of seed) whose light-use efficiency is up 17% compared with wild-type, with 25% more biomass produced. That goes up even further to 40% biomass gain if they also engineer in RNA interference for a wild-type glycolate transporter, forcing the plant to go more through the new enzymes. What’s more, they’re optimistic that this can be translated to other more useful C3 plants, including food sources. This will also allow these plants to thrive even more if carbon dioxide levels keep increasing (and allow them to take even more of it up). It looks like the plants produce larger leaf area earlier in their life cycle, and the hope is that this will allow for larger biomass showing up as seeds (for grain crops) and tubers (as with potatoes).

This is good news. Increased crop yields would allow us to feed the Earth’s population while plowing up less of the planet than we would have to otherwise, and figuring out how to engineer plants to use carbon dioxide more effectively is no bad thing, either. So while always thinking that we can rig up something better than evolution is not the way to go, just assuming that we have to take the cards we’re dealt isn’t sound, either. Anyone who works in biomedicine has already put their bet down against that second attitude, anyway!

Now, what you think of such means might be another matter. To take up that question, let me recommend Charles Mann’s The Wizard and the Prophet, which is a history of the Green Revolution and more besides. Mann has a nice discussion of just these sorts of foodcrop-based issues, but (as he discusses) the questions raised go far beyond the borders of the simple little area of growing enough food for everyone. We’ll be hitting those soon enough in biomedicine, at the rate things are going. . .

27 comments on “Room For Improvement”

  1. milkshake says:

    the reason why evolution did not optimize the efficiency of CO2 fixation or photorespiration better could be a trade-off, maybe some sort of evolutionary disadvantage would come from doing so. But food crops grow in man-controlled environment: they don’t have to be fittest, in evolutionary terms

    1. NPs says:

      Agreed, it shouldn’t be framed as an efficiency competition between humans and nature but rather humans and nature optimizing towards different goals. Ours is increased consumable biomass and nature is working towards increased survival.

    2. MrXYZ says:

      Will these plants require higher amounts of fertilizer or other nutrients because of the increased growth rate?

      1. loupgarous says:

        Quoting Derek:

        “They now have field-tested plants (tobacco as a test case, since it has easy genetics, is robust, and produces large amounts of seed) whose light-use efficiency is up 17% compared with wild-type, with 25% more biomass produced. That goes up even further to 40% biomass gain if they also engineer in RNA interference for a wild-type glycolate transporter, forcing the plant to go more through the new enzymes. What’s more, they’re optimistic that this can be translated to other more useful C3 plants, including food sources. This will also allow these plants to thrive even more if carbon dioxide levels keep increasing (and allow them to take even more of it up). It looks like the plants produce larger leaf area earlier in their life cycle, and the hope is that this will allow for larger biomass showing up as seeds (for grain crops) and tubers (as with potatoes).”

        More leaf area should require more nitrogen (thus fertilizer) because photosynthetic activity depends on enzyme catalysts such as RuBisCo. But speculatively, it shouldn’t be in direct proportion to either seeds (as in grain crops) or tubers (like potatoes).

        I wouldn’t be shocked to see this team play with potato DNA next, as potatoes and tobacco (which this report deals with) both belong to family Solanaceae, the “nightshades”.

        1. loupgarous says:

          I left out the real answer to your question:

          “Will these plants require higher amounts of fertilizer or other nutrients because of the increased growth rate?

          .

          I think the nitrogen demand will be higher in the leaves, where photosynthesis happens. But the enzyme catalysts involved are available for reuse, so there shouldn’t be a steady demand for nitrogen or other enzyme-related nutrients throughout the plant’s life cycle.

          But seeds are made both of protein and carbohydrates. Later in the redesigned plant’s life cycle, an increase in seed yield should also increase demand for nitrogen and/or other enzyme-related nutrients, more so in proportion to their mass than tuber plants like potatoes.

          Speculating, again, demand for nitrogen and other plant nutrients should increase in redesigned plants along the lines in Derek’s article. But the leaves should use most of the increase as more photosynthetic enzymes are made, but this should happen early in the plant’s life cycle. Demand for those nutrients later in the plant’s life cycle should be comparatively modest (mostly amino acids for reproductive tissues such as seeds and tubers). Most of the increased biomass should be carbohydrates.

