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Project Reports

• Project 11 Isolation and Genomic Sequencing

  This projects seeks to understand the early evolution of eukaryotic cells by comparing the genomes of diverse eukaryotic microbes and asking what genes are shared and when features of the eukaryotic cell evolved.

  ROADMAP OBJECTIVES: 3.4 4.2

• Education and Public Outreach

  Our ongoing Education and Public Outreach activities include: (1) a Massively Open Online Course (MOOC) in which over 36,000 students have participated worldwide; (2) workshops for middle school and high school teachers; (3) formal in person and online for-credit courses at the University of Illinois Urbana-Champaign in which 240 students have participated; informal courses in Yellowstone in collaboration with the Yellowstone Association Institute; and (4) ongoing development and writing of a new book.

  ROADMAP OBJECTIVES: 6.1 6.2

• Project 10: Identifying Key Innovations in the Origin of the Cell

  Identifying essential functions of conserved hypothetical genes holds the key to understanding the origins of key innovations in the origin of the cell. Our goal is to take a comparative genomic approach to define the molecular machinery that differentiate the Bacterial from its sister lineage that later diverged to became the Archaea and Eukaryotes. One of the obstacles clouding our view of these early cells from a comparative approach is the large number of conserved hypothetical genes present in Archaeal and Eukaryote genomes whose cellular functions are unknown. Our approach is to identify which conserved hypothetical genes are essential to the function of the model crenarchaeon Sulfolobus islandicus. The Crenarchaea are one of the major lineages with in the Archaeal domain with close ties in function to the cellular biology of Eukaryotes. The essential gene profile has not been identified within any organism in this lineage and holds the key to understanding the origin of cellular features in central processing of genomic information through replication, recombination, repair and the shaping of the chromosome.

  ROADMAP OBJECTIVES: 3.4 4.2 5.1 6.1 6.2

• Project 7 Control of Evolvability and Chromosomal Rearrangement by Stress

  Evolution of the genome happens predominantly by gross chromosomal rearrangements (GCR), usually involving non-homologous recombination, and point mutation or single nucleotide variation (SNV). GCR re-assorts domains and regulatory functions, and frequently changes gene copy number, allowing further evolution. SNV changes coding sequences, modifying the properties of encoded macromolecules and their regulation. We are able to measure both SNV and GCR in the same assay in Escherichia coli, and have established that both are dramatically up-regulated in response to stress. Through many year’s work, we have learnt many details of these mechanisms, but some of the outstanding questions are crucial to understanding the significance of stress in evolution, notably the signaling and execution of the pathway from stress to mutation, and how the decision is made between SNV and GCR. This project aims to answer these questions.

  ROADMAP OBJECTIVES: 5.1

• Project 8 Culturing Microbial Communities in Controlled Stress Micro-Environments

  This project explores the adaptation and evolution of organisms under controlled environmental conditions, and compares the behavior across two Domains of Life in order to identify and quantify universal aspects of evolutionary response.

  ROADMAP OBJECTIVES: 6.1 6.2

• Project 9: Evolution Through the Lens of Codon Usage

  The sequences of protein encoding genes are subject to multiple levels of selection. First, amino acid changes that adversely alter protein function are unlikely to survive. In addition, the genetic code of organisms is degenerate; it includes alternative (synonymous) codons for most of the amino acids. Codon usages in a genome are generally viewed as a balance between drift and selection for rapid and accurate translation of mRNAs into proteins. This balance defines the native codon usage of the organism. Later, it was recognized that many horizontally transferred genes have distinctive codon usages. It was assumed that these reflected the codon usages of the organisms that contributed the genes. We viewed this as an opportunity to identify those sources.

  These studies of this have led us to discover that: (i) most of the recently acquired genes come from such closely related organisms that their distinctive codon usages cannot be attributed to a phylogenetically distant source; (ii) the transfers commonly exceed recognized boundaries of microbial species; (iii) after their acquisition, some of the genes do not drift to match the native codon usage of the recipient; (iv) many of the genes that are most up-regulated under starvation conditions have this same codon usage; and (v) a distinctive stress/starvation-associated codon usage is a recurring theme that is observed in diverse Bacteria and Archaea.

  These studies entailed the development of a variety of new codon usage analysis tools. We are making these tools available, and are integrating them into the RAST genome annotation and analysis server at Argonne National Laboratory.

  ROADMAP OBJECTIVES: 5.1 5.2 5.3

• Project 5: The Origins of Life’s Diversity

  The huge diversity of life poses a major challenge to ecological theory and a major source of optimism for astrobiology. Ecological theory argues that a single environmental niche should be colonized by a single species of organism, or perhaps a small community, and so the diversity of life should be essentially a measure of the number of niches present. The huge diversity of life does suggest, however, that the ability of life to explore, colonize and especially create environmental niches has been drastically underestimated. Accordingly, the likelihood of extraterrestrial life arising is also underestimated, or at least inadequately estimated, by our present understanding of biological evolution. This project attempts to solve this problem by developing a new theory for niche diversity.

  ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2

• Project 1: Dynamics of Self-Programming Systems

  This project is a theoretical attempt to understand how evolution can arise from inanimate physical systems. The key idea is that matter can organize into structures that not only replicate and carry information, but are able to program and reprogram themselves functionally. We have already been able to construct simple computer programs that can increase their complexity in an open-ended way, but in this grant period we have been building a mathematical formulation of how this arises using recursive function theory. We have also been trying to develop cellular automata meta-programming pairs that can co-evolve complexity.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 5.3 6.2

• 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 2.1 3.1 3.2 3.3 3.4

• Project 3: The Origin of Homochirality

  A universal aspect of living systems on Earth is their homochirality: Life uses dextrorotary sugars and levorotary amino acids. The reasons for this are hotly debated and not close to being settled. However, the leading idea is that autocatalytic reactions grew exponentially fast at the origin of life, and whatever chiral symmetry breaking was accidentally present became amplified subsequently. We are calculating the way in which this can take place using statistical mechanics, and also trying to see how a uniform homochirality could be stable to spatial fluctuations.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 7.1 7.2

• Project 4: Rapid Evolution in Stressed Populations: Theory

  Evolution is typically thought of as occurring over millions of years. But recently it has become clear that we have grossly over-estimated this time scale. Perhaps the most famous example of this is the rapid evolution of resistance of bacteria, worldwide, to modern antibiotics. Similarly, early life has an evolution time scale problem: given the age of the Earth and the known age of the Last Universal Common Ancestor, life must have arisen and evolved the majority of the complexity of the modern cell in less than a billion years. This project is a theoretical attempt to understand how a fluctuating environment can accelerate evolution rate, and lead to evolution on ecosystem time scales. Eventually, this work will join up with the experimental work being done by our team, using the GeoBioCell, in Project 8.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 5.3 6.1

• Project 6. Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

  Methanogenic archaea derive energy from simple starting materials, producing methane and carbon dioxide in the process. The chemical simplicity of the growth substrates and versatility of the organisms in extreme environments provide for a possibility that they could exist on other planets. By characterizing the evolution of methanogens from the most simple to most complex organism as well as their growth characteristics under controlled environments, we hope to address the question as to whether they could exist on planets such as Mars, where bursts of methane have been seen, yet no source has yet been identified.

  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 7.2

• Project 12 Enrichment of Eukaryotic DNA

  This projects seeks to understand the early evolution of eukaryotic cells by comparing the genomes of diverse eukaryotic microbes and asking what genes are shared and when features of the eukaryotic cell evolved.

  ROADMAP OBJECTIVES: 3.4 4.2

• Project 13: Experimental Determination of the Existence of the Darwinian Transition

  Life on our planet can be divided into three domains: Archaea, Bacteria and Eukarya. While some genes may be shared among the domains of life, others especially those involved in information processing namely DNA replication, transcription and translation are often unique to a particular domain. It has, therefore, been proposed that the molecular machineries that carry out these processes (replication, transcription and translation) have crossed a so-called Darwinian threshold where the molecular machineries have become gelled and therefore intolerant of new components. This project is examining the Darwinian threshold hypothesis by testing the interchangeability of the components of the DNA replication machinery across the domains of life. Further experiments will examine the capacity of biomolecules involved in translation and transcription to substitute for their counterparts across the domains of life.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 5.3