2015 Annual Science Report

Astrobiology Roadmap Objective 3.4 Reports Reporting  |  JAN 2015 – DEC 2015

Project Reports

  • Inv 1 – Geochemical Reactor: Energy Production at Water-Rock Interfaces

    INV 1 examines water-rock interactions in the lab and in the field, to characterize the geochemical gradients that could be present at water-rock interfaces on Earth and other worlds, taking into account different ocean and crustal chemistries. We have fully investigated serpentinization as the most likely of all possible environments for life’s emergence on Earth as well as other water-rich worlds – a key goal for astrobiology as stated in the NASA Astrobiology Roadmap 2008. (Russell, 2015). Serpentinization is now recognized as fundamental to delivering the appropriate chemical disequilibria at the emergence of life. And the fact that this process is likely inevitable on any icy, wet and rocky planet makes its study fundamental to emergence of life, habitability and habitancy. Nevertheless, notwithstanding the thermodynamic drives to CO2 reduction during the process, great uncertainty exists over just what kind of organic molecules (if any) are delivered to the submarine springs and consequential precipitate mounds. In attempts to clarify what these might be we have undertaken thermodynamic modelling and experimental investigations of the serpentinization process.

    ROADMAP OBJECTIVES: 2.2 3.1 3.2 3.3 3.4 4.1
  • Project 1: The Origin of Homochirality

    Small biological molecules are frequently chiral, meaning that they can exist in both right-handed and left-handed forms. The two forms are identical except for the mirror symmetry that they break, and so would be expected to participate in chemical reactions in a way that does not depend on their chirality. When assembled into polymers, the resulting chains would therefore be expected to consist of a mixture of right and left-handed forms of the small molecules, a so-called racemic state. The surprise is that this is not true for the molecules of life. All chiral amino acids used by biology are left-handed and all chiral sugars are right-handed. That is, they are homochiral. This project is concerned with trying to find an explanation for this ubiquitous phenomenon, a universal aspect of all life on Earth. The specific question that is addressed is whether homochirality is a generic phenomenon of living systems, one that would be anticipated to arise if life were found elsewhere in the universe. Or is it instead some frozen accident related to the specific way that life arose on Earth? This question has been hotly debated in one form or other for over a hundred years, certainly since the time that Lord Kelvin coined the term “homochirality”. It is important for the Illinois NASA Astrobiology Institute for Universal Biology, because it is one of the two most evident universal phenomena of all life on Earth, the other being the universal genetic code. The phenomenon is important for another reason. The magnitude of the homochirality is 100%. It is not a slight imbalance in the abundance of right-handed vs. left-handed molecules. Thus, it is an unambiguous signal to measure, either from biological samples or remotely due to the effects of homochirality on the scattering of light waves. Specifically, homochiral solutions or suspensions will affect the polarization plane of electromagnetic waves, and so can readily be detected through optical means. The most exciting possibility in this regard is that if homochirality can be firmly established as a biological phenomenon, then its presence can be used as a biosignature of non-terrestrial life.

    ROADMAP OBJECTIVES: 1.2 3.2 3.4 4.1 4.2 7.1 7.2
  • Project 2: Cells as Engines and the Serpentinization Hypothesis for the Origin of Life

    All life is, and must be, “powered” since all of its most essential and distinguishing processes have to be driven “up-hill” against their natural thermodynamic direction. By the 2nd law of thermodynamics, however, a process can only be made to proceed up-hill by being mechanistically linked, via a molecular device functioning as an engine, to another, more powerful, process that is moving in its natural, down-hill direction. On fundamental principles, we argue, such engine-mediated conversion activities must also have been operating at, and indeed have been the cause of, life’s emergence. But what then were life’s birthing engines, what sources of power drove them, what did they need to produce, and how did they arise in an entirely lifeless world? Promising potential answers to these and other questions related to the emergence of life are provided by the Alkaline Hydrothermal Vent/serpentinization (“AHV”) hypothesis, whose original propounder and lead proponent, Dr. Michael Russell of JPL, is a co-investigator on this project. The goal of the project is specifically to clarify the essential mechanistic modus operandi of all molecular engines that power life, and to see how the most fundamental and prerequisite of these could have arisen, and operated, in the structures and flows produced by the serpentinization process. Importantly, candidate answers to these questions can be put to definitive laboratory tests.

