Genomes and Genes
Summary: Ribulose substituted by one or more phosphoric acid moieties.
- Mitchell R, Theobald J, Parry M, Lawlor D. Is there scope for improving balance between RuBP-regeneration and carboxylation capacities in wheat at elevated CO2?. J Exp Bot. 2000;51 Spec No:391-7 pubmed..This showed that the observed balance between carboxylation and RuBP-regeneration capacities in young wheat leaves could be consistent with adaptation to the current, or even the preindustrial pCa. ..
- McCormick K, Hingre K, Brown J, Mick G. Activation of in situ glycolytic flux by bisphosphorylated compounds: studies in porous rat adipocytes. Biochim Biophys Acta. 1992;1135:1-7 pubmed..In conclusion, F2,6DP is the pre-eminent in situ regulator of in situ adipocyte glycolysis, especially at higher ATP levels, although other sugars containing two phosphoryl groups may under certain conditions cause activation. ..
- Yasueda H, Kawahara Y, Sugimoto S. Bacillus subtilis yckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression. J Bacteriol. 1999;181:7154-60 pubmed..subtilis. In conclusion, we found an active yckG (for HPS)-yckF (for PHI) gene structure (now named hxlA-hxlB) in a nonmethylotroph, B. subtilis, which inherently preserves the RuMP pathway. ..
- Bumann M, Djafarzadeh S, Oberholzer A, Bigler P, Altmann M, Trachsel H, et al. Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. J Biol Chem. 2004;279:37087-94 pubmed
- Borisjuk L, Neuberger T, Schwender J, Heinzel N, Sunderhaus S, Fuchs J, et al. Seed architecture shapes embryo metabolism in oilseed rape. Plant Cell. 2013;25:1625-40 pubmed publisher..We conclude that in vivo metabolic fluxes are locally regulated and connected to seed architecture, driving the embryo toward an efficient use of available light and space. ..
- Long S, Zhu X, Naidu S, Ort D. Can improvement in photosynthesis increase crop yields?. Plant Cell Environ. 2006;29:315-30 pubmed..50%. Because some changes could be achieved by transgenic technology, the time of the development of commercial cultivars could be considerably less than by conventional breeding and potentially, within 10-15 years. ..
- Kato N, Yurimoto H, Thauer R. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci Biotechnol Biochem. 2006;70:10-21 pubmed..Thus the enzyme system plays a different role in bacteria and archaea by catalyzing the forward and reverse reactions respectively. ..
- van Lun M, van der Spoel D, Andersson I. Subunit interface dynamics in hexadecameric rubisco. J Mol Biol. 2011;411:1083-98 pubmed publisher..These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance. ..
- Oja V, Eichelmann H, Laisk A. The size of the lumenal proton pool in leaves during induction and steady-state photosynthesis. Photosynth Res. 2011;110:73-88 pubmed publisher..The accumulation of electrons in reduced compounds of the stroma and cytosol is the natural cause for accumulation of a stoichiometric pool of lumenal protons during this transient event. ..
- Dani D, Sainis J. Isolation and characterization of a thylakoid membrane module showing partial light and dark reactions. Biochim Biophys Acta. 2005;1669:43-52 pubmed..Most of the components of this module remained together even after sucrose density gradient centrifugation. This is the first report on the isolation of a photosynthetic module involving membrane and soluble proteins. ..
- Kondo H, Nakamura Y, Dong Y, Nikawa J, Sueda S. Pyridoxine biosynthesis in yeast: participation of ribose 5-phosphate ketol-isomerase. Biochem J. 2004;379:65-70 pubmed
- Kane K, Moheb A, Fukushi Y, Roy R, Huner N, Ibrahim R, et al. Daphnetin methylation stabilizes the activity of phosphoribulokinase in wheat during cold acclimation. Biochem Cell Biol. 2012;90:657-66 pubmed publisher..The results also show that cold acclimation does not alter the level of TaPRK mRNA or its enzyme activity, and thus ensures the stable generation of ribulose 1,5-biphosphate. ..
- Kapralov M, Smith J, Filatov D. Rubisco evolution in Câ‚„ eudicots: an analysis of Amaranthaceae sensu lato. PLoS ONE. 2012;7:e52974 pubmed publisher..Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco. ..