          1. aairfccha says:

            Growing unmodified wheat in a CO2 enriched atmosphere increases both biomass and grain yield, however the grain contained less proteins.

            https://www.ncbi.nlm.nih.gov/pubmed/19778369

          2. MrXYZ says:

            Many thanks for the detailed answer. I tend to be a believer in unexpected consequences. So while for something like this, moving forward with more field trials makes sense, I think we should be prepared for surprises. For example, we are assuming that photorespiration is a bug (that we can and should engineer away), but it could also be feature (i.e. giving some fitness advantage to the plant that we’re not aware of yet).

  2. loupgarous says:

    The mathematical physicist Freeman Dyson proposed planting of vast tracts of fast-growing trees (fir, pine, that sort of thing) to sequester carbon dioxide from the air. The biomass would be a welcome bonus to foresters (especially “tree farmers” who are constantly planting large tracts of land in pine to harvest later). Engineering strains of these trees to grow and turn CO2 into biomass shoujld make this proposal more feasible.

    Another use for re=engineered plants of this kind would be, if we embark on the project, for human colonies on Mars, where faster-growing, more efficient, carbon dioxide-loving plants for food and reclamation fo CO2 from closed environments might not just be a good idea, but vital.

    The objection that engineered plants like this aren’t desirable because evolution didn’t select for this new trait the people in Illinois developed is weak. Man’s been selecting for desirable traits in food crops and various ornamental plants for centuries, moving desirable plants like maize and tomatoes across the oceans for cultivation and use. Animal husbandry also makes extensive use of artificial selection to discover, isolate and foster desirable traits.

    Milkshake’s right – we don’t have the environment that existed when evolution selected the traits we now foster in our flora and fauna. The mere presence of humans, capable of liberating enough energy and energy-trapping gases to change the environment requires we take responsibility for what we do – because we are controlling the environment globally now.

    Folks like the late Robert Heilbroner (in his 1974 An Inquiry Into The Human Prospect, updated into an “I told you so” edition in 1991) tell us we need to curtail the human race’s activities to a level the Earth can support – using less energy for luxuries such as transport faster than bicycling and local climate control such as air conditioning.

    This new development, applied to create new and more robust forests, may let Man take positive action toward an Earth that can better absorb the things we humans put in the environment that make it less livable, while growing more food to feed us all with less damage to the environment.

    1. Emjeff says:

      Thanks, Al Gore. Here’s the usual lecture from the elites stating that “we” have to give things up for the good of the planet. Meanwhile, people like Al are driven to the airport in limos, then step on their G4 and fly all over the world to tell other people to stop flying and driving. I’ll start worrying about climate change when the elite start flying coach.

      1. loupgarous says:

        Unlike Al Gore, I have neither millions invested in “green” enterprises waiting for global warming tulip mania to kick in, nor a credulous attitude toward every report of global warming or a starring role in a movie the British schools require a disclaimer stating its factual deficiencies before their kids can see it in school.

        I just live on the Gulf of Mexico coast and notice how big hurricanes seem to be increasingly common, and noticed the role of heat in ocean water plays in how tropical storms become big hurricanes.

        I didn’t mean to trigger you by mentioning a few facts.
        I’ll just run everything past Exxon/Mobil’s PR people from now on before I post.

        1. dearieme says:

          “I just live on the Gulf of Mexico coast and notice how big hurricanes seem to be increasingly common”.

          I understand that the facts are otherwise. Do you have a source for your claim?

          1. Niklas B says:

            Appears to be a bit of a mixed bag, according to https://www.c3we.ucar.edu/impact-climate-change-gulf-mexico-hurricanes

            Quote:
            – A tendency towards fewer hurricanes in the Gulf of Mexico and a slight reduction in the proportion of Atlantic hurricanes entering the Gulf.
            – An increased proportion of category 3, 4, and 5 storms in the Gulf of Mexico.
            – Increased precipitation for all cyclones in the Gulf of Mexico (on the order of 30-40%).

            The characteristics of hurricanes in the Gulf of Mexico in the future are projected to be similar in size and track speed to current hurricanes.

            These simulations predict a ~10% increase in cyclone damage potential for the most intense hurricanes.

          2. cancer_man says:

            Both IPCC and the National Hurricane Center say there has been no increase in magnitude or frequency of hurricanes in the past hundred years.

