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Archaea
Volume 1, Issue 5, Pages 347-352
http://dx.doi.org/10.1155/2005/314760
Research Article

Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes

Division of Science and Mathematics, University of Minnesota, Morris, 600 E. 4th Street, Morris, MN 56267, USA

Received 7 June 2004; Accepted 15 September 2004

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [45 citations]

The following is the list of published articles that have cited the current article.

  • Bettina Siebers, and Peter Schönheit, “Unusual pathways and enzymes of central carbohydrate metabolism in Archaea,” Current Opinion in Microbiology, vol. 8, no. 6, pp. 695–705, 2005. View at Publisher · View at Google Scholar
  • Meike Goenrich, Rudolf K. Thauer, Hiroya Yurimoto, and Nobuo Kato, “Formaldehyde activating enzyme (Fae) and hexulose-6-phosphate synthase (Hps) in Methanosarcina barkeri: A possible function in ribose-5-phosphate biosynthesis,” Archives of Microbiology, vol. 184, no. 1, pp. 41–48, 2005. View at Publisher · View at Google Scholar
  • Hiroya Yurimoto, Nobuo Kato, and Yasuyoshi Sakai, “Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism,” The Chemical Record, vol. 5, no. 6, pp. 367–375, 2005. View at Publisher · View at Google Scholar
  • Michael Kaufmann, “The role of the COG database in comparative and functional genomics,” Current Bioinformatics, vol. 1, no. 3, pp. 291–300, 2006. View at Publisher · View at Google Scholar
  • Izumi Orita, Takaaki Sato, Hiroya Yurimoto, Nobuo Kato, Haruyuki Atomi, Tadayuki Imanaka, and Yasuyoshi Sakai, “The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis,” Journal Of Bacteriology, vol. 188, no. 13, pp. 4698–4704, 2006. View at Publisher · View at Google Scholar
  • Izumi Orita, Takaaki Sato, Hiroya Yurimoto, Nobuo Kato, Haruyuki Atomi, Tadayuki Imanaka, and Yasuyoshi Sakai, “The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis,” Journal of Bacteriology, vol. 188, no. 13, pp. 4698–4704, 2006. View at Publisher · View at Google Scholar
  • Milanko R. Stupar, “Eukaryotes arose after genetic recombination,” Archive of Oncology, vol. 14, no. 1-2, pp. 11–14, 2006. View at Publisher · View at Google Scholar
  • Christine C. Milburn, Henry J. Lamble, Alex Theodossis, David W. Hough, Michael J. Danson, Steven D. Bull, and Garry L. Taylor, “The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus,” Journal of Biological Chemistry, vol. 281, no. 21, pp. 14796–14804, 2006. View at Publisher · View at Google Scholar
  • Nobuo Kato, Hiroya Yurimoto, and Rudolf K. Thauer, “The Physiological Role of the Ribulose Monophosphate Pathway in Bacteria and Archaea,” Bioscience, Biotechnology, and Biochemistry, vol. 70, no. 1, pp. 10–21, 2006. View at Publisher · View at Google Scholar
  • Ulrike Jahn, Wolfgang Eisenreich, Michael Hügler, Harald Huber, and Georg Fuchs, “Insights into the autotrophic CO2 fixation pathway of the archaeon Ignicoccus hospitalis: Comprehensive analysis of the central carbon metabolism,” Journal of Bacteriology, vol. 189, no. 11, pp. 4108–4119, 2007. View at Publisher · View at Google Scholar
  • Roger A. Garrett, and Hans-Peter Klenkpp. 1–388, 2007. View at Publisher · View at Google Scholar
  • Nobuyuki Yoshida, Hiroshi Egami, Naoko Ohhata, Tohoru Katsuragi, Yoshiki Tani, and Hiroshi Takagi, “An extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4, isolated from crude oil,” Journal of Bacteriology, vol. 189, no. 19, pp. 6824–6831, 2007. View at Publisher · View at Google Scholar
  • Michaela Falb, Kerstin Müller, Lisa Königsmaier, Tanja Oberwinkler, Patrick Horn, Susanne Gronau, Orland Gonzalez, Friedhelm Pfeiffer, Erich Bornberg-Bauer, and Dieter Oesterhelt, “Metabolism of halophilic archaea,” Extremophiles, vol. 12, no. 2, pp. 177–196, 2008. View at Publisher · View at Google Scholar
  • Milanko Stupar, “Nucleogenesis and origin of organelles,” Archive of Oncology, vol. 16, no. 3-4, pp. 88–92, 2008. View at Publisher · View at Google Scholar
  • Hiroya Yurimoto, Nobuo Kato, and Yasuyoshi Sakai, “Genomic organization and biochemistry of the ribulose monophosphate pathway and its application in biotechnology,” Applied Microbiology and Biotechnology, vol. 84, no. 3, pp. 407–416, 2009. View at Publisher · View at Google Scholar
  • Ivan A. Berg, Daniel Kockelkorn, W. Hugo Ramos-Vera, Rafael F. Say, Jan Zarzycki, Michael Hügler, Birgit E. Alber, and Georg Fuchs, “Autotrophic carbon fixation in archaea,” Nature Reviews Microbiology, vol. 8, no. 6, pp. 447–460, 2010. View at Publisher · View at Google Scholar
  • Laura L. Grochowski, and Robert H. White, “Biosynthesis of the Methanogenic Coenzymes,” Comprehensive Natural Products II, pp. 711–748, 2010. View at Publisher · View at Google Scholar
  • Sung-Ho Yun, Sang Oh Kwon, Gun Wook Park, Jin Young Kim, Sung Gyun Kang, Jung-Hyun Lee, Young-Ho Chung, Soohyun Kim, Jong-Soon Choi, and Seung Il Kim, “Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth,” Journal of Proteomics, vol. 74, no. 10, pp. 1926–1933, 2011. View at Publisher · View at Google Scholar
  • Guenter Raddatz, Sonja-Verena Albers, Fabian Blombach, Nikos Kyrpides, Christa Lanz, Markus Rampp, Andrea Rosinus, Kira S. Makarova, Stephan C. Schuster, Reinhard Hensel, Bettina Siebers, Melanie Zaparty, Britta Tjaden, Steve D. Bell, Arnulf Kletzin, André Plagens, Mathias von Jan, and Hans-Peter Klenk, “The complete genome sequence of Thermoproteus tenax: A physiologically versatile member of the Crenarchaeota,” PLoS ONE, vol. 6, no. 10, 2011. View at Publisher · View at Google Scholar
  • Iain Anderson, Carla Risso, Dawn Holmes, Susan Lucas, Alex Copeland, Alla Lapidus, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Samuel Pitluck, Elizabeth Saunders, Thomas Brettin, John C. Detter, Cliff Han, Roxanne Tapia, Frank Larimer, Miriam Land, Loren Hauser, Tanja Woyke, Derek Lovley, Nikos Kyrpides, and Natalia Ivanova, “Complete genome sequence of Ferroglobus placidus AEDII12DO,” Standards in Genomic Sciences, vol. 5, no. 1, pp. 50–60, 2011. View at Publisher · View at Google Scholar
  • Carmen Scheuner, Markus Göker, Iris Porat, Hans-Peter Klenk, Nikos Kyrpides, Iain Anderson, Kostas Mavromatis, Sean D. Hooper, and Natalia Ivanova, “Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes,” PLoS ONE, vol. 6, no. 5, 2011. View at Publisher · View at Google Scholar
  • Andreas Pickl, Ulrike Johnsen, and Peter Schoenheit, “Fructose Degradation in the Haloarchaeon Haloferax volcanii Involves a Bacterial Type Phosphoenolpyruvate-Dependent Phosphotransferase System, Fructose-1-Phosphate Kinase, and Class II Fructose-1,6-Bisphosphate Aldolase,” Journal Of Bacteriology, vol. 194, no. 12, pp. 3088–3097, 2012. View at Publisher · View at Google Scholar
  • Riku Aono, Takaaki Sato, Ayumu Yano, Shosuke Yoshida, Yuichi Nishitani, Kunio Miki, Tadayuki Imanaka, and Haruyuki Atomi, “Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway,” Journal Of Bacteriology, vol. 194, no. 24, pp. 6847–6855, 2012. View at Publisher · View at Google Scholar
  • Anja Spang, Anja Poehlein, Pierre Offre, Sabine Zumbrägel, Susanne Haider, Nicolas Rychlik, Boris Nowka, Christel Schmeisser, Elena V. Lebedeva, Thomas Rattei, Christoph Böhm, Markus Schmid, Alexander Galushko, Roland Hatzenpichler, Thomas Weinmaier, Rolf Daniel, Christa Schleper, Eva Spieck, Wolfgang Streit, and Michael Wagner, “ The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations ,” Environmental Microbiology, vol. 14, no. 12, pp. 3122–3145, 2012. View at Publisher · View at Google Scholar
  • Jacob P Beam, Zackary J Jay, Mark A Kozubal, and William P Inskeep, “Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park,” The ISME Journal, 2013. View at Publisher · View at Google Scholar
  • Takaaki Sato, and Haruyuki Atomipp. 307–330, 2013. View at Publisher · View at Google Scholar
  • Miriam Kolog Gulko, Mike Dyall-Smith, Orland Gonzalez, and Dieter Oesterhelt, “How Do Haloarchaea Synthesize Aromatic Amino Acids?,” Plos One, vol. 9, no. 9, 2014. View at Publisher · View at Google Scholar
  • John A. Raven, and Peter J. Ralph, “Enhanced biofuel production using optimality, pathway modification and waste minimization,” Journal of Applied Phycology, 2014. View at Publisher · View at Google Scholar
  • Xue Guo, Huaqun Yin, Yili Liang, Qi Hu, Xishu Zhou, Yunhua Xiao, Liyuan Ma, Xian Zhang, Guanzhou Qiu, and Xueduan Liu, “Comparative Genome Analysis Reveals Metabolic Versatility and Environmental Adaptations of Sulfobacillus thermosulfidooxidans Strain ST,” Plos One, vol. 9, no. 6, 2014. View at Publisher · View at Google Scholar
  • Christopher Braesen, Dominik Esser, Bernadette Rauch, and Bettina Siebers, “Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation,” Microbiology and Molecular Biology Reviews, vol. 78, no. 1, pp. 89–175, 2014. View at Publisher · View at Google Scholar
  • Xiao-Yang Zhi, Ji-Cheng Yao, Hong-Wei Li, Ying Huang, and Wen-Jun Li, “Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes,” Molecular Phylogenetics and Evolution, 2014. View at Publisher · View at Google Scholar
  • Boung-Hyuk Yoo, Eun-Hee Park, Jin-Ho Seo, and Myoung-Dong Kim, “Cloning of the Transketolase Gene from Erythritol-Producing Yeast Candida magnoliae,” Journal of Microbiology and Biotechnology, vol. 24, no. 10, pp. 1389–1396, 2014. View at Publisher · View at Google Scholar
  • Vincenzo Carbone, Linley R. Schofield, Yanli Zhang, Carrie Sang, Debjit Dey, Ingegerd M. Hannus, William F. Martin, Andrew J. Sutherland-Smith, and Ron S. Ronimus, “Structure and evolution of the archaeal lipid synthesis enzyme sn-Glycerol-1-phosphate dehydrogenase,” Journal of Biological Chemistry, vol. 290, no. 35, pp. 21690–21704, 2015. View at Publisher · View at Google Scholar
  • Riku Aono, Takaaki Sato, Tadayuki Imanaka, and Haruyuki Atomi, “A pentose bisphosphate pathway for nucleoside degradation in Archaea,” Nature Chemical Biology, 2015. View at Publisher · View at Google Scholar
  • Andreas Pickl, and Peter Schönheit, “The oxidative pentose phosphate pathway in the haloarchaeon Haloferax volcanii involves a novel type of glucose-6-phosphate dehydrogenase – the archaeal Zwischenferment,” FEBS Letters, 2015. View at Publisher · View at Google Scholar
  • Sergio Esposito, “Nitrogen Assimilation, Abiotic Stress and Glucose 6-Phosphate Dehydrogenase: The Full Circle of Reductants,” Plants, vol. 5, no. 2, pp. 24, 2016. View at Publisher · View at Google Scholar
  • James J. Moran, Laura M. Whitmore, Nancy G. Isern, Margaret F. Romine, Krystin M. Riha, William P. Inskeep, and Helen W. Kreuzer, “Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park,” Extremophiles, 2016. View at Publisher · View at Google Scholar
  • Yuki Makino, Takaaki Sato, Hiroki Kawamura, Shin-ichi Hachisuka, Ryo Takeno, Tadayuki Imanaka, and Haruyuki Atomi, “An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism,” Nature Communications, vol. 7, pp. 13446, 2016. View at Publisher · View at Google Scholar
  • Jacqueline Wolf, Helge Stark, Katharina Fafenrot, Andreas Albersmeier, Trong K. Pham, Katrin B. Müller, Benjamin H. Meyer, Lena Hoffmann, Lu Shen, Stefan P. Albaum, Theresa Kouril, Kerstin Schmidt-Hohagen, Meina Neumann-Schaal, Christopher Bräsen, Jörn Kalinowski, Phillip C. Wright, Sonja-Verena Albers, Dietmar Schomburg, and Bettina Siebers, “ A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose ,” Molecular Microbiology, 2016. View at Publisher · View at Google Scholar
  • Christopher T Straub, Benjamin M Zeldes, Gerrit J Schut, Michael WW Adams, and Robert M Kelly, “Extremely thermophilic energy metabolisms: biotechnological prospects,” Current Opinion in Biotechnology, vol. 45, pp. 104–112, 2017. View at Publisher · View at Google Scholar
  • Simone Balzer Le, Tonje Marita Bjerkan Heggeset, Tone Haugen, Ingemar Nærdal, and Trygve Brautaset, “6-Phosphofructokinase and ribulose-5-phosphate 3-epimerase in methylotrophic Bacillus methanolicus ribulose monophosphate cycle,” Applied Microbiology and Biotechnology, 2017. View at Publisher · View at Google Scholar
  • Julian Quehenberger, Lu Shen, Sonja-Verena Albers, Bettina Siebers, and Oliver Spadiut, “Sulfolobus – A Potential Key Organism in Future Biotechnology,” Frontiers in Microbiology, vol. 8, 2017. View at Publisher · View at Google Scholar
  • Takunari Kono, Sandhya Mehrotra, Chikako Endo, Natsuko Kizu, Mami Matusda, Hiroyuki Kimura, Eiichi Mizohata, Tsuyoshi Inoue, Tomohisa Hasunuma, Akiho Yokota, Hiroyoshi Matsumura, and Hiroki Ashida, “A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea,” Nature Communications, vol. 8, pp. 14007, 2017. View at Publisher · View at Google Scholar
  • Kristopher A. Hunt, Ryan M. Jennings, William P. Inskeep, and Ross P. Carlson, “Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community,” PLOS Computational Biology, vol. 14, no. 9, pp. e1006431, 2018. View at Publisher · View at Google Scholar
  • Julie A. Maupin-Furlow, “Vitamin B1 (Thiamine) Metabolism and Regulation in Archaea,” B Group Vitamins - Current Uses and Perspectives, 2018. View at Publisher · View at Google Scholar