Linking the Central Dogma of Biology to Life’s Adaptations and Detectability in Spaceflight, Laboratory, and Planetary Analog Environments

Committee: Dr. Christopher E. Carr (Advisor), Dr. Jennifer B. Glass, Dr. Jill Mikucki, Dr. Frances Rivera-Hernández, Dr. James J. Wray

Date and Time: Friday July 11, 10am

Location: ES&T L1255, https://gatech.zoom.us/j/93788301639

Life on Earth has evolved to proliferate across an extensive range of habitats. Evidence of life is detectable throughout extremes of temperature, salinity, radiation, pH, nutrient availability, and other environmental stressors. The inferred history and known habitable range of life on Earth suggests that an origin and/or persistence of life may be possible on other planetary bodies. Life can be defined as a self-sustaining chemical system capable of Darwinian evolution. All known life on Earth conforms to this definition through the central dogma of biology, which traces the flow of information from genetic material into cellular machinery. DNA stores genetic information and its mutation and copying facilitates evolution. DNA is transcribed into RNA, which is then translated into amino acid sequences or polypeptides by ribosomes. These polypeptides are then processed into biologically functional proteins. Here, we present three complementary investigations demonstrating how detection and characterization of DNA, RNA, and ribosomes can inform the search for extraterrestrial life.

First, we study “life as we know it” in a spaceflight context: organisms can epigenetically modify their DNA through a chemical tag known as methylation, which modulates cellular defense and regulation. As part of the Genomic Enumeration of Antibiotic Resistance in Space (GEARS) mission, we extend on-orbit sequencing capabilities to profile genomic methylation of microbes sampled from the International Space Station. Here, we present results from the mission’s pre-flight Experiment Verification Test, including spaceflight isolate culturing, sequencing, microbial identification, and bioinformatic profiling of antibiotic resistance indicators and methylation. This work enabled the now-accomplished first sequencing of unknown organisms in space, and is expected to yield the first methylome generated from data collected in space.

Next, we show how the central dogma informs detection of “life as we don’t know it.” Life of a separate origin may differ biochemically from known life on Earth. However, such life is likely to have its own equivalent to the central dogma, raising the opportunity to target translation as a biosignature. Making and operating ribosomes is the most energetically expensive thing that life does. This reflects the centrality of translation as an emergent requirement of life as a chemical system capable of Darwinian evolution. We propose that a molecular apparatus capable of performing translation, similar to a ribosome, could serve as evidence of life that does not share a common origin with life on Earth. We then show that such a biosignature could be detectable with solid-state nanopore instrumentation, demonstrating capabilities to detect and distinguish between DNA, RNA, and ribosomes. Such instrumentation could be integrated into high-priority proposed planetary missions such as the Enceladus Orbilander, providing a tool to search for signs of life regardless of composition or relation to life on Earth.

Finally, we investigate how life as we know it can epigenetically modify its DNA in the extreme environmental conditions of a deep-sea hypersaline anoxic basin (DHAB). By integrating instrumentation and methodologies used in the GEARS project, we profile genomic methylation in two highly abundant bacterial species. Observed patterns of differential methylation with depth suggest that these species may be utilizing genomic methylation to adapt to harsh deep-sea conditions across a halocline, particularly by modifying the DNA that codes for ribosomal RNA. Given the high energetic cost of producing and maintaining ribosomes, this modification represents a potential adaptation to optimize metabolism in a resource-depleted environment. Future work will aim to confirm this hypothesis and refine regulatory mechanisms.

We provide a roadmap to single molecule detection and characterization of life beyond Earth and reveal a new level of integration within the framework of the central dogma via epigenomic regulation of translation. We show that biological and solid-state nanopore instrumentation can interrogate the molecules of life as we know it and can likely be extended to seek evidence of life as we don’t know it. Thus, single-molecule methods can enable future in situ space and planetary missions to search for biosignatures in potential resource-limited ecosystems with rare and disparate signs of life.