Biochemical Characterization of Uracil-DNA Glycosylase from Pyrococcus furiosus

We report the characterization of a uracil-DNA glycosylase（UDG） from the hyperthermophilic archaea Pyrococcus furiosus（P, furiosus）. P. furiosus UDG（PfUDG） has high sequence similarity to the families IV and V UDGs（thermostable UDG family and PaUDG-b family）. PfUDG excises uracil from various DNA substrates with the following order： U/T=U/C〉U/G=U/AP=U/-〉U/U=U/I=U/A. The optimal temperature and pH value for uracil exci- sion by PfUDG are 70 ℃ and 9.0, respectively. The removal of U is inhibited by the divalent ions of Fe, Ca, Zn, Cu, Co, Ni and Mn, as well as a high concentration of NaC1. The phosphorothioates near uracil strongly inhibit the exci- sion of uracil by PfUDG. Interestingly, pfuDNA（Pyrococcusfuriosus DNA） polymerase, which tightly binds the ura- cil-carrying oligonucleotide, does not inhibit the excision by Pfl.IDG, suggesting PfUDG in vivo functions as the re- pair enzyme to excise uracil damage in genome.

Helical Repeats of Left-Handed DNA

DNA is generally assumed as a right-handed double helix and Z-DNA is a special kind of left-handed DNA infrequently found in nature. However, the finding of a zero linking number topoisomer supports a hypothesis that the two strands of DNA are winding ambidextrously, rather than plectonemically. It logically leads to a notion that the left-handed DNA is as common as right-handed DNA and the amount of left-handed DNA in a positively supercoiled plasmid prevails that of the right-handed DNA. In this report, the helical repeat of left-handed DNA, 12 bp per turn, was determined by a new method. How the positively supercoiled DNA was generated in hyperthermophiles and why their DNA can withstand the extreme high temperature are answered from an alternative theory.

Core Metabolic Features and Hot Origin of Bathyarchaeota

The archaeal phylum Bathyarchaeota comprises highly diversified subgroups and is considered to be one of the most abundant microorganisms on earth. The metabolic features and evolution of this phylum still remain largely unknown. In this article, a comparative metabolic analysis of 15 newly reconstructed and 36 published metagenomic assembled genomes (MAGs) spanning 10 subgroups was performed, revealing the core metabolic features of Bathyarchaeota—namely, protein, lipid, and benzoate degradation;glycolysis;and the Wood–Ljungdahl (WL) pathway, indicating an acetyl-CoA-centralized metabolism within this phylum. Furthermore, a partial tricarboxylic acid (TCA) cycle, acetogenesis, and sulfur-related metabolic pathways were found in specific subgroups, suggesting versatile metabolic capabilities and ecological functions of different subgroups. Intriguingly, most of the MAGs from the Bathy-21 and -22 subgroups, which are placed at the phylogenetic root of all bathyarchaeotal lineages and likely represent the ancient Bathyarchaeota types, were found in hydrothermal environments and encoded reverse gyrase, suggesting a hyperthermophilic feature. This work reveals the core metabolic features of Bathyarchaeota, and indicates a hot origin of this archaeal phylum.

Denaturing Effects of Urea and Guanidine Hydrochloride on Hyperthermophilic Esterase from Aeropyrum pernix K1

The changes in the activity and the conformation of the hyperthermophilic esterase derived from aerobic thermophilic Aeropyrum pernix K1 （ APE1547 ） were studied during denaturation by guanidine hydrochlofide （ GdnHC1 ） and urea. The denaturation course of APE1547 was followed by the steady-state and time resolved fluorescence methods. An increase in the denaturant concentration in the denatured system can significantly enhance the inactivation and unfolding of APE1547. The enzyme can be completely inactivated with a urea concentration of 2.7 mol/L or a GdnHCl concentration of 7.5 mol/L. The fluorescence emission maximum of the enzyme protein red shifts in magnitude to a maximum value（355 nm） when the concentration of GdnHCl is 5.1 mol/L. The experimental results indicate that APE1547 has a high resistance to urea. Unfolding of APE1547 in GdnHCI（4. 2-6.0 mol/L） was shown to be an irreversible process. The present results indicate that the ion pairs in this protein may be a key factor for the stability of this esterase.