          3. gippgig says:

            Great source for tropical cyclone information that covers this sort of issue:
            http://www.wunderground.com/cat6

          4. loupgarous says:

            First, I’ll mention that the National Hurricane Center’s Dr. Chris Landsea resigned from an IPCC study in tropical storms back in 2005 when IPCC announced the outcome of a study he co-authored on global warming’s impact on number and severity of tropical storms – before Landsea and his co-authors were done analyzing the data. That was one of a number of highly-publicized exposes of shoddy science by IPCC’s leadership. I’m aware of the tendency of IPCC to court publicity for studies that affirm the existence of global warming and possible harms coming from that.

            I am still agnostic about global warming in general, and would like to see more actual proof of harms arising from it.

            But the paper cited by Niklas B
            https://www.c3we.ucar.edu/impact-climate-change-gulf-mexico-hurricanes
            trends to affirm more really damaging hurricanes are here (in North America as a whole) and more are coming.

            The increase in their effects cannot entirely be blamed on increases in their severity. I don’t know about other areas, but the Gulf of Mexico coast has steadily become more populous over the past decades. Areas in low-lying areas which were never even settled in previous decades now have large housing developments on them – a pattern which persists even after Katrina and other catastrophic tropical storms.

            But the storms are getting worse, if not more numerous.

  3. John Wayne says:

    Don’t forget the third way to fix carbon; crassulacean acid metabolism. This is used by plants to minimize water loss and is a really cool adaption.

    When a normal plant opens its stoma to absorb CO2 it looses hundreds of water molecules for each CO2 absorbed in the exchange. This water loss is used to drive fluid movement (instead of using an explicit pump like a heart). When water is the limiting reagent, minimizing its loss becomes an evolutionary advantage. This water loss is temperature dependent. CAM plants absorb CO2 at night, and store it as malic acid in vacuoles. During the day, this stored CO2 is used for synthesis when the photochemical energy is available. Familiar plants that use this method are pineapple, agave and jade. Some plants with this adapation only use it, others can switch between metabolic strategies. Cool stuff.

    Why aren’t there more than three carbon fixing adaptions that are mechanistically similar? I’d guess the current method is in a local minimum of efficiency. Give it a few billion more years, or a new planetary starting point, and you may end up with something new. The new thing could be better, or worse. You could image that plants from an alien biosphere could be at a significant advantage or disadvantage compared with those on earth, leading to potential issues with contaminating invasive organisms on a grandiose scale.

    Biology is an impressive chemist.

    1. John Wayne says:

      Addendum: biology is an impressive chemist, and a terrible overlord. You are no longer efficient; out of the pool.

  4. krv says:

    Here is an article which posits an explanation for rubisco’s inefficiency. Briefly, it first arose in an environment largely deprived of O2 and learnt to discriminate between CO2/O2 later at the cost of catalytic efficiency.
    https://www.sciencedirect.com/science/article/pii/S095816691730099X

  5. gippgig says:

    Alternate carbon-dioxide-fixing photosynthetic pathways have emerged (in bacteria). Look up Carbon fixation in Wikipedia.

    1. Derek Lowe says:

      Are any of those non-Calvin-cycle and photosynthetic?

      1. Anonymous Machine Learning Algorithm says:

        Yes, it seems green sulfur bacteria at least, use the Reductive citric acid cycle (reverse krebs), and are (as hinted by their color) photosynthetic. Wikipedia lists a few others but I didn’t look far enough to see which are chemo vs photosynthetic.

      2. John Wayne says:

        If my read of the wikipedia entry facilitated understanding, those additional mechanisms are not photosynthetic.

  6. Ken says:

    I’m sure I’ve read at least three science fiction stories with this premise. Somewhat encouragingly, only two were dystopian hell-worlds where humanity struggled to survive.

    1. Lucky Crystal says:

      I spent my Master’s Degree chasing the structure of RUBISCO in a Billion year old algae. The little $&#€£&!@** loved conditions that made a mockery of basic physiology. i.e. pH low as hell, temps way too hot to be comfortable, and nutrient profiles that would worry most medicinal chemists. Lingering too long in the lower transition elements, flirting heavily with the Langthanides and Actinides, and just to mix it up loving some weak electromagnetic non-metallic elements. It was weird. What did they use? “Lawn Grass?”

  7. ENES says:

    A bit off topic but a fascinating account of how grains domesticated us. What we see as the menu of food crops today, according to Scott, is a small number that humans have selected and not as robust as their wild peers.
    https://youtu.be/oQgQRmx19HA

  8. ex-London Chemist says:

    GM plants? The EU would never allow it…..

    1. Nameless says:

      It practically has done that. If CRISPR is used to modify then it doesn‘t have to be labeled as such. Then it can be exported to the EU and sold.

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