Origem da Vida:Como a Matriz sugeriu, ferro e sulfa vindo do nucleo terrestre

(Registrado para posterior pesquisa)

NAI – NASA Astrophisic Institute
Workshop Without Walls
Molecular Paleontology and Resurrection:
Rewinding the Tape of Life

Iron-Sulfur Enzyme Evolution – A Pathway to Understanding the Transition from the Abiotic to the Biotic Earth.

John Peters
Montana State University
The main emphasis of our research at the Astrobiology Biogeocatalysis
Research Center at Montana State University is premised in the assumption that
the relationship between iron-sulfur mineral structure and catalytic reactivity is
simply too strong to be coincidental. Our assertion then is that gaining a better
understanding of this relationship together with understanding the chemistry by
which modifications are introduced in both mineral and biological iron-sulfur
motifs to tune their reactivity provides a means to understand the transition
between the abiotic and biotic Earth. Recently, we have made significant
progress in our understanding of how different classes of iron-sulfur based
metalloenzymes are assembled in biology and these results have had profound
implications in the way we view their respective evolutionary trajectories. These
insights have contributed to our ability to rationalize potential pathways of abiotic
reactive iron-sulfur cluster evolution via ligand assisted catalysis that we believe
may be mirrored in biology today.
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Narrowing the Gap between Hadean and Abiotic Earth by
Catalytic Processes on Iron-Sulfur Mineral Surfaces and Particles

Robert Szilagyi
Montana State University
The Mineral Thrust team members at the Astrobiology Biogeocatalysis Research
Center at Montana State University have made considerable progress toward
describing the formation of the building blocks of life (Stage II) from abundant, yet
inert small molecules that are characteristic for Hadean Earth (Stage I). From
chemical laboratory experiments that mimic hydrothermal conditions in and
around black smokers, fresh iron(II) sulfur precipitates and pyrite particles were
shown to produce considerable amount of ammonia from nitrite/nitrate/nitric
oxide small molecules. Experiments involving biologically inspired heterometal
substitutions (Mo, V, Ni) are in progress to extend the scope of the above
reactions toward other nitrogen substrate, in particularly to dinitrogen. Molecular
beam/surface scattering experiments under experimental conditions that are
relevant to exposed Fe-S mineral surfaces to Hadean atmosphere were able to
generate highly reactive, reduce Fe-S phase on pyrite. The modified pyrite
surface was characterized by synchrotron-radiation based multi-edge X-ray
spectroscopic measurements. Reactivity studies already indicate considerably
higher ammonia formation by the reduced pyrite phase than for example a
metallic iron surface used in the Haber-Bosch industrial ammonia synthesis.
Realistic size virtual chemical models have been developed for explaining the
mechanistic details of the above processes. These theoretical modeling efforts
link the above hydrothermal experiments with plausible mineral surface
modifications by atmospheric processes.
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Early Prebiotic Chemistry
Session Chair: Nicholas Hud
Ancestral Biopolymers
Nick Hud
Georgia Institute of Technology
Since the Miller-Urey experiment demonstrated the spontaneous formation of
small biological molecules in a model prebiotic reaction, chemists have been
investigating possible abiotic routes by which biological building blocks (e.g.
amino acids, nucleobases, sugars) could have spontaneously formed the first
polymers of life. The discovery that RNA can catalyze reactions has made RNA a
particularly attractive candidate as the first polymer of life (the “RNA world”
hypothesis).  However, a prebiotic pathway by which RNA polymers could have formed and replicated without the aid of coded proteins remains unresolved.
Before the discovery of catalytic RNA, there was substantial focus on the
possibility that non-coded polypeptides were the first biopolymers of life. While
notable progress has been made towards the realization of plausible prebiotic
routes for the synthesis of both RNA and non-coded peptides, it looks
increasingly likely that the first polymers of life were somewhat different from
those found in contemporary life and/or that other prebiotic molecules, not
currently found in life,
(Sugerindo que a fórmula da Matriz vinda de LUCA como sistema fechado sofreu aqui mutação para sistema aberto)
 facilitated the rise of the first biopolymers. For example, the
first biopolymers might have been comprised of different chemical building blocks
that allowed the facile assembly of RNA-like and protein-like polymers, which
provided the catalytic power necessary to begin the course of chemical evolution
that eventually resulted in the appearance of RNA, DNA and coded protein
synthesis. Some recent advances and remaining questions regarding the
possible origins of our ancestral biopolymers will be discussed.
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A Search for Structural Alternatives of RNA
Ram Krishnamurty
Scripps Research Institute
Our work is focused on gaining an understanding of the chemical criteria that led
to the selection of RNA (DNA) as informational systems.1 We address this – by
synthesizing potentially natural structural alternatives that may have had a
chance to self-assemble, by studying their properties (such as base-pairing), and
by comparing them with those properties relevant to the functioning of RNA.
Such an approach (a) provides chemical facts that may contain clues to RNA’s origin; (b) allows for the possibility of finding informational systems that could be
more ‘primitive’ than RNA
; and (c) permits insights into the structure-function
relationship of RNA.
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Paleogenetics. Bringing Experimental Methods to Bear on Historical Models for Earth

