Bacteria, among the simplest and smallest of living things, should never be called primitive. They have a genetic code, a membrane, and metabolism — the three essentials for independent life — and not just in token form, but in highly productive and robust instances. They thrive in almost every environment. The most abundant of all, the cyanobacteria, perform the wizardry of photosynthesis, giving oxygen to the world and forming the foundation of the food chain.

Humans have a mixed relationship with cyanobacteria. We need them, but some cause harm. The USGS tells about cyanobacteria that sometimes bloom in large numbers, producing potent cyanotoxins that kill fish, cattle, and even people (see the CDC FAQ page about cyanotoxin blooms). Formerly called blue-green algae, cyanobacteria are now classified as bacteria, not algae, because they are prokaryotes, not eukaryotes like true algae. Some live in colonies or strands with a bit of role differentiation; many others live independently as autotrophs, organisms that make their own food. They live in freshwater, soil, and salt water. Prochlorococcus, which lives in the ocean, may be the most abundant species of life on earth. It produces about 20 percent of the oxygen we breathe. 

Another important role cyanobacteria play is in nitrogen fixation. A review article in Frontiers in Microbiology calls them “A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability.” They can crack the tough triple bonds of N₂ molecules at ambient temperatures with an enzyme called nitrogenase. Agricultural engineers would love to learn this trick but have so far not succeeded. Cyanobacteria also are important for carbon sequestration in discussions of climate change mitigation. Others live in biotic crusts that form the foundation for ecosystems in deserts (see “Intelligent Design in the Dirt”) and other hostile environments like cliff walls exposed to the sun (“Living Murals: Wall Art Made by Photosynthetic Bacteria”). The few that cause harm, therefore, are more than compensated for by the vast majority that do our planet good.

Light-Driven Motor Control

Face it: anything running on ATP synthase is not primitive! This key molecular rotary engine, running at up to 6,000 RPM, is one of the most efficient machines known inside or outside of life. Energy from sunlight powers machines upstream from ATP synthase that deliver protons through a membrane channel to turn the engine. The details of this incomparable nanoscale engine have been discussed in detail elsewhere and need not be reviewed here. Suffice it to say, ATP synthase in bacteria, the smallest and most “primitive” of life forms, poses a severe challenge to naturalistic origin-of-life theories. How could any life form get by without this irreducibly complex system? 

Now, scientists have learned that the machine in a model species of cyanobacterium has a unique regulatory mechanism to prevent ATP waste at night when the photosynthetic machinery cannot run. Robert L. Burnap from Oklahoma State University writes in Current Biology:

Because the photosynthetic and respiratory electron transport chains in cyanobacteria are located in the same bioenergetic membrane, regulation of the shared F₁F_O ATP synthase is needed to prevent wasteful ATP futile cycling. The newly discovered regulatory protein Atp-theta, which is widely distributed in cyanobacteria, is shown to provide such a function. [Emphasis added.]

This solves a problem in a unique way for cyanobacteria. Unlike higher plants, cyanobacteria use their ATP synthase rotors in both photosynthesis and in respiration. ATP synthase, though, is a reversible motor. If the proton motive force (PMF) drops, thermodynamics favors hydrolysis of ATP back into protons, like a waterwheel reversing direction. In darkness, the upstream machines cannot keep adequate PMF. Without regulation, this could lead to a catastrophic loss of ATP during the night. 

Indeed, cyanobacteria possess a true circadian clock and use it to commit resources for the deployment of new photosynthetic machinery precisely before dawn, providing testament to the fact that the ATP synthase remains active far into the night, albeit at lower rates that match lower nocturnal metabolic fluxes. Thus, the regulation of the F₁F_O ATP synthase in cyanobacteria presents unique regulatory challenges that have resisted understanding.

