RE: Citric Acid Cycle Labeling In C3 Plants

[davidrhodes124]

Photosynthetic cyanobacteria can fix CO₂ (or HCO₃^-) like plants (Calvin cycle and PEP-carboxylase). But these organisms are unlikely to be of relevance in a cave environment with no light!

Many bacteria can trap CO₂ (or HCO₃^-) via pyruvate carboxylase and incorporate it into citrate, oxaloacetate, and aspartate (see earlier post on Metabolic Engineering and Metabolic Flux Analysis).

But some bacteria, and I think these would be the most interesting in a cave environment, metabolizing CaCO₃, would be capable of running the citric acid cycle (TCA cycle or Krebs Cycle) in reverse (see Reverse Krebs cycle). Recently a novel variant of this reverse TCA cycle has been discovered:

Nunoura, T., Chikaraishi, Y., Izaki, R., Suwa, T., Sato, T., Harada, T., Mori, K., Kato, Y., Miyazaki, M., Shimamura, S., Yanagawa, K., Shuto, A., Ohkouchi, N., Fujita, N., Takaki, Y., Atomi, H., Takai, K. A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile. Science 359: 559-563 (2018)

Comments

[qiyi]

I'll check that out. We found lots of Nitrospira and others capable of using nitrite/HCO3 (chemolithotrophs) and Fe/Mn sulphur bacteria.

[davidrhodes124]

Nitrospira seems to use a reverse TCA cycle for CO₂ fixation:

Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., Rattei, T., Damsté, J.S., Spieck, E., Le Paslier, D., Daims, H. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci. U.S.A. 107: 13479-13484 (2010)

[qiyi]

Another good one! This was the info we needed at the same time we were finding and hypothesizing. My expertise was in technical methodology and experimental approaches to get the data and compile sequences. Colleagues were better than me at interpretation of the physiological systems. Some of my microbiology collaborators include Penelope Boston, Hazel Barton, Diana Northup. Recently I discovered that many phylogenetic trees from artificial substrates were not published in a recent book, so they are fair game for a new post!

[qiyi]

I've read that one several times now. I last worked on that in 2007-2008, and I had no idea so much was known! From 2008-2011 I was looking at Bacteroides 16S sequences. I'm working on some of our Mammoth Cave bacterial data.

[davidrhodes124]

The pace of discovery in biological sciences is staggering ... it's getting hard to keep up with the literature.