Ancient Bacteria Research Articles

Steroids and ion channels in evolution: From bacteria to synapses and mind. Evolutionary role of steroid regulation of GABAA receptors

Ion channels are vital components of plasma membranes. This article presents an evolutionary view of the biochemical mechanism of controlling activity of ion channels by rigid lipids, such as steroids or biophysically similar molecules, which were instrumental in formation and control of ion channels in cell membranes at the very origin of life. Such regulatory mechanisms exist in all cellular forms of life from ancient bacteria to humans and participate in a diversity of biological functions, from the most basic, such as maintenance of cell shape, homeostasis, feeding, cell fusion, and reproduction to the most intricate, such as the mind. Learning about the regulation of membrane ion channels by steroids and like molecules is important for understanding the evolution of life and various aspects of cell and organism physiology, for unraveling the mysteries of mind, and for practical purposes such as developing new pharmacotherapies.

Ancient bacteria show evidence of DNA repair.

Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.

Barely alive: Ancient bacteria survive in the slow lane

Science NewsVolume 172, Issue 9 p. 131-132 This Week Barely alive: Ancient bacteria survive in the slow lane Brian Vastag, Brian VastagSearch for more papers by this author Brian Vastag, Brian VastagSearch for more papers by this author First published: 30 September 2009 https://doi.org/10.1002/scin.2007.5591720903AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume172, Issue91 September 2007Pages 131-132 RelatedInformation

A likely role for anoxygenic photosynthetic microbes in the formation of ancient stromatolites.

Although cyanobacteria are the dominant primary producers in modern stromatolites and other microbialites, the oldest stromatolites pre-date geochemical evidence for oxygenic photosynthesis and cyanobacteria in the rock record. As a step towards the development of laboratory models of stromatolite growth, we tested the potential of a metabolically ancient anoxygenic photosynthetic bacterium to build stromatolites. This organism, Rhodopseudomonas palustris, stimulates the precipitation of calcite in solutions already highly saturated with respect to calcium carbonate, and greatly facilitates the incorporation of carbonate grains into proto-lamina (i.e. crusts). The appreciable stimulation of the growth of proto-lamina by a nonfilamentous anoxygenic microbe suggests that similar microbes may have played a greater role in the formation of Archean stromatolites than previously assumed.

Hyperthermostable and oxygen resistant hydrogenases from a hyperthermophilic bacterium Aquifex aeolicus: Physicochemical properties

The discovery of hydrogenases in hyperthermophiles has important ramifications not only in microbial physiology and evolution but also in biotechnologies. These organisms are the source of extremely stable enzymes (regarding temperature, pressure, and O 2 ). Aquifex aeolicus is a microaerophilic, hyperthermophilic bacterium containing three [NiFe] hydrogenases. It is the most hyperthermophilic bacterium known to date and grows at 85 °C under a H 2 / CO 2 / O 2 atmosphere. The Aquificales represent the earliest branching order of the bacterial domain indicating that they are the most ancient bacteria. Two Aquifex hydrogenases (one membrane-bound and one soluble) have been purified and characterized. In contrast to the majority of the [NiFe] hydrogenases, the hydrogenases from A. aeolicus are rather tolerant to oxygen. The molecular basis of the oxygen resistance of Aquifex hydrogenases has been investigated. The great stability of Aquifex hydrogenases with respect to oxygen and high temperatures make these enzymes good candidates for biotechnological uses.

Bacterial Symbionts May Prove a Double-Edged Sword for the Sharpshooter

Bacterial Symbionts May Prove a Double-Edged Sword for the Sharpshooter

La paléomicrobiologie

The objective of Paleomicrobiology which forms part of microbiology, is to establish microbial diagnosis of ancient infectious diseases. One can consider the adjective “ancient” as devoted to specimens preceding microbial identification as developed at the end of XIX th century. Ancient microorganisms can be detected in environment samples as well as in “ancient” human samples. Skeletons constitute the major source of human material containing potentially ancient bacteria and we have shown that dental pulp, protected in dental cavities in skeletons, forms a particularly interesting material for identification of ancient bacteraemic agents. Molecular biology methods are the best current approach for detection of microorganisms in ancient specimens. Ancient tuberculosis has given rise to the most frequent published studies, and we have contributed to the diagnosis of ancient plague by using new original methods such as “suicide” PCR, and an original genotypic technique, the Multi Spacer Typing (MST).

