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Journal articles on the topic 'Hyperthermophilic enzymes'

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Published: 4 June 2021

Last updated: 3 February 2022

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1

Vieille, Claire, and Gregory J. Zeikus. "Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability." Microbiology and Molecular Biology Reviews 65, no. 1 (March 1, 2001): 1–43. http://dx.doi.org/10.1128/mmbr.65.1.1-43.2001.

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SUMMARY Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of >80°C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.

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2

Sakuraba, Haruhiko, Kazunari Yoneda, Kumiko Yoshihara, Kyoko Satoh, Ryushi Kawakami, Yoshihiro Uto, Hideaki Tsuge, Katsuyuki Takahashi, Hitoshi Hori, and Toshihisa Ohshima. "Sequential Aldol Condensation Catalyzed by Hyperthermophilic 2-Deoxy-d-Ribose-5-Phosphate Aldolase." Applied and Environmental Microbiology 73, no. 22 (September 28, 2007): 7427–34. http://dx.doi.org/10.1128/aem.01101-07.

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ABSTRACT Genes encoding 2-deoxy-d-ribose-5-phosphate aldolase (DERA) homologues from two hyperthermophiles, the archaeon Pyrobaculum aerophilum and the bacterium Thermotoga maritima, were expressed individually in Escherichia coli, after which the structures and activities of the enzymes produced were characterized and compared with those of E. coli DERA. To our surprise, the two hyperthermophilic DERAs showed much greater catalysis of sequential aldol condensation using three acetaldehydes as substrates than the E. coli enzyme, even at a low temperature (25°C), although both enzymes showed much less 2-deoxy-d-ribose-5-phosphate synthetic activity. Both the enzymes were highly resistant to high concentrations of acetaldehyde and retained about 50% of their initial activities after a 20-h exposure to 300 mM acetaldehyde at 25°C, whereas the E. coli DERA was almost completely inactivated after a 2-h exposure under the same conditions. The structure of the P. aerophilum DERA was determined by X-ray crystallography to a resolution of 2.0 Å. The main chain coordinate of the P. aerophilum enzyme monomer was quite similar to those of the T. maritima and E. coli enzymes, whose crystal structures have already been solved. However, the quaternary structure of the hyperthermophilic enzymes was totally different from that of the E. coli DERA. The areas of the subunit-subunit interface in the dimer of the hyperthermophilic enzymes are much larger than that of the E. coli enzyme. This promotes the formation of the unique dimeric structure and strengthens the hydrophobic intersubunit interactions. These structural features are considered responsible for the extremely high stability of the hyperthermophilic DERAs.

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3

Littlechild, J. A., J. E. Guy, and M. N. Isupov. "Hyperthermophilic dehydrogenase enzymes." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 255–58. http://dx.doi.org/10.1042/bst0320255.

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Archaeal dehydrogenases are often found to be of a specific class of dehydrogenase which has low sequence identity to the equivalent bacterial and eukaryotic counterparts. This paper focuses on two different types of hyperthermophilic dehydrogenase enzyme that have been cloned and over-expressed in Escherichia coli. The crystallographic structures of the apo form of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) from Sulfolobus solfataricus and the related holo form of GAPDH from Methanothermus fervidus have been solved to high resolution. The zinc-containing structure of ADH (alcohol dehydrogenase) from Aeropyrum pernix has also been solved as a quaternary complex with the cofactor NADH and the inhibitor octanoic acid. The results show that despite the low sequence identity to the related enzymes found in other organisms the fold of the protein chain is similar. The archaeal GAPDH enzymes show a relocation of the active site which is a feature of evolutionary interest. The high thermostability of these three archaeal dehydrogenases can be attributed to a combination of factors including an increase in the number of salt bridges and hydrophobic interactions, a higher percentage of secondary structure and the presence of disulphide bonds.

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4

Pandey, Raj Kumar, Anupam Barh, Dinesh Chandra, Satish Chandra, Vishakha Pandey Pankaj, and Lakshmi Tewari. "Biotechnological Applications of Hyperthermophilic Enzymes." International Journal of Current Research and Academic Review 5, no. 3 (March 20, 2016): 39–47. http://dx.doi.org/10.20546/ijcrar.2016.403.005.

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5

IMANAKA, Tadayuki, and Shinsuke FUJIWARA. "Thermostable Enzymes of Hyperthermophilic Archaea." Journal of Japan Oil Chemists' Society 46, no. 5 (1997): 525–33. http://dx.doi.org/10.5650/jos1996.46.525.

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6

Adams, Michael W. W., and Robert M. Kelly. "Finding and using hyperthermophilic enzymes." Trends in Biotechnology 16, no. 8 (December 1998): 329–32. http://dx.doi.org/10.1016/s0167-7799(98)01193-7.

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7

Comfort, Donald A., Swapnil R. Chhabra, Shannon B. Conners, Chung-Jung Chou, Kevin L. Epting, Matthew R. Johnson, Kristen L. Jones, Amitabh C. Sehgal, and Robert M. Kelly. "Strategic biocatalysis with hyperthermophilic enzymes." Green Chemistry 6, no. 9 (2004): 459. http://dx.doi.org/10.1039/b406297c.

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8

Cowan, Don A. "Hyperthermophilic enzymes: biochemistry and biotechnology." Geological Society, London, Special Publications 87, no. 1 (1995): 351–63. http://dx.doi.org/10.1144/gsl.sp.1995.087.01.27.

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9

Massant, J., and N. Glansdorff. "Metabolic channelling of carbamoyl phosphate in the hyperthermophilic archaeon Pyrococcus furiosus: dynamic enzyme–enzyme interactions involved in the formation of the channelling complex." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 306–9. http://dx.doi.org/10.1042/bst0320306.

