Whole-Genome Transcriptional Profiling of Bradyrhizobium japonicum during Chemoautotrophic Growth

ABSTRACT Bradyrhizobium japonicum is a facultative chemoautotroph capable of utilizing hydrogen gas as an electron donor in a respiratory chain terminated by oxygen to provide energy for cellular processes and carbon dioxide assimilation via a reductive pentose phosphate pathway. A transcriptomic analysis of B. japonicum cultured chemoautotrophically identified 1,485 transcripts, representing 17.5% of the genome, as differentially expressed when compared to heterotrophic cultures. Genetic determinants required for hydrogen utilization and carbon fixation, including the uptake hydrogenase system and components of the Calvin-Benson-Bassham cycle, were strongly induced in chemoautotrophically cultured cells. A putative isocitrate lyase (aceA; blr2455) was among the most strongly upregulated genes, suggesting a role for the glyoxylate cycle during chemoautotrophic growth. Addition of arabinose to chemoautotrophic cultures of B. japonicum did not significantly alter transcript profiles. Furthermore, a subset of nitrogen fixation genes was moderately induced during chemoautotrophic growth. In order to specifically address the role of isocitrate lyase and nitrogenase in chemoautotrophic growth, we cultured aceA, nifD, and nifH mutants under chemoautotrophic conditions. Growth of each mutant was similar to that of the wild type, indicating that the glyoxylate bypass and nitrogenase activity are not essential components of chemoautotrophy in B. japonicum.

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The possible role of some enzymes in sclerotia formation in Aspergillus ochraceus

Canadian Journal of Microbiology ◽

10.1139/m83-117 ◽

1983 ◽

Vol 29 (6) ◽

pp. 718-723 ◽

Cited By ~ 2

Author(s):

Nachman Paster ◽

Ilan Chet

Keyword(s):

Isocitrate Lyase ◽

Tricarboxylic Acid Cycle ◽

Glyoxylate Cycle ◽

Pentose Phosphate ◽

Aspergillus Ochraceus ◽

Phosphogluconate Dehydrogenase ◽

Cycle Plays ◽

Glucose 6 Phosphate Dehydrogenase ◽

The Glyoxylate Cycle

The role of some enzymes in sclerotia production by Aspergillus ochraceus was studied using a sclerotia-producing strain grown under conditions in which sclerotia production was either favoured or inhibited. In addition, a mutant strain incapable of producing sclerotia was used. No significant differences in patterns of soluble proteins, polyphenol oxidase, and esterases could be detected electrophoretically by gel electrophoresis, while the peroxidase pattern of both the sclerotia-producing strain and the mutant showed three bands as compared with two bands that appeared when sclerotia formation was inhibited. The activities of the tricarboxylic acid cycle enzymes, malate dehydrogenase and succinate dehydrogenase, and those of the pentose-phosphate pathway, glucose-6 phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, were almost identical in sclerotia- and nonsclerotia-producing mycelia. The activities of isocitrate lyase and malate synthetase, key enzymes of the glyoxylate cycle, and that of glyoxylate dehydrogenase which is related to this cycle were significantly reduced when sclerotia formation was inhibited either by methionine or by high levels of CO2. It is suggested that the glyoxylate cycle plays an important role in sclerotia formation in the fungus.

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Co-ordinate regulation of genes involved in storage lipid mobilization in Arabidopsis thaliana

Biochemical Society Transactions ◽

10.1042/bst0290283 ◽

2001 ◽

Vol 29 (2) ◽

pp. 283-286 ◽

Cited By ~ 54

Author(s):

E. L. Rylott ◽

M. A. Hooks ◽

I. A. Graham

Keyword(s):

Arabidopsis Thaliana ◽

Enzyme Activities ◽

Phosphoenolpyruvate Carboxykinase ◽

Isocitrate Lyase ◽

Glyoxylate Cycle ◽

Molecular Genetic ◽

Regulation Of Gene Expression ◽

Growth Period ◽

Malate Synthase ◽

The Glyoxylate Cycle

Molecular genetic approaches in the model plant Arabidopsis thaliana (ColO) are shedding new light on the role and control of the pathways associated with the mobilization of lipid reserves during oilseed germination and post-germinative growth. Numerous independent studies have reported on the expression of individual genes encoding enzymes from the three major pathways: β-oxidation, the glyoxylate cycle and gluconeogenesis. However, a single comprehensive study of representative genes and enzymes from the different pathways in a single plant species has not been done. Here we present results from Arabidopsis that demonstrate the co-ordinate regulation of gene expression and enzyme activities for the acyl-CoA oxidase- and 3-ketoacyl-CoA thiolasemediated steps of β-oxidation, the isocitrate lyase and malate synthase steps of the glyoxylate cycle and the phosphoenolpyruvate carboxykinase step of gluconeogenesis. The mRNA abundance and enzyme activities increase to a peak at stage 2, 48 h after the onset of seed germination, and decline thereafter either to undetectable levels (for malate synthase and isocitrate lyase) or low basal levels (for the genes of β-oxidation and gluconeogenesis). The co-ordinate induction of all these genes at the onset of germination raises the possibility that a global regulatory mechanism operates to induce the expression of genes associated with the mobilization of storage reserves during the heterotrophic growth period.

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Isocitrate lyase fromAspergillus nidulans: crystallization and X-ray analysis of a glyoxylate cycle enzyme

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444997002680 ◽

1997 ◽

Vol 53 (4) ◽

pp. 488-490 ◽

Cited By ~ 1

Author(s):

S. J. Langridge ◽

P. J. Baker ◽

J. R. De Lucas ◽

S. E. Sedelnikova ◽

G. Turner ◽

...

Keyword(s):

Isocitrate Lyase ◽

Glyoxylate Cycle ◽

X Ray ◽

Cycle Enzyme

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Transcriptional Response of Soybean Suspension-cultured Cells Induced by Nod Factors Obtained from Bradyrhizobium japonicum USDA110

Plant and Cell Physiology ◽

10.1093/pcp/pcf160 ◽

2002 ◽

Vol 43 (11) ◽

pp. 1314-1322

Author(s):

Tsuneo Hakoyama ◽

Tadashi Yokoyama ◽

Hiroshi Kouchi ◽

Ken-ichi Tsuchiya ◽

Hisatoshi Kaku ◽

...

Keyword(s):

Bradyrhizobium Japonicum ◽

Cultured Cells ◽

Transcriptional Response ◽

Nod Factors ◽

Suspension Cultured Cells

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Regulation of nitrogenase activity in Bradyrhizobium japonicum/soybean symbiosis by plant N status as determined by shoot C:N ratio

Physiologia Plantarum ◽

10.1111/j.1399-3054.1996.tb05708.x ◽

1996 ◽

Vol 98 (3) ◽

pp. 529-538 ◽

Cