The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Smidt, Hauke, Van Der Oost, John, De Vos, Willem M.
Efficient host-vector systems have been developed for the versatile, strictly anaerobic, halo- and fumarate-respiring gram-positive bacterium Desulfitobacterium dehalogenans. An electroporation-based...
López-Contreras, Ana M., Smidt, Hauke, Van Der Oost, John, Claassen, Pieternel A. M., Mooibroek, Hans, De Vos, Willem M.
Growth and the production of acetone, butanol, and ethanol by Clostridium beijerinckii NCIMB 8052 on several polysaccharides and sugars were analyzed. On crystalline cellulose, growth and solvent...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Voorhorst, Wilfried G. B., Gueguen, Yannick, Geerling, Ans C. M., Schut, Gerti, Dahlke, Isabell, Thomm, Michael, ...
The genetic organization, expression, and regulation of the celB locus of the hyperthermophilic archaeon Pyrococcus furiosus were analyzed. This locus includes the celB gene, which codes for an...
Smidt, Hauke, Song, Donglin, Van Der Oost, John, De Vos, Willem M.
To allow for the molecular analysis of halorespiration by the strictly anaerobic gram-positive bacterium Desulfitobacterium dehalogenans, halorespiration-deficient mutants were selected and...
Smidt, Hauke, Van Leest, Maarten, Van Der Oost, John, De Vos, Willem M.
To characterize the expression and possible regulation of reductive dehalogenation in halorespiring bacteria, a 11.5-kb genomic fragment containing the o-chlorophenol reductive dehalogenase-encoding...
Otten, Marijke F., Van Der Oost, John, Reijnders, Willem N. M., Westerhoff, Hans V., Ludwig, Bernd
Paracoccus denitrificans strains with mutations in the genes encoding the cytochrome c550, c552, or c1 and in combinations of these genes were constructed, and their growth characteristics were...
ADP-Dependent Phosphofructokinases in Mesophilic and Thermophilic Methanogenic Archaea
Verhees, Corné H., Tuininga, Judith E., Kengen, Servé W. M., Stams, Alfons J. M., Van Der Oost, John, De Vos, Willem M.
Phosphofructokinase (PFK) is a key enzyme of the glycolytic pathway in all domains of life. Two related PFKs, ATP-dependent and PPi-dependent PFK, have been distinguished in bacteria and eucarya, as...
Ward, Donald E., Kengen, Servé W. M., Van Der Oost, John, De Vos, Willem M.
Alanine aminotransferase (AlaAT) was purified from cell extracts of the hyperthermophilic archaeon Pyrococcus furiosus by multistep chromatography. The enzyme has an apparent molecular mass of 93.5...
Plasmid pGS5 from the Hyperthermophilic Archaeon Archaeoglobus profundus Is Negatively Supercoiled
López-García, Purificación, Forterre, Patrick, Van Der Oost, John, Erauso, Gaël
We present evidence that, in contrast to plasmids from other hyperthermophilic archaea, which are in the relaxed to positively supercoiled state, plasmid pGS5 (2.8 kb) from Archaeoglobus profundus is...
Characterization of Plasmid pRT1 from Pyrococcus sp. Strain JT1
Ward, Donald E., Revet, Ingrid M., Nandakumar, Renu, Tuttle, Jon H., De Vos, Willem M., Van Der Oost, John, ...
We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon Pyrococcus sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some...
Verhees, Corné H., Akerboom, Jasper, Schiltz, Emile, De Vos, Willem M., Van Der Oost, John
The Pyrococcus furiosus fbpA gene was cloned and expressed in Escherichia coli, and the fructose-1,6-bisphosphatase produced was subsequently purified and characterized. The dimeric enzyme showed a...
López-Contreras, Ana M., Martens, Aernout A., Szijarto, Nora, Mooibroek, Hans, Claassen, Pieternel A. M., Van Der Oost, John, ...
The genome sequence of Clostridium acetobutylicum ATCC 824, a noncellulolytic solvent-producing strain, predicts the production of various proteins with domains typical for cellulosomal subunits....
Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus
Leonard, Philip M., Smits, Sander H.J., Sedelnikova, Svetlana E., Brinkman, Arie B., De Vos, Willem M., Van Der Oost, John, ...