DNA similarity analysis of a putative ancient bacterial isolate obtained from amber

Bacterial isolate BCA16, a putatively ancient bacterium apparently recovered from the abdominal contents of an insect preserved in amber, was identified by DNA similarity analysis as belonging to similarity group III of the Bacillus sphaericus complex. Thus, it is closely related to strains of this species frequently isolated from soil. Although some strains of B. sphaericus are pathogenic for mosquito larvae, isolate BCA16 is nonpathogenic.

Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution

The editing reactions catalyzed by aminoacyl-tRNA synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated tRNAs. We report that the isolated editing domain of leucyl-tRNA synthetase from the deep-rooted bacterium Aquifex aeolicus (alphabeta-LeuRS) catalyzes the hydrolytic editing of both mischarged tRNA(Leu) and minihelix(Leu). Within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when transplanted into the inactive Escherichia coli LeuRS editing domain. Likewise, fusion of the beta-subunit of alphabeta-LeuRS to the E. coli editing domain activates its editing function. These results suggest that alphabeta-LeuRS still carries the basic features from a primitive synthetase molecule. It has a remarkable capacity to transfer autonomous active modules, which is consistent with the idea that modern synthetases arose after exchange of small idiosyncratic domains. It also has a unique alphabeta-heterodimeric structure with separated catalytic and tRNA-binding sites. Such an organization supports the tRNA/synthetase coevolution theory that predicts sequential addition of tRNA and synthetase domains.

Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria

Past studies of cold-acclimated bacteria have focused primarily on organisms not capable of sub-zero growth. Siberian permafrost isolates Exiguobacterium sp. 255-15 and Psychrobacter sp. 273-4, which grow at subzero temperatures, were used to study cold-acclimated physiology. Changes in membrane composition and exopolysaccharides were defined as a function of growth at 24, 4 and −2.5 °C in the presence and absence of 5% NaCl. As expected, there was a decrease in fatty acid saturation and chain length at the colder temperatures and a further decrease in the degree of saturation at higher osmolarity. A shift in carbon source utilization and antibiotic resistance occurred at 4 versus 24 °C growth, perhaps due to changes in the membrane transport. Some carbon substrates were used uniquely at 4 °C and, in general, increased antibiotic sensitivity was observed at 4 °C. All the permafrost strains tested were resistant to long-term freezing (1 year) and were not particularly unique in their UVC tolerance. Most of the tested isolates had moderate ice nucleation activity, and particularly interesting was the fact that the Gram-positive Exiguobacterium showed some soluble ice nucleation activity. In general the features measured suggest that the Siberian organisms have adapted to the conditions of long-term freezing at least for the temperatures of the Kolyma region which are −10 to −12 °C where intracellular water is likely not frozen.

Isolation, free-living capacities, and genome structure of "Candidatus Glomeribacter gigasporarum," the endocellular bacterium of the mycorrhizal fungus Gigaspora margarita.

"Candidatus Glomeribacter gigasporarum" is an endocellular beta-proteobacterium present in the arbuscular mycorrhizal (AM) fungus Gigaspora margarita. We established a protocol to isolate "Ca. Glomeribacter gigasporarum" from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. They are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. Isolated bacteria could not be grown in any of the 19 culture media tested, but they could be kept alive for up to 4 weeks. PCR-based investigations of purified DNA from isolated bacteria did not confirm the presence of all genes previously assigned to "Ca. Glomeribacter gigasporarum." In particular, the presence of nif genes could not be detected. Pulsed-field gel electrophoresis analyses allowed us to estimate the genome size of "Ca. Glomeribacter gigasporarum" to approximately 1.4 Mb with a ca. 750-kb chromosome and a 600- to 650-kb plasmid. This is the smallest genome known for a beta-proteobacterium. Such small genome sizes are typically found in endocellular bacteria living permanently in their host. Altogether, our data suggest that "Ca. Glomeribacter gigasporarum" is an ancient obligate endocellular bacterium of the AM fungus G. margarita.

Methylhopanoids: Molecular indicators of ancient bacteria and a petroleum correlation tool

Methylhopanoids are organic compounds synthesized by certain bacteria, that when preserved in sediments act as molecular fossils or biomarkers for organic matter inputs from specific bacterial sources. Two series of methylhopanoids occur, each mainly deriving from a distinct bacterial source: cyanobacteria (2-methyl) and methanotrophic bacteria (3-methyl). The abundance and composition of methylhopanoids within sediments of modern depositional environments varies widely, apparently due to different bacterial communities contributing to the sedimentary organic matter. Comparable molecular characteristics are found in oils and their source rocks. Consequently, methylhopanoids are valuable in oil-oil and oil-source rock correlations, distinguishing between samples related to different depositional environments. In particular, abundant 3β-methylhopanoids (from methanotrophic bacteria or an additional unknown bacterial source) are characteristic of some modern alkaline saline lake environments. Comparable compositional features in the methylhopanes of oils allow the assignment of lacustrine oils offshore West Africa to two distinct lacustrine source rock facies, and to distinguish between different marine source facies, thus refining oil-source rock correlation.

Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans.

N-acylamino acid racemase (NAAAR) catalyzes the racemization of N-acylamino acids and can be used in concert with an aminoacylase to produce enantiopure alpha-amino acids, a process that has potential industrial applications. Here we have cloned and characterized an NAAAR homologue from a radiation-resistant ancient bacterium, Deinococcus radiodurans. The expressed NAAAR racemized various substrates at an optimal temperature of 60 degrees C and had Km values of 24.8 mM and 12.3 mM for N-acetyl-D-methionine and N-acetyl-L-methionine, respectively. The crystal structure of NAAAR was solved to 1.3 A resolution using multiwavelength anomalous dispersion (MAD) methods. The structure consists of a homooctamer in which each subunit has an architecture characteristic of enolases with a capping domain and a (beta/alpha)7 beta barrel domain. The NAAAR.Mg2+ and NAAAR.N-acetyl-L-glutamine.Mg2+ structures were also determined, allowing us to define the Lys170-Asp195-Glu220-Asp245-Lys269 framework for catalyzing 1,1-proton exchange of N-acylamino acids. Four subsites enclosing the substrate are identified: catalytic site, metal-binding site, side-chain-binding region, and a flexible lid region. The high conservation of catalytic and metal-binding sites in different enolases reflects the essentiality of a common catalytic platform, allowing these enzymes to robustly abstract alpha-protons of various carboxylate substrates efficiently. The other subsites involved in substrate recognition are less conserved, suggesting that divergent evolution has led to functionally distinct enzymes.

Binding to pyruvylated compounds as an ancestral mechanism to anchor the outer envelope in primitive bacteria.

Electron microscopy of isolated cell walls of the ancient bacterium Thermus thermophilus revealed that most of the peptidoglycan (PG) surface, apart from the septal region, was shielded against specific alphaPG antibodies. On the other hand, an antiserum raised against S-layer-attached cell wall fragments (alphaSAC) bound to most of the surface except for the septal regions. Treatments with alpha-amylase and pronase E made the entire cell wall surface uniformly accessible to alphaPG and severely decreased the binding of alphaSAC. We concluded that a layer of strongly bound secondary cell wall polymers (SCWPs) covers most of the cell wall surface in this ancient bacterium. A preliminary analysis revealed that such SCWPs constitute 14% of the cell wall and are essentially composed of sugars. Enzyme treatments of the cell walls revealed that SCWP was required in vitro for the binding of the S-layer protein through the S-layer homology (SLH) motif. The csaB gene was necessary for the attachment of the S-layer-outer membrane (OM) complex to the cell wall in growing cells of T. thermophilus. In vitro experiments confirmed that cell walls from a csaB mutant bound to the S-layer with a much lower affinity ( approximately 1/10) than that of the wild type. CsaB was found to be required for pyruvylation of components of the SCWP and for immunodetection with alpha-SAC antiserum. Therefore, the S-layer-OM complex of T. thermophilus binds to the cell wall through the SLH motif of the S-layer protein via a strong interaction with a highly immunogenic pyruvylated component of the SCWP. Immuno-cross-reactive compounds were detected with alphaSAC on cell walls of other Thermus spp. and in the phylogenetically related microorganism Deinococcus radiodurans. These results imply that the interaction between the SLH motif and pyruvylated components of the cell wall arose early during bacterial evolution as an ancestral mechanism for anchoring proteins and outer membranes to the cell walls of primitive bacteria.

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.

Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55-65 degrees C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria, the distribution of thermophily in derived bacterial lineages, the inferred G + C content of ancient ribosomal RNA, and the geological record combined with assumptions concerning molecular clocks. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.

Using thermal inactivation kinetics to calculate the probability of extreme spore longevity: implications for paleomicrobiology and lithopanspermia.

Thermal inactivation kinetics with extrapolation were used to model the survival probabilities of spores of various Bacillus species over time periods of millions of years at the historical ambient temperatures (25-40 degrees C) encountered within the 250 million-year-old Salado formation, from which the putative ancient spore-forming bacterium Salibacillus marismortui strain 2-9-3 was recovered. The model indicated extremely low-to-moderate survival probabilities for spores of mesophiles. but surprisingly high survival probabilities for thermophilic spores. The significance of the results are discussed in terms of the survival probabilities of (i) terrestrial spores in ancient geologic samples and (ii) spores transported between planets within impact ejecta.

