Hyperthermophiles in the history of life

Today, hyperthermophilic ('superheat-loving') bacteria and archaea are found within high-temperature environments, representing the upper temperature border of life. They grow optimally above 80 degrees C and exhibit an upper temperature border of growth up to 113 degrees C. Members of the genera, Pyrodictium and Pyrolobus, survive at least 1h of autoclaving. In their basically anaerobic environments, hyperthermophiles (HT) gain energy by inorganic redox reactions employing compounds like molecular hydrogen, carbon dioxide, sulphur and ferric and ferrous iron. Based on their growth requirements, HT could have existed already on the early Earth about 3.9Gyr ago. In agreement, within the phylogenetic tree of life, they occupy all the short deep branches closest to the root. The earliest archaeal phylogenetic lineage is represented by the extremely tiny members of the novel kingdom of Nanoarchaeota, which thrive in submarine hot vents. HT are very tough survivors, even in deep-freezing at -140 degrees C. Therefore, during impact ejecta, they could have been successfully transferred to other planets and moons through the coldness of space.     

Large-Scale Cultivation of Acidophilic Hyperthermophiles for Recovery of Secreted Proteins

An electric water heater was modified for large-scale cultivation of aerobic acidophilic hyperthermophiles to enable recovery of secreted proteins. Critical changes included thermostat replacement, redesign of the temperature control circuit, and removal of the cathodic anticorrosion system. These alterations provided accurate temperature and pH control. The bioreactor was used to cultivate selected strains of the archaeon Sulfolobus solfataricus and other species within this genus. Reformulation of a basal salts medium facilitated preparation of large culture volumes and eliminated sterilization-induced precipitation of medium components. Substrate induction of synthesis of the S. solfataricus-secreted alpha-amylase during growth in a defined medium supported the utility of the bioreactor for studies of physiologically regulated processes. An improved purification strategy was developed by using strong cation-exchange chromatography for recovery of the alpha-amylase and the processing of large sample volumes of acidic culture supernatant. These findings should simplify efforts to study acidophilic hyperthermophilic microbes and their secreted proteins.     

Hyperthermophiles and the problem of DNA instability

Rates of chemical decomposition of DNA at the optimal growth temperatures of hyperthermophiles seem incongruent with the requirements of accurate genome replication. The peculiar physiology, ecology and phylogeny of hyperthermophiles combine to suggest that these prokaryotes have solved a molecular problem (spontaneous loss of native DNA structure) of a magnitude that well-studied microorganisms do not face. The failure of DNA base composition to correlate with optimal growth temperature among hyperthermophiles provides indirect evidence that other mechanisms maintain their chromosomal DNA in the duplex form. Studies in vitro indicate that DNA primary structure is more difficult to maintain at extremely high temperature than is secondary structure, yet hyperthermophiles exhibit only modest levels of spontaneous mutation. Radiation sensitivity studies also indicate that hyperthermophiles repair their DNA efficiently in vivo , and underlying mechanisms are beginning to be examined. Several enzymes of DNA metabolism from hyperthermophilic archaea exhibit unusual biochemical features that may ultimately prove relevant to DNA repair. However, genomic sequencing results suggest that many DNA repair genes of hyperthermophilic archaea may not be recognized because they are not sufficiently related to those of well-studied organisms.     

Approaches To New Vaccines

ABSTRACT:?

The explosive technological advances in the fields of immunology and molecular biology in the last 5 years had an enormous impact on the identification of candidate vaccines against diseases, which until a few years ago seemed uncontrollable. Increased knowledge of the immune system has helped to define the mechanisms that underlie successful immunization and is now being exploited to develop improved versions of existing vaccines and new vaccines against emerging pathogens, tumors, or autoimmune diseases. An understanding of the mechanisms of action of novel adjuvants and the development of new vector and delivery systems will have a major impact on vaccine strategies. The use of DNA encoding antigens from pathogenic viruses, bacteria, and parasites as vaccines is a new approach that is receiving considerable attention. This and other innovative approaches, including vaccine production in plants, are appraised in this review. The successful eradication of smallpox and the imminent eradication of poliomyelitis by worldwide immunization campaigns provide positive examples of how the vaccine-mediated approach can lead to disease elimination; with the advent of new vaccines and improved delivery systems, there is no scientific reason why these successes cannot be repeated.     

New Approaches to Principal Component Analysis for Trees

Object Oriented Data Analysis is a new area in statistics that studies populations of general data objects. In this article we consider populations of tree-structured objects as our focus of interest. We develop improved analysis tools for data lying in a binary tree space analogous to classical Principal Component Analysis methods in Euclidean space. Our extensions of PCA are analogs of one dimensional subspaces that best fit the data. Previous work was based on the notion of tree-lines.     

The Archaeology of City-States: Cross Cultural Approaches

The Archaeology of City-States: Cross Cultural Approaches. Deborah L. Nichols and Thomas H. Charlton. eds. Washington, DC: Smithsonian Institution Press, 1997. 335 pp.     