The LrpA protein from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the Lrp/AsnC family of transcriptional regulatory proteins, of which the Escherichia coli leucine-responsive...
Substrate-Induced Production and Secretion of Cellulases by Clostridium acetobutylicum
López-Contreras, Ana M., Gabor, Krisztina, Martens, Aernout A., Renckens, Bernadet A. M., Claassen, Pieternel A. M., Van Der Oost, John, ...
Clostridium acetobutylicum ATCC 824 is a solventogenic bacterium that grows heterotrophically on a variety of carbohydrates, including glucose, cellobiose, xylose, and lichenan, a linear polymer of...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...
Kessler, Alexandra, Brinkman, Arie B., Van Der Oost, John, Prangishvili, David
The double-stranded DNA genomes of the crenarchaeal rudiviruses SIRV1 (32 kb) and SIRV2 (35 kb) were previously sequenced. Here we present results of the analysis of gene expression of these viruses...
Chiaraluce, Roberta, Gianese, Giulio, Angelaccio, Sebastiana, Florio, Rita, Van Lieshout, Johan F. T., Van Der Oost, John, ...
The family 16 endo-β-1,3 glucanase from the extremophilic archaeon Pyrococcus furiosus is a laminarinase, which in 7.9 M GdmCl (guanidinium chloride) maintains a significant amount of tertiary...
The semi-phosphorylative Entner–Doudoroff pathway in hyperthermophilic archaea: a re-evaluation
Ahmed, Hatim, Ettema, Thijs J. G., Tjaden, Britta, Geerling, Ans C. M., Van Der Oost, John, Siebers, Bettina
Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner–Doudoroff) pathway generally proceeds via a non-phosphorylative...
Verhees, Corné H, Koot, Denise G M, Ettema, Thijs J G, Dijkema, Cor, De Vos, Willem M, Van Der Oost, John
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...
DNA family shuffling of hyperthermostable beta-glycosidases.
Kaper, Thijs, Brouns, Stan J J, Geerling, Ans C M, De Vos, Willem M, Van Der Oost, John
The structural compatibility of two hyperthermostable family 1 glycoside hydrolases, Pyrococcus furiosus CelB and Sulfolobus solfataricus LacS, as well as their kinetic potential were studied by...
Kluskens, Leon D, Voragen, Alphons G J, De Vos, Willem M, Van Der Oost, John
The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PelA) in the extracellular medium. The...
The unique features of glycolytic pathways in Archaea.
Verhees, Corné H, Kengen, Servé W M, Tuininga, Judith E, Schut, Gerrit J, Adams, Michael W W, De Vos, Willem M, ...
An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved,...
Koutsopoulos, Sotirios, Van Der Oost, John, Norde, Willem
Conformational characteristics and the adsorption behavior of endo-β-1,3-glucanase from the hyperthermophilic microorganism Pyrococcus furiosus were studied by circular dichroism, steady-state and...
Machielsen, Ronnie, Uria, Agustinus R., Kengen, Servé W. M., Van Der Oost, John
The gene encoding a novel alcohol dehydrogenase that belongs to the aldo-keto reductase superfamily has been identified in the hyperthermophilic archaeon Pyrococcus furiosus. The gene, referred to as...
Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family
Thaw, Paul, Sedelnikova, Svetlana E., Muranova, Tatyana, Wiese, Sebastian, Ayora, Sylvia, Alonso, Juan C., ...
The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC)...
Gödde, Carolin, Sahm, Kerstin, Brouns, Stan J. J., Kluskens, Leon D., Van Der Oost, John, De Vos, Willem M., ...
A gene encoding a subtilisin-like protease, designated islandisin, from the extremely thermophilic bacterium Fervidobacterium islandicum (DSMZ 5733) was cloned and actively expressed in Escherichia...
Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family
Thaw, Paul, Sedelnikova, Svetlana E., Muranova, Tatyana, Wiese, Sebastian, Ayora, Sylvia, Alonso, Juan C., ...
Brouns, Stan J. J., Smits, Nicole, Wu, Hao, Snijders, Ambrosius P. L., Wright, Phillip C., De Vos, Willem M., ...
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....
Gábor, Krisztina, Veríssimo, Carla S., Cyran, Barbara C., Ter Horst, Paul, Meijer, Nienke P., Smidt, Hauke, ...
The recently identified CprK branch of the CRP (cyclic AMP receptor protein)-FNR (fumarate and nitrate reduction regulator) family of transcriptional regulators includes proteins that activate the...
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Smidt, Hauke, Van Der Oost, John, De Vos, Willem M.
Efficient host-vector systems have been developed for the versatile, strictly anaerobic, halo- and fumarate-respiring gram-positive bacterium Desulfitobacterium dehalogenans. An electroporation-based...
López-Contreras, Ana M., Smidt, Hauke, Van Der Oost, John, Claassen, Pieternel A. M., Mooibroek, Hans, De Vos, Willem M.
Growth and the production of acetone, butanol, and ethanol by Clostridium beijerinckii NCIMB 8052 on several polysaccharides and sugars were analyzed. On crystalline cellulose, growth and solvent...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Voorhorst, Wilfried G. B., Gueguen, Yannick, Geerling, Ans C. M., Schut, Gerti, Dahlke, Isabell, Thomm, Michael, ...
The genetic organization, expression, and regulation of the celB locus of the hyperthermophilic archaeon Pyrococcus furiosus were analyzed. This locus includes the celB gene, which codes for an...
Smidt, Hauke, Song, Donglin, Van Der Oost, John, De Vos, Willem M.
To allow for the molecular analysis of halorespiration by the strictly anaerobic gram-positive bacterium Desulfitobacterium dehalogenans, halorespiration-deficient mutants were selected and...
Smidt, Hauke, Van Leest, Maarten, Van Der Oost, John, De Vos, Willem M.
To characterize the expression and possible regulation of reductive dehalogenation in halorespiring bacteria, a 11.5-kb genomic fragment containing the o-chlorophenol reductive dehalogenase-encoding...
Otten, Marijke F., Van Der Oost, John, Reijnders, Willem N. M., Westerhoff, Hans V., Ludwig, Bernd
Paracoccus denitrificans strains with mutations in the genes encoding the cytochrome c550, c552, or c1 and in combinations of these genes were constructed, and their growth characteristics were...
ADP-Dependent Phosphofructokinases in Mesophilic and Thermophilic Methanogenic Archaea
Verhees, Corné H., Tuininga, Judith E., Kengen, Servé W. M., Stams, Alfons J. M., Van Der Oost, John, De Vos, Willem M.
Phosphofructokinase (PFK) is a key enzyme of the glycolytic pathway in all domains of life. Two related PFKs, ATP-dependent and PPi-dependent PFK, have been distinguished in bacteria and eucarya, as...
Ward, Donald E., Kengen, Servé W. M., Van Der Oost, John, De Vos, Willem M.
Alanine aminotransferase (AlaAT) was purified from cell extracts of the hyperthermophilic archaeon Pyrococcus furiosus by multistep chromatography. The enzyme has an apparent molecular mass of 93.5...
Plasmid pGS5 from the Hyperthermophilic Archaeon Archaeoglobus profundus Is Negatively Supercoiled
López-García, Purificación, Forterre, Patrick, Van Der Oost, John, Erauso, Gaël
We present evidence that, in contrast to plasmids from other hyperthermophilic archaea, which are in the relaxed to positively supercoiled state, plasmid pGS5 (2.8 kb) from Archaeoglobus profundus is...
Characterization of Plasmid pRT1 from Pyrococcus sp. Strain JT1
Ward, Donald E., Revet, Ingrid M., Nandakumar, Renu, Tuttle, Jon H., De Vos, Willem M., Van Der Oost, John, ...
We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon Pyrococcus sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some...
Verhees, Corné H., Akerboom, Jasper, Schiltz, Emile, De Vos, Willem M., Van Der Oost, John
The Pyrococcus furiosus fbpA gene was cloned and expressed in Escherichia coli, and the fructose-1,6-bisphosphatase produced was subsequently purified and characterized. The dimeric enzyme showed a...
López-Contreras, Ana M., Martens, Aernout A., Szijarto, Nora, Mooibroek, Hans, Claassen, Pieternel A. M., Van Der Oost, John, ...