- Jin L, Zhou H, Zhao S, Yang W, Niu S, Wang D. [Cloning and characterization of a new antibacterial target, 3,4-dihydroxy-2-butanone-4-phosphate synthase]. Wei Sheng Wu Xue Bao. 2012;52:1415-20 pubmed..5 and 25 degrees C and in the presence of Mg2+. DHBPs could be highly expressed in soluble form in E. coli BL21 strain, and the recombinant protein has activity to hydrolyze Ru5P. ..
- Chen G, Yong Z, Liao Y, Zhang D, Chen Y, Zhang H, et al. Photosynthetic acclimation in rice leaves to free-air CO2 enrichment related to both ribulose-1,5-bisphosphate carboxylation limitation and ribulose-1,5-bisphosphate regeneration limitation. Plant Cell Physiol. 2005;46:1036-45 pubmed..It appears that the photosynthetic acclimation in rice leaves is related to both ribulose-1,5-bisphosphate (RuBP) carboxylation limitation and RuBP regeneration limitation. ..
- Bracher A, Eisenreich W, Schramek N, Ritz H, Götze E, Herrmann A, et al. Biosynthesis of pteridines. NMR studies on the reaction mechanisms of GTP cyclohydrolase I, pyruvoyltetrahydropterin synthase, and sepiapterin reductase. J Biol Chem. 1998;273:28132-41 pubmed..On the other hand, the reaction catalyzed by sepiapterin reductase does not involve any detectable incorporation of solvent protons into tetrahydrobiopterin. ..
- Richter G, Volk R, Krieger C, Lahm H, Rothlisberger U, Bacher A. Biosynthesis of riboflavin: cloning, sequencing, and expression of the gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of Escherichia coli. J Bacteriol. 1992;174:4050-6 pubmed..Sequence homology indicates that gene luxH of Vibrio harveyi and the central open reading frame of the Bacillus subtilis riboflavin operon code for 3,4-dihydroxy-2-butanone 4-phosphate synthase. ..
- Templeton P, Litman E, Metzner S, Ahn N, Sousa M. Structure of mediator of RhoA-dependent invasion (MRDI) explains its dual function as a metabolic enzyme and a mediator of cell invasion. Biochemistry. 2013;52:5675-84 pubmed publisher..Thus, structural elements in MRDI distal from the MTR-1-P catalytic site are responsible for the invasion phenotype. ..
- Schrader S, Kleinbeck K, Sharkey T. Rapid heating of intact leaves reveals initial effects of stromal oxidation on photosynthesis. Plant Cell Environ. 2007;30:671-8 pubmed..Measurements of triose-phosphate levels and NADP-malate dehydrogenase activation (a stromal redox proxy) indicated that the regeneration of RuBP by the Calvin cycle was limited by the availability of redox power. ..
- Hikosaka K, Ishikawa K, Borjigidai A, Muller O, Onoda Y. Temperature acclimation of photosynthesis: mechanisms involved in the changes in temperature dependence of photosynthetic rate. J Exp Bot. 2006;57:291-302 pubmed..Physiological and biochemical causes for the change in these parameters are discussed. ..
- Igamberdiev A, Shen T, Gardeström P. Function of mitochondria during the transition of barley protoplasts from low light to high light. Planta. 2006;224:196-204 pubmed..The oligomycin-treated protoplasts were deficient in cytosolic ATP and thereby unable to support Calvin cycle operation. This resulted in a delayed capacity to adjust to a sudden increase in light intensity. ..
- Nakano T, Ohki I, Yokota A, Ashida H. MtnBD is a multifunctional fusion enzyme in the methionine salvage pathway of Tetrahymena thermophila. PLoS ONE. 2013;8:e67385 pubmed publisher..Our results suggest that the MtnB domain of T. thermophila MtnBD acquired the new function to catalyze both the dehydratase and enolase reactions through evolutionary gene mutations, rather than fusion of MSP genes. ..
- Takahashi N, Washio J, Mayanagi G. Metabolomics of supragingival plaque and oral bacteria. J Dent Res. 2010;89:1383-8 pubmed publisher..These pathways and changes in metabolites observed in supragingival plaque were similar to the integration of metabolite profiles in Streptococcus and Actinomyces. ..
- Sørhagen K, Laxa M, Peterhansel C, Reumann S. The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence. Plant Biol (Stuttg). 2013;15:723-36 pubmed publisher..The analyses further support the idea that photorespiration and non-photorespiratory peroxisomal metabolism play multi-faceted roles in pathogen defence beyond metabolism of reactive oxygen species. ..