Microaerophilic growth of Wolinella recta ATCC 33238

Abstract The influence of oxygen on growth and fumarate-dependent respiration of Wolinella recta ATCC 33238 was studied in continuous culture. Steady states were obtained with formate-limited cultures grown at a specific growth rate of 0.1 h⁻¹ with different levels of oxygenation. The extent of aeration was regulated by means of a redox control system permitting reproducible cultivation at oxygen levels below the detection limit of conventional lead-silver probes. The ratio of succinate produced to that of formate consumed (Suc/For) decreased from 0.99 in strictly anaerobic cultures to 0.06–0.10 in aerated cultures. The growth yield did not change significantly with increasing redox readings: 4.9–5.2 g cell carbon/mol formate. The ability to use O₂ as the sole electron acceptor was demonstrated in a chemostat culture with formate as electron donor and succinate as carbon source. Washed cells from all chemostat cultures comsumed O₂ with formate as electron donor at a high rate (2.1–3.7 μmol/min per mg protein) and possessed b - and c -type cytochromes and CO-binding pigments. These results clearly indicated the microaerophilic nature of W. recta .     

Occurrence of 1-Glyceryl-1-myo-Inosityl Phosphate in Hyperthermophiles

The accumulation of compatible solutes was studied in the hyperthermophilic bacterium Aquifex pyrophilus as a function of the temperature and the NaCl concentration of the growth medium. Nuclear magnetic resonance analysis of cell extracts revealed the presence of α- and β-glutamate, di-mannosyl-di-myo-inositol phosphate, di-myo-inositol phosphate, and an additional compound here identified as 1-glyceryl-1-myo-inosityl phosphate. All solutes accumulated by A. pyrophilus are negatively charged at physiological pH. The intracellular levels of di-myo-inositol phosphate increased in response to supraoptimal growth temperature, while α- and β-glutamate accumulated in response to osmotic stress, especially at growth temperatures below the optimum. The newly discovered compound, 1-glyceryl-1-myo-inosityl phosphate, appears to play a double role in osmo- and thermoprotection, since its intracellular pool increased primarily in response to a combination of osmotic and heat stresses. This work also uncovered the nature of the unknown compound, previously detected in Archaeoglobus fulgidus (L. O. Martins et al., Appl. Environ. Microbiol. 63:896-902, 1997). The curious structural relationship between diglycerol phosphate (found only in Archaeoglobus species), di-myo-inositol phosphate (a canonical solute of hyperthermophiles), and the newly identified solute is highlighted. This is the first report on the occurrence of 1-glyceryl-1-myo-inosityl phosphate in living systems.     

极端嗜热微生物及其高温适应机制的研究进展

极端嗜热微生物在高温条件下生长繁殖,其必然具有适应高温环境的特殊细胞结构、基因类型以及生理生化机制。极端嗜热微生物的研究对探索生命的起源以及极端嗜热微生物的开发和应用具有重要意义。对极端嗜热微生物中细胞膜、核酸分子、蛋白质分子、代谢产物和辅酶的高温适应机制的研究进展进行了概述,旨为极端嗜热微生物以及来源于极端嗜热微生物的各种生物分子的开发和应用提供理论依据。     

Boranophosphate Oligonucleotides: New Synthetic Approaches

Abstract

Recently our laboratory reported a new backbone-modified class of oligonucleotides, with a borane (B₃3?) group replacing one of the non-bridging oxygen atoms. Here we present two new approaches to synthesize the boranophosphate oligonucleotides. All-stereoregular boranophosphate oligonucleotides can be prepared by enzymatic template extension reactions using nucleoside a-boranotriphosphates, which are good substrates for a number of polymerases. Larger scale synthesis of boranophosphate oligonucleotides can be carried out by effective chemical synthesis using the H-phosphonate approach, instead of previously used phosphoramidite methodology. The main advantage of H-phosphonate methodology is the ability to carry out one boronation reaction, after oligonucleotide chain elongation has been completed, using mild conditions without base damage and producing the desired boranophosphate oligonucleotides in high yield.     

Nitrate Dissimilation Under Microaerophilic Conditions by a Magnetic Spirillum

During microaerophilic growth of magnetic spirillum MS-1 on tartrate and nitrate, a maximal cell density was obtained at an initial oxygen partial pressure of 17 Pa. A transient accumulation of nitrous oxide and a 1:2 (mol/mol) stoichiometry between tartrate oxidation and nitrate reduction were observed, indicating that the organism carried out a respiratory type of metabolism.     

The Universal Ancestor and the Ancestor of Bacteria Were Hyperthermophiles

The definition of the node of the last universal common ancestor (LUCA) is justified in a topology of the unrooted universal tree. This definition allows previous analyses based on paralogous proteins to be extended to orthologous ones. In particular, the use of a thermophily index (based on the amino acids propensity to enter the [hyper] thermophile proteins more frequently) and its correlation with the optimal growth temperature of the various organisms allow inferences to be made on the habitat in which the LUCA lived. The reconstruction of ancestral sequences by means of the maximum likelihood method and their attribution to the set of mesophilic or hyperthermophilic sequences have led to the following conclusions: the LUCA was a hyperthermophile organism, as were the ancestors of the Archaea and Bacteria domains, while the ancestor of the Eukarya domain was a mesophile. These conclusions are independent of the presence of hyperthermophile bacteria in the sample of sequences used in the analysis and are therefore independent of whether or not these are the first lines of divergence in the Bacteria domain, as observed in the topology of the universal tree of ribosomal RNA. These conclusions are thus more easily understood under the hypothesis that the origin of life took place at a high temperature.     

Post-Viking Microbiology: New Approaches,New Data,New Insights

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.