    ROADMAP OBJECTIVES: 1.1 1.2 3.1 3.2 3.3 3.4
  • Project 3: Theory for the Darwinian Transition

    One of the key puzzles of astrobiology concerns the precision, uniqueness and rapidity of early evolution. In order for life to have evolved the main components of the modern cell as early 3.8 billion years ago, with a unique genetic code that is virtually optimal in terms of minimizing translational errors, the mode of evolution would have had to be different from the current vertical transmission of genes. We had shown in 2006 that the collective mechanism of horizontal gene transfer (HGT) is the only one capable of solving the puzzle of early evolution. The HGT means that the evolutionary process before LUCA can be thought of as a network of interactions rather than a tree, as would be the case in vertical gene transfer. The multiple connectivity of the network accelerates the evolution and allows rapid convergence to a unique, near-optimal genetic code. With all these advantages of HGT, why would it ever stop? Our project uses computer simulation of digital organisms in order to address these generic questions about the exit of life from the collective, progenote phase to the current era of vertically dominated evolution.

    This project is potentially important for understanding biosignatures of life. Even on Earth, we are familiar with the tree-like structure of individual organismal lineages. If life were a network, as we believe that it once was, the usual phylogenetic pattern of individuality and species would not apply. If we encounter life on other planets, we cannot be sure if it will be in the collective (progenote) phase or the vertical-dominated phase. Thus it is interesting to understand better the inexorability and timing of the Darwinian Transition.

    ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 6.2
  • Ancient Gene Families and HGT

    We have identified a subset of genes that appear to have been horizontally transferred from very ancient lineages that diverged earlier than the ancestor of the 3 known Domains of life.

    ROADMAP OBJECTIVES: 3.2 3.4
  • Project 4: Experiment on Darwinian Transition

    Carl Woese proposed that life started as semi-autonomous subcellular forms named progenotes. The progenotes lacked cell membranes and readily exchanged information, suggesting that aspects of information processing had already been developed. Woese further hypothesized that certain early life processes crossed a Darwinian threshold, where incorporation of new components of a processes was not tolerated. We aim at determining whether translation, transcription, and replication have crossed the Darwinian threshold. To determine whether DNA replication has crossed the Darwinian Threshold, interchangeability of the DNA replication processivity factor known as the sliding clamp is being examined. It is only in the presence of the sliding clamp that DNA polymerases in extant organisms can gain the speed required to replicate their genomes. In Bacteria, the sliding clamp is the -subunit of Pol-III and in Archaea and Eukarya the functional homolog is proliferating cell nuclear antigen (PCNA). We have, therefore, expressed and purified a sliding clamp from each of the three domains of life (E. coli -subunit, M. acetivorans PCNA, and human PCNA). Sliding clamps are loaded in a clamp loader dependent manner; therefore, we have cloned, expressed and purified an archaeal clamp loader from M. acetivorans. Our next step is to determine whether an archaeal clamp loader can interact with each of the sliding clamps from the three domains of life and whether any of the interactions leads to loading of the sliding clamps onto DNA to orchestrate processive DNA synthesis.

    ROADMAP OBJECTIVES: 3.2 3.4 4.2
  • Project 4: Co-Evolution of Escherichia Coli and Its Parasite Bdellovibrio Bacteriovorus: An Experimental Model for Eukaryogenesis

    This project seeks to address a long-standing question in the early evolution of life on Earth: how and why did simpler cell types (prokaryotes) transition into more complex (eukaryotic) cells (i.e. eukaryogeneis)? Because this conversion happened millions of years ago and left scant fossil evidence, we have been attempting to “re-create” a similar transformation in the lab that can be easily manipulated and studied in detail. A greater understanding of the events that ocurred both before and after eukaryogenesis will not only help NASA scientists predict what extraterrestrial life might look like, it will also help us understand how modern eukaryotic cells function and evolve.

    ROADMAP OBJECTIVES: 3.3 3.4 5.1 6.2
  • Stellar Effects on Planetary Habitability and the Limits of the Habitable Zone

    In this task, VPL team members studied the interaction between stellar radiation (including light) and planetary atmospheres to better understand the limits of planetary habitability and the effects of stellar radiation on planetary evolution. Work this year spanned climate modeling to atmospheric escape. We showed that multiple stable states of climate could exist for water-rich worlds, including both habitable and uninhabitable states, suggesting that water-rich planets in the habitable zone are not necessarily habitable. Atmospheric escape models were used to illustrate how the pre-main sequence evolution of M-dwarf stars could strip the gaseous envelopes from mini-Neptune planets, transforming them into potentially-habitable, Earth-sized rocky bodies. We also showed that pre-main sequence evolution could lead to strong atmospheric escape of water on otherwise habitable worlds, potentially rendering them uninhabitable. We defined the first metric to rank an exoplanet’s potential to support surface liquid water based on fundamental data from transit observations. Observational work was also undertaken to characterize the frequency and characteristics of stellar flares on M dwarf stars from Kepler data, as input to future work on characterizing the effect of stellar flares on habitability.