The genome sequence of Clostridium acetobutylicum ATCC 824, a noncellulolytic solvent-producing strain, predicts the production of various proteins with domains typical for cellulosomal subunits....
Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus
Leonard, Philip M., Smits, Sander H.J., Sedelnikova, Svetlana E., Brinkman, Arie B., De Vos, Willem M., Van Der Oost, John, ...
The LrpA protein from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the Lrp/AsnC family of transcriptional regulatory proteins, of which the Escherichia coli leucine-responsive...
Substrate-Induced Production and Secretion of Cellulases by Clostridium acetobutylicum
López-Contreras, Ana M., Gabor, Krisztina, Martens, Aernout A., Renckens, Bernadet A. M., Claassen, Pieternel A. M., Van Der Oost, John, ...
Clostridium acetobutylicum ATCC 824 is a solventogenic bacterium that grows heterotrophically on a variety of carbohydrates, including glucose, cellobiose, xylose, and lichenan, a linear polymer of...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...
Kessler, Alexandra, Brinkman, Arie B., Van Der Oost, John, Prangishvili, David
The double-stranded DNA genomes of the crenarchaeal rudiviruses SIRV1 (32 kb) and SIRV2 (35 kb) were previously sequenced. Here we present results of the analysis of gene expression of these viruses...
Chiaraluce, Roberta, Gianese, Giulio, Angelaccio, Sebastiana, Florio, Rita, Van Lieshout, Johan F. T., Van Der Oost, John, ...
The family 16 endo-β-1,3 glucanase from the extremophilic archaeon Pyrococcus furiosus is a laminarinase, which in 7.9 M GdmCl (guanidinium chloride) maintains a significant amount of tertiary...
Gödde, Carolin, Sahm, Kerstin, Brouns, Stan J. J., Kluskens, Leon D., Van Der Oost, John, De Vos, Willem M., ...
A gene encoding a subtilisin-like protease, designated islandisin, from the extremely thermophilic bacterium Fervidobacterium islandicum (DSMZ 5733) was cloned and actively expressed in Escherichia...
The semi-phosphorylative Entner–Doudoroff pathway in hyperthermophilic archaea: a re-evaluation
Ahmed, Hatim, Ettema, Thijs J. G., Tjaden, Britta, Geerling, Ans C. M., Van Der Oost, John, Siebers, Bettina
Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner–Doudoroff) pathway generally proceeds via a non-phosphorylative...
Verhees, Corné H, Koot, Denise G M, Ettema, Thijs J G, Dijkema, Cor, De Vos, Willem M, Van Der Oost, John
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...
DNA family shuffling of hyperthermostable beta-glycosidases.
Kaper, Thijs, Brouns, Stan J J, Geerling, Ans C M, De Vos, Willem M, Van Der Oost, John
The structural compatibility of two hyperthermostable family 1 glycoside hydrolases, Pyrococcus furiosus CelB and Sulfolobus solfataricus LacS, as well as their kinetic potential were studied by...
Kluskens, Leon D, Voragen, Alphons G J, De Vos, Willem M, Van Der Oost, John
The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PelA) in the extracellular medium. The...
The unique features of glycolytic pathways in Archaea.
Verhees, Corné H, Kengen, Servé W M, Tuininga, Judith E, Schut, Gerrit J, Adams, Michael W W, De Vos, Willem M, ...
An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved,...
Koutsopoulos, Sotirios, Van Der Oost, John, Norde, Willem
Conformational characteristics and the adsorption behavior of endo-β-1,3-glucanase from the hyperthermophilic microorganism Pyrococcus furiosus were studied by circular dichroism, steady-state and...
Machielsen, Ronnie, Uria, Agustinus R., Kengen, Servé W. M., Van Der Oost, John
The gene encoding a novel alcohol dehydrogenase that belongs to the aldo-keto reductase superfamily has been identified in the hyperthermophilic archaeon Pyrococcus furiosus. The gene, referred to as...
Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family
Thaw, Paul, Sedelnikova, Svetlana E., Muranova, Tatyana, Wiese, Sebastian, Ayora, Sylvia, Alonso, Juan C., ...
The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC)...
Brouns, Stan J. J., Smits, Nicole, Wu, Hao, Snijders, Ambrosius P. L., Wright, Phillip C., De Vos, Willem M., ...
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....