Steve Benner Foundation for Applied Molecular Evolution

The reductionist approach to biology in the last century has placed chemical structures behind most biological phenomena. Unfortunately, the more complete our chemical description has become, the more it has become clear that a description of the parts of biological systems does not necessarily provide us with an understanding of the whole.

One way to add perspective to molecular descriptions of life is to use tools from molecular evolution to determine the history of biological molecules.

 Unfortunately, historical hypotheses that account for modern biology concern events in the past, considered by many to be inaccessible to experiment, and therefore less than “scientific”.

The emerging field of paleogenetics seeks to address this problem by a process that infers the structures of ancient genes and proteins by analysis of the structures of their descendents, resurrects those proteins using biotechnology, and examines thm experimentally in the laboratory. This talk will describe recent advances in paleogenetics, including proteins that test hypotheses about how ancient life adapted to challenges millions of years ago. We will discuss how paleogenetics helps us understand how mammals adapted to the global cooling of the past 40 million years, how fungi adapted to the emergence of angiosperms in the age of the dinosaurs, and how the resurrections of ancestral proteins can help us understand human disease.

 

Making Sense of Life’s Amino Acid Alphabet

Steve Freeland University of Hawaii

The Last Universal Common Ancestor (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded proteins. It appears that some of these amino acids were present through non-biological syntheses prior to the origin of life, while the rest evolved as inventions of early metabolism. However, it also appears that many alternatives were available, so what factors led biological evolution on our planet to define its standard amino acid alphabet?  

Sugestão da Matriz: O padrão básico de todos os amino-ac idos – o carbono central com quatro ligações – é cópia da Matriz. Por isso ele se tornou o padrão doas aminoacidos constituintes dos seres vivos.

One possibility is that natural selection favoured a set of amino acids with clear, non-random properties – a set of especially useful building blocks. A simple test of this idea idea reveals that life’s “choice” of amino acids
exhibit values for each of size, charge and hydrophobicity that spread more
broadly and more evenly than any chance sampling of what was likely available
to early life. Indeed, amino acids of the standard alphabet are also overrepresented
within the small fraction of alternative alphabets found to out-perform
evolution’s choice. While much remains unanswered, this study offers suggests a
fundamental explanatory logic at the heart of molecular evolution that hints at
possibilities for a truly universal biochemistry.

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( O que está em vermelho não fou lido ainda)


