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PubMed2006

Prebiotic materials from on and off the early Earth.

One of the greatest puzzles of all time is how did life arise? It has been universally presumed that life arose in a soup rich in carbon compounds, but from where did these organic molecules come? In this article, I will review proposed terrestrial sources of prebiotic organic molecules, such as Miller-Urey synthesis (including how they would depend on the oxidation state of the atmosphere) and hydrothermal vents and also input from space. While the former is perhaps better known and more commonly taught in school, we now know that comet and asteroid dust deliver tons of organics to the Earth every day, therefore this flux of reduced carbon from space probably also played a role in making the Earth habitable. We will compare and contrast the types and abundances of organics from on and off the Earth given standard assumptions. Perhaps each process provided specific compounds (amino acids, sugars, amphiphiles) that were directly related to the origin or early evolution of life. In any case, whether planetary, nebular or interstellar, we will consider how one might attempt to distinguish between abiotic organic molecules from actual signs of life as part of a robotic search for life in the Solar System.

Earth, Planet↗
PubMed2002

Exact results for hydrogen recombination on dust grain surfaces.

The recombination of hydrogen in the interstellar medium, taking place on surfaces of microscopic dust grains, is an essential process in the evolution of chemical complexity in interstellar clouds. Molecular hydrogen plays an important role in absorbing the heat that emerges during gravitational collapse, thus enabling the formation of structure in the universe. The H2 formation process has been studied theoretically, and in recent years also by laboratory experiments. The experimental results were analyzed using a rate equation model. The parameters of the surface that are relevant to H2 formation were obtained and used in order to calculate the recombination rate under interstellar conditions. However, it turned out that, due to the microscopic size of the dust grains and the low density of H atoms, the rate equations may not always apply. A master equation approach that provides a good description of the H2 formation process was proposed. It takes into account both the discrete nature of the H atoms and the fluctuations in the number of atoms on a grain. In this paper we present a comprehensive analysis of the H2 formation process, under steady state conditions, using an exact solution of the master equation. This solution provides an exact result for the hydrogen recombination rate and its dependence on the flux, the surface temperature, and the grain size. The results are compared with those obtained from the rate equations. The relevant length scales in the problem are identified and the parameter space is divided into two domains. One domain, characterized by first order kinetics, exhibits high efficiency of H2 formation. In the other domain, characterized by second order kinetics, the efficiency of H2 formation is low. In each of these domains we identify the range of parameters in which, due to the small size of the grains, the rate equations do not account correctly for the recombination rate and the master equation is needed.

Journal Article↗
PubMed2001

Perspective: From mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology.

The generation of mutants in model organisms by geneticists and developmental biologists over the last century has occasionally produced phenotypes that are startlingly reminiscent of those seen in other species. Such extreme mutations have generally been dismissed by evolutionary geneticists since the "modern synthesis" as irrelevant to adaptation and speciation. But only in recent years has information on the molecular bases of mutant phenotypes become widely available, and thus work on testing the relevance of such extreme mutations to the generation of phylogenetic diversity has just begun. Here we evaluate whether evolutionary mimics are, in fact, useful for pinpointing the genetic differences that distinguish morphological variants generated during evolution. Examples come from both plants and animals, and range from intraspecific to interordinal taxonomic ranges. The use of mutationally defined candidate genes to predict evolutionary mechanisms has so far been most fruitful in explaining intraspecific variants, where it has been effective in both plants and animals. In several cases these efforts were facilitated or supported by parallel results from quantitative trait loci studies, in which natural alleles controlling continuous variation in developmental model organisms were mapped to mutationally defined genes. However, despite these successes the approach's utility seems to rapidly decay as a function of phylogenetic distance. This suggests that the divergence of developmental genetic systems is great even in closely related organisms and may become intractable at larger distances. We discuss this result in the context of what it teaches us about development, the future prospects of the candidate gene approach, and the historical debate over process in micro- and macroevolution.

