nai

Project Reports

• BioInspired Mimetic Cluster Synthesis: Bridging the Structure and Reactivity of Biotic and Abiotic Iron-Sulfur Motifs

  Bioinspired synthetic techniques are bridging the gap between iron sulfur (FeS) mineral surfaces that demonstrate chemical reactivity and the highly evolved FeS cluster centers observed in biological metalloenzymes. An emerging paradigm in biology relating to the synthesis of certain complex iron sulfur clusters involves the modification of standard FeS clusters through radical chemistry catalyzed by radical S-adenosylmethionine (SAM) enzymes. In our attempts to examine potential sources for prebiotic and/or early biotic catalysts, we have initiated a new experimental line that probes the ability of short conserved FeS amino acid motifs that are present in modern day enzymes for their ability to coordinate FeS clusters capable of initiating small molecule radical reactions.

  ROADMAP OBJECTIVES: 3.1 3.2 3.3 3.4 7.1 7.2

• Project 1A: Interaction Between Lipid Membranes and Mineral Surfaces

  The goal of our work was to determine whether the surface chemistry or physical properties of mineral surfaces in contact with model “protocells” may have controlled the rupture/integrity of the protocell membranes. We hypothesized that mineral surface/lipid head group interface chemistry may have acted as a Darwinian selection force for the types of protocells which survived. We used a variety of experimental techniques including fluorimetric analysis of vesicle rupture in contact with mineral particles, bulk adsorption isotherms for lipids on oxide particles, Atomic Force Micropscopy and Neutron Reflectivity studies of lipid bilayer formation on planar oxide surfaces. The results could be explained by a modified version of the Deraguin-Landau-Verwey-Ovebeek (DLVO) theory for colloidal stability. Results indicated that lipid vesicles and bilayers are more stable at the positively-charged corundum surface in the low and mid-pH range than at the negatively-charged surface at high pH. Thus, protocells which came in contact with mineral surfaces having a positive surface charge would have maintained their integrity while those contacting negatively-charged surfaces would have been ruptured. Our results may suggest that mineral surface chemistry and lipid head group chemistry may have acted as a Darwinian “evolutionary stress” to select the most robust types of vesicles which “survived.”

  Our project addresses NASA Astrobiology Institute’s (NAI) Roadmap goals of understanding the origins of cellularity and the evolution of mechanisms for survival at environmental limits, and NASA’s Strategic Goal of advancing scientific knowledge of the origin and evolution of the Earth’s biosphere and the potential for life elsewhere.

  ROADMAP OBJECTIVES: 3.4

• Habitability of Icy Worlds

  Habitability of Icy Worlds investigates the habitability of liquid water environments in icy worlds, with a focus on what processes may give rise to life, what processes may sustain life, and what processes may deliver that life to the surface. Habitability of Icy Worlds investigation has three major objectives. Objective 1, Seafloor Processes, explores conditions that might be conducive to originating and supporting life in icy world interiors. Objective 2, Ocean Processes, investigates the formation of prebiotic cell membranes under simulated deep-ocean conditions, and Objective 3, Ice Shell Processes, investigates astrobiological aspects of ice shell evolution.

  ROADMAP OBJECTIVES: 1.1 2.1 2.2 3.1 3.2 3.3 3.4 4.1 5.1 6.1 6.2 7.1 7.2

• Cosmic Distribution of Chemical Complexity

  The three tasks of this project explore the connections between chemistry in space and the origin of life. We start by tracking the formation and evolution of chemical complexity in space, from simple carbon-rich molecules such as formaldehyde and acetylene to complex species including amino acids, nucleic acids and polycyclic aromatic hydrocarbons. The work focuses on carbon-rich species that are interesting from a biogenic perspective and on understanding their possible roles in the origin of life on habitable worlds. We do this by measuring the spectra and chemistry of analog materials in the laboratory, by remote sensing with small spacecraft, and by analysis of extraterrestrial samples returned by spacecraft or that fall to Earth as meteorites. We then use these results to interpret astronomical observations made with ground-based and orbiting telescopes.

  ROADMAP OBJECTIVES: 1.1 2.1 2.2 3.1 3.2 3.4 4.3 7.1 7.2

• Ecology of Extreme Environments: Characterization of Energy Flow, Bioenergetics, and Biodiversity in Early Earth Analog Ecosystems

  The distribution of organisms and their metabolic functions on Earth is rooted, at least in part, to the numerous adaptive radiations that have resulted in the ability to occupy new ecological niches through evolutionary time. Such responses are recorded in extant organismal geographic distribution patterns (e.g., habitat range), as well as in the genetic record of organisms. The extreme variation in the geochemical composition of present day hydrothermal environments is likely to encompass many of those that were present on early Earth, when key metabolic processes are thought to have evolved. Environments such Yellowstone National Park (YNP), Wyoming harbor >12,000 geothermal features that vary widely in temperature and geochemical composition. Such environments provide a field laboratory for examining the tendency for guilds of organisms to inhabit particular ecological niches and to define the range of geochemical conditions tolerated by that functional guild (i.e., habitat range or zone of habitability). In this aim, we are examining the distribution and diversity of genes that encode for target metalloproteins in YNP environments that harbor geochemical properties that are thought to be similar to those that characterize early Earth. Using a number of newly developed computational approaches, we have been able to deduce the primary environmental parameters that constrain the distribution of a number of functional processes and which underpin their diversity. Such information is central to constraining the parameter space of environment types that are likely to have facilitated the emergence of these metal-based biocatalysts.

