Getting through the winter - we all get by with a little help from our pigments

Metagenomics is an important tool in allowing us to quickly determine which genes are present communities, this revolutionary tool was used to discover a ‘new’ type of rhodopsin in microbial communities (Proteorhodopsin), previous to this, scientist knew about bacteriorhodopsins, in the membranes of archaea (halobacterium genus) for some time, but considered it to be a unique feature to this extremely halophilic archaea (C. B. Munn & Azam, 2011). Studies on Proteorhodopsins (PR) revealed that the bacteria were using PR as a novel way to syntheses ATP, without fixing CO₂. This gave scientists some indication that cells may use this mechanism to survive in periods of resource deprivation, yet the wide reaching dispersal of this protein (discovered using GOS) suggests there may be other use or a major physiological benefit of Proteorhodopsins.

The discovery of PR was followed by a number of studies which attempted to determine the variation, function and mechanism of PR’s (Beja et al. (2001), Walter et al. (2007), Gomez-Consarnau et al. (2010)), this studies gave great framework on how PR work, showing PR as a survival mechanism, by synthesising ATP directly from light energy. Wanting to further explore the distribution especially in polar regions which represent some of the harshest conditions on the planet Nguyen et al. (2015) conducted an ambitious 8-month study, spanning the entire polar winter, aiming to report the seasonal occurrence and diversity of the proteorhodopsin (PR) expression in the polar oceans.

An interesting seasonal pattern of PR expression was discovered with a decreased expression from early to late winter, which indicated a reduced functional usage of PR’s in the darkness of the winters, although the expression of PR’s never ceased. This sustained expression suggesting that the bacterium can regulate PR expression rather than being constituently expressed. Beginning to give us more insight into the purpose of this protein in the cells, initially used for ATP synthesis as a secondary synthesis mechanism in low nutrient conditions, but when light is restricted PR may continue to be useful for non-ATP forming functions, which could include environmental biosensing or as a transport mechanism for small solutes. Throughout the polar winter Gammaproteobacteria like-PR sequences were dominant, but surprisingly there was a transition in the second most common sequences from Flavobacteria-like PR in early winter to Alphaproteobacteria-like PR in late winter, following carbon dynamics where patterns in expression were consistent with community succession, as identified by DNA community fingerprinting. This displacement of one type of PR for another may suggest that the different ecotypes of PR that exist give the microbes it belongs to a different niche in the ecosystem, and creates competition between species when they are exposed to harsh conditions for a sustained period of times, giving some microbes a physiological edge and allowing one or two species to dominate, shifting community dynamics.

This paper offers us great insight into how cells use PR’s to exploit biological resources at times where survival is difficult and competition maybe high, although the findings and the pattern of expression over the year are clear, it brings few definite answers to how and why bacteria use PR’s, although suggesting at increased survival under harsh conditions no mechanism has been proposed. The multifunctional of this protein is a topic which needs to be addressed to give clear answers on the purpose of this protein other than ATP synthesis, which will allow us to being to discover the further complexity of microbial metabolism and survival especially in harsh conditions such as the polar winters. 

References

Reviewed paper: Nguyen, D., Maranger, R., Balagué, V., Coll-Lladó, M., Lovejoy, C., & Pedrós-Alió, C. (2015). Winter diversity and expression of proteorhodopsin genes in a polar ocean. The ISME Journal, 9(8), 1835–1845. doi:10.1038/ismej.2015.1. http://www.nature.com/ismej/journal/v9/n8/abs/ismej20151a.html

Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M., & DeLong, E. F. (2001). Proteorhodopsin phototrophy in the ocean. Nature, 411(6839), 786–789. doi:10.1038/35081051

Gómez-Consarnau, L., Akram, N., Lindell, K., Pedersen, A., Neutze, R., Milton, D. L., … Pinhassi, J. (2010). Proteorhodopsin Phototrophy promotes survival of marine bacteria during starvation. PLoS Biology, 8(4), e1000358. doi:10.1371/journal.pbio.1000358

Munn, C. B., & Azam, F. (2011). Marine microbiology: Ecology and applications (2nd ed.). New York: Bios Scientific Publ.

Walter, J. M., Greenfield, D., Bustamante, C., & Liphardt, J. (2007). Light-powering Escherichia coli with proteorhodopsin. Proceedings of the National Academy of Sciences, 104(7), 2408–2412. doi:10.1073/pnas.0611035104