Animals↗
PubMed2006

Evolutionary conservation of neuropeptide expression in the thymus of different species.

Evidence suggests that the immune and neuroendocrine systems cross talk by sharing ligands and receptors. Hormones and neuropeptides produced by the neuroendocrine system often modulate the function of lymphoid organs and immune cells. We have previously reported the intrathymic expression of somatostatin (SOM) in the mouse and that several neuropeptides, most notably calcitonin-gene-related peptide (CGRP), neuropeptide Y (NPY), SOM and substance P (SP), can modulate thymocyte development. However, little is known about the intrathymic expression of these neuropeptides either in the mouse or in other species. Moreover, a comparative analysis of the expression of these molecules would highlight the evolutionary importance of intrathymic neuroendocrine interactions in T-cell development. We have studied the expression of different neuropeptides in the thymus of zebrafish, Xenopus, avians, rodent, porcine, equine and human by immunohistochemistry and reverse transcription-polymerase chain reaction. We found that CGRP, NPY, SOM, SP and vasointestinal polypeptide (VIP) are expressed in the thymus of all species investigated. The thymic location of many of these neuropeptides was conserved and appears to be within the stromal compartments. Interestingly, in the avian thymus the expression of CGRP, SOM and SP appears to change depending on the age of the tissue. These findings suggest that neuropeptides may play an important role in T-cell development and provide further evidence of cross talk between the immune and neuroendocrine systems.

Animals↗
PubMed1981

Pyruvate dehydrogenase complex from baker's yeast. 2. Molecular structure, dissociation, and implications for the origin of mitochondria.

1. Pyruvate dehydrogenase complex from Saccharomyces cerevisiae is similar in size (s20,w 77 S) and flavin content (1.3--1.4 nmol/mg) to the complexes from mammalian mitochondria. 2. The relative molecular masses of the constituent polypeptide chains, as determined by dodecylsulfate gel electrophoresis at different gel concentrations, were: lipoate acetyltransferase (E2), 58 000; lipoamide dehydrogenase (E3), 56 000; pyruvate dehydrogenase (E1), alpha-subunit, 45 000, and beta-subunit, 35 000. Gel chromatography in the presence of 6 M guanidine . HCl gave a value of 52 000 for E2 indicating anomalous electrophoretic migration as described for the E2 components of other pyruvate dehydrogenase complexes. Thus, the organization and subunit Mr values are similar with the mammalian complexes and virtually identical with the complexes of gram-positive bacteria but differ greatly from the pyruvate dehydrogenase complexes of gram-negative bacteria. 3. The complex was resolved into its component enzymes by the following methods. E1 was obtained by treatment of the complex with elastase followed by gel chromatography on Sepharose CL-2B using a reverse ammonium sulfate gradient for elution. E2 was isolated by gel filtration of the complex in the presence of 2 M KBr, and E3 was obtained by hydroxyapatite chromatography in 8 M urea. The isolated enzymes reassociated spontaneously to give pyruvate dehydrogenase overall activity.

Biological Evolution↗
PubMed1983

Classification of phospholipases A2 according to sequence. Evolutionary and pharmacological implications.

The sequences of 32 phospholipases A2 (EC 3.1.1.4) were systematically compared on the basis of polypeptide chain length and similarity at selected amino acid positions around the active site. Two difference matrices were constructed and the various groupings present in the data were expressed in dendrogram form. The two methods of comparison yielded different results, and this is seen as a consequence of separate aspects of phospholipase evolution being highlighted in each case. It appears that, although Elapid snake venom phospholipases are very similar in terms of overall conformation, the area around their active sites distinguishes them into two major groups, namely the Asian Elapids and the marine/Australasian Elapids. Further, the Asian Elapids seem to have active-site vicinities which are closer to those in the mammalian pancreatic phospholipases. The relevance of the classifications to structure/activity relationships (especially beta-neurotoxicity) and phospholipase evolution is discussed.

