Watching 'jumping genes' in action: Real-time observation of transposon activity in living cells

Siv Schwink
6/13/2016

Asst. Professor of Physics Thomas E. Kuhlman
Asst. Professor of Physics Thomas E. Kuhlman
Swanlund Professor of Physics Nigel Goldenfeld
Swanlund Professor of Physics Nigel Goldenfeld
“Jumping genes” are ubiquitous. Every domain of life hosts these sequences of DNA that can “jump” from one position to another along a chromosome; in fact, nearly half the human genome is made up of jumping genes. Depending on their specific excision and insertion points, jumping genes can interrupt or trigger gene expression, driving genetic mutation and contributing to cell diversification. Since their discovery in the 1940s, researchers have been able to study the behavior of these jumping genes, generally known as transposons or transposable elements (TE), primarily through indirect methods that infer individual activity from bulk results.  However, such techniques are not sensitive enough to determine precisely how or why the transposons jump, and what factors trigger their activity.

Reporting in the Proceedings of the National Academy of Sciences, scientists at the University of Illinois at Urbana-Champaign have observed jumping gene activity in real time within living cells. The study is the collaborative effort of physics professors Thomas Kuhlman and Nigel Goldenfeld, at the Center for the Physics of Living Cells, a National Science Foundation Physics Frontiers Center.

Real time transposable element activity in a small colony of bacteria, where excision of the transposable element causes the cell to light up (false colored green), and the excision reaction is caused by transposase protein (false colored magenta). Video courtesy of T.E. Kuhlman and N. Goldenfeld, University of Illinois at Urbana-Champaign, reproduced with permission from Proceedings of the National Academy of Sciences USA.
Real time transposable element activity in a small colony of bacteria, where excision of the transposable element causes the cell to light up (false colored green), and the excision reaction is caused by transposase protein (false colored magenta). Video courtesy of T.E. Kuhlman and N. Goldenfeld, University of Illinois at Urbana-Champaign, reproduced with permission from Proceedings of the National Academy of Sciences USA.

"In this study, we were able to see that there is actually more of this jumping gene action going on than might have been expected from previous studies,” said Kuhlman, whose team performed the in vivo experiments. “What’s more, we learned that the rates at which these genes jump depend sensitively on how the cells are growing—if there is food available for the cells to grow, for example. In other words, jumping gene activation isn’t entirely random, it’s dependent on environmental feedback."

To observe these individual cellular-evolution events in living cells, Kuhlman’s team devised a synthetic biological system using the bacterium Escherichia coli. The scientists coupled the expression of fluorescent reporters—genes that encode (in this case, blue and yellow) fluorescent proteins—to the jumping activity of the transposons. The scientists could then visually record the transposon activity using fluorescent microscopy.

University of Illinois Assistant Professor of Physics Thomas E. Kuhlman discusses upcoming experiments with graduate students Gloria Lee and Hyuneil Kim in his laboratory at the Center for the Physics of Living Cells. Photo by L. Brian Stauffer, University of Illinois at Urbana-Champaign
University of Illinois Assistant Professor of Physics Thomas E. Kuhlman discusses upcoming experiments with graduate students Gloria Lee and Hyuneil Kim in his laboratory at the Center for the Physics of Living Cells. Photo by L. Brian Stauffer, University of Illinois at Urbana-Champaign
“These are genes that hop around and change location within the genome of a cell,” said Kuhlman. “We hooked that activity up to a molecular system, such that when they start hopping around, the whole cell fluoresces. In our experiment, cells fluoresced most when they weren’t very happy. One school of thought suggests that an increased mutation rate like this might be an advantage in such unhappy conditions, for cells to diversify.”

In order to help design the experiment and to calculate what would have happened if the jumping occurred in a purely random fashion, Goldenfeld’s team developed computer simulations of the growth of bacterial colonies and predicted what the experimental signal would look like in the random case. These calculations showed that the experiments could not simply be interpreted as random transposon activity and even provided clues as to sources of non-randomness, including environmental feedback and heredity.

