BU team studies photosynthesis evolution (and discovers new Rhodobacter species from Yellowstone)

The evolution of phototrophic bacteria and photosynthesis in general is certainly an interesting but complex topic. It is commonly well accepted that anoxygenic phototrophy evolved well before the gradual oxygenation of the Earth. This means that the photosynthetic machinery of anaerobic phototrophic bacteria (like purple and green bacteria) evolved well before the existence of oxygenic photosynthesis of algae and plants.

One of the best studied model organisms for studying photosynthesis in purple non-sulfur bacteria is Rhodobacter. Members of the genus Rhodobacter all perform anoxygenic photosynthesis, but can also grow aerobic (but when doing so repress the synthesis of photosynthetic pigments). They also fix nitrogen and thereby play key roles in biogeochemical cycles.

A novel Rhodobacter species, designated strain M37P, was isolated a couple of years ago by Dr. Robert Ramaley (a collaborator from UNMC on this project) from the Mushroom hot spring runoff within the Lower Geyser Basin of Yellowstone National Park.

(a) Colonies of Rhodobacter calidifons M37P grown on dark incubated media plates. (b) Dark (left) and light (right) incubated aerobic liquid cultures of M37P. (c) Absorption spectra of extracted pigments from dark incubated (red) and light incubated (black) aerobic Rhodobacter calidifons M37P cultures.

“When we first tried to grow and characterize this new Rhodobacter species from Yellowstone National Park, we were quite surprised and puzzled that this species could not be grown anaerobically.” says Dr. Kyndt, who was one of the leads on the study. Up until that point, all Rhodobacter species were easily grown under anaerobic photosynthetic conditions. “It’s easier to show that something can be done in science, than proving that something cannot be done. The latter takes a lot more experiments, replications, and time.”- Dr. John Kyndt.

After several cultivation attempts from both the BU team and the collaborating lab from Dr. Ramaley at UNMC, the team had to conclude that this new species was a so-called aerobic, anoxygenic phototroph (AAP). The unique physiology, whereby the cells make a red-pink pigment in the dark, but loose the pigment in the light, was consistent with the species being an AAP. This was the first AAP identified in the large Rhodobacter genus.

Genome sequencing by BU biology student Sydney Robertson, and further genomic analysis by a visiting biochemistry student from New Mexico State University, Isabella Shoffstall, revealed some clues from the genome that relate to those unique features. This new strain does not contain the RuBisCo gene for fixation of CO2, which is typical for AAP’s. RuBisCO is an essential protein in the Calvin-Benson-Bassham cycle that catalyzes the addition of carbon dioxide to ribulose-1,5-bisphosphate. The new genome also lacks the genes for the Light Harvesting complex II, which is typically an important photosystem component in Rhodobacter (and other photosynthetic bacteria) and augments the collection of solar energy.   

The student research also led to the discovery that this new strain contains a unique xanthorhodopsin protein, which likely contributes to the cells red-pink color. Xanthorhodopsins (XR) are light-harvesting proton pumps with a dual chromophore. They have one retinal molecule, similar to archaeal bacteriorhodopsin and the rhodopsin in your eyes that allow you to read this text, but in addition, XR also contains an additional carotenoid antenna chromophore which allows the cells to utilize a wider range of light for energy conversion. No other Rhodobacter species contains rhodopsin.

(a) Superimposed structures of Rba. sp. M37P xanthorhodopsin (RXR; red) and the Salinibacter ruber xanthorhodopsin (light gray, PDB entry 3DDL) The retinal and salinixanthin chromophores from XR are labeled in yellow and orange, respectively. (b) Detailed structural image of the 3-omega motif formed by pi-stacking of aromatic residues in helix A, B, and the B-C loop. RXR residues are labeled in red and Salinibacter XR residues shown in gray.

However, a clue for this uniqueness might come from the environmental conditions where this new strain was isolated. An earlier metagenomics study of the Mushroom Hot Spring had shown an unexpected diversity of potential retinal-based phototrophy in this area (although only partial genomes were found, and it was uncertain whether these were producing functional rhodopsins). This new xanthorhodopsin-containing Rhodobacter was isolated from the same area (albeit it at a lower temperature point) and possibly obtained the rhodopsin gene through horizontal gene transfer from nearby organisms. Blue-green light (450-550 nm) is not absorbed very well by the chlorophyll a, phycocyanin and carotenoids of cyanobacteria and algae in that area, and the presence of an antenna chromophore in xanthorhodopsin certainly provides a selective advantage in the complex microbial community of the Mushroom Spring runoff area.

“It is fascinating to see how diverse and adaptable bacterial species are, and how, with the power of genome sequencing we can find new clues about this diversity and adaptability of life in general.” says Dr. Kyndt.

The findings and a full detailed description were recently published in the journal Microorganisms and can be accessed here:

https://www.mdpi.com/2076-2607/10/6/1169

This collaborative project has provided some additional insight in the possible evolution of bacterial anoxygenic photosynthesis and the adaptation of bacterial species to varying environmental conditions, but (as often in science) also raised more questions about the complexity of this evolution. The team is planning to continue this research and more detailed studies on the Rhodobacter xanthorhodopsin and this new clade of species are already underway.   

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