Burnap relates a discovery by Song et al., who expected a “hypothetical protein” might act as a regulator. It had escaped detection due to its small mass (8 kDa), but they finally found it. Called Atp-theta, it is upregulated by the circadian clock in darkness, and downregulated at first light of dawn. This molecule binds to the “crankshaft” (gamma subunit) of the engine, preventing its reverse direction in low-power mode. Burnap speculates that this regulator may work like a ratchet, along with other regulatory molecules, to ensure “transient inhibition of wasteful ATP hydrolysis upon the light to dark transition” in these tiny living factories. He admits, though, that this new discovery raises additional questions. It will probably turn out to be more sophisticated than shown in his simplified model diagram.

More Light on Cyanobacteria Photosynthesis

Another paper elucidated the light-harvesting mechanism called Photosystem II (PSII) in a model cyanobacterium. Writing in PNAS, Gisriel et al. used the super-resolution technique of cryo-electron microscopy to discover the structure of PSII in less than 2-angstrom resolution: that is 2 ten-billionths of a meter!

Photosystem II (PSII) is a photo-oxidoreductase that harnesses light energy to use water to make fuel. Water oxidation occurs at a metal cluster in the active site called the oxygen-evolving complex (OEC). Understanding PSII function has provided design principles for synthetic solar fuel catalysts; however, the details of water oxidation are obscured by the multiple states through which the mechanism proceeds, differences between species, and lability of the OEC. To better understand PSII function, we solved its structure from Synechocystis sp. PCC 6803. We observe significant differences compared with PSII from thermophilic cyanobacteria that highlight the need for reexamination of previous data using this structure for interpretation. 

Compared to thermophilic cyanobacteria, the structure of the OEC in this mesophilic species that is easily cultured in a lab shows unique features. Interestingly, they speak of a “water wheel” as part of the mechanism of action. (Learn how “water wires” participate in enzymatic processes at the molecular scale in this previous article.)

The proposed mechanism involved residues near the water wheel in the Large channel … and was substantiated by similarities in substrate gating of acetylcholinesterase. In part, it involved conformational changes in aromatic residues. It may be that the PsbV-Tyr159 sidechain undergoes a conformational change in the gating of the Large channel. Future molecular dynamics simulations may allow for more insight into this possibility. If a gating mechanism does exist in Synechocystis 6803 PSII involving PsbV, it is presently unclear whether similar mechanisms are observed in other cyanobacteria because of low sequence identity between PsbV from different species (SI Appendix, Table S8). In any case, the differences observed between PSII structures from mesophilic and thermophilic cyanobacteria suggest differences in proton egress and/or substrate water delivery between organisms. However, the light-saturated rate of oxygen evolution by PSII appears comparable between mesophilic and thermophilic cyanobacteria….

These observations are challenging not only because of the diminutive size of the parts, but because of the “dynamic nature of the structure and challenges in modeling OEC atoms.” Some of the differences could be due to lab procedures, or the state of the molecules when flash-frozen for cryo-EM. It’s also possible that the high temperatures in the habitats of thermophilic cyanobacteria impose additional design requirements for its equipment. Nevertheless, this is a significant achievement to look so closely at molecular machinery that runs with exquisite precision to produce fuel from light and water. We can look forward to further glimpses of nanotechnology going on in “primitive” organisms. 

Warm Little Ponds Need Not Apply

Consider the distance between proposed origin-of-life models and this! Can lipid bubbles capturing random nucleotides by chance handle this level of sophistication? No genetic code; no metabolism; no regulatory networks? Everywhere biochemists look, in the “simplest” cells, they find factories of molecular machines, run by digital code, that work extremely well and can reproduce themselves. No origin-of-life model comes close.

Tellingly, the PNAS paper’s predominant mention of “evolution” is not about Darwinism but about the “oxygen-evolving complex” in PSII, as in a complex machine that gives off (“evolves”) oxygen. There is this one passing tribute to evolution: “understanding its enzymatic function is relevant to a variety of fields including synthetic photocatalysis, crop optimization, biofuel production, and evolutionary biology.” The ending three words could be excised without loss of science. Belnap’s sole use of the word in his Current Biology article is similarly expungeable: “it is … not surprising that a variety of mechanisms have evolved in different species to regulate F₁F_O ATP synthase activity.” 

As usual, the closer authors look at the details, the less they tend to talk about Darwinian evolution.