Surface-Catalyzed Peptide Formation on Sulfide Minerals
Shohei Ohara
Carnegie Institution of Washington
The formation of peptide from amino acids in dilute solutions on the early Earth
remains an enigma for the origins of life. Hypotheses by Wächtershäuser [1, 2]
and Russell and Hall [3] propose that sulfide minerals could catalyze the
production of the first peptides. Huber and Wächtershäuser [4] reported that
dipeptides were formed via reactions amino acids in the presence of a (Ni,Fe)S
precipitate with CO and H2S (or CH3SH) at 100ºC. However, the formation of
COS, has been shown to be a condensation agent for peptide formation [5].
Consequently, a special role of metal sulfides for peptide formation has not been
demonstrated. We present results that show peptide formation is significantly
enhanced in the presence of pyrite (FeS2), chalcopyrite (CuFeS2) or sphalerite
(ZnS). That the peptization reaction is surface catalyzed is supported by the fact
that the yield of peptide strongly correlates with mineral surface area.
Interestingly the yield of peptide with sphalerite or chalcopyrite was much higher
than that with pyrite under the same surface-area condition. In the crystal
structure of sphalerite and chalcopyrite, metal atom is coordinated by a
tetrahedron of sulfurs. On the other hand, each iron atom in the structure of pyrite
is surrounded by six sulfur atoms at the corners of an octahedron. Crystal
structure of sulfide mineral may be related to the catalytic effect for the peptide
formation.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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Linking the Evolutionary Record to the Geological Record
Session Chair: Eric Gaucher
Between a Rock and Hot Place: What Do Microbial Genomes Tell Us About
the Natural History of the Interactions of Microorganisms With Mercury?
Tamar Barkay
Rutgers University
Mercuric reductase (MerA) is central to the mercury (Hg) resistance (mer)
system, catalyzing the reduction of ionic Hg to volatile Hg(0). A total of 213 merA
homologues were identified in sequence databases, the majority of which
belonged to microbial lineages that occupy oxic environments. merA was absent
among phototrophs and in lineages that inhabit anoxic environments.
Phylogenetic reconstructions of MerA indicate that (i) merA originated in a
thermophilic bacterium following the divergence of the Archaea and Bacteria with
a subsequent acquisition in Archaea via horizontal gene transfer (HGT), (ii) HGT
of merA was rare across phylum boundaries, and (iii) MerA from marine bacteria
formed distinct and strongly supported lineages. Collectively, these observations
suggest that a combination of redox, light, and salinity conditions constrain MerA
to microbial lineages that occupy environments where the most oxidized and
toxic form of Hg, Hg(II), predominates. Further, taxon-specific distribution of
MerA with and without a 70 amino acid N terminal extension may reflect
intracellular levels of thiols. In conclusion, MerA likely evolved following the
widespread oxygenation of the biosphere in a thermal environment and its
subsequent evolution has been modulated by the interactions of Hg with the
intra- and extra-cellular environment of the organism.
Ancient Proteins as Proxies for Precambrian Environments Hosting Life
(pH and Temperature)
Eric Gaucher
Georgia Institute of Technology
The recent accumulation of DNA sequence data, combined with advances in
evolutionary theory and computational power, have paved the way for innovative
approaches to understand the origins, evolution, and distribution of life and its
constituent biomolecules. One approach to understand ancestral states follows a
present-day-backwards strategy, whereby genomic sequences from extant
(modern) organisms are incorporated into evolutionary models that estimate the
extinct (ancient) character states of genes no longer present on Earth. These
inferred ancestral gene sequences act as hypotheses that can be tested in the
laboratory through the resurrection of the ancestral proteins themselves. Results
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
9
from functional assays of the protein products from these ancient genes provide
insight into their activities, interactions, binding-specificities, environments, etc.
This talk will describe our attempts to understand how early life evolved on Earth
and the types of environmental conditions that hosted this life. In particular, the
talk will focus on Precambrian life in regards to temperature and pH.
Linking Trace Metal Availability and Nitrogenase Evolution: Influence of the
Late-Archean Marine Nickel Famine on the Emergence of Molybdenum-
Based Nitrogen Fixation
Jennifer Glass
Arizona State University
Exploring links between metal bioavailability and evolution of metalloenzymes
has the potential to connect the geological record with the genetic record. In
modern biological systems, molybdenum (Mo)-nitrogenase is the primary
enzyme responsible for the conversion of dinitrogen to ammonia. However, in the
low-Mo Archean ocean, it is thought that nitrogen fixation was catalyzed by
