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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
NASA NTRS1981

A model for protocellular coordination of nucleic acid and protein syntheses

The proteinoid model for the coordination of protein synthesis with nucleic acid coding within the evolving protocell is discussed. Evidence for the self-ordering of amino acid chains, which would enhance the catalytic activity of a lysine-rich proteinoid, is presented, along with that for the preferential formation of microparticles, particularly proteinoid microparticles, in various solutions. Demonstrations of the catalytic activity of lysine-rich proteinoids in the synthesis of peptide and internucleotide bonds are pointed out. The view of evolution as a two stage sequence in which the geological synthesis of peptides evolved to the protocellular synthesis of peptides and oligonucleotides is discussed, and contrasted with the alternative view, in accord with the central dogma, that nucleic acids arose first then governed the production of proteins and protocells.

Fox, S. W.↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗
NASA NTRS1993

The RNA World: Life Before DNA and Protein

All of the life that is known, all organisms that exist on Earth today or are known to have existed on Earth in the past, are of the same life form: a life form based on DNA and protein. It does not necessarily have to be that way. Why not have two competing life forms on this planet? Why not have biology as we know it and some other biology that occupies its own distinct niche? Yet that is not how evolution has played out. From microbes living on the surface of antarctic ice to tube worms lying near the deep-sea hydrothermal vents, all known organisms on this planet are of the same biology. Looking at the single known biology on Earth, it is clear that this biology could not have simply sprung forth from the primordial soup. The biological system that is the basis for all known. life is far too complicated to have arisen spontaneously. This brings us to the notion that something else something simpler, must have preceded life based on DNA and protein. One suggestion that has gained considerable acceptance over the past decade is that DNA and protein-based life was preceded by RNA-based life in a period referred to as the 'RNA world'. Even an RNA-based life form would have been fairly complicated - not as complicated as our own DNA- and protein-based life form - but far too complicated, according to prevailing scientific thinking, to have arisen spontaneously from the primordial soup. Thus, it has been argued that something else must have preceded RNA-based life, or even that there was a succession of life forms leading from the primordial soup to RNA-based life. The experimental evidence to support this conjecture is not strong because, after all, the origin of life was a historical event that left no direct physical record. However, based on indirect evidence in both the geological record and the phylogenetic record of evolutionary history on earth, it is possible to reconstruct a rough picture of what life was like before DNA and protein.

Joyce, Gerald F.↗
NASA NTRS1985

The search for extraterrestrial life: Recent developments; Proceedings of the Symposium, Boston University, MA, June 18-21, 1984

The conference presents papers on the history of the search for extraterrestrial life, the scientific rationale and methods used in the search for other planetary systems, the detection of distant planets with the Space Telescope, planetary searches using optical astrometric interferometers, and infrared spectral identification of complex organic molecules in interstellar grains. Also considered are universal protein ancestors from hydrogen cyanide and water, astronomical sources of polarized light and their role in determining molecular chirality on earth, the universal diagrams and life in the universe, the precambrian evolution of terrestrial life and a thermodynamic approach to the occurrance and appearance of galactic life forms. Papers are also presented on the Ohio Seti program, lunar reflections of terrestrial radio leakage, the multichannel spectrum analyzer, software implementation of detection algorithms for the MCSA, the Serendip II design, galactic colonization and competition in a young galactic disk, implications of ancient and future migrations, extraterrestrial intelligence, the ineviability and the possible structures of supercivilizations, planetary, interplanetary and interstellar organic matter, and universal aspects of biological evolution.

Papagiannis, M. D.↗
NASA NTRS2014

Cofactors in the RNA World

RNA world theories figure prominently in many scenarios for the origin and early evolution of life. These theories posit that RNA molecules played a much larger role in ancient biology than they do now, acting both as the dominant biocatalysts and as the repository of genetic information. Many features of modern RNA biology are potential examples of molecular fossils from an RNA world, such as the pervasive involvement of nucleotides in coenzymes, the existence of natural aptamers that bind these coenzymes, the existence of natural ribozymes, a biosynthetic pathway in which deoxynucleotides are produced from ribonucleotides, and the central role of ribosomal RNA in protein synthesis in the peptidyl transferase center of the ribosome. Here, we uses both a top-down approach that evaluates RNA function in modern biology and a bottom-up approach that examines the capacities of RNA independent of modern biology. These complementary approaches exploit multiple in vitro evolution techniques coupled with high-throughput sequencing and bioinformatics analysis. Together these complementary approaches advance our understanding of the most primitive organisms, their early evolution, and their eventual transition to modern biochemistry.

RNA↗
NASA NTRSDate not supplied

Life Finds A Way, the Dynamics of E. Coli Evolution in Microgravity

Investigating the evolutionary dynamics of Escherichia coli in microgravity offers a unique opportunity to understand microbial adaptation to extreme environments. Here, we explored the effects of simulated microgravity (SµG) on gene expression and genome evolution of Escherichia coli REL606, a strain continuously evolved and documented terrestrially for 35 years. We used transcriptomic profiling over a 24-hour growth cycle to examine how short-term exposure to SµG under glucose-limiting and glucose-replete conditions may influence the genetic adaptations in microbial populations. Pathway analyses of differentially expressed genes suggest that SµG may alter cell membrane structure and function across all conditions, while changes to protein synthesis machinery were uniquely observed in glucose-replete samples. Furthermore, altered expression of several prophage genes across conditions in SµG samples and upregulation of general stress response factors hints at the potential for stress-induced mutagenesis in response to microgravity. We further investigated the impact of long-term exposure to SµG on genome evolution and observed a more rapid accumulation of base substitutions and deletions in SµG sample genomes across time. Specifically, mutations in the mraZ and elyC genes suggest a mechanism for increased production of peptidoglycan in the cell membrane. These findings offer insights into bacterial adaptations in long-term microgravity environments and pave the way for further detailed investigations.

Brittney Lozzi↗
NASA NTRS2000

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

Review, Tutorial↗
NASA NTRS2003

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Evolution, Molecular↗
NASA NTRS1971

Primordial organic chemistry and the origin of life.

Aspects of Darwinian revolution are discussed together with spontaneous generation, the inorganic chemical evolution, the primitive atmosphere, and interstellar matter. The significance of the change of the earth's reducing atmosphere to an atmosphere with oxidizing characteristics is considered. Experiments regarding the abiogenic synthesis of nucleic acids and proteins are reported. It was found that micromolecules can be formed in simulation experiments. The condensation reaction taking place in the presence of water was studied together with the condensation reaction taking place in the relative absence of water or under hypohydrous conditions. Jupiter simulation studies were conducted, and lunar and meteorite material was analyzed.

Ponnamperuma, C.↗
NASA NTRS1992

Origin and early evolution of photosynthesis

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

NASA Program Exobiology↗
NASA NTRS1998

The origin and evolution of oxygenic photosynthesis

The evolutionary developments that led to the ability of photosynthetic organisms to oxidize water to molecular oxygen are discussed. Two major changes from a more primitive non-oxygen-evolving reaction center are required: a charge-accumulating system and a reaction center pigment with a greater oxidizing potential. Intermediate stages are proposed in which hydrogen peroxide was oxidized by the reaction center, and an intermediate pigment, similar to chlorophyll d, was present.

Review, Tutorial↗
NASA NTRS2000

Biological Moleculars: Have Most of Our Problems Already Been Solved?

Evolution has resulted in biological machinery that engineers have great reason to envy and at present can only poorly mimic. This is not just a curiosity as biological systems perform many functions that are desired industrial processes. Examples include photosynthesis, chemosynthesis, energy storage, low temperature chemical conversion, reproducible manufacture of chemical compounds, etc. The bases of biological machinery are the proteins and nucleic acids that comprise living organisms. Each molecule functions as a part of a biological machine. In many cases the molecule can be properly regarded as a stand alone machine of its own. Concepts and methods for harnessing the power of biological molecules exist but are often overlooked in the industrial world. Some are old and appear crude but are quite effective, e.g. the fermentation of grains and fruits. Currently, there is a revolution in progress regarding the harnessing biological processes. These include techniques such as genetic manipulation via polymerase chain reaction, forced evolution also known as evolution in a test tube, determination of molecular structure, and combinatorial chemistry. The following is a brief discussion on how these processes are performed and how they may relate to industrial and aerospace processes.

Downey, James P.↗
NASA NTRS1983

Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence

Prokaryotic and eukaryotic evolutionary trees are developed from protein and nucleic-acid sequences by the methods of numerical taxonomy. Trees are presented for bacterial ferredoxins, 5S ribosomal RNA, c-type cytochromes , cytochromes c2 and c', and 5.8S ribosomal RNA; the implications for early evolution are discussed; and a composite tree showing the branching of the anaerobes, aerobes, archaebacteria, and eukaryotes is shown. Single lines are found for all oxygen-evolving photosynthetic forms and for the salt-loving and high-temperature forms of archaebacteria. It is argued that the eukaryote mitochondria, chloroplasts, and cytoplasmic host material are descended from free-living prokaryotes that formed symbiotic associations, with more than one symbiotic event involved in the evolution of each organelle.

Dayhoff, M. O.↗
NASA NTRS2005

"The Evolution of Photosynthesis and the Transition from an Anaerobic to an Aerobic World"

This project was focused on elucidating the evolution of photosynthesis, in particular the evolutionary developments that preceded and accompanied the transition from anoxygenic to oxygenic photosynthesis. Development of this process has clearly been of central importance to evolution of life on Earth. Photosynthesis is the mechanism that ultimately provides for the energy needs of most surface-dwelling organisms. Eukaryotic organisms are absolutely dependent on the molecular oxygen that has been produced by oxygenic photosynthesis. In this project we have employed a multidisciplinary approach to understand some of the processes that took place during the evolution of photosynthesis. In this project, we made excellent progress in the overall area of understanding the origin and evolution of photosynthesis. Particular progress has been made on several more specific research questions, including the molecular evolutionary analysis of photosynthetic components and biosynthetic pathways (2,3, 5, 7, 10), as well as biochemical characterization of electron transfer proteins related to photosynthesis and active oxygen protection (4,6,9). Finally, several review and commentary papers have been published (1, 8, 1 1). A total of twelve publications arose out of this grant, references to which are given below. Some specific areas of progress are highlighted and discussed in more detail.

Blankenship, Robert E.↗
NASA NTRS2004

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.

Evolution, Molecular↗
NASA NTRS1986

Microbial contributions to the Precambrian Earth

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

Margulis, L.↗
NASA NTRS1994

Evolution of heliobacteria: implications for photosynthetic reaction center complexes

The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

NASA Program Exobiology↗