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Project Reports

• Amino Acid Alphabet Evolution

  A genetically encoded alphabet of just 20 amino acids has produced the universe of protein structures and functions found throughout Earth’s biosphere. Relationships within this amino acid alphabet are responsible for fundamental biological phenomena, such as protein folding and patterns of molecular evolution. In attempting to unravel these relationships, considerable scientific ingenuity has been spent developing systems to simplify the genetically encoded alphabet of 20 amino acids while minimizing the associated loss of chemical diversity. These efforts present an opportunity to generate a composite picture of the properties that link the amino acids as a set. We are therefore investigating whether different simplification schemes (“simplified amino acid alphabets”), including those derived from very different approaches, can be combined to create a coherent description of amino acid similarity. By understanding the organization and relationships between amino acids on Earth, we hope to shed light on the chemical logic to be expected as a product of evolution in extraterrestrial environments.

  An extensive scientific literature has converged on surprisingly clear agreement that a subset of only around half of the 20 genetically encoded amino acids was likely present from the inception of genetic coding (the “early” amino acids), and an equal sized subset was incorporated through subsequent evolution (the “late” amino acids). A further widespread assumption is that, as the set expanded, natural selection favored the addition of amino acids that extended the range of protein structures and functions. We initiated a quantitative investigation for consilience between these two important ideas.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 6.2 7.1 7.2

• Biosignatures in Ancient Rocks

  The Biosignatures in Ancient Rocks group investigates the co-evolution of life and environment on early Earth using a combination of geological field work, geochemical analysis, genomics, and numerical simulation.

  ROADMAP OBJECTIVES: 1.1 3.2 4.1 4.2 4.3 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Atmospheric Oxygen and Complex Life

  Our team is working to understand what the world looked like just before and just after the evolution of animals. This encompasses field geology (identifying rocks of that age), chemical analysis of those rocks, and close examination of the small, enigmatic fossilized forms within those same geologic units. To synthesize these interdisciplinary approaches, our team also works to contribute overview/review papers that speak to the contribution from each field.

  ROADMAP OBJECTIVES: 4.1 4.2 6.1 6.2

• Deconstruction of the Ribosome

  In the ribosome, RNA and protein are fully interdependent, part of the highly complex system of translation. We demonstrate here that isolated Domain III of 23S rRNA from Thermus thermophilus retains function after being split essentially in half. Chemical footprinting shows that a core of Domain III (DIII^core), obtained replacement of helices 54-59 with a simple stem-loop, folds to a near-native state in the presence of Mg²⁺ ions. Both DIII and DIII^core form specific complexes with ribosomal protein L23 in vivo, as indicated with a yeast three-hybrid experiment. L23 has a globular domain on the LSU surface and an extension (L23peptide) that penetrates into the ribosomal large subunit. In the assembled LSU, L23peptide (amino acids 58-79) traverses the surface of DIII^core. In solution, DIII^core forms a stable 1:1 complex with L23peptide, as observed with spectroscopic assay. The experiments described here are intended to recapitulate steps in early ribosomal evolution. We have previously proposed that some of the extensions of ribosomal proteins are molecular fossils that predate the globular protein domains in evolution. In our favored model of ribosomal origins, small independently-folding RNA elements associated with short peptides. Such complexes assembled to form a primitive peptidyl transferase center. The PTC evolved into the modern LSU, in a series of cooptions that left unaltered the basic structure and function of the PTC. This model predicts a continuous size distribution of folding and assembly elements within the LSU. We anticipate autonomy and specificity of folding and interaction of small, mid-sized and large rRNA and protein components.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2

• 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

• Biomechanics of Rangeomorph Fauna

  The oldest evidence of complex communities of lifeforms come from Newfoundland, Canada. The fossil beds discovered there are dominated by rangeomorphs, which look superficially like underwater plants, but probably got their nutrition by direct uptake of dissolved resources in the water. Here, we use models of water flow in the community to see how these complex organisms could have competed with bacteria for organic matter or reduced compounds in the water. Ultimately, we have determined that by sticking up off the sea floor, rangeomorphs could take advantage of sheer forces created by moving water, and gain an advantage over bacteria in competition for nutrients. The benefits of sticking up into water flow may have driven the early evolution of complex life on earth. Ongoing work seeks to clarify the transitions between flow regimes across stages of community succession from prokaryotic mats to eukaryotic communities