nitrogenase enzymes that contained vanadium (V) or iron (Fe) in place of Mo.
During dinitrogen reduction these “alternative” forms of nitrogenase expend
significant energy in the form of hydrogen gas, resulting in the need for an
additional ~8 (V-nitrogenase) and ~32 (Fe-nitrogenase) mol ATP per catalytic
cycle when compared to Mo-nitrogenase. A fraction of this energy can be
recovered if the hydrogen produced by nitrogenase is recycled by Ni-Fe
hydrogenases. We propose that a drop in marine Ni concentrations 2.7 billion
years ago (Konhauser et al., 2009, Nature) may have impaired the activity of
these hydrogenase enzymes, leading to a reduced ability of organisms to recycle
the hydrogen produced by alternative nitrogenases. In combination with transient
pulses of Mo into the ocean as a result of increased oxidative weathering during
this period, this marine Ni famine could have provided the evolutionary impetus
for the evolution of the more efficient Mo-containing form of nitrogenase, resulting
in drastic changes to the late Archean and/or early Proterozoic nitrogen cycle.
Physiological, paleochemical, and phylogenetic evidence in support of this
hypothesis will be discussed.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
10
The Utilization of MALDI Surfaces to Improve Detection of Abioticaly
Polymerized RNA
Lauren Cassidy
Rensselaer Polytechnic Institute
Metal is the standard desorption platform for Matrix assisted laser
adsorption/desorption ionization – Mass Spectrometry (MALDI-MS) but other
surfaces have been shown to offer advantages for particular types of analytes or
applications. One such substrate is fused silica, which has been employed for
matrix-free Laser Desorption/Ionization (LDI)detection of small mass analytes
and for affinity MALDI-MS in which binding ligands are immobilized at the fused
silica surface. In the presence of matrix, the in crease in analyte desorption
potential remains, independent of the matrix used. This suggests that the surface
composition actively influences the analyte desorption potential. The present
work reports improved MALDI-MS detection of longer (>10-mer) RNA
oligonucleotides at unmodified fused silica surfaces compared to stainless steel
surfaces. In contrast, positively charged analytes, including proteins and
peptides, showed the expected increase in detectability on the steel surface
compared to the fused silica surface. Neutral saccharide polymers were also
examined and found to have a minor amplification in detection. The RNA
oligonucleotides were abiotically synthesized from activated monomers on
catalytic clay surfaces. The results are relevant to rapid screening of abiotic
polymerization towards elucidating pathways to life on Earth.
Alternative Biochemistry and Arsenic, or Life as We Might Not Expect It
Felisa Wolfe-Simon
US Geological Survey
Life on Earth is metabolically diverse and yet maintains a biochemical unity. That
is, all known biology is composed of essentially identical components such as
DNA/RNA, proteins and lipids made of carbon, hydrogen, nitrogen, oxygen,
phosphorus and sulfur; while the physiology of organisms can be highly varied.
The basis for all life starts with chemical underpinnings. This chemical potential
manifests in four metabolic strategies used by life on Earth today, all of which
most likely evolved in the distant past. However, a single metabolism is not linked
to a unique microbe, for example some microbes, like Cyanobacteria, may utilize
known biological processes (e.g. photosynthesis) in alternative ways with
relatively unexplored yet potentially significant biogeochemistry. In addition to
well-known microbes with unexpected metabolism, current research is also
addressing this “unity of biochemistry” to identify potential alternatives to
“CHNOPS”-based life; for example the substitution of arsenic for phosphorus.
Taken together, variations on these themes of microbial metabolic flexibility and
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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alternative biochemistry may help us search for “alien” life either elsewhere in the
Universe or a “shadow biosphere” right here at home on Earth.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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Reconstruction & Resurrection
Session Chair: Betul Kacar Arslan
Evolution of Photosynthesis
Robert Blankenship
Washington University in St. Louis
Energy conversion of sunlight by photosynthetic organisms has changed Earth
and life on it. Photosynthesis arose early in Earth’s history and the earliest forms
of photosynthetic life were almost certainly anoxygenic (non oxygen evolving)
The invention of oxygenic photosynthesis and the subsequent rise of
atmospheric oxygen about 2.4 billion years ago revolutionized the energetic and
enzymatic fundamentals of life. The repercussions of this revolution are
manifested in novel biosynthetic pathways of photosynthetic cofactors and the
modification of existing and alternative modes of photosynthetic carbon fixation,