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Protection of thermolabile metabolites and coenzymes is a somewhat neglected but essential aspect of the molecular physiology of hyperthermophiles. Detailed information about the mechanisms used by thermophiles to protect these thermolabile metabolites and coenzymes is still scarce. A case in point is CP (carbamoyl phosphate), a precursor of pyrimidines and arginine, which is an extremely labile and potentially toxic intermediate. Recently we obtained the first evidence for a physical interaction between two hyperthermophilic enzymes for which kinetic evidence had suggested that these enzymes channel a highly thermolabile and potentially toxic intermediate. By physically interacting with each other, CKase (carbamate kinase) and OTCase (ornithine carbamoyltransferase) prevent thermodenaturation of CP in the aqueous cytoplasmic environment. The CP channelling complex involving CKase and OTCase or ATCase (aspartate carbamoyltransferase), identified in hyperthermophilic archaea, provides a good model system to investigate the mechanism of metabolic channelling and the molecular basis of protein–protein interactions in the physiology of extreme thermophiles.

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10

Maurelli, Luisa, and Alessandra Morana. "Hyperthermophilic Enzymes: Their Potential in Biotechnology." Current Biotechnology 2, no. 4 (December 31, 2013): 313–24. http://dx.doi.org/10.2174/18722083113076660032.

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11

Maurelli, Luisa, and Alessandra Morana. "Hyperthermophilic enzymes: their potential in biotechnology." Current Biotechnology 999, no. 999 (September 1, 2013): 13–14. http://dx.doi.org/10.2174/22115501113026660032.

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12

SEVERAL AUTHORS, SEVERAL AUTHORS. "ChemInform Abstract: Enzymes from Hyperthermophilic Microorganisms." ChemInform 26, no. 15 (August 18, 2010): no. http://dx.doi.org/10.1002/chin.199515290.

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13

Nishimasu, Hiroshi, Shinya Fushinobu, Hirofumi Shoun, and Takayoshi Wakagi. "Identification and Characterization of an ATP-Dependent Hexokinase with Broad Substrate Specificity from the Hyperthermophilic Archaeon Sulfolobus tokodaii." Journal of Bacteriology 188, no. 5 (March 1, 2006): 2014–19. http://dx.doi.org/10.1128/jb.188.5.2014-2019.2006.

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ABSTRACT As a new member of the glucose-phosphorylating enzymes, the ATP-dependent hexokinase from the hyperthermophilic crenarchaeon Sulfolobus tokodaii was purified, identified, and characterized. Our results revealed that the enzyme differs from other known enzymes in primary structure and its broad substrate specificity for both phosphoryl donors and acceptors.

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14

Fukuda, Wakao, Yulia Sari Ismail, Toshiaki Fukui, Haruyuki Atomi, and Tadayuki Imanaka. "Characterization of an archaeal malic enzyme from the hyperthermophilic archaeonThermococcus kodakaraensisKOD1." Archaea 1, no. 5 (2005): 293–301. http://dx.doi.org/10.1155/2005/250757.

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Although the interconversion between C4 and C3 compounds has an important role in overall metabolism, limited information is available on the properties and regulation of enzymes acting on these metabolites in hyperthermophilic archaea. Malic enzyme is one of the enzymes involved in this interconversion, catalyzing the oxidative decarboxylation of malate to pyruvate as well as the reductive carboxylation coupled with NAD(P)H. This study focused on the enzymatic properties and expression profile of an uncharacterized homolog of malic enzyme identified in the genome of a heterotrophic, hyperthermophilic archaeonT hermococcus kodakaraensisKOD1 (Tk-Mae). The amino acid sequence ofTk-Mae was 52–58% identical to those of malic enzymes from bacteria, whereas the similarities to the eukaryotic homologs were lower. Several catalytically important regions and residues were conserved in the primary structure ofTk-Mae. The recombinant protein, which formed a homodimer, exhibited thermostable malic enzyme activity with strict divalent cation dependency. The enzyme preferred NADP+rather than NAD+, but did not catalyze the decarboxylation of oxaloacetate, unlike the usual NADP-dependent malic enzymes. The apparent Michaelis constant (Km) ofTk-Mae for malate (16.9 mM) was much larger than those of known enzymes, leading to no strong preference for the reaction direction. Transcription of the gene encodingTk-Mae and intracellular malic enzyme activity inT. kodakaraensiswere constitutively weak, regardless of the growth substrates. Possible roles ofTk-Mae are discussed based on these results and the metabolic pathways ofT. kodakaraensisdeduced from the genome sequence.

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15

de Miguel Bouzas, Trinidad, Jorge Barros-Velazquez, and Tomas Gonzalez Villa. "Industrial Applications of Hyperthermophilic Enzymes: A Review." Protein & Peptide Letters 13, no. 7 (July 1, 2006): 645–51. http://dx.doi.org/10.2174/092986606777790548.

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16

Pletnev, S., S. Kozlov, and A. Wlodawer. "Structural studies of hyperthermophilic enzymes fromPyrococcus horikoshii." Acta Crystallographica Section A Foundations of Crystallography 61, a1 (August 23, 2005): c256. http://dx.doi.org/10.1107/s0108767305089075.

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17

George, G. N., Y. Gea, R. C. Prince, S. Mukund, and M. W. W. Adams. "Tungsten oxo-thiolate enzymes from hyperthermophilic bacteria." Journal of Inorganic Biochemistry 43, no. 2-3 (August 1991): 241. http://dx.doi.org/10.1016/0162-0134(91)84231-w.

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18

Imanaka, Tadayuki, and Haruyuki Atomi. "Catalyzing ?Hot? Reactions: Enzymes from Hyperthermophilic Archaea." Chemical Record 2, no. 3 (May 2002): 149–63. http://dx.doi.org/10.1002/tcr.10023.