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• Extremophile Ribosomes

  Diapausing embryos (resting eggs) from brachionid rotifers are able to withstand desiccation and thermal stress. Resting eggs can remain viable for decades, and develop normally once placed in a permissive environment that allows for hatching, growth and development. The exact mechanisms of resistance are not known, although several molecules have been suggested to confer protection during desiccation and thermal stress. In this study, we have identified by mass spectrometry two thermostable proteins, LEA (late embryogenesis abundant) and VTG (vitellogenin-like), found exclusively in the resting eggs of Brachionus manjavacas. This is the first observation that LEA proteins may play a role in thermostability and the first report of a VTG-like protein in the phylum Rotifera. These proteins exhibited increased expression in rotifer resting eggs when compared to amictic females. Our data suggest the existence of alternate pathways of desiccation and thermal resistance in brachionid rotifers.

  ROADMAP OBJECTIVES: 3.2 4.2 5.3

• Ironing Out the RNA World

  In RNA World models of evolution, RNA was once the primary biopolymer of genetics and catalysis (1). Ancient RNA-based life would have inhabited an earth with abundant soluble iron and no free oxygen (2,3). Anoxic life persisted for around 1.0-1.5 billion years before photosynthesis began producing substantial free oxygen. The ‘great oxidation’ led to Fe²⁺/O₂ mediated cellular damage (4) and depletion of soluble iron from the biosphere (5). We hypothesize that Fe2²⁺ was an RNA cofactor when iron was benign and abundant and that Fe²⁺ was replaced by Mg²⁺ during the great oxidation. The RNA-Fe²⁺ to RNA-Mg²⁺ hypothesis is in close analogy with known metal substitutions in some metalloproteins (6-11). An ancestral ribonucleotide reductase (RNR), for example, spawned di-iron, di-manganese, and iron-manganese RNRs (12). Our hypothesis is supported by observations (13) that (i) RNA folding is conserved between complexes with Fe2+ and Mg²⁺ and (ii) at least some phosphoryl transfer ribozymes are more active in the presence of Fe²⁺ than Mg²⁺. Here, we demonstrate that reversing the putative metal substitution in an anoxic environment, by removing Mg²⁺ and adding Fe²⁺, expands the catalytic repertoire of some RNAs. Fe²⁺ can confer on RNA a previously uncharacterized ability to catalyze single electron transfer. Catalysis is specific, in that it is dependent on the type of RNA. The 23S rRNA and tRNA, some of the most abundant and ancient RNAs (14), are found to be efficient electron transfer ribozymes in the presence of Fe²⁺. Therefore, the catalytic competence of ancient RNAs may have been greater in early earth conditions than in extant conditions, and the experiments described here may be reviving latent function.

  ROADMAP OBJECTIVES: 4.1 4.2

• Ediacaran-Cambrian Diversification of Animals

  We have continued our focus on the record of the early origin of animals, focusing on the fossil record of the Ediacaran and Early Cambrian. Our comprehensive analysis of the Ediacaran-Cambrian diversification of animals, using a new database of first occurrences combined with new molecular clock results (in collaboration with Peterson’s group), was published last year in Science. Erwin and Valentine completed the first comprehensive book on the Cambrian explosion, which is in press and due for release in late 2012 or early 2013.

  ROADMAP OBJECTIVES: 4.2

• Geochemical Signals for Low Oxygen Worlds

  We are studying the physiology of sulfate reducing bacteria, organisms that perform a key microbial metabolism in anoxic worlds. By calibrating microbial sulfur isotope effects, we can infer the redox level of paleoenvironments in the geologic past by studying sedimentary records. The sulfur cycle is intimately linked to the redox budget of the Earth’s surface, such that this study will help inform us about the evolution of aerobic environments, a key process that set the stage for animal evolution. Similarly, we also are studying the role of oxygen in controlling the budget and transformations of nitrogen in the ocean. Nitrogen is a critical nutrient limiting marine production, and the balance of its redox cycling controls how much nitrogen is added or removed from the ocean by redox-sensitive processes.