- Crafts Brandner S, Salvucci M. Sensitivity of photosynthesis in a C4 plant, maize, to heat stress. Plant Physiol. 2002;129:1773-80 pubmed..We conclude that inactivation of Rubisco was the primary constraint on the rate of Pn of maize leaves as leaf temperature increased above 30 degrees C. ..
- Whitney S, Sharwood R, Orr D, White S, Alonso H, Galmés J. Isoleucine 309 acts as a C4 catalytic switch that increases ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) carboxylation rate in Flaveria. Proc Natl Acad Sci U S A. 2011;108:14688-93 pubmed publisher..Coengineering a catalytically faster C(3) rubisco and a CO(2)-concentrating mechanism within C(3) crop species could enhance their efficiency in resource use and yield. ..
- Grochowski L, Xu H, White R. Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway. J Bacteriol. 2005;187:7382-9 pubmed publisher..Additional work has demonstrated that ribulose-5-phosphate is derived by the loss of formaldehyde from D-arabino-3-hexulose-6-phosphate, catalyzed by the protein product of the MJ1447 gene...
- Akana J, Fedorov A, Fedorov E, Novak W, Babbitt P, Almo S, et al. D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily. Biochemistry. 2006;45:2493-503 pubmed publisher..Instead, this "superfamily" may result from assembly from smaller modules, including the conserved phosphate binding motif associated with the C-terminal (beta/alpha)(2)-quarter barrel...
- Portais J, Tavernier P, Gosselin I, Barbotin J. Relevance and isotopic assessment of hexose-6-phosphate recycling in micro-organisms. J Biotechnol. 2000;77:49-64 pubmed..The model was initially designed for the study of micro-organisms producing polysaccharides, but it can be extended to other situations. ..
- Tamoi M, Nagaoka M, Miyagawa Y, Shigeoka S. Contribution of fructose-1,6-bisphosphatase and sedoheptulose-1,7-bisphosphatase to the photosynthetic rate and carbon flow in the Calvin cycle in transgenic plants. Plant Cell Physiol. 2006;47:380-90 pubmed
- Graille M, Meyer P, Leulliot N, Sorel I, Janin J, van Tilbeurgh H, et al. Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes. Biochimie. 2005;87:763-9 pubmed..The yeast enzyme associates as a homotetramer similarly to the archaeal protein. The effect of an inactivating mutation (Arg189 to Lys) is discussed in view of the information brought by this structure. ..
- Gordon G, McKinlay J. Calvin cycle mutants of photoheterotrophic purple nonsulfur bacteria fail to grow due to an electron imbalance rather than toxic metabolite accumulation. J Bacteriol. 2014;196:1231-7 pubmed publisher..rubrum, but not of Rp. palustris, grew photoheterotrophically on malate without electron acceptors or H2 production. The mechanism by which Rs. rubrum grows under these conditions remains to be elucidated. ..
- Tao L, Tanzer J. Novel sucrose-dependent adhesion co-factors in Streptococcus mutans. J Dent Res. 2002;81:505-10 pubmed..The multidrug efflux pump mutant failed to colonize the rats. Three other mutants colonized the rats by reverting to the wild type. Therefore, these four factors may contribute to S. mutans sucrose-dependent adhesion...
- Maire V, Martre P, Kattge J, Gastal F, Esser G, Fontaine S, et al. The coordination of leaf photosynthesis links C and N fluxes in C3 plant species. PLoS ONE. 2012;7:e38345 pubmed publisher..These results open a new avenue for predicting photosynthetic capacity and leaf nitrogen content in vegetation models. ..
- Zhu C, Ziska L, Zhu J, Zeng Q, Xie Z, Tang H, et al. The temporal and species dynamics of photosynthetic acclimation in flag leaves of rice (Oryza sativa) and wheat (Triticum aestivum) under elevated carbon dioxide. Physiol Plant. 2012;145:395-405 pubmed publisher..These data suggest that the basis for photosynthetic acclimation with elevated [CO?] may be more closely associated with enhanced rates of senescence, and, as a consequence, may be temporally dynamic, with significant species variation. ..