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19

Ronimus, Ron S., and Hugh W. Morgan. "Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism." Archaea 1, no. 3 (2003): 199–221. http://dx.doi.org/10.1155/2003/162593.

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Enzymes of the gluconeogenic/glycolytic pathway (the Embden-Meyerhof-Parnas (EMP) pathway), the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle and the Entner-Doudoroff pathway are widely distributed and are often considered to be central to the origins of metabolism. In particular, several enzymes of the lower portion of the EMP pathway (the so-called trunk pathway), including triosephosphate isomerase (TPI; EC 5.3.1.1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12/13), phosphoglycerate kinase (PGK; EC 2.7.2.3) and enolase (EC 4.2.1.11), are extremely well conserved and universally distributed among the three domains of life. In this paper, the distribution of enzymes of gluconeogenesis/glycolysis in hyperthermophiles—microorganisms that many believe represent the least evolved organisms on the planet—is reviewed. In addition, the phylogenies of the trunk pathway enzymes (TPIs, GAPDHs, PGKs and enolases) are examined. The enzymes catalyzing each of the six-carbon transformations in the upper portion of the EMP pathway, with the possible exception of aldolase, are all derived from multiple gene sequence families. In contrast, single sequence families can account for the archaeal and hyperthermophilic bacterial enzyme activities of the lower portion of the EMP pathway. The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.

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20

Pedone, Emilia, Gabriella Fiorentino, Simonetta Bartolucci, and Danila Limauro. "Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea." Antioxidants 9, no. 8 (August 3, 2020): 703. http://dx.doi.org/10.3390/antiox9080703.

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To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2•−) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.

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21

Filipovic, M., S. Ognjanovic, and M. Ognjanovic. "Evidence of molecular adaptation to extreme environments and applicability to space environments." Serbian Astronomical Journal, no. 176 (2008): 81–86. http://dx.doi.org/10.2298/saj0876081f.

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This is initial investigation of gene signatures responsible for adapting microscopic life to the extreme Earth environments. We present preliminary results on identification of the clusters of orthologous groups (COGs) common to several hyperthermophiles and exclusion of those common to a mesophile (non-hyperthermophile): Escherichia coli (E. coli K12), will yield a group of proteins possibly involved in adaptation to life under extreme temperatures. Comparative genome analyses represent a powerful tool in discovery of novel genes responsible for adaptation to specific extreme environments. Methanogens stand out as the only group of organisms that have species capable of growth at 0?C (Metarhizium frigidum (M. frigidum) and Methanococcoides burtonii (M. burtonii)) and 110?C (Methanopyrus kandleri (M. kandleri)). Although not all the components of heat adaptation can be attributed to novel genes, the chaperones known as heat shock proteins stabilize the enzymes under elevated temperature. However, highly conserved chaperons found in bacteria and eukaryots are not present in hyperthermophilic Archea, rather, they have a unique chaperone TF55. Our aim was to use software which we specifically developed for extremophile genome comparative analyses in order to search for additional novel genes involved in hyperthermophile adaptation. The following hyperthermophile genomes incorporated in this software were used for these studies: Methanocaldococcus jannaschii (M. jannaschii), M. kandleri, Archaeoglobus fulgidus (A. fulgidus) and three species of Pyrococcus. Common genes were annotated and grouped according to their roles in cellular processes where such information was available and proteins not previously implicated in the heat-adaptation of hyperthermophiles were identified. Additional experimental data are needed in order to learn more about these proteins. To address non-gene based components of thermal adaptation, all sequenced extremophiles were analyzed for their GC contents and aminoacid hydrophobicity. Finally, we develop a prediction model for optimal growth temperature.

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22

Xavier, Karina B., Ralf Peist, Marina Kossmann, Winfried Boos, and Helena Santos. "Maltose Metabolism in the Hyperthermophilic Archaeon Thermococcus litoralis: Purification and Characterization of Key Enzymes." Journal of Bacteriology 181, no. 11 (June 1, 1999): 3358–67. http://dx.doi.org/10.1128/jb.181.11.3358-3367.1999.

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ABSTRACT Maltose metabolism was investigated in the hyperthermophilic archaeon Thermococcus litoralis. Maltose was degraded by the concerted action of 4-α-glucanotransferase and maltodextrin phosphorylase (MalP). The first enzyme produced glucose and a series of maltodextrins that could be acted upon by MalP when the chain length of glucose residues was equal or higher than four, to produce glucose-1-phosphate. Phosphoglucomutase activity was also detected inT. litoralis cell extracts. Glucose derived from the action of 4-α-glucanotransferase was subsequently metabolized via an Embden-Meyerhof pathway. The closely related organism Pyrococcus furiosus used a different metabolic strategy in which maltose was cleaved primarily by the action of an α-glucosidase, ap-nitrophenyl-α-d-glucopyranoside (PNPG)-hydrolyzing enzyme, producing glucose from maltose. A PNPG-hydrolyzing activity was also detected in T. litoralis, but maltose was not a substrate for this enzyme. The two key enzymes in the pathway for maltose catabolism in T. litoralis were purified to homogeneity and characterized; they were constitutively synthesized, although phosphorylase expression was twofold induced by maltodextrins or maltose. The gene encoding MalP was obtained by complementation in Escherichia coli and sequenced (calculated molecular mass, 96,622 Da). The enzyme purified from the organism had a specific activity for maltoheptaose, at the temperature for maximal activity (98°C), of 66 U/mg. AKm of 0.46 mM was determined with heptaose as the substrate at 60°C. The deduced amino acid sequence had a high degree of identity with that of the putative enzyme from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 (66%) and with sequences of the enzymes from the hyperthermophilic bacteriumThermotoga maritima (60%) and Mycobacterium tuberculosis (31%) but not with that of the enzyme from E. coli (13%). The consensus binding site for pyridoxal 5′-phosphate is conserved in the T. litoralis enzyme.

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23

Hotta, Yuji, Satoshi Ezaki, Haruyuki Atomi, and Tadayuki Imanaka. "Extremely Stable and Versatile Carboxylesterase from a Hyperthermophilic Archaeon." Applied and Environmental Microbiology 68, no. 8 (August 2002): 3925–31. http://dx.doi.org/10.1128/aem.68.8.3925-3931.2002.

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ABSTRACT We have found that the hyperthermophilic archaeon Pyrobaculum calidifontis VA1 produced a thermostable esterase. We isolated and sequenced the esterase gene (estPc ) from strain VA1. estPc consisted of 939 bp, corresponding to 313 amino acid residues with a molecular mass of 34,354 Da. As estPc showed significant identity (30%) to mammalian hormone-sensitive lipases (HSLs), esterase of P. calidifontis (Est) could be regarded as a new member of the HSL family. Activity levels of the enzyme were comparable or higher than those of previously reported enzymes not only at high temperature (6,410 U/mg at 90°C), but also at ambient temperature (1,050 U/mg at 30°C). The enzyme displayed extremely high thermostability and was also stable after incubation with various water-miscible organic solvents at a concentration of 80%. The enzyme also exhibited activity in the presence of organic solvents. Est of P. calidifontis showed higher hydrolytic activity towards esters with short to medium chains, with p-nitrophenyl caproate (C6) the best substrate among the p-nitrophenyl esters examined. As for the alcoholic moiety, the enzyme displayed esterase activity towards esters with both straight- and branched-chain alcohols. Most surprisingly, we found that this Est enzyme hydrolyzed the tertiary alcohol ester tert-butyl acetate, a feature very rare among previously reported lipolytic enzymes. The extreme stability against heat and organic solvents, along with its activity towards a tertiary alcohol ester, indicates a high potential for the Est of P. calidifontis in future applications.

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24

Montalvo-Rodriguez, Rafael, Cynthia Haseltine, Kathy Huess-LaRossa, Tom Clemente, Jimmy Soto, Paul Staswick, and Paul Blum. "Autohydrolysis of plant polysaccharides using transgenic hyperthermophilic enzymes." Biotechnology and Bioengineering 70, no. 2 (2000): 151–59. http://dx.doi.org/10.1002/1097-0290(20001020)70:2<151::aid-bit4>3.0.co;2-d.

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25

Adams, M. W. W., and R. M. Kelly. "Thermostability and thermoactivity of enzymes from hyperthermophilic archaea." Bioorganic & Medicinal Chemistry 2, no. 7 (July 1994): 659–67. http://dx.doi.org/10.1016/0968-0896(94)85015-1.

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26

Tang, Christina, Carl D. Saquing, Pooja K. Sarin, Robert M. Kelly, and Saad A. Khan. "Nanofibrous membranes for single-step immobilization of hyperthermophilic enzymes." Journal of Membrane Science 472 (December 2014): 251–60. http://dx.doi.org/10.1016/j.memsci.2014.08.037.

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27

Kohda, Jiro, Hirofumi Kawanishi, Ken-Ichiro Suehara, Yasuhisa Nakano, and Takuo Yano. "Stabilization of free and immobilized enzymes using hyperthermophilic chaperonin." Journal of Bioscience and Bioengineering 101, no. 2 (February 2006): 131–36. http://dx.doi.org/10.1263/jbb.101.131.

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28

Leuschner, C., and G. Antranikian. "Heat-stable enzymes from extremely thermophilic and hyperthermophilic microorganisms." World Journal of Microbiology & Biotechnology 11, no. 1 (January 1995): 95–114. http://dx.doi.org/10.1007/bf00339139.

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29

Baldasseroni, Fulvio, and Stefano Pascarella. "Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness." International Journal of Biological Macromolecules 44, no. 4 (May 2009): 353–60. http://dx.doi.org/10.1016/j.ijbiomac.2009.02.002.

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30

Sakuraba, Haruhiko, Shuichiro Goda, and Toshihisa Ohshima. "Unique sugar metabolism and novel enzymes of hyperthermophilic archaea." Chemical Record 3, no. 5 (2004): 281–87. http://dx.doi.org/10.1002/tcr.10066.

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31

Ronimus, R. S., and H. W. Morgan. "Central Metabolic Pathways of Hyperthermophiles: Important Clues on how Metabolism Gives Rise to Life." Symposium - International Astronomical Union 213 (2004): 367–73. http://dx.doi.org/10.1017/s0074180900193568.

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Vital clues on life's origins within the galaxy exist here on present day Earth. Life is currently divided into the three domains Bacteria, Archaea and Eukarya based on the phylogeny of small ribosomal subunit RNA (16S/18S) gene sequences. The domains are presumed to share a “last universal common ancestor” (LUCA). Hyperthermophilic bacteria and archaea, which are able to thrive at 80°C or higher, dominate the bottom of the tree of life and are thus suggested to be the least evolved, or most “ancient”. Geochemical data indicates that life first appeared on Earth approximately 3.8 billion years ago in a hot environment. Due to these considerations, hyperthermophiles represent the most appropriate microorganisms to investigate the origins of metabolism. The central biochemical pathway of gluconeogenesis/glycolysis (the Embden-Meyerhof pathway) which produces six carbon sugars from three carbon compounds is present in all organisms and can provide important hints concerning the early development of metabolism. Significantly, there are a number of striking deviations from the textbook canonical reaction sequence that are found, particularly in hyperthermophilic archaea. In this paper the phylogenetic istribution of enzymes of the pathway is detailed; overall, the distribution pattern provides strong evidence for the pathway to have developed from the bottom-up.