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 5.1 7.1

• Geochemical Signatures of Multicellular Life

  Sterols are essential membrane components of eukaryotes but their structural diversity varies across different eukaryotic lineages. Our research aimed to determine if are any systematic variations in sterol structures between Metazoa and their immediate unicellular relatives. We found that there is a stepwise reduction in production of 24-alkyl sterol on the path toward eumetazoa suggesting an evolutionary preference for C27 sterols among animals and their kin. A major exception to this finding are the Demosponges which produce a structurally diverse array of sterols.
  We also completed a study of sediments and oils in the South Oman Salt Basin that reported an array of unusual hydrocarbon patterns that are likely to be biosignatures for early metazoa.

  ROADMAP OBJECTIVES: 4.2 5.1

• Resurrection of an Ancestral Peptidyl Transferase

  Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro, and in vivo. The resulting model of the ancestral ribosome presented here incorporates about 20% of the extant 23S rRNA and fragments of four ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure, and (iii) form native complexes with ribosomal protein fragments. Footprinting experiments support formation of predicted secondary and tertiary structure. Gel shift, spectroscopic and yeast three-hybrid assays show specific interactions between ancestral rRNA and ribosomal protein fragments, independent of other, more recent, components of the ribosome. This robustness suggests that the catalytic core of the ribosome is an ancient construct that has survived billions of years of evolution without major changes in structure. Collectively, the data here support a model in which ancestors of the large and small subunits originated and evolved independently of each other, with autonomous functionalities.

  ROADMAP OBJECTIVES: 3.2 4.2

• Postdoctoral Fellow Report: Steven Mielke

  S. P. Mielke completed an NAI NASA Postdoctoral Program (NPP) fellowship during September 1, 2011 to February 29, 2012. His postdoctoral research has provided the basis for the project: “The Long-Wavelength Limit for Oxygenic Photosynthesis.” He continues this research as a Research Associate at Rockefeller University.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• RiboVision: Visualization and Analysis of Ribosomes

  Ribosomes present special problems and opportunities related to visualization and analysis because they are exceeding complex and information-rich. Many structures have determined at near-atomic resolution, a large number of rRNAs have been sequenced, and each is a large macromolecular assembly with many components and highly complex function. We are devising visualization and analysis methods in analogy with Google Maps, but applied to the ribosome.

  ROADMAP OBJECTIVES: 3.2 4.2

• Habitability of Extrasolar Planets

  We model if and under what conditions some of the recently detected Super-Earths – small, Earth-sized planets that have been discovered in in the classical Habitable Zone Sun-like stars – could be habitable. These models explore the underlying physics of planetary atmospheres and their remotely detectable features.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 6.2 7.2

• 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

• Stromatolites in the Desert: Analogs to Other Worlds

  In this task biologists go to field sites in Mexico to better understand the environmental effects on growth rates for freshwater stromatolites. 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 characterizing their metabolisms and gas outputs, for use in planetary models of ancient environments.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 5.3 6.1 6.2

• The Long Wavelength Limit for Oxygenic Photosynthesis

  Photosynthesis produces signs of life (biosignatures) on a planetary scale: atmospheric oxygen and the reflectance signature of photosynthetic pigments. Oxygenic photosynthesis is therefore a primary target in NASA’s search for life on habitable planets in other solar systems. An unanswered question is what the upper limit is to the photon wavelength at which oxygenic photosynthesis can remain viable. On other planets that have a parent star very different spectrally from our Sun, can we expect oxygen from plants of different colors from those on Earth?