    ROADMAP OBJECTIVES: 1.1 1.2 3.4
  • RPL and Expedition 357: Serpentinization and Life at the Atlantis Massif

    Circulating hydrothermal fluids associated with mid-ocean ridges represent some of the most prominent examples of the intersection between chemical energy and the biosphere. The Lost City Hydrothermal Field, which sits atop the Atlantis Massif near the Mid Atlantic Ridge hosts a microbial ecosystem which feeds off the products of serpentinization. IODP Expedition 357, which sailed in Fall 2015, obtained rock cores and fluids from the Atlantis Massif, which are being used for the coordinated investigation of serpentinization processes and life. Lost City is known to sustain abiogenic organosynthesis reactions and as such has been suggested to be an analogue to prebiotic early Earth environments and potential extraterrestrial habitats.

    ROADMAP OBJECTIVES: 3.1 3.4 5.1 5.2 5.3 7.2
  • Project 7: Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

    Methanogens represent the largest diversity among the archaea and have the unique ability to generate methane from simple compounds such as carbon dioxide, acetate and methylamines which were common in the anaerobic environments of early Earth and perhaps Mars. Methane biosynthesis also requires the presence/uptake of important ions such as sulfates, sulfides, carbonates, phosphates, and various light metal ions. In this project, we are attempting to analyze the evolution of the methanogens’ central cellular functions of translation, transcription, replication, and metabolism. To accomplish this, we are constructing the metabolic and regulatory networks of Methanosarcina acetivorans, the most complex methanogen known, and using these models to establish a framework for studying the evolution of methanogens. Results will be tested through microfluidic studies using varying carbon and ion sources.

    ROADMAP OBJECTIVES: 1.1 2.1 3.1 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2 7.1
  • Project 8: The Evolution of the Eukaryote-Archaea Common Ancestor

    The goals of our lab with respect to the NAI project are to describe early evolutionary via genomic and cellular comparisons of diverse eukaryotes to diverse archaea. We are interested in comparing genomes from diverse free-living eukaryotes to investigate the origins and evolution of eukaryotic complexity. Evolutionary reconstructions of early eukaryotes are challenged by a lack of sufficient taxonomic sampling. Few genomes of free-living microbial eukaryotes are sequenced, despite their critical importance in ecology, evolution, and basic cellular biology. The real challenge to protistan genomics is actually quite mundane; it concerns the lack of available and cultivatable free-living protists (mainly heterotrophs) in the laboratory. Yet, a better understanding of the genomic content diverse eukaryotes facilitates the evolutionary analysis of archaeal genomes. To address these issues of poor taxonomic sampling of eukaryotic genomes, my lab has developed a molecular method to separate eukaryotic DNA from bacterial DNA. We have demonstrated conclusively that we can separate eukaryotic chromatin from a mixture of eukaryotic and bacterial genomic DNA. This method will be widely applicable to the study of protistan genomics. Currently, our lab is in the process of assembling and annotating ten eukaryotic genomes from my lab’s culture collection of over 100 amoeboid protists from diverse phylogenetic groups. Many of these amoeba represent novel phyla-level lineages of eukaryotes.

    One amoebal genome is form is Nuclearia sp., which is an amoeboid protist closely and a member of a primary “supergroup” of eukaryotes – the Optisthokonts. This supergroup includes all animals, fungi, and several types of unicellular or colonial protists including choanoflagllates. Thus, genomic analyses of Nuclearia will inform the evolution of complexity and multicelllularity in both Fungi and Animals.

    ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2
  • Project 9: Metapopulation Structure

    Although often modeled as a single well mixed populations, microbes in terrestrial systems likely exist as metapopulations, isolated but connected by infrequent migration. This can change the evolution of complexity, increasing the effect of genetic drift and decreasing the effect of selection. It can increase diversity and the rate at which complexity evolves. We have argued that metapopulation structure may have existed in early life and been responsible for the rapid evolution of LUCA and diversification across the tree of life. We investigate microbial genome evolution in metapopulations in Yellowstone National Park. We find that indeed they represent evidence for both natural selection and genetic drift shaping these populations.

    ROADMAP OBJECTIVES: 3.2 3.4 4.2 6.2
  • NAI ARC Communications

    The ARC NAI Team interacts with a number of institutions that fall outside the NAI proper. These include universities and other domestic and international organizations, chief of which are Langston University, the Chickasaw and Choctaw Nations, and the Dutch Astrochemistry Network, which is part of the Netherlands Organization for Scientific Research (NWO).

    ROADMAP OBJECTIVES: 3.1 3.2 3.4
  • Laboratory Studies

    The Laboratory Studies project uses a variety of cryo-vacuum systems to study the physical and chemical properties of astrophysically relevant materials to better understand the extent to which these materials can be converted in more complex organic materials of astrophysical and astrobiological importance. We concentrate on mimicking conditions found in astrophysically relevant environments involving low temperatures, low pressures, and high radiation fields. The main processes we explore are the photolytic processing of mixed molecular ices and organics and chemistry that occurs at gas-solid interfaces.

    ROADMAP OBJECTIVES: 3.1 3.2 3.4