electron carriers and pigments. The evolutionary history of photosynthetic
organisms is further complicated by lateral gene transfer that involved
photosynthetic components, as well as endosymbiotic events. An expanding
wealth of genetic information together with biochemical, biophysical and
physiological data reveals a mosaic of photosynthetic features. In combination,
these data provide an increasingly robust framework to formulate and evaluate
hypotheses concerning the origin and evolution of photosynthesis.
Nitrogenase Evolution
Eric Boyd
Montana State University
The emergence of metalloenzymes capable of activating substrates such as
CO2, N2, and H2, were significant advancements in biochemical reactivity and in
the evolution of complex life. Examples of such enzymes include [FeFe]- and
[NiFe]-hydrogenase that function in H2 metabolism and Mo-, V-, and Fenitrogenases
that function in N2 reduction. Many of these metalloenzymes have
closely related paralogs (evolutionary relatives with differing function) that
catalyze distinctly different chemistries, an example being nitrogenase and its
closely related paralog protochlorophyllide reductase that functions in the
biosynthesis of bacteriochlorophyll (photosynthesis). While the amino acid
composition of nitrogenase and protochlorophyllide reductase is similar, their
active site compositions are very different. Whereas nitrogenase binds an
elaborative metallocluster (FeMo-co), protochlorophyllide reductase binds an
intermediate substrate during the synthesis of chlorophyll. The biochemical
reactivity and substrate specificity of nitrogenase is a direct consequence of the
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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composition and molecular structure of the active site metallocluster (FeMo-co),
which requires a number of accessory proteins to synthesize. By specifically
focusing on the origin of proteins required to synthesize FeMo-co, we have been
able to obtain significant insight into the evolution of this functional process, and
to place a number of key events in the evolution of this process in geologic time.
Here, we report on the origin of the metallocluster at the active site of the
nitrogenase reductase and discuss ongoing efforts aimed at resurrecting and
biochemically characterizing intermediate states during the stepwise evolution of
this metalloprotein.
Reconstructing Synthetase Paralog Ancestors: Composition, Horizontal
Transfer, and Recombination
Greg Fournier
Massachusetts Institute of Technology
The evolution of aminoacyl-tRNA synthetases (aaRS) is an essential part of the
emergence of protein synthesis. Currently, it is unknown to what extent the
duplication and divergence of aaRS paralogs impacted the establishment of the
current genetic code; code disambiguation, expansion, or takeover from an RNAbased
system are all plausible scenarios. Ancestral reconstruction of aaRS
paralog ancestors followed by probabilistic composition analysis can determine
the likelihood of each hypothesis, as sites containing cognate amino acids
preserve a record of which residues were likely available to be incorporated at
that early time. Such deep ancestral reconstructions are sensitive to artifacts
resulting from branch-specific compositional bias, structural constraints, and
horizontal gene transfer followed by intragenic recombination. We propose
methodologies for dealing with these complex evolutionary factors, and show
preliminary results for the probabilistic reconstruction of the TyrRS/TrpRS
paralog ancestor supporting the late addition of Trp to the genetic code via
paralog divergence and neofunctionalization.
Recapitulating the Evolutionary History of Elongation Factor Proteins
Betül Kacar Arslan
Georgia Institute of Technology
All living organisms evolve by adaptively responding to changes in their habitat.
Little is known, however, about the interaction between environmental changes
and an organism’s adaptation to these changes as it navigates along a particular
evolutionary trajectory. To assess the role of contingency in evolution, an
experimental time machine is constructed. The system is composed of inserting
previously resurrected genes from the Elongation Factor (EF–‐Tu) gene family
into a modern bacterial genome and then monitoring evolution in action.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
14
Replaying the evolution of ancestral genes is intended to directly address the
question of whether the mutation/adaptation path previously traversed in natural
history is the only possible path. Results from this study will shed light on the
universal features of the evolutionary process that can be used to study life here
on Earth and potentially elsewhere in the cosmos.
A Changing View of Viruses in the Evolution and Ecology of Life
Mark Young
Montana State University
The main emphasis of our research at the Astrobiology Biogeocatalysis
Research Center at Montana State University is to try to gain insights into the
role of viruses might have played in the evolution of early life on Earth. Viruses
