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Summary: Thermococcales, a major order of archaea inhabiting the iron‐ and sulfur‐rich anaerobic parts of hydrothermal deep‐sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS2 in iron–sulfur‐rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS2 in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero‐valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero‐valent sulfur, significant amounts of Fe3S4 greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non‐mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron‐sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high‐temperature hydrothermal environments. [ABSTRACT FROM AUTHOR]

Oligopeptide permease A (OppA) plays an important role in cell nutrition, uptake of cell wall peptides, and various signaling processes. In Thermococcales, OppA is a major protein present in membrane vesicles, suggesting that archaeal OppAs may be involved in processes other than peptide scavenging. No structural studies of archaeal OppAs have been reported to date. In this study, OppA of the thermophilic archaeon Thermococcus kodakaraensis was expressed in Escherichia coli and purified after a series of purification steps. According to mass spectrometry and N-terminal amino acid sequencing, the initial methionine of the purified protein was mainly processed. OppA mixed with the peptide bradykinin was crystallized by sitting-drop vapor-diffusion method. The crystal belonged to P212121 space group with the unit-cell parameters a = 84.06 Å, b = 109.62 Å, c = 75.07 Å. [ABSTRACT FROM AUTHOR]

Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB. [ABSTRACT FROM AUTHOR]

The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 - Sulfolobus islandicus rod-shaped virus 2, TPV1 - Thermococcus prieurii virus 1, and PAV1 - Pyrococcus abyssi virus 1). Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope) over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles. [ABSTRACT FROM AUTHOR]

The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. The earliest traces of life were preserved by the precipitation of silica on organic structures. The study of the in situ and experimental fossilisation of microorganisms allows better understanding of the fossilisation processes and helps identification of traces of life in ancient rocks. In a continuation of these studies, we present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 -- Sulfolobus islandicus Virus 2, TPV1 -- Thermococcus prieurii virus 1, and PAV1 -- Pyrococcus abyssi virus 1). Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope) over several months. However differences in the silicification process were noticed, depending on the viral structure and composition. The fossilisation mechanism is similar to that of the fossilisation of microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles. [ABSTRACT FROM AUTHOR]

We present here the 2.6Å resolution crystal structure of the pT26-6p protein, which is encoded by an ORF of the plasmid pT26-2, recently isolated from the hyperthermophilic archaeon, Thermococcus sp. 26,2. This large protein is present in all members of a new family of mobile elements that, beside pT26-2 include several virus-like elements integrated in the genomes of several Thermococcales and Methanococcales (phylum Euryarchaeota). Phylogenetic analysis suggested that this protein, together with its nearest neighbor (organized as an operon) have coevolved for a long time with the cellular hosts of the encoding mobile element. As the sequences of the N and C-terminal regions suggested a possible membrane association, a deletion construct (739 amino acids) was used for structural analysis. The structure consists of two very similar β-sheet domains with a new topology and a five helical bundle C-terminal domain. Each of these domains corresponds to a unique fold that has presently not been found in cellular proteins. This result supports the idea that proteins encoded by plasmid and viruses that have no cellular homologues could be a reservoir of new folds for structural genomic studies. [ABSTRACT FROM AUTHOR]

The effect of physiological concentrations of KCl and MgCl2 on the chemical stability of double-stranded and single-stranded DNA has been studied at temperatures typical for hyperthermophiles. These two salts protect both double and single-stranded DNA against heat-induced cleavage by inhibiting depurination. High KCl concentrations also protect DNA cleavage at apurinic sites, while high MgCl2 concentrations stimulate this cleavage. It has been previously proposed that salt protects double-stranded DNA against depurination by stabilizing the double helix. However, the inhibition of the depurination of single-stranded DNA by KCl and MgCl2 indicates that this effect is more probably due to a direct interaction of salts with purine nucleotides. These results suggest that the number and nature of heat-induced DNA lesions which have to be repaired might be quite different from one hyperthermophile to another, depending on their intracellular salt concentration. High salt concentrations might be also useful to protect DNA in long polymerase chain reaction (PCR) experiments and for long-term preservation. [ABSTRACT FROM AUTHOR]