Unintelligent Designer News - Fixing the Designer's Incompetence

Rubisco in every green cell.
Compensating with quantity for what it lacks in quality

Rubisco proton production can enhance CO2 acquisition | RIPE

Scientists working on the Illinois-based Realizing Increased Photosynthetic Efficiency (RIPE) project are trying to improve Earth's food production capability by improving on probably the most abundant protein enzyme on Earth, Rubisco.

The reason you rarely hear an intelligent [sic] design Creationist talking about Rubisco, apart from the fact that few of them know enough biology to know anything about it, is that, for the few who do understand it, it is a major embarrassment.

Quite simply, as an example of sheer incompetence in design, Rubisco, or to give it its full name, ribulose-1,5-bisphosphate carboxylase/oxygenase, is hard to beat. It is the key enzyme involved in photosynthesis so is at the basis of almost all life on Earth, and is probably the most abundant protein on Earth, being in all the photosynthesising cells of every green plant. And it is probably the least efficient of all enzymes, being only capable of about 4 reactions per second, against the hundreds or thousands of reactions for most enzymes. Indeed, the reason it is so abundant, is probably because it is so inefficient. Green plants need lots of it to compensate with quantity what it lacks in quantity.

It is responsible for fixing CO₂ in the initial stages of converting CO₂ and water into glucose. The problem is, it finds it hard to distinguish between CO₂ and O₂, so it wastes about 20% of its time doing something destructive that costs the plant energy that could be used to increase the glucose yield.

In evolutionary terms, this is easily explained because evolution is utilitarian and builds on what is there. Once living organisms evolved a Rubisco, it had an advantage over organisms that couldn't utilise CO₂, so this put all their descendants on an evolutionary path in which they were dependent on an inefficient enzyme but could not scrap the design and start again - something that would have been no problem for an intelligent designer. Also, since photosynthesis is the source of O₂, Rubisco evolved in an environment in which molecular oxygen was a rarity, so its inability to differentiate between CO₂ and O₂ was not the problem it later became. Again, an intelligent designer, who should have foreseen that his design was going to produced lots of O₂, should have foreseen the problem it would become.

However, many photosynthetic organisms have evolved mechanisms to overcome some of Rubisco’s limitations. Among these organisms are microalgae and cyanobacteria from aquatic environments, which have efficiently functioning Rubisco enzymes sitting inside liquid protein droplets and protein compartments called pyrenoids and carboxysomes.

Inside Rubisco compartments, these protons can speed up Rubisco by increasing the amount of CO2 available. The protons do this by helping the conversion of bicarbonate into CO2. Bicarbonate is the major source of CO2 in aquatic environments and photosynthetic organisms that use bicarbonate can tell us a lot about how to improve crop plants.

The outcomes of this study provide an insight into the correct function of specialized Rubisco compartments and give us a better understanding of how we expect them to perform in plants.

Ben Long, Lead researcher
Realizing Increased Photosynthetic Efficiency
Plant Science Division,
Research School of Biology,
The Australian National University, Acton, ACT, Australia

In fact, this inefficiency has been the driver of ways to improve the efficiency of Rubisco in some photosynthesising organisms, some of which are being studied by scientists on the RIPE project in cooperation with Australian National University Research School of Biology.

“However, many photosynthetic organisms have evolved mechanisms to overcome some of Rubisco’s limitations,” said Ben Long who led this recent study published in PNAS for a research project called Realizing Increased Photosynthetic Efficiency (RIPE). RIPE, which is led by Illinois in partnership with the Australian National University (ANU), is engineering crops to be more productive by improving photosynthesis. RIPE is supported by the Bill & Melinda Gates Foundation, Foundation for Food & Agriculture Research, and U.K. Foreign, Commonwealth & Development Office.

“Among these organisms are microalgae and cyanobacteria from aquatic environments, which have efficiently functioning Rubisco enzymes sitting inside liquid protein droplets and protein compartments called pyrenoids and carboxysomes,” said lead researcher Long from the ANU Research School of Biology.

How these protein compartments assist in the Rubisco function is not entirely known. The team from ANU aimed to find the answer by using a mathematical model that focused on the chemical reaction Rubisco carries out. As it collects CO2 from the atmosphere, Rubisco also releases positively charged protons.

“Inside Rubisco compartments, these protons can speed up Rubisco by increasing the amount of CO2 available. The protons do this by helping the conversion of bicarbonate into CO2,” said Long. “Bicarbonate is the major source of CO2 in aquatic environments and photosynthetic organisms that use bicarbonate can tell us a lot about how to improve crop plants.”

The mathematical model gives the ANU team a better idea as to why these special Rubisco compartments might improve the enzyme’s function and it also gives them more insight into how they may have evolved. One hypothesis from the study suggests that periods of low CO2 in the earth’s ancient atmosphere may have been the trigger for the cyanobacteria and microalgae to evolve these specialized compartments, while they might also be beneficial for organisms that grow in dim light environments.

ANU members of the Realizing Increased Photosynthetic Efficiency (RIPE) project are trying to build these specialized Rubisco compartments in crop plants to assist in increasing yield. “The outcomes of this study,” explained Long, “provide an insight into the correct function of specialized Rubisco compartments and give us a better understanding of how we expect them to perform in plants.”

The researcher have published their findings, open access, in PNAS:

Significance

Rubisco is arguably the most abundant protein on Earth, and its catalytic action is responsible for the bulk of organic carbon in the biosphere. Its function has been the focus of study for many decades, but recent discoveries highlight that in a broad array of organisms, it undergoes liquid–liquid phase separation to form membraneless organelles, known as pyrenoids and carboxysomes, that enhance CO₂ acquisition. We assess the benefit of these condensate compartments to Rubisco function using a mathematical model. Our model shows that proton production via Rubisco reactions, and those carried by protonated reaction species, can enable the elevation of condensate CO₂ to enhance carboxylation. Application of this theory provides insights into pyrenoid and carboxysome evolution.

Abstract

Membraneless organelles containing the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO2 concentrating mechanisms to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO₂ fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO₂ within the organelle via a colocalized carbonic anhydrase (CA) and inwardly diffusing HCO₃−, which have accumulated in the cytoplasm via dedicated transporters. Here, we present a concept in which we consider the net of two protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction–diffusion compartment model to investigate functional advantages these protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO3− accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived protons to drive the conversion of HCO3− to CO₂ via colocalized CA, enhancing both condensate [CO₂] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (phosphoglycerate) plays an important role in modulating internal pH and CO₂ generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO₃− accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO₂ and low light environments.

Long, Benedict M.; Förster, Britta; Pulsford, Sacha B.; Price, G. Dean; Badger, Murray R. Rubisco proton production can drive the elevation of CO₂ within condensates and carboxysomes
Proceedings of the National Academy of Sciences May 2021, 118 (18) e2014406118; DOI: 10.1073/pnas.2014406118

Copyright: © The authors. Published by the National Academy of Sciences of the United States of America
Open access Reprinted under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Just imagine what a different world we would be living in if Rubisco really had been intelligently designed by a creative deity who was everything Creationists like to imagine their putative designer is, including competent, omniscient and omnipotent as well as perfect. As it is, we have inherited a world in which living things were produced by a utilitarian, unthinking natural mechanism with no plan and no ability to design or even to scrap a bad design and start again. Consequently, we are hard-pressed to produce enough food and need to employ scientists to try to improve on things to compensate for the bad designs evolution has come up with.

Incidentally, that applies in so many other areas of life too, including medical science, none of which would be necessary without bad design and parasites like worms, protozoa, bacteria and viruses.

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