Low stability for monomeric human chaperonin protein 10: interprotein interactions contribute majority of oligomer stability

Co-chaperonin protein 10 (cpn10, GroES in Escherichia coli) is a ring-shaped heptameric protein that facilitates substrate folding when in complex with cpn60 (GroEL in E. coli). The cpn10 from the hyperthermophilic, ancient bacterium Aquifex aeolicus (Aacpn10) has a 25-residue C-terminal extension in each monomer not found in any other cpn10 protein. Earlier in vitro work has shown that this tail is not needed for heptamer assembly or protein function. Without the tail, however, the heptamers (Aacpn10del-25) readily aggregate into fibrillar stacked rings. To explain this phenomenon, we performed binding experiments with a peptide construct of the tail to establish its specificity for Aacpn10del-25 and used cryo-electron microscopy to determine the three-dimensional (3D) structure of the GroEL–Aacpn10–ADP complex at an 8-Å resolution. We found that the GroEL–Aacpn10 structure is similar to the GroEL–GroES structure at this resolution, suggesting that Aacpn10 has molecular interactions with cpn60 similar to other cpn10s. The cryo-electron microscopy density map does not directly reveal the density of the Aacpn10 25-residue tail. However, the 3D statistical variance coefficient map computed from multiple 3D reconstructions with randomly selected particle images suggests that the tail is located at the Aacpn10 monomer–monomer interface and extends toward the cis-ring apical domain of GroEL. The tail at this location does not block the formation of a functional co-chaperonin/chaperonin complex but limits self-aggregation into linear fibrils at high temperatures. In addition, the 3D variance coefficient map identifies several regions inside the GroEL–Aacpn10 complex that have flexible conformations. This observation is in full agreement with the structural properties of an effective chaperonin.

Iron-Sulfur Cluster Biosynthesis: THERMATOGA MARITIMA IscU IS A STRUCTURED IRON-SULFUR CLUSTER ASSEMBLY PROTEIN

Genetic evidence has indicated that Isc proteins play an important role in iron-sulfur cluster biogenesis. In particular, IscU is believed to serve as a scaffold for the assembly of a nascent iron-sulfur cluster that is subsequently delivered to target iron-sulfur apoproteins. We report the characterization of an IscU from Thermatoga maritima, an evolutionarily ancient hyperthermophilic bacterium. The stabilizing influence of a D40A substitution allowed characterization of the holoprotein. Mössbauer (delta = 0.29 +/- 0.03 mm/s, DeltaE(Q) = 0.58 +/- 0.03 mm/s), UV-visible absorption, and circular dichroism studies of the D40A protein show that T. maritima IscU coordinates a [2Fe-2S]2+ cluster. Thermal denaturation experiments demonstrate that T. maritima IscU is a thermally stable protein with a thermally unstable cluster. This is also the first IscU type domain that is demonstrated to possess a high degree of secondary and tertiary structure. CD spectra indicate 36.7% alpha-helix, 13.1% antiparallel beta-sheet, 11.3% parallel beta-sheet, 20.2% beta-turn, and 19.1% other at 20 degrees C, with negligible spectral change observed at 70 degrees C. Cluster coordination also has no effect on the secondary structure of the protein. The dispersion of signals in 1H-15N heteronuclear single quantum correlation NMR spectra of wild type and D40A IscU supports the presence of significant tertiary structure for the apoprotein, consistent with a scaffolding role, and is in marked contrast to other low molecular weight Fe-S proteins where cofactor coordination is found to be necessary for proper protein folding. Consistent with the observed sequence homology and proposed conservation of function for IscU-type proteins, we demonstrate T. maritima IscU-mediated reconstitution of human apoferredoxin.

The question of uniqueness of ancient bacteria

The question of uniqueness of ancient bacteria

Martian water: are there extant halobacteria on Mars?

On Earth, life exists in all niches where water exists in liquid form for at least a portion of the year. On Mars, any liquid water would have to be a highly concentrated brine solution. It is likely, therefore, that any present-day Martian microorganisms would be similar to terrestrial halophiles. Even if present-day life does not exist on Mars, it is an interesting speculation that ancient bacteria preserved in salt deposits could be retrieved from an era when the climate of Mars was more conducive to life.