High-throughput Screening of the Enantioselectivity of Hyperthermophilic Mutant Esterases from Archaeon Aeropyrum pernix K1 for Resolution of (R,S)-2-Octanol Acetate

To identify the desired hypertherrnophilic variants within a mutant esterase library for the resolution of （R, S）-2- octanol acetate, a simple, reliable, and versatile method was developed in this study. We built a screening strategy including two steps, first we selected agar plate with substrate to screen the enzymatic activity; secondly we used a pH indicator to screen the enantioselectivity. This method could rapidly detect favorable mutants with high activity and enantioselectivity. A total of 96. 2% of tedious screening work can be precluded using this screening strategy. It is an effective screening for alkyl ester and can be applied to relative screening researches. The four improved mutants were screened from the mutant esterase library. Their enantioselectivities, activities, and structures were investigated at different temperatures.

Study on a Specific Site Tyr^(444) on a Hyperthermophilic Enzyme APE1547

Hyperthermophilic enzyme APE1547 is an extremely thermostable recombinant protein from thermophilic archaeon Aeropyrumpernix K1. The Tyr444 located in the catalytic domain adjacent to the catalytic amino acid Ser445 and formed hydrogen bond with Ile567. To study the effect of Tyr444 on the activity of APE1547, site-directed mutagenesis was applied. Two mutant enzymes T444S and T444G were created. Comparison of the mutant enzymes with wide enzyme, the thermostability of mutants T444S and T444G decreased by 10%-20%, but the catalytic efficiency of mutants toward pNPC8 and Ac-Leu-pNA increased 1.33 and 1.75 fold respectively. Molecular modeling shows that the elimination of hydrogen bond between Tyr444 and Ile567 is the cause of the decrease in thermostability and increase in catalytic efficiency. These observations suggest that Tyr444 plays an important role in the catalytic ability and thermostability of this enzyme.

Molecular Basis for Stereospecific Hydrolysis of Ethyl Mandelate by Thermophilic Esterase

The stereospecific hydrolysis of mandelate can be effectively catalyzed by hyperthermophilic acylpeptide esterase APE 1547（Aeropyrum pernix esterase 1547）. APE 1547 used in this reaction showed a remarkable stereodi-scrimination in favour of R-mandelic acid（99% e.e.） with an enantiomeric ratio E〉200. The results of computer simulation are consistent with the experimental results. It can be inferred that the R-substrate adopted a binding mode productive of the reaction due to the formation of the hydrogen bond at the active site of APE 1547.

Statistical Optimization of Medium Components for Improved Product Ion of Recombinant Hyperthermophilic Esterase

The optimization of nutrient levels for the production of recombinant hyperthermophilie esterase by E. coli was carried out with response surface methodology（RSM） based on the central composite rotatable design（CCRD）. A 24 central composite rotatable design was used to study the combined effect of the nutritional constituents like yeast extract, peptone, mineral salt and trace metals. The P-value of the coefficient for the linear effect of peptone concentration was 0. 0081 and trace metals solution was less than 0. 0001, suggesting that these were the principal variables with significant effect on the hyperthermophilic esterase production. The predicted optimal hyperthermophilie esterase yield was 269. 17 U/mL, whereas an actual experimental value of 284. 58 U/mL was obtained.

A novel alcohol dehydrogenase in the hyperthermophilic crenarchaeon Hyperthermus butylicus

Hyperthermus butylicus is a hyperthermophilic crenarchaeon that produces 1-butanol as an end product.A thermostable alcohol dehydrogenase(ADH)must be present in H.butylicus to act as the key enzyme responsible for this production;however,the gene that encodes the ADH has not yet been identified.A novel ADH,HbADH2,was purified from a cell-free extract of H.butylicus,and its characteristics were determined.The gene that encodes HbADH2 was demonstrated to be HBUT_RS04850 and annotated as a hypothetical protein in H.butylicus.HbADH2 was found to be a primary-secondary ADH capable of using a wide range of substrates,including butyraldehyde and butanol.Butyraldehyde had the highest specificity constant,calculated as k_(cat)/K_(m),with kcat and apparent K_(m) values of 8.00±0.22 s^(-1) and 0.59±0.07 mM,respectively.The apparent Km values for other substrates,including ethanol,1-propanol,2-propanol,butanol,acetaldehyde,propanal,and acetone,were 4.36±0.42,4.69±0.41,3.74±0.46,2.44±0.30,1.27±0.18,1.55±0.20,and 0.68±0.04 mM,respectively.The optimal pH values for catalyzing aldehyde reduction and alcohol oxidation were 6.0 and 9.0,respectively,while the optimal temperature was higher than 90°C due to the increase in enzymatic activity from 60℃ to 90℃.Based on its substrate specificity,enzyme kinetics,and thermostability,HbADH2 may be the ADH that catalyzes the production of 1-butanol in H.butylicus.The putative conserved motif sites for NAD(P)^(+)and iron binding were identified by aligning HbADH2 with previously characterized Fe-containing ADHs.