Amino Acid Sequence↗
PubMed1984

Primary structures of the alpha-crystallin A chains of twenty-eight mammalian species, chicken and frog.

The amino acid sequences of the alpha-crystallin A chains of 28 mammalian species, representing 14 different orders, have been analyzed, mainly on the basis of amino acid compositions of the composing peptides. The alpha A sequences of chicken and a frog have been completely determined by Edman degradation. A method is described to transport eye lenses, to be used for protein sequence studies, at ambient temperature in a solution of guanidine . HCl. The number of cysteine residues in different alpha A chains could be determined by alkaline urea gel electrophoresis after aminoethylation . In some cases the alpha A chains have been isolated from total lens extracts in a single ion-exchange chromatographic step. The average rate of substitutions in the evolution of the alpha A chains is moderately slow, approximately 3 amino acid substitutions per 100 residues in 100 million years, but varies considerably in different lineages. Substitutions involving changes in charge are strongly underrepresented; the alpha A chains tend to keep their net charge constant throughout evolution. Analysis of the types of substitutions suggests a directional trend leading to an increase in functional density of alpha A in the course of evolution.

Amino Acid Sequence↗
PubMed1984

Nucleotide sequence of the respiratory D-lactate dehydrogenase gene of Escherichia coli.

The structural gene for the respiratory D-lactate dehydrogenase of Escherichia coli, a membrane-bound flavoenzyme, has been subcloned from a 7 X 10(3)-base-pair chromosomal HindIII fragment containing the gene [Young, I. G., Jaworowski, A., and Poulis, M. (1982) Biochemistry 21, 2092-2095]. The complete nucleotide sequence of the 2340-base-pair PstI-SmaI subclone has been determined on both strands by the dideoxy chain termination method. A single large open reading frame is present in the nucleotide sequence. The reading frame is preceded by a good ribosome binding site and numerous possible promoter sequences, and is followed by a typical rho-independent termination sequence. The reading frame predicts that the D-lactate dehydrogenase polypeptide consists of 571 amino acids (including the initiating methionine residue) with Mr = 64613. The protein does not have a low overall polarity, nor does it contain unusually hydrophobic stretches. It appears to contain a short repeat which is homologous with the well characterized L-lactate dehydrogenases in the vicinity of the 'essential' cysteine residue. Apart from this, homology with other proteins of known sequence has not been detected.

Amino Acid Sequence↗
PubMed1985

The sequence of 967 amino acids at the carboxyl-end of rat thyroglobulin. Location and surroundings of two thyroxine-forming sites.

The entire rat thyroglobulin mRNA sequence (about 8500 nucleotides) has been cloned in five recombinant plasmids containing overlapping cDNA inserts. The 3' end of the mRNA is precisely defined by the poly (A) tail found in the furthest 3' end clone. Evidence that most of the 5' end is cloned come from size considerations and from a primer extension experiment. At the 3' end of the mRNA only one long open reading frame is present in the sequence of 3018 nucleotides that has been established. In the deduced protein sequence we have localized two thyroxine-forming sites in a region containing a high concentration of tyrosine residues.

Amino Acid Sequence↗
PubMed1985

Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species.

The nucleotide sequences of the 5S ribosomal RNAs of the bacteria Agrobacterium tumefaciens, Alcaligenes faecalis, Pseudomonas cepacia, Aquaspirillum serpens and Acinetobacter calcoaceticus have been determined. The sequences fit in a generally accepted model for 5S RNA secondary structure. However, a closer comparative examination of these and other bacterial 5S RNA primary structures reveals the potential of additional base pairing and of multiple equilibria between a set of slightly different alternative secondary structures in one area of the molecule. The phylogenetic position of the examined bacteria is derived from a 5S RNA sequence alignment by a clustering method and compared with the position derived on the basis of 16S ribosomal RNA oligonucleotide catalogs.

Bacteria↗