are the most abundant life-like entities on Earth and we presume wherever life
exists. In particular, we have been focused on the identification and
understanding of archaeal viruses from high temperature acidic environments
found in hot springs located in Yellowstone National Park USA and other hot
spring environments worldwide. These unusual environments are dominated by
Archaea and their viruses. Little is known about viruses that replicate in hosts
belonging to the domain Archaea. Our assertion is that by understanding
biochemical details of present day archaeal viruses and their relationship to virus
associated with hosts belong to the domains Bacteria and Eukarya that we will
gain insights into the origins and evolutionary role of viruses. This presentation
will provide a general introduction into what we know about the role of viruses in
the ecology and evolution of life followed by specific examples of how we are
gaining new insights by examining archaeal viruses from extreme environments.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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Molecules and Microbes
Session Chair: Eric Boyd
The Origins of Transmembrane Ion Channels
Andrew Pohorille
NASA Ames Research Center
Even though membrane proteins that mediate transport of ions and small
molecules across cell walls are among the largest and least understood
biopolymers in contemporary cells, it is still possible to shed light on their origins
and early evolution. The central observation is that transmembrane portions of
most ion channels are simply bundles of α-helices. By combining results of
experimental and computer simulation studies on synthetic models and natural
channels, mostly of non-genomic origin, we show that the emergence of α-helical
channels was protobiologically plausible, and did not require highly specific
amino acid sequences. Despite their simple structure, such channels could
possess properties that, at the first sight, appear to require markedly larger
complexity. Specifically, we explain how the antiamoebin and trichotoxin
channels, which are made of identical helices, 16 and 18 amino acids in length,
achieve efficiency comparable to that of highly evolved channels. On the basis of
our results, we propose that channels evolved further towards high structural
complexity because they needed to acquire mechanisms for precise regulation
rather than improve efficiency. In general, even though architectures of
membrane proteins are not nearly as diverse as those of water-soluble proteins,
they are sufficiently flexible to adapt readily to the functional demands arising
during evolution.
Extracellular Polymeric Substances As Armor Against Cytotoxic Minerals
Nita Sahai
University of Wisconsin, Madison
We explored the effect of extracellular polymeric substances (EPS) on bacterial
cell viability in suspensions of nanoparticulate metal oxides, and the mechanisms
of potential oxide cytotoxicity. We worked with a model biofilm former, a wild
type strain of Pseudomonas aeruginosa PAO1 (WT) that makes copious biofilm,
and an isogenic mutant δ-psl (MT) incapable of biofilm formation. We chose
model nanoparticulate oxides, amorphous silica (am. SiO2), anatase (b-TiO2),
and g-Al2O3, of primary particle sizes ~100 – 250 nm, and representing a
spectrum of surface charge at culture medium pH ~ 6-6.5. For EPS-devoid MT
cells, all three oxides investigated were cytotoxic, reducing cell viability by 20-
60% within 6 h compared to their oxide-free blanks. Cytotoxicity increased as
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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am. SiO2 < b-TiO2 ≤ γ-Al2O3. By comparison, WT viability was unaffected by
presence of nanoparticles. Thus, nanoparticles are potentially cytotoxic, the
extent of toxicity is mineral-dependent, and EPS shields against potential nanooxide
toxicity. Separately, the amount of EPS generated by WT cells, initially
gently washed to remove all EPS, was higher at 6 h in all oxide suspensions
versus oxide-free blanks, suggesting that EPS production is induced in response
to the stress of nanopartices. HRTEM analysis coupled with high-pressure
freezing and substitution techniques showed that positively-charged γ-Al2O3
particles penetrated into the intra-cellular space of MT cells, which have a
negative surface charge. In contrast, negatively-charged am. SiO2 and neutrallycharged
anatase were located only extra-cellularly. Thus, electrostatic forces
controlled the initial nanoparticle approach to the cell surface. Once inside the
MT cell, speculatively, γ-Al2O3 or a soluble Al(III) species bonded to
polyphosphates, disrupting normal cell-function, and decreasing viability. For
anatase, the concentration of highly reactive oxygen species (hROS) was two
orders of magnitude greater than on am. SiO2 or γ-Al2O3. When hROS activity
was quenched by catalase , MT cell viability was much higher in anatase
suspensions, and closer to oxide-free blanks. Thus, hROS on anatase caused
cell lysis by membrane peroxidation. Our results show that degree of toxicity and