  The cyanobacterium, Acaryochloris marina serves as a model organism for oxygenic photosynthesis adapted to low light and red-shifted light environments similar to what may be found on habitable planets orbiting M stars. Until A. marina was discovered in 1996, all known oxygenic photosynthesis relied on the pigment chlorophyll a (Chl a). A. marina instead uses chlorophyll d, which can absorb the far-red and near-infrared light in A. marina’s habitat. We use photoacoustics in the lab to measure the energy storage efficiency of A. marina with lasers, and molecular electrostatics modeling to surmise how replacement of Chl a by Chl d in A. marina affects arrangements within the photosystem molecules. We are finding that A. marina can perform oxygenic photosynthesis quite efficiently in its unique light niche.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Micro-RNAs as Phylogenetic Markers

  Since the beginning of 2011, we have published 12 peer-reviewed papers centered on three themes. First, we have pioneered the use of microRNAs (miRNAs) – small 22 nucleotide non-coding RNAs – as phylogenetic characters, and have recently gained new insights into the relationships of vertebrates, arthropods, brachiopods, and flies. Second, we have noted that the number of miRNAs an organism possesses seems related to their relative morphological complexity such that more complex animals have many more miRNAs than simple animals. Third, in a recent Science paper (Erwin et al.2012) we summarized all of our molecular-clock work to date which strongly suggests that bilaterians have a fairly extensive cryptic Precambrian history, which when coupled with our miRNA work makes this missing record even more enigmatic, and the resolution of this paradox is the focus of our current and much of our future NASA-sponsored work.

  ROADMAP OBJECTIVES: 4.2

• Molecular Basis for Complexity Development

  Cadherins are large, multi-domain proteins that are also cell surface receptors which function in cell adhesion, cell polarity, and tissue morphogenesis. They are considered essential to the appearance of animal life. We found cadherin genes in Capsaspora owczarzaki and the choanoflagellate Salpingoeca rosetta suggesting that this protein family predates the divergence of the C. owczarzaki, choanoflagellate, and metazoan lineages.

  ROADMAP OBJECTIVES: 4.2

• Interdisciplinary Studies of Earth’s Seafloor Biosphere

  The remote deep sediment-buried ocean basaltic crust is Earth’s largest aquifer and host to the least known and potentially one of the most significant biospheres on Earth. CORK observatories have provided unparalleled access to this remote environment. They are enabling groundbreaking research in crustal fluid flow, (bio)geochemical fluid/crustal alteration, and the emerging field of deep crustal biosphere

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Project 3A: Stable Isotope and Mineralogical Studies of Banded Iron Formations – O Isotopes by SIMS

  During the past year, we have made advances in technique development for analysis of mineral chemistry and stable isotope ratios in minerals. Applications to magnetite in Banded Iron Formation (BIF) have lead to the proposal that silician magnetite forms only in low oxygen fugacity conditions and are thus a signature for the former presence of reduced organic matter. Petrography and in situ analysis of δ¹⁸O by SIMS has shown that the earliest quartz cements in 1.85 Ga Granular Iron formation (GIF) consistently have high δ¹⁸O showing that earlier reports of more variable compositions included altered material.

  ROADMAP OBJECTIVES: 4.1 4.2 7.2

• Understanding Past Earth Environments

  For much of the history Earth, life on the planet existed in an environment very different than that of modern-day Earth. Thus, the ancient Earth represents a planet with a biosphere that is both dramatically different than the one in which we live, but that is also accessible to detailed study. As such, it serves as a model for what types of biospheres we may find on other planets. A particular focus of our work was on the “Early Earth” (formation through to about 500 million years ago), a timeframe poorly represented in the geological and fossil records but comprises the majority of Earth’s history. We have studied the composition and pressure of the ancient atmosphere; modeled the effects of clouds on such a planet; studied the sulfur, oxygen and nitrogen cycles; and explored atmospheric formation of molecules that were likely important to the origins of life on Earth.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1

• Paleontological Investigations of the Advent and Maintenance of Multicellular Life

  Cohen and Knoll (2012) published a monograph on scale microfossils in the ca. 800 million year old Fifteen Mile group, northwestern Canada. These fossils, document defenses against protistan predation and are the most diverse eukaryotic fossils known from pre-Ediacaran rocks. Justin Strauss discovered a rich new assemblage of testate microfossils in Neoproterozoic strata from northwestern Canada and undergraduate student Ross Anderson completed a senior thesis on testate protists from shales from the Neoproterozoic Dalradian succession in Scotland.