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32

Tanaka, Takeshi, Fumikazu Takahashi, Toshiaki Fukui, Shinsuke Fujiwara, Haruyuki Atomi, and Tadayuki Imanaka. "Characterization of a Novel Glucosamine-6-Phosphate Deaminase from a Hyperthermophilic Archaeon." Journal of Bacteriology 187, no. 20 (October 15, 2005): 7038–44. http://dx.doi.org/10.1128/jb.187.20.7038-7044.2005.

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ABSTRACT A key step in amino sugar metabolism is the interconversion between fructose-6-phosphate (Fru6P) and glucosamine-6-phosphate (GlcN6P). This conversion is catalyzed in the catabolic and anabolic directions by GlcN6P deaminase and GlcN6P synthase, respectively, two enzymes that show no relationship with one another in terms of primary structure. In this study, we examined the catalytic properties and regulatory features of the glmD gene product (GlmD Tk ) present within a chitin degradation gene cluster in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Although the protein GlmD Tk was predicted as a probable sugar isomerase related to the C-terminal sugar isomerase domain of GlcN6P synthase, the recombinant GlmD Tk clearly exhibited GlcN6P deaminase activity, generating Fru6P and ammonia from GlcN6P. This enzyme also catalyzed the reverse reaction, the ammonia-dependent amination/isomerization of Fru6P to GlcN6P, whereas no GlcN6P synthase activity dependent on glutamine was observed. Kinetic analyses clarified the preference of this enzyme for the deaminase reaction rather than the reverse one, consistent with the catabolic function of GlmD Tk . In T. kodakaraensis cells, glmDTk was polycistronically transcribed together with upstream genes encoding an ABC transporter and a downstream exo-β-glucosaminidase gene (glmATk ) within the gene cluster, and their expression was induced by the chitin degradation intermediate, diacetylchitobiose. The results presented here indicate that GlmD Tk is actually a GlcN6P deaminase functioning in the entry of chitin-derived monosaccharides to glycolysis in this hyperthermophile. This enzyme is the first example of an archaeal GlcN6P deaminase and is a structurally novel type distinct from any previously known GlcN6P deaminase.

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33

Shima, S., R. K. Thauer, and U. Ermler. "Hyperthermophilic and salt-dependent formyltransferase from Methanopyrus kandleri." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 269–72. http://dx.doi.org/10.1042/bst0320269.

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Methanopyrus kandleri is a hyperthermophilic methanogenic archaeon, which grows on H2 and CO2 as its sole energy source. Its growth temperature optimum is 98°C. One of the interesting characteristics of this archaeon is its high intracellular salt content. The organism has been reported to contain the trianionic cDPG (cyclic 2,3-diphosphoglycerate) and K+ at concentrations of 1.1 and 3 M, respectively. Reflecting the high cellular salt concentration, the enzymes in this organism are adapted not only to high temperature but also to high salt concentrations. The formyltransferase from M. kandleri was characterized extensively with respect to thermo- and halophilicity. The crystal structure of the formyltransferase at 1.73 Å shows the enzyme to be composed of four identical subunits of molecular mass 32 kDa. The formyltransferase is thermostable and active only at relatively high concentrations of potassium phosphate (1 M) or other salts with strongly hydrated anions (strong salting-out salts). Potassium phosphate and potassium cDPG were found to be equivalent in activating and stabilizing the enzyme. At low concentrations of these salts, the enzyme is inactive and thermolabile. It was shown by equilibrium sedimentation analysis that the enzyme is in a monomer/dimer/tetramer equilibrium, the equilibrium constant being dependent on the concentration of salts: the higher oligomeric species increase with increasing salt concentrations. Evidence was provided that the monomer is both inactive and thermolabile. Experiments using a mutation which is directed to break surface ion pairs between two dimers indicated that dimerization is required for activity and tetramerization leads to thermostability.

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Negron, Leonardo, Mark L. Patchett, and Emily J. Parker. "Expression, Purification, and Characterisation of Dehydroquinate Synthase from Pyrococcus furiosus." Enzyme Research 2011 (April 5, 2011): 1–10. http://dx.doi.org/10.4061/2011/134893.

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Dehydroquinate synthase (DHQS) catalyses the second step of the shikimate pathway to aromatic compounds. DHQS from the archaeal hyperthermophile Pyrococcus furiosus was insoluble when expressed in Escherichia coli but was partially solubilised when KCl was included in the cell lysis buffer. A purification procedure was developed, involving lysis by sonication at 30∘C followed by a heat treatment at 70∘C and anion exchange chromatography. Purified recombinant P. furiosus DHQS is a dimer with a subunit Mr of 37,397 (determined by electrospray ionisation mass spectrometry) and is active over broad pH and temperature ranges. The kinetic parameters are KM (3-deoxy-D-arabino-heptulosonate 7-phosphate) 3.7 μM and kcat 3.0 sec-1 at 60∘C and pH 6.8. EDTA inactivates the enzyme, and enzyme activity is restored by several divalent metal ions including (in order of decreasing effectiveness) Cd2+, Co2+, Zn2+, and Mn2+. High activity of a DHQS in the presence of Cd2+ has not been reported for enzymes from other sources, and may be related to the bioavailability of Cd2+ for P. furiosus. This study is the first biochemical characterisation of a DHQS from a thermophilic source. Furthermore, the characterisation of this hyperthermophilic enzyme was carried out at elevated temperatures using an enzyme-coupled assay.

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Benedetti, Manuel, Valeria Vecchi, Zeno Guardini, Luca Dall’Osto, and Roberto Bassi. "Expression of a Hyperthermophilic Cellobiohydrolase in Transgenic Nicotiana tabacum by Protein Storage Vacuole Targeting." Plants 9, no. 12 (December 18, 2020): 1799. http://dx.doi.org/10.3390/plants9121799.

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Plant expression of microbial Cell Wall Degrading Enzymes (CWDEs) is a valuable strategy to produce industrial enzymes at affordable cost. Unfortunately, the constitutive expression of CWDEs may affect plant fitness to variable extents, including developmental alterations, sterility and even lethality. In order to explore novel strategies for expressing CWDEs in crops, the cellobiohydrolase CBM3GH5, from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, was constitutively expressed in N. tabacum by targeting the enzyme both to the apoplast and to the protein storage vacuole. The apoplast targeting failed to isolate plants expressing the recombinant enzyme despite a large number of transformants being screened. On the opposite side, the targeting of the cellobiohydrolase to the protein storage vacuole led to several transgenic lines expressing CBM3GH5, with an enzyme yield of up to 0.08 mg g DW−1 (1.67 Units g DW−1) in the mature leaf tissue. The analysis of CBM3GH5 activity revealed that the enzyme accumulated in different plant organs in a developmental-dependent manner, with the highest abundance in mature leaves and roots, followed by seeds, stems and leaf ribs. Notably, both leaves and stems from transgenic plants were characterized by an improved temperature-dependent saccharification profile.

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Kobayashi, Kazuo, Masaru Kato, Yutaka Miura, Masako Kettoku, Toshihiro Komeda, and Akihiro Iwamatsu. "Gene Analysis of Trehalose-producing Enzymes from Hyperthermophilic Archaea inSulfolobales." Bioscience, Biotechnology, and Biochemistry 60, no. 10 (January 1996): 1720–23. http://dx.doi.org/10.1271/bbb.60.1720.

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Andrade, Carolina M. M. C., Nei Pereira Jr., and Garo Antranikian. "Extremely thermophilic microorganisms and their polymer-hidrolytic enzymes." Revista de Microbiologia 30, no. 4 (December 1999): 287–98. http://dx.doi.org/10.1590/s0001-37141999000400001.

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Thermophilic and hyperthermophilic microorganisms are found as normal inhabitants of continental and submarine volcanic areas, geothermally heated sea-sediments and hydrothermal vents and thus are considered extremophiles. Several present or potential applications of extremophilic enzymes are reviewed, especially polymer-hydrolysing enzymes, such as amylolytic and hemicellulolytic enzymes. The purpose of this review is to present the range of morphological and metabolic features among those microorganisms growing from 70oC to 100°C and to indicate potential opportunities for useful applications derived from these features.

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Fernandes, Gabriela Cabral, Elwi Guillermo Machado Sierra, Paul Brear, Mariana Rangel Pereira, and Eliana G. M. Lemos. "From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase." Microorganisms 9, no. 2 (February 14, 2021): 393. http://dx.doi.org/10.3390/microorganisms9020393.

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For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca2+, Ba2+, Mn2+ and Mg2+ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co2+. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications.

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Brouns, Stan J. J., Nicole Smits, Hao Wu, Ambrosius P. L. Snijders, Phillip C. Wright, Willem M. de Vos, and John van der Oost. "Identification of a Novel α-Galactosidase from the Hyperthermophilic Archaeon Sulfolobus solfataricus." Journal of Bacteriology 188, no. 7 (April 1, 2006): 2392–99. http://dx.doi.org/10.1128/jb.188.7.2392-2399.2006.

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ABSTRACT Sulfolobus solfataricus is an aerobic crenarchaeon that thrives in acidic volcanic pools. In this study, we have purified and characterized a thermostable α-galactosidase from cell extracts of S. solfataricus P2 grown on the trisaccharide raffinose. The enzyme, designated GalS, is highly specific for α-linked galactosides, which are optimally hydrolyzed at pH 5 and 90°C. The protein consists of 74.7-kDa subunits and has been identified as the gene product of open reading frame Sso3127. Its primary sequence is most related to plant enzymes of glycoside hydrolase family 36, which are involved in the synthesis and degradation of raffinose and stachyose. Both the galS gene from S. solfataricus P2 and an orthologous gene from Sulfolobus tokodaii have been cloned and functionally expressed in Escherichia coli, and their activity was confirmed. At present, these Sulfolobus enzymes not only constitute a distinct type of thermostable α-galactosidases within glycoside hydrolase clan D but also represent the first members from the Archaea.

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Haseltine, Cynthia, Rafael Montalvo-Rodriguez, Elisabetta Bini, Audrey Carl, and Paul Blum. "Coordinate Transcriptional Control in the Hyperthermophilic Archaeon Sulfolobus solfataricus." Journal of Bacteriology 181, no. 13 (July 1, 1999): 3920–27. http://dx.doi.org/10.1128/jb.181.13.3920-3927.1999.

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ABSTRACT The existence of a global gene regulatory system in the hyperthermophilic archaeon Sulfolobus solfataricus is described. The system is responsive to carbon source quality and acts at the level of transcription to coordinate synthesis of three physically unlinked glycosyl hydrolases implicated in carbohydrate utilization. The specific activities of three enzymes, an α-glucosidase (malA), a β-glycosidase (lacS), and an α-amylase, were reduced 4-, 20-, and 10-fold, respectively, in response to the addition of supplementary carbon sources to a minimal sucrose medium. Western blot analysis using anti-α-glucosidase and anti-β-glycosidase antibodies indicated that reduced enzyme activities resulted exclusively from decreased enzyme levels. Northern blot analysis of malA and lacSmRNAs revealed that changes in enzyme abundance arose primarily from reductions in transcript concentrations. Culture conditions precipitating rapid changes in lacS gene expression were established to determine the response time of the regulatory system in vivo. Full induction occurred within a single generation whereas full repression occurred more slowly, requiring nearly 38 generations. SincelacS mRNA abundance changed much more rapidly in response to a nutrient down shift than to a nutrient up shift, transcript synthesis rather than degradation likely plays a role in the regulatory response.