toxicity mechanisms depend on surface chemistry on specific nanominerals. We
hypothesize that EPS either evolved to, or plays a redundant role in, protecting
against potential nanoparticle cytotoxicty.
Cuatro Cienegas: A Precambrian Park
Janet Siefert
Rice University
The Cuatro Cienegas Bolson, an oasis in the Chihuahuan desert in the state of
Coahuila, Mexico is a rare place. It has a biological endemism equal to the
Galapagos, it presents anomalous elemental stoichiometry with regards to
phosphorus, and its hydrologic system is dominated by living stromatolitic
features. As such it has proven a distinctive opportunity for the field of
Astrobiology. CCB is a reasonable proxy for an earlier time in earth’s history, the
late Precambrian, the biological frontier when microbial life was giving way to the
dominance of more complex eukaryotic organisms. It is an extant ecological time
machine that provides investigative collaborative opportunity for geochemists,
geologists, biologists, and population biologists to study the evolutionary process
of earth based life, especially microbial ones. It can and is being prospected for
the designing of biosignatures of past and present life that can be used in our
search for life extra-terrestrially. We summarize research efforts that began with
microbial population biology based projects and expanded into correlative efforts
in biogeochemistry, comparative genomics. We outline the future of CCB as a
Precambrian Park for Astrobiology.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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Yellowstone Microbial Diversity: A Glimpse into the Early Archaen
Wesley Swingley
University of California, Merced
Unique Split tRNA Genes Found in Archaea Suggest Gene Evolution May
Have Occurred at the RNA Level
Kosuke Fujishima
Keio University
Transfer RNA (tRNA) is an essential molecule involved in the process of protein
biosynthesis, which translates the genetic information into protein. Generally
tRNAs are encoded on a single gene with no intervention. However, unique types
of tRNA genes have been discovered from deep-branching species so-called
‘split tRNA’, which the 5’ and 3’ tRNA halves are encoded on two separate genes
of hyperthermophilic archaeon Nanoarchaeum equitans. The discovery of this
disrupted tRNA genes has raised the possibility that ancestral tRNA was once
encoded as a short tRNA half sequences and later efficient combination was
selected to form the cloverleaf structure to correspond with the variation of amino
acids. Recently our group has discovered ten novel split tRNA genes in the
genome sequence of deep-branching hyperthermoacidophilic crenarchaeon
Caldivirga maquilingensis. We found that all ten split tRNAs were individually
transcribed and joined in various combinations to generate all of the six missing
tRNAs encoding glycine, alanine and glutamate. Notably, the three mature
tRNA(Gly) with synonymous codons are created through the different
combinations of five short transcripts like a jigsaw, representing a first example of
functional RNA molecule made from three individual transcripts. Discovery of the
split tRNA genes from two deep-branching archaeal phylum (Nanoarchaeota and
Crenarchaeota) suggests that genes encoding short tRNA fragments may have
already existed in the common ancestor of Archaea. These findings also provide
a new idea that gene evolution at early stages may have taken place at RNA
level, which the short gene products could have been used in multiple
combinations to produce more longer and functional RNAs (and genes via
reverse transcription) through trial and error.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
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The Evolutionary History of Protein Synthesis
Session Chair: Loren Williams
On the Origin of Translation
Eugene Koonin
National Institutes of Health
The origin of the translation system is the central and the hardest problem in the
study of the origin of life and one of the hardest in all evolutionary biology. The
problem has a clear catch 22 aspect: high translation fidelity hardly can be
achieved without a complex, highly evolved set of RNAs and proteins but an
elaborate protein machinery could not evolve without an accurate translation
system. The origin of the genetic code and whether it evolved on the basis of a
stereochemical correspondence between amino acids and their cognate codons
(or anticodons), through selectional optimization of the code vocabulary, as a
“frozen accident” or via a combination of all these routes is another wide open
problem despite extensive theoretical and experimental studies. According to the
Darwinian Continuity Principle, a scenario for the evolution of a complex system
must consist of plausible elementary steps, each conferring a distinct advantage
on the evolving ensemble of genetic elements. Evolution of the translation
system seems to be conceivable only in a compartmentalized ensemble of
replicating, co-selected RNA segments, i.e., in a RNA World containing
