Hopanoid Biomarkers

One important piece of evidence that geobiologists use to understand ancient life on Earth is the organic remains that are preserved in rocks. Certain lipids (fat-like molecules that are composed of mainly carbon and hydrogen) are very resistant to degradation, and under the right geologic conditions can be preserved in recognizable form for billions of years. Many of these lipids consist of little more than straight hydrocarbon chains, and when you find them in rocks there is no telling what sorts of creatures produced them. However, certain structurally complex lipids carry much more information, because their unique carbon skeletons can be recognized in ancient deposits and (in some cases) tell us who produced them. We call such structures "molecular fossils", or biomarkers.

An important group of biomarkers is the hopanoids, large molecules containing five rings with an extended tail hanging off one end (see figure above). They are unique to bacteria, but otherwise are quite widely distributed. However, hopanoids with a specific structural modification (a methyl group added to C-2 on the lower left-hand side of the molecule) have a much more limited distribution. Roger Summons has hypothesized that the dominant source of 2-methylhopanes in the environment is cyanobacteria, and that when you find them in rocks (including very old rocks) you can infer that cyanobacteria were alive and well at that time. This has lead to the rather controversial conclusion that cyanobacteria arose, and were conducting photosynthesis, well before O2 first accumulated in the Earth's atmosphere.

One of the problems with 2-methylhopanes (and indeed most biomarkers) is that its very hard to tell how many different organisms have the ability to make that particular compound. We know of only a couple species outside the cyanobacteria that make 2-methylhopanes, but then again there are still tens of thousands of organisms that have not been specifically tested for this ability. We cannot possibly culture and measure all these creatures, so we need a better way forward. A second problem is that the link between 2-methylhopanes and photosynthesis is circumstantial - what if distant cyanobacterial ancestors produced hopanes but did not photosynthesize?

To understand many of these issues, we been collaborating with Diane Newman and Roger Summons (MIT) to understand the specificity of this biomarker. In particular, we would like to know what genes regulate the production of hopanoids and/or their methylation, what environmental factors influence the production of 2-methylhopanoids, and what those molecules do in the cell. We are working in the model organism Rhodopseudomonas palustris, which is an anoxygenic phototrophic bacterium. It's not a cyanobacterium, but it is much easier to work with. Diane's lab is carrying out a detailed genetic study of methylhopane regulation and production, while Roger and I are working on improved GC/MS and LC/MS analytical techniques for their detection and structural characterization, and conducting surveys of related organisms.

Recent papers on this subject:

Neubauer C, Dalleska NF, Cowley ES, Shikuma NJ, Wu C-H, Sessions AL, and Newman DK (2015) Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation. Geobiology DOI:10.1111/gbi.12143.

Doughty DM, Dieterle M, Sessions AL, Fischer WW, Newman DK (2014) Probing the subcellular localization of hopanoid lipids in bacteria using NanoSIMS. PLoS One 9, e84455.

Ricci JN, Coleman ML, Welander PV, Sessions AL, Summons RE, Spear JR, Newman DK (2014) Diverse capacity for 2-methylhopanoid production correlates with a specific ecological nicheThe ISME Journal 8, 675-684.

Sessions AL, Zhang L, Welander PV, Doughty D, Summons RE, Newman DK (2013) Identification and quantification of polyfunctionalized hopanoids by high temperature gas chromatography-mass spectrometry. Organic Geochemistry 56120-130.

Doughty DM, Coleman ML, Hunter RC, Sessions AL, Summons RE, and Newman DK (2011) The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1. Proceedings of the National Academy of Sciences 108, E1045-E1051.

Welander P.V., Coleman M.L., Sessions A.L., Summons R.E., Newman D.K. (2010) Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes. Proceedings of the National Academy of Sciences 107, 8537-8542.

Welander P.V., Hunter R.C., Zhang L., Sessions A.L., Summons R.E., and Newman D.K. (2009) Hopanoids play a role in membrane integrity and pH homeostasis in Rhodopseudomonas palustris TIE-1Journal of Bacteriology 191, 6145-6156.  

 Rashby S.E., Sessions A.L., Summons R.E., and Newman D.K. (2007). Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph. Proceedings of the National Academy of Science 104, 15099-15104.

Copyright 2015 by Alex Sessions. All rights reserved.