  ROADMAP OBJECTIVES: 4.2

• 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

• The Development of Sensory and Nervous Systems in the Basal Branches of the Animal Tree

  Animals interact with the world through complex sensory structures (eyes, ears, antennas, etc.), which are coordinated by collections of neurons. While the nervous and sensory systems of animals are incredibly diverse, a growing body of evidence suggests that many of these systems are controlled by similar sets of genes. We are looking at early branching and understudied lineages of the animal family tree (using the jellyfish Aurelia and the worm Neanthes respectively) to see if these animals use similar genes during neurosensory development as the better-studied fruit fly and mouse. This research is critical for determining which structures are shared between animals because of common ancestry (known as homologous structures) and those that evolved independently in different lineages. Ultimately, such research informs how morphologically and behaviorally complex animals evolve.

  ROADMAP OBJECTIVES: 4.1 4.2

• The Neoproterozoic Carbon Cycle

  We are studying the dynamics of the rise of oxygen during the Neoproterozoic (1 billion years ago to 543 million years ago) through culturing experiments, models and observations (see the progress report on the Unicellular Protists). We are testing the predictions of the following “anti-priming” hypothesis: if more easily degradable organic matter was degraded in oxic environments, this may have slowed down the degradation of organic matter in anaerobic environments and the overall degradation of organic matter, increasing the concentration of oxygen in the atmosphere and the surface ocean. We are currently developing theoretical predictions and testing these ideas by laboratory enrichment cultures of anaerobic microbes that degrade complex substrates in the presence and absence of labile organic compounds.

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 5.2 6.1 6.2

• Stoichiometry of Life, Task 3a: Ancient Records – Geologic

  Fossil and chemical fingerprints of animal life first appear in the geologic record around 600 million years ago. The four billion years of Earth history before this milestone were marked by dramatic changes that we take for granted today but that set the stage for our existence. Among the key events recorded in very old rocks is the first rise of oxygen in the atmosphere and ocean about 2.5 billion years ago following two billion years of a virtually oxygen-free world. And this evolving chemical state was the backdrop against which photosynthesis first evolved; simple, single-celled organisms appeared and diversified; and the first eukaryotic life evolved as a forerunner to the complex animals that would follow one-to-two billion years later. Our work is exploring the evolving compositions of the early atmosphere and ocean and their cause-and-effect relationships with the evolution of life—spanning the middle 50% of Earth history from the first production of oxygen via photosynthesis to the first appearance of animals. Darwin would have been pleased to know that early rocks tell us a convincingly strong: long before the animals, the oceans were teeming with life and that this life set the stage, in so many ways, for the later evolution of animals. Our sophisticated geochemical tracers are changing our view of the early environmental conditions that facilitated, and just as often throttled, the rise of life and the ways life can passively and intentionally modify its own environment—not unlike the lessons we are learning about our relationship with the changing ocean, atmosphere, and climate today.

  ROADMAP OBJECTIVES: 4.1 4.2

• Understanding the Shuram Excursion

  The Shuram carbon isotopic excursion – one of the largest deviations in Earth history- was first discovered in Oman before being found in deposits across the planet. While the causes of this isotopic excursion are as yet unknown, one hypothesis implicates major changes in Ediacaran carbon cycling that occurred simultaneously with the advent of complex life. Alternative hypotheses posit that it is simply a diagenetic anomaly. This research demonstrated that the Shuram Formation carbonates were formed in equilibrium with a fluid with the same oxygen isotopic composition as seawater and at ~50C.

  ROADMAP OBJECTIVES: 4.1 4.2

• Unicellular Protists of the Neoproterozoic

  We investigated 1) how microbial processes shape some sedimentary rocks, 2) how microbial processes influence the isotopic composition of sulfur-rich minerals that are used to understand the evolution of oxygen and the cycling of carbon in the past, 3) searched for fossils of organisms that lived between 716 and 635 million years ago, surviving times when ice covered entire oceans, even at the equator and 4) used these fossils, recovered from limestone rocks, to understand the cycling of carbon during this unusual time.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 6.1 7.1

• Task 3.5.1 Titan Genetics

  This project seeks to determine what chemical structures might support the genetic component of Darwinian evolution in Titan environments.

  ROADMAP OBJECTIVES: 2.2 3.2 4.2 6.2