ribozymes with versatile activities. Evolution has no foresight, so translation
apparently could not evolve in the RNA World through selection for protein
synthesis and must have been a by-product of evolution driven by selection for
another function, i.e., the translation system must have evolved via the
exaptation route. The least far fetched possibility seems to be that the
evolutionary process that eventually led to the emergence of translation started
with the selection of ribozymes binding abiogenic amino acids that stimulated
ribozyme-catalyzed reactions. The following conceptual scenario can be
envisaged:
i) binding of amino acids to a ribozyme resulting in an enhancement of its
catalytic activity
ii) evolution of the amino-acid-stimulated ribozyme into a peptide ligase
(predecessor of the large ribosomal subunit) yielding, initially, a unique
peptide activating the original ribozyme and, possibly, other ribozymes
in the ensemble
iii) evolution of self-charging proto-tRNAs that were selected, initially, for
accumulation of amino acids, and subsequently, for delivery of amino
acids to the peptide ligase
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
19
iv) joining of the peptide ligase with a distinct RNA molecule (predecessor
of the small ribosomal subunit carrying a built-in template for more
efficient, complementary binding of charged proto-tRNAs
v) evolution of the ability of the peptide ligase to assemble peptides
using exogenous RNAs as template for complementary binding of
charged proto-tRNAs, yielding peptides with the potential to activate
different ribozymes
vi) evolution of the translocation function of the protoribosome leading to
the production of increasingly longer peptides (the first proteins), i.e.,
the origin of translation.
The RNA World roots of the translation system are not sheer speculation but can
be partially inferred from comparative sequence analysis of proteins involved in
translation. In particular, evolutionary history of aminoacyl-tRNA synthetases
indicates that in the primordial translation system the adaptor function was
performed by RNA molecules.
Time Points in Ribosomal Evolution
George Fox
University of Houston
Numerous, but not all, major components of the modern translation machinery
are found in all branches of living systems. This implies that the ribosome was
largely functional at the time of the last universal common ancestor but still being
actively refined. Examples are used to show that it is possible to estimate the
relative age of various ribosomal components using a variety of timing events. As
a result, it is possible to obtain a general timeline for the development of the
ribosomal machinery. This timeline provides insight to when the genetic code
emerged. In addition, studies of the ribosome have implications for the
emergence of homochirality in modern proteins.
A Hierarchical Model for the Evolution of Ribosomal RNA
Sergey Steinberg
University of Montreal
The emergence of the ribosome constituted a pivotal step in the evolution of life.
This event happened nearly four billion years ago, and any traces of early stages
of ribosome evolution are generally thought to have completely eroded away.
Surprisingly, a detailed analysis of the structure of the modern ribosome reveals
a concerted and modular scheme of its early evolution.
NAI Workshop Without Walls ABSTRACTS Nov 8-10, 2010
Molecular Paleontology and Resurrection: Rewinding the Tape of Life
20
What Does the Ribosome Say about Pre-LUCA Biopolymers?
Loren Williams
Georgia Institute of Technology
The ribosome, which synthesizes protein in all living systems, is one of life’s most
ancient molecular machines. The ribosome is our most direct macromolecular
connection to the distant evolutionary past, and to life before LUCA. Here we
describe our method for establishing chronologies of ancient ribosomal origin and
evolution. We have computationally sectioned ribosomal structures into
concentric shells, like an onion, either the site of peptidyl transfer or the decoding
center is the origin. This approximation allows shell-by-shell comparisons: we
effectively drill into the ribosome and study the rings, like a tree. This method
captures clear and significant information along the evolutionary timeline, well
before LUCA. For the large subunit, sequence and conformational similarity
between bacteria and archaea are greatest near peptidyl transferase center and
diverge smoothly with distance from it. Thus, the oldest regions of the ribosome
are more conserved than recent regions. More importantly, the method shows
that the conformation, interactions and abundance of both RNA and protein
change over evolutionary time. The arrival of coded protein in biology is recorded
in ribosomal structure and is announced by changes in densities, conformations
and interactions of biopolymers. Some of the most ancient protein elements
appear to be molecular fossils of non-coded peptide ancestors. Ancient RNAmagnesium
assemblies are not required with the advent of coded protein.

 

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