  ROADMAP OBJECTIVES: 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3

• Project 1B: Extracellular Polymeric Substances (EPS) and Bacterial Toxicity of Oxides

  Our interdisciplinary project examined the hypotheses that (1) bacterial cell membranes are ruptured in contact with specific mineral surfaces, (2) biofilm-forming extra-cellular polymeric substances (EPS) may have evolved to shield against membrane rupture (cell lysis), (3) differences in cell-wall structure of Gram-negative and Gram-positive bacteria may influence the susceptibility of cells to toxic minerals and (4) mineral toxicity depends on its surface chemistry and nanoparticle size.

  We have confirmed that the viability of wild-type bacterial cells which make EPS and biofilm is higher than that of mutant-type bacteria when exposed to oxide minerals. The effect is seen for both Gram negative and Gram positive bacteria, where the latter are less susceptible to the toxicity of minerals (Xu et al., 2012, Astrobiology; Zhu et al., in prep.). Thus, the thicker peptidoglycan outermost layer of the Gram positive cell surface provides an additional layer of protection compared to the less rigid, phospholipid outer membrane of the Gram negative bacteria (Zhu et al., in prep.). Most interestingly, EPS production could be induced by exposure to toxic minerals. The toxicity of the minerals depends on their surface chemistry (surface charge, ability to generate photocatalytic reactive oxygen species (ROS)) and size (Xu et al., in review).

  By understanding the mechanisms for membranolysis, especially under the extreme conditions of high radiation and heavy impacts during early planetary history, the project addresses the NASA Astrobiology Institute’s (NAI) Roadmap goals of understanding the origins of cellularity, the evolution of mechanisms for survival at environmental limits, and preservation of biosignatures, and NASA’s Strategic Goal of advancing scientific knowledge of the origin and evolution of the Earth’s biosphere and the potential for life elsewhere.

  ROADMAP OBJECTIVES: 3.4 5.1

• Experimental Evolution and Genomic Analysis of an E. Coli Containing a Resurrected Ancestral Gene

  We have previously described a paleo-experimental evolution system that combines Ancestral Sequence Reconstruction (ASR) with experimental evolution in the laboratory. Briefly, we designed a system that is composed of an organism with a short generation time and a protein under strong selective constraints in the modern host but whose ancestral genotype and phenotype, if genomically integrated, causes the modern host to be less fit than a modern population hosting the modern form of the protein. The modern organism hosting the resurrected protein would obviously need to be viable, but sick. E. coli and a protein, whose ancestral sequences are available termed Elongation Factor-Tu (EF-Tu), turned out to be ideal for this type of experiment.

  ROADMAP OBJECTIVES: 3.4 4.1

• Origins of Functional Proteins and the Early Evolution of Metabolism

  The main goal of this project is to identify critical requirements for the emergence of biological complexity in early habitable environments by examining key steps in the origins and early evolution of functional proteins and metabolic reaction networks. In particular, we investigate whether protein functionality can arise from an inventory of polypeptides that might have naturally existed in habitable environments. We attempt the first demonstration of multiple origins of a single enzymatic function. We investigate experimentally how primordial proteins could evolve through the diversification of their structure and function and thus demonstrate key steps in the earliest evolution of protein functions.

  ROADMAP OBJECTIVES: 3.2 3.4

• Metabolic Networks From Cells to Ecosystems

  Members of the Segre’ group use systems biology approaches to study the complex network of metabolic reactions that allow microbial cells to survive and reproduce under varying environmental conditions. The resource allocation problem that underlies these fundamental processes changes dramatically when multiple cells can compete or cooperate with each other, for example through metabolic cross-feeding. Through mathematical models of microbial ecosystems and computer simulations of spatially structured cell populations, the Segre’ team aims at understanding the environmental conditions and evolutionary processes that favor the emergence of multicellular organization in living systems.

  ROADMAP OBJECTIVES: 3.4 4.2 5.2 6.1

• Reconstruction of Ancient Proteins

  The genetic code is one of the most ancient and universal aspects of biology on Earth, and determines how specific DNA sequences get interpreted as peptide sequences, which then fold into all the proteins necessary for the growth and function of living cells. To a large extent, this code is determined by a class of proteins that specify which RNA adaptor molecules (tRNA) become attached to which amino acids, aminoacyl-tRNA synthetases. Therefore, reconstructing the amino acid sequences of the ancestors of these synthetases, existing ~4 billion years ago, can tell us the mechanisms by which the genetic code arose, and how it evolved to the modern form inherited by all known living organisms.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2

• Measuring Interdisciplinarity Within Astrobiology Research

  To integrate the work of the diverse scientists working on astrobiology, we have harvested and analyzed thousands of astrobiology documents to reveal areas of potential connection. This framework allows us to identify crossover documents that guide scientists quickly across vast interdisciplinary libraries, suggest productive interdisciplinary collaborations, and provide a metric of interdisciplinary science.

  ROADMAP OBJECTIVES: 1.1 1.2 2.1 2.2 3.1 3.2 3.3 3.4 4.1 4.2 4.3 5.1 5.2 5.3 6.1 6.2 7.1 7.2