“Our work involved a good deal of computational image analysis, followed by statistical analysis,” said Goldenfeld. “To extract signals and conclusions from the raw data, simulation and theoretical calculations were integral to the experimental design and interpretation.  This sort of collaborative project was really only possible with the unique structure provided by the Center for the Physics of Living Cells.” 

 

E. coli cells carrying a “wildtype” version of the transposable element grow in a monolayer within a microfluidic device; a single cell is seen to light up green upon experiencing a transposable element event. Video courtesy of T.E. Kuhlman, University of Illinois at Urbana-Champaign

“The over-arching long-term research goal is a deeper understanding of how evolution works at the molecular level. Direct observation of how genomes in cells restructure themselves allows for a precise determination of adaptation rates and may shed light on a host of important evolutionary questions, ranging from the emergence of life to the spread of cancer, where cells undergo rapid mutations and transformations of their genomes,” added Kuhlman.

Kuhlman and Goldenfeld are members of the Carl R. Woese Institute for Genomic Biology and the Department of Physics at the University of Illinois at Urbana-Champaign. The work involved several graduate students, including lead author Hyuneil Kim, Gloria Lee, Nicholas Sherer and Michael Martini. 

This release is based upon research performed at the Center for the Physics of Living Cells, a Physics Frontiers Center supported by the National Science Foundation, and at the NASA Astrobiology Institute for Universal Biology supported by NASA, both located on the University of Illinois at Urbana-Champaign campus. Kuhlman’s research is additionally supported by a 2015 Sloan Research Fellowship from the Alfred P. Sloan Foundation. The conclusions presented are those of the scientists, and not necessarily those of the funding agencies.

Recent News

  • In the Media

Paul Kwiat asks his volunteers to sit inside a small, dark room. As their eyes adjust to the lack of light, each volunteer props his or her head on a chin rest—as you would at an optometrist’s—and gazes with one eye at a dim red cross. On either side of the cross is an optical fiber, positioned to pipe a single photon of light at either the left or the right side of a volunteer’s eye.

Even as he verifies the human eye’s ability to detect single photons, Kwiat, an experimental quantum physicist at the University of Illinois at Urbana–Champaign, and his colleagues are setting their sights higher: to use human vision to probe the very foundations of quantum mechanics, according to a paper they submitted to the preprint server arXiv on June 21.

  • Research
  • Biological Physics

Scientists at the University of Illinois at Urbana-Champaign have predicted new physics governing compression of water under a high-gradient electric field. Physics Professor Aleksei Aksimentiev and his post doctoral researcher James Wilson found that a high electric field applied to a tiny hole in a graphene membrane would compress the water molecules travelling through the pore by 3 percent. The predicted water compression may eventually prove useful in high-precision filtering of biomolecules for biomedical research.

  • Research
  • Biological Physics
  • Biophysics

A new synthetic enzyme, crafted from DNA rather than protein, flips lipid molecules within the cell membrane, triggering a signal pathway that could be harnessed to induce cell death in cancer cells.   

Researchers at University of Illinois at Urbana-Champaign and the University of Cambridge say their lipid-scrambling DNA enzyme is the first in its class to outperform naturally occurring enzymes – and does so by three orders of magnitude. They published their findings in the journal Nature Communications.

  • Accolades
  • High Energy Physics

Assistant Professor of Physics Thomas Faulkner has been selected by the US Department of Energy (DOE) Office of Science to receive an Early Career Award. The DOE Early Career Research Program, now in its ninth year, provides award recipients with significant funding over a five year period. Faulkner is among 84 scientists at U.S. universities and DOE-supported national laboratories to be selected this year. He is one of only two scientists at the University of Illinois at Urbana-Champaign to receive the honor this year.

The Early Career Award recognizes promising scientists within 10 years of having earned their doctoral degrees, working in research areas supported by the DOE Office of Science. Faulkner’s research proposal in theoretical high-energy physics is entitled, “New perspectives on QFT and gravity from quantum entanglement.”