Ring by Ring

Posted on Nov 18, 2019

A collaboration of current and former EAPS researchers reveals the genes that enable GDGTs to cyclize 

by Fatima Husain

The stratigraphic expression of Milankovich cycles at the Cretaceous- Paleogene boundary offshore in Zumaia, Basque Country. Courtesy Fatima Husain

Nestled within sediments that accumulate in marine environments, a certain class of molecule-sized fossils sneakily record surface water temperature changes over time. For almost two decades, scientists have used these molecules called glycerol dibiphytanyl glycerol tetraether lipids, or GDGTs, to reconstruct climate trends experienced over both regional and local marine environments via the TEX86 paleotemperature proxy. But they did so conditionally because, until now, no one has understood exactly the mechanisms by which the complex membrane-spanning GDGTs encoded information about temperature, or which organisms actually contributed to the sedimentary GDGT signals — all they had were hypotheses and correlations. 

Now, with the advent of a collaboration of scientists currently and formerly associated with the MIT Department of Earth, Atmospheric and Planetary Sciences, that’s set to change. 

Paula Welander, a former postdoctoral researcher in the department, now an Associate Professor of Earth Systems Science at Stanford University, recently led an effort to understand just how GDGTs are built, as well as how that information relates to the GDGTs produced in the oceans today and, potentially, in the distant past. 

In a study published last month in PNAS, Welander, along with first-author Zhirui Zeng and their colleagues, employed a combined organic geochemical, bioinformatic and microbiological approach to fill in the details on GDGT biosynthesis. To start, the researchers identified a related type of archaeon, called Sulfolobus acidocaldarius, that produced GDGTs with rings, much like the GDGTs produced by marine organisms. While S. acidocaldarius does not grow in marine environments,  a genetically tractable archaeal system is already in place for this model organism — that is, scientists can genetically manipulate it by inserting or deleting genes and seeing how those changes affect its physiology and its membrane lipids. S. acidocaldarius is also well-characterized, and also grows quickly, enabling researchers to study their manipulations within days, rather than weeks or months. 

Within S. acidocaldarius, the researchers found three genes that might encode the ring-building mechanisms in GDGTs, and, deleted them one by one. These mutants showed them that only two of the deletions affected the number of rings present in the GDGTs. When they performed the two deletions together, the GDGTs produced no longer contained any rings. To further confirm the roles the two genes play in ring-building, the researchers expressed the genes in another organism that doesn’t normally produce GDGTs with rings, Methanosarcina acetivorans. Once the genes were expressed, M. acetivorans began to produce GDGTs containing rings. 

To study the GDGTs produced, Welander, a microbiologist, turned to former EAPS postdoctoral researcher Xiaolei Liu, now assistant professor of organic geochemistry at the University of Oklahoma, and Roger Summons, the Schlumberger Professor of Geobiology at MIT. Professor Liu, the world’s leading expert on identifying GDGTs by mass spectrometry, was not only able to confirm that two genes were needed to make the cyclized GDGT, but also that they operated in a sequential manner. One gene adds rings near the center of the molecule and the second gene adds more rings to the outer edges.

Summons adds: “This was an exciting collaboration to participate in because earlier work conducted in our laboratory suggested that there may be multiple clades of archaea contributing to the TEX86 signal in the ocean. The new research shows that this does not seem to be the case and that it is one clade, the marine Thaumarchaeota, that appears responsible thereby improving the focus for future research directions.”

To read more about this work, and the researchers’ further findings, visit https://news.stanford.edu/2019/10/07/archaea-hold-clues-ancient-ocean-temperatures/. To read previous coverage related to this topic, visit https://summons.mit.edu/sulfolobus-survival/

This study detailed in this article was funded by the Simons Foundation Collaboration on the Origins of Life, the National Science Foundation, and the U.S. Department of Energy.