- Zhu J, Burgner J, Harms E, Belitsky B, Smith J. A new arrangement of (beta/alpha)8 barrels in the synthase subunit of PLP synthase. J Biol Chem. 2005;280:27914-23 pubmed..The distribution of conserved surfaces in the PdxS dodecamer was used to predict a docking site for the glutaminase partner, PdxT. ..
- Merz A, Yee M, Szadkowski H, Pappenberger G, Crameri A, Stemmer W, et al. Improving the catalytic activity of a thermophilic enzyme at low temperatures. Biochemistry. 2000;39:880-9 pubmed..In support of this interpretation, the rate of trypsinolysis or of thermal denaturation is accelerated significantly in the activated protein variants. ..
- Henkes S, Sonnewald U, Badur R, Flachmann R, Stitt M. A small decrease of plastid transketolase activity in antisense tobacco transformants has dramatic effects on photosynthesis and phenylpropanoid metabolism. Plant Cell. 2001;13:535-51 pubmed
- Schlee S, Dietrich S, Kurćon T, DELANEY P, Goodey N, Sterner R. Kinetic mechanism of indole-3-glycerol phosphate synthase. Biochemistry. 2013;52:132-42 pubmed publisher..The liberation of the product from the active site is the rate-limiting step of the overall reaction. Our results confirm the importance of flexible active loops for substrate binding and catalysis by sIGPS. ..
- Yamori W, Suzuki K, Noguchi K, Nakai M, Terashima I. Effects of Rubisco kinetics and Rubisco activation state on the temperature dependence of the photosynthetic rate in spinach leaves from contrasting growth temperatures. Plant Cell Environ. 2006;29:1659-70 pubmed..This study suggests that photosynthetic performance is largely determined by the Rubisco kinetics at low temperature and by Rubisco Kinetics and the Rubisco activation state at high temperature. ..
- Spencer N, Hopkinson D. Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE). Ann Hum Genet. 1980;43:335-42 pubmed..6. Electrophoretic analysis of RPE and RPI isozyme patterns in extracts of man/mouse hybrid cells indicates that RPE is probably a dimer and RPI may also be polymeric. ..
- Terashima I, Hanba Y, Tazoe Y, Vyas P, Yano S. Irradiance and phenotype: comparative eco-development of sun and shade leaves in relation to photosynthetic CO2 diffusion. J Exp Bot. 2006;57:343-54 pubmed..To increase the mesophyll surface area, the leaf can either be thicker or have smaller cells. Issues of cell size are discussed to understand plasticity in leaf thickness. ..
- Tavender T, Halliday N, Hardie K, Winzer K. LuxS-independent formation of AI-2 from ribulose-5-phosphate. BMC Microbiol. 2008;8:98 pubmed publisher..It does not contribute to AI-2 formation in wildtype E. coli and S. aureus under the conditions tested, but may be responsible for the AI-2-like activities reported for other organisms lacking the luxS gene. ..
- Chistoserdova L, Gomelsky L, Vorholt J, Gomelsky M, Tsygankov Y, Lidstrom M. Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph. Microbiology. 2000;146 ( Pt 1):233-8 pubmed..This function is in contrast to Methylobacterium extorquens AM1, in which the H4MPT-linked pathway is essential...
- Yurimoto H, Kato N, Sakai Y. Genomic organization and biochemistry of the ribulose monophosphate pathway and its application in biotechnology. Appl Microbiol Biotechnol. 2009;84:407-16 pubmed publisher..Heterologous expression of HPS and PHI in various organisms allows them to metabolize and detoxify formaldehyde, and we also review recent progress in such applications in biotechnology. ..
- Wise E, Yew W, Akana J, Gerlt J, Rayment I. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2005;44:1816-23 pubmed
- Pearce F. Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies. Biochem J. 2006;399:525-34 pubmed publisher..Our observations also illustrate the phylogenetic diversity of mechanisms for regulating Rubisco and raise questions about whether an activase-like mechanism should be expected outside the green-algal/higher-plant lineage...
- Xiong Y, DeFraia C, Williams D, Zhang X, Mou Z. Deficiency in a cytosolic ribose-5-phosphate isomerase causes chloroplast dysfunction, late flowering and premature cell death in Arabidopsis. Physiol Plant. 2009;137:249-63 pubmed publisher..These results demonstrate that a deficiency in the non-oxidative phase of the cytosolic oxPPP has pleiotropic effects on plant growth and development and causes premature cell death. ..