Rapid progress of DNA replication studies in Archaea,the third domain of life

Archaea,the third domain of life,are interesting organisms to study from the aspects of molecular and evolutionary biology.Archaeal cells have a unicellular ultrastructure without a nucleus,resembling bacterial cells,but the proteins involved in genetic information processing pathways,including DNA replication,transcription,and translation,share strong similarities with those of Eukaryota.Therefore,archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells.Moreover,the hyperthermophilic archaea provide very stable proteins,which are especially useful for the isolation of replisomal multicomplexes,to analyze their structures and functions.This review focuses on the history,current status,and future directions of archaeal DNA replication studies.

Effect of DNA binding protein Ssh12 from hyperthermophilic archaeon Sulfolobus shibatae on DNA supercoiling

An 11.5-ku DNA binding protein, designated as Sshl2, was purified from the hyperthermophilic archaeon Sulfolobus shibatae by column chromatography in SP Sepharose, DNA cellulose and phosphocellulose. Sshl2 accounts for about 4 % of the total cellular protein. The protein is capable of binding to both negatively supercoiled and relaxed DNAs. Nick closure analysis revealed that Sshl2 constrains negative supercoils upon binding to DNA. While the ability of the protein to constrain supercoils is weak at 22℃ , it is enhanced substantially at temperatures higher than 37℃ . Both the cellular content and supercoil-constraining ability of Sshl2 suggest that the protein may play an important role in the organization and stabilization of the chromosome of S. shibatae.

Deletion of the topoisomeraseⅢgene in the hyperthermophilic archaeon Sulfolobus islandicus results in slow growth and defects in cell cycle control

Topoisomerase III （topo III）, a type IA topoisomerase, is widespread in hyperthermophilic archaea. In order to interrogate the in vivo role of archaeal topo III, we constructed and characterized a topo III gene deletion mutant of Sulfolobus islandicus. The mutant was ,viable but grew more slowly than the wild-type strain, especially in a nutrient-poor medium. Flow cytometry analysis revealed changes of the mutant in growth cycle characteristics including an increase in proportion of cells containing either more than two genome equivalents or less than one genome equivalent in exponentially-growing cultures. As shown by fluorescence microscopy, a fraction of mutant cells in the cultures were drastically enlarged, and at least some of the enlarged cells were apparently capable of resuming cell division. The mutant also shows a different tran- scriptional profile from that of the wild-type strain. Our results suggest that the enzyme may serve roles in chromosomal segregation and control of the level of supercoiling in the cell.

Induction of the Sulfolobus shibatae virus SSV1 DNA replication by mitomycin C

The temperate virus SSV1 from the hyper-thermophilic archaeon Sulfolobus shibatae provides a useful model system for the study of archaeal DNA replication. Southern hybridization showed that SSV1 existed primarily as a provirus in its host that was grown without shaking. Upon UV or mitomycin C induction, the cellular level of free SSV1 DNA increased drastically whereas that of integrated viral DNA remained unchanged. The results of mitomycin C induction were more reproducible than those of UV induction. We found that, when the cells that had been grown without shaking were shaken, the replication of SSV1 DNA was also induced. Based on our results, we developed a method for the induction of SSY1 DNA replication by mitomycin C. When the S. shibatae virus production was induced using this method, the cellular level of free SSV1 DNA started to increase 10 h after induction, and peaked after 12-15 h. A fully induced S. shibatae cell contained -50 molecules of free SSV1 DNA. The development of this induction

Evolutionary conservation and DNA binding properties of the Ssh7 proteins from Sulfolobus shibatae

The thermoacidophilic archaeon Sulfolobus shibatae synthesizes a large amount of the 7-ku DMA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S. shibatae. These two genes, designated ssh7a and ssh7b, have been cloned, sequenced and expressed in Escherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, the c/s-regulatory sequences of the ssh7a and ssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein in Sulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation of Sulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DNA fragments was analyzed by electrophoretic mobility shift assays. Both native and recombinant forms of the protein behaved in a similar fashion in the assays, suggesting that the interaction of Ssh7 with DNA is not affected either by specific lysine methylation found in the native Ssh7 proteins or by the difference between the two Ssh7 isomers in amino acid sequence. Our data show that Ssh7 binds duplex DNA fragments with a binding size of - 6.6 base pairs and an apparent dissociation constant of (0.7-1.0)×10-7 mol/L under the assay conditions employed in the present study. In addition, Ssh7 binds more tightly to negatively supercoiled DNA than to linear or relaxed DNA.