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Danson, Michael J., and David W. Hough. "Promiscuity in the Archaea: The enzymology of their metabolic pathways." Biochemist 27, no. 1 (February 1, 2005): 17–21. http://dx.doi.org/10.1042/bio02701017.

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The pathways of central metabolism provide the metabolic connections between the catabolic (degradative) and anabolic (biosynthetic) routes in all living organisms. In hyperthermophilic Archaea, we have discovered a promiscuous central metabolic pathway that catabolizes a variety of sugars using a single set of enzymes. This article explores the structural basis of this promiscuity in enzymes that have to maintain their integrity at temperatures approaching 100°C.

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Hutchins, Andrea M., James F. Holden, and Michael W. W. Adams. "Phosphoenolpyruvate Synthetase from the Hyperthermophilic Archaeon Pyrococcus furiosus." Journal of Bacteriology 183, no. 2 (January 15, 2001): 709–15. http://dx.doi.org/10.1128/jb.183.2.709-715.2001.

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ABSTRACT Phosphoenolpyruvate synthetase (PpsA) was purified from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme catalyzes the conversion of pyruvate and ATP to phosphoenolpyruvate (PEP), AMP, and phosphate and is thought to function in gluconeogenesis. PpsA has a subunit molecular mass of 92 kDa and contains one calcium and one phosphorus atom per subunit. The active form has a molecular mass of 690 ± 20 kDa and is assumed to be octomeric, while approximately 30% of the protein is purified as a large (∼1.6 MDa) complex that is not active. The apparentKm values and catalytic efficiencies for the substrates pyruvate and ATP (at 80°C, pH 8.4) were 0.11 mM and 1.43 × 104 mM−1 · s−1 and 0.39 mM and 3.40 × 103mM−1 · s−1, respectively. Maximal activity was measured at pH 9.0 (at 80°C) and at 90°C (at pH 8.4). The enzyme also catalyzed the reverse reaction, but the catalytic efficiency with PEP was very low [k cat/Km = 32 (mM · s)−1]. In contrast to several other nucleotide-dependent enzymes from P. furiosus, PpsA has an absolute specificity for ATP as the phosphate-donating substrate. This is the first PpsA from a nonmethanogenic archaeon to be biochemically characterized. Its kinetic properties are consistent with a role in gluconeogenesis, although its relatively high cellular concentration (∼5% of the cytoplasmic protein) suggests an additional function possibly related to energy spilling. It is not known whether interconversion between the smaller, active and larger, inactive forms of the enzyme has any functional role.

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VERHEES, Corné H., Denise G. M. KOOT, Thijs J. G. ETTEMA, Cor DIJKEMA, Willem M. de VOS, and John van der OOST. "Biochemical adaptations of two sugar kinases from the hyperthermophilic archaeon Pyrococcus furiosus." Biochemical Journal 366, no. 1 (August 15, 2002): 121–27. http://dx.doi.org/10.1042/bj20011597.

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The hyperthermophilic archaeon Pyrococcus furiosus possesses a modified Embden—Meyerhof pathway, including an unusual ADP-dependent glucokinase (ADP-GLK) and an ADP-dependent phosphofructokinase. In the present study, we report the characterization of a P. furiosus galactokinase (GALK) and its comparison with the P. furiosus ADP-GLK. The pyrococcal genes encoding the ADP-GLK and GALK were functionally expressed in Escherichia coli, and the proteins were subsequently purified to homogeneity. Both enzymes are specific kinases with an optimal activity at approx. 90°C. Biochemical characterization of these enzymes confirmed that the ADP-GLK is unable to use ATP as the phosphoryl group donor, but revealed that GALK is ATP-dependent and has an extremely high affinity for ATP. There is a discussion about whether the unusual features of these two classes of kinases might reflect adaptations to a relatively low intracellular ATP concentration in the hyperthermophilic archaeon P. furiosus.

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Littlechild, Jenny. "Cures from the ends of the earth: Novel thermostable enzymes and the pharmaceutical industry." Biochemist 27, no. 1 (February 1, 2005): 27–29. http://dx.doi.org/10.1042/bio02701027.

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Enzymes that are found naturally in thermophilic and hyperthermophilic organisms are being used as robust biocatalysts in the fine-chemical and pharmaceutical industries. Knowledge of their biochemical properties and three-dimeasional structures has proved invaluable in understanding their mechanism and in optimizing their commercial use.

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Kobus, Stefanie, Pablo Perez-Garcia, Astrid Hoeppner, Nicholas Holzscheck, Filip Kovacic, Wolfgang R. Streit, Karl-Erich Jaeger, Jennifer Chow, and Sander H. J. Smits. "Igni18, a novel metallo-hydrolase from the hyperthermophilic archaeon Ignicoccus hospitalis KIN4/I: cloning, expression, purification and X-ray analysis." Acta Crystallographica Section F Structural Biology Communications 75, no. 4 (April 1, 2019): 307–11. http://dx.doi.org/10.1107/s2053230x19002851.

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The hyperthermophilic crenarchaeon Ignicoccus hospitalis KIN4/I possesses at least 35 putative genes encoding enzymes that belong to the α/β-hydrolase superfamily. One of those genes, the metallo-hydrolase-encoding igni18, was cloned and heterologously expressed in Pichia pastoris. The enzyme produced was purified in its catalytically active form. The recombinant enzyme was successfully crystallized and the crystal diffracted to a resolution of 2.3 Å. The crystal belonged to space group R32, with unit-cell parameters a = b = 67.42, c = 253.77 Å, α = β = 90.0, γ = 120.0°. It is suggested that it contains one monomer of Igni18 within the asymmetric unit.

