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Project Reports

• Cosmic Distribution of Chemical Complexity

  This project explores the connections between chemistry in space and the origin of life. It is comprised of three tightly interwoven tasks. We track the formation and evolution of chemical complexity in space starting with simple carbon-rich molecules such as formaldehyde and acetylene. We then move on to more 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: 2.1 2.2 3.1 3.2 3.4 4.3 7.1 7.2

• Culturing Microbial Communities in Controlled Stress Micro-Environments

  In NAI Theme 4B, our goal in Year 1 has been to initiate our understanding of how cells structure their genomes in response to specific environmental stresses and to determine whether or not such mechanisms have been a major force in directing the evolution of cells in natural environments over evolutionary time. Natural environments are typically rather heterogeneous at small scales, as established by sampling from geothermal hot spring communities, and so it is important to understand the generic impact on the evolution and structure of microbial communities. Our first step towards probing this phenomenon has been to culture living bacterial populations within a small specially constructed microfluidic device (called the GeoBioCell), where strong physical, chemical and biological gradients can be imposed under carefully controlled conditions.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 5.3 6.1

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

  In order to study the historical pathways and modern mechanisms of protein evolution in a complex cellular environment, we combined ancestral sequence reconstruction with experimental evolution. Our first goal was to identify how ancestral states of a protein effect cellular behavior by directly engineering an ancient gene inside a modern genome. We could then identify the evolutionary steps of this organism harboring the ancient gene by subjecting it to laboratory evolution, and directly monitoring the resulting changes within the integrated ancient gene as well as the rest of the host genome.

  ROADMAP OBJECTIVES: 3.4 4.1 5.1 5.2 6.1 6.2

• 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. Specifically, we investigate whether protein functionality can arise from an inventory of polypeptides that might have naturally existed in habitable environments; we attempt to demonstrate multiple origins of a single enzymatic function; we investigate how primordial proteins could evolve through the diversification of their structure and functions; and we determine how simple proteins could carry out seemingly complex functions.

  ROADMAP OBJECTIVES: 3.2 3.4

• Mining Archaeal Genomes for Signatures of Very Early Life

  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 b-subunit of Pol-III and in Archaea and Eukarya the functional homolog is proliferating cell nuclear anti-gen (PCNA). We have, therefore, expressed and purified a sliding clamp from each of the three domains of life (E. coli beta-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

• The Nature of the Last Archaeal and Eukaryal Ancestor

  The evolutionary history of the eukaryotic cell is intimately linked evolution of atmospheric oxygen and with the endosymbiosis of bacterial symbionts to become the mitochondrial organelles. This project seeks to understand the evolutionary history of the eukaryotic cell using contemporary analogs of ancestral anaerobic eukaryotes (rumen ciliates), which are often associated with endosymbiotic archaea and bacteria in tightly associated communities. We study the evolution of this association using state-of-the-art metagenomic and ecological methods to gain a better understanding of the evolution of these types of associations and thus of eukaryotic evolutionary history.

  ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.2 6.1

• Genetic Evolution and the Origin of Life

  In this task biologists and chemists use field and laboratory work to better understand the environmental effects on growth rates for freshwater stromatolites and the mechanisms that govern their adaptation to their environment. Stromatolites are microbial mat communities that have the ability to calcify under certain conditions. They are believed to be an ancient form of life, that may have dominated the planet’s biosphere more than 2 billion years ago. Our work focuses on understanding these communities as a means of understanding environmental impacts on evolution, and characterizing their metabolisms and gas outputs, for use in planetary models of ancient environments. This year we also started a new project looking at the chemical affinities of the building blocks of life, as a way to understand how life might have initially formed from these chemical precursors.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.2 5.3 6.1 6.2

• Thermodynamics of Life

  Although thermodynamics dictates that all spontaneous processes must be purely dissipative and “destructive” (the notoriously ungenerous face of the “2nd law”), under particular circumstances a spontaneous process can be a compound of two mechanistically coupled sub-processes only one of which (necessarily the larger one), is dissipative while its coupled, lesser partner is literally “driven” to be creative and generative – that is, a process that can “do work”, “build stuff”, and “make things happen”. A system functioning in this way is technically an engine and all living systems are necessarily, examples of such thermodynamically compound and creative “engine” systems – while at the same time operating internally via a complex, interlinked clockwork of such engines.
  Moreover, living systems inherently belong to a special thermodynamic subclass of such engines, namely those that are “autocatalytic” (self-growing and self-stabilizing) in their operation. Arguably, in fact, it is the property of being autocatalytic thermodynamic engines which at root underlies the potency and magic of living systems and which at the same time constitutes life’s most assuredly universal, fundamental, and primitive property. However, as of yet, we understand the implications of these thermodynamic facts quite poorly – notwithstanding that they seem certain to materially impact questions regarding the origin of life, evolutionary dynamics, and community, trophic, and ecology-level organization.
  The present project undertakes to redress this situation to some extent by investigating the formal dynamical behavior of model systems made up of interacting, thermodynamically driven, autocatalytic engines.

  ROADMAP OBJECTIVES: 3.3 3.4 4.2 5.1 5.2

• Molecular Biosignatures: Reconstructing Events by Comparative Genomics

  Reconstructing ancient events in genome evolution provides a valuable narrative for planetary history. Phylogenetic analysis of protein families within microbial lineages can be used to detect horizontal gene transfers and the evolution of new metabolic pathways and physiologies, many of which are significant in reconstructing ancient ecologies and biogeochemical events. These gene transfers can also be used to constrain molecular clock models for early life evolution, applying principles of stratigraphy and date calibration. A better understanding of gene evolution, including partial horizontal gene transfer, is needed to improve these inferences and avoid systematic errors.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 4.3 5.1 5.2 6.1