Peering Into the Gray Cloud Using Spaceflown RNA

colinkruseColin Kruse, Wyatt Lab manager and researcher, is looking for genes not yet identified as related to gravity response in plants. To do this, Colin and Dr. Sarah Wyatt enlisted the help of NASA to germinate seedlings in microgravity conditions aboard the International Space Station. The spaceflown samples have since returned to earth and Colin will soon complete the next milestone in the NASA-sponsored BRIC-20 microgravity experiment. Using RNA extracted from spaceflown seedlings and ground controls, Colin hopes to  identify the genes involved in the plant signalling biochemical pathway.

Gravity plays a fundamental role in plant growth. Plants respond to gravity by sending roots down toward perceived gravity and stems up against it. A plant’s response to gravity breaks down into four main events:

  1. Perception: the plant perceives a change in gravity
  2. Transduction: a biochemical reaction alerting related plant systems of the change
  3. Transmission: the plant transports Auxin to trigger a response
  4. Response: the stem bends against the perceived gravity vector

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Plant scientists have invested a significant amount of research on unlocking plant gravitropic response but have yet to present a complete picture of the biochemical pathway of signal transduction that links the biophysical action of perception to a biochemical signal that regulates gravitropic effects on plant growth. For this reason, the signal transduction events are described as a “gray cloud” – meaning, they have a good idea of the biochemical components and many of the genes involved but do not yet see a clear path that describes the precise way a plant signals for the transport of Auxin to allow the stem to bend.

Dr. Sarah Wyatt has been researching plant gravitropic signaling for a long time but the BRIC-20 experiment is unique because it is the first time she has been able to perform research on seedlings germinated in space. Until now, Dr. Wyatt and her team of researchers have studied gravity response using a group of Arabidopsis (common name) gps mutants she discovered as a post-doc researcher using gravity persistent signaling (GPS) treatment.

Colin and Proma Basu, Wyatt Lab graduate student researcher, have the potential to finally define the signal transduction pathway using the BRIC-20 spaceflown seedlings. Proma performed a proteomic analysis of a portion of the seedlings to determine what proteins were present at the point they were fixed in space, and Colin will analyze the RNA data. The two sample results will be compared and contrasted to corroborate and strengthen the results of each.

The next steps for Colin is one final quality control measure on the experimental method to ensure they have a good understanding of how the fixative may impact the RNA-Seq analysis. Then Colin will package the spaceflown and ground control samples and send them to co-principle investigator, Dr. Darron Luesse, who will submit the samples to the Genome Technology Access Center (GTAC) at Washington University in St. Louis for RNA-Seq analysis.

When Colin receives the gene expression data back from Dr. Luesse, he will compare his results from the BRIC-20 spaceflown experiment to other data sets the lab has collected using ground-based experimental methods to look for gene expression that overlaps. This process should help him to peer into the gray cloud of signal transduction to identify novel genes regulating plant gravitropic response not identifiable by Earth-based research models. And in doing so, define the biochemical pathway between plant perception and subsequent response to changes in gravity.

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