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Yang, Sung-Jae, Hee-Seob Lee, Cheon-Seok Park, Yong-Ro Kim, Tae-Wha Moon, and Kwan-Hwa Park. "Enzymatic Analysis of an Amylolytic Enzyme from the Hyperthermophilic Archaeon Pyrococcus furiosus Reveals Its Novel Catalytic Properties as both an α-Amylase and a Cyclodextrin-Hydrolyzing Enzyme." Applied and Environmental Microbiology 70, no. 10 (October 2004): 5988–95. http://dx.doi.org/10.1128/aem.70.10.5988-5995.2004.

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ABSTRACT Genomic analysis of the hyperthermophilic archaeon Pyrococcus furiosus revealed the presence of an open reading frame (ORF PF1939) similar to the enzymes in glycoside hydrolase family 13. This amylolytic enzyme, designated PFTA (Pyrococcus furiosus thermostable amylase), was cloned and expressed in Escherichia coli. The recombinant PFTA was extremely thermostable, with an optimum temperature of 90°C. The substrate specificity of PFTA suggests that it possesses characteristics of both α-amylase and cyclodextrin-hydrolyzing enzyme. Like typical α-amylases, PFTA hydrolyzed maltooligosaccharides and starch to produce mainly maltotriose and maltotetraose. However, it could also attack and degrade pullulan and β-cyclodextrin, which are resistant to α-amylase, to primarily produce panose and maltoheptaose, respectively. Furthermore, acarbose, a potent α-amylase inhibitor, was drastically degraded by PFTA, as is typical of cyclodextrin-hydrolyzing enzymes. These results confirm that PFTA possesses novel catalytic properties characteristic of both α-amylase and cyclodextrin-hydrolyzing enzyme.

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Guiral, M., C. Aubert, and M. T. Giudici-Orticoni. "Hydrogen metabolism in the hyperthermophilic bacterium Aquifex aeolicus." Biochemical Society Transactions 33, no. 1 (February 1, 2005): 22–24. http://dx.doi.org/10.1042/bst0330022.

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Aquifex aeolicus is a microaerophilic, hydrogen-oxidizing, hyperthermophilic bacterium containing three [NiFe] hydrogenases. Two of these three enzymes (one membrane-bound and one soluble) have been purified and characterized. The Aquifex hydrogenases are thermostable and tolerant to oxygen. A cellular function for the three hydrogenases has been proposed. The two membrane-bound periplasmic hydrogenases may function in energy conservation, whereas the soluble cytoplasmic hydrogenase is probably involved in the CO2 fixation pathway.

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Unsworth, Larry D., John van der Oost, and Sotirios Koutsopoulos. "Hyperthermophilic enzymes − stability, activity and implementation strategies for high temperature applications." FEBS Journal 274, no. 16 (August 2007): 4044–56. http://dx.doi.org/10.1111/j.1742-4658.2007.05954.x.

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Jongsareejit, Boonsri, Shinsuke Fujiwara, Masahiro Takagi, and Tadayuki Imanaka. "Comparison of two glutamate producing enzymes from the hyperthermophilic archaeonPyrococcussp. KOD1." FEMS Microbiology Letters 158, no. 2 (January 1998): 243–48. http://dx.doi.org/10.1111/j.1574-6968.1998.tb12827.x.

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Shimosaka, Takahiro, Hiroya Tomita, and Haruyuki Atomi. "Regulation of Coenzyme A Biosynthesis in the Hyperthermophilic Bacterium Thermotoga maritima." Journal of Bacteriology 198, no. 14 (May 9, 2016): 1993–2000. http://dx.doi.org/10.1128/jb.00077-16.

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ABSTRACTRegulation of coenzyme A (CoA) biosynthesis in bacteria and eukaryotes occurs through feedback inhibition targeting type I and type II pantothenate kinase (PanK), respectively. In contrast, the activity of type III PanK is not affected by CoA. As the hyperthermophilic bacteriumThermotoga maritimaharbors only a single type III PanK (Tm-PanK), here we examined the mechanisms that regulate CoA biosynthesis in this organism. We first examined the enzyme responsible for the ketopantoate reductase (KPR) reaction, which is the target of feedback inhibition in archaea. A classical KPR homolog was not present on theT. maritimagenome, but we found a homolog (TM0550) of the ketol-acid reductoisomerase (KARI) fromCorynebacterium glutamicum, which exhibits KPR activity. The purified TM0550 protein displayed both KPR and KARI activities and was designatedTm-KPR/KARI. WhenT. maritimacell extract was subjected to anion-exchange chromatography, the fractions containing high levels of KPR activity also displayed positive signals in a Western blot analysis using polyclonal anti-TM0550 protein antisera, strongly suggesting thatTm-KPR/KARI was the major source of KPR activity in the organism. The KPR activity ofTm-KPR/KARI was not inhibited in the presence of CoA. We thus examined the properties ofTm-PanK and the pantothenate synthetase (Tm-PS) of this organism.Tm-PS was not affected by CoA. Surprisingly however,Tm-PanK was inhibited by CoA, with almost complete inhibition in the presence of 400 μM CoA. Our results suggest that CoA biosynthesis inT. maritimais regulated by feedback inhibition targeting PanK, althoughTm-PanK is a type III enzyme.IMPORTANCEBacteria and eukaryotes regulate the biosynthesis of coenzyme A (CoA) by feedback inhibition targeting type I or type II pantothenate kinase (PanK). The hyperthermophilic bacteriumThermotoga maritimaharbors a single type III PanK (Tm-PanK), previously considered to be unaffected by CoA. By examining the properties of three enzymes involved in CoA biosynthesis in this organism, we found thatTm-PanK, although a type III enzyme, is inhibited by CoA. The results provide a feasible explanation of how CoA biosynthesis is regulated inT. maritima, which may also apply for other bacteria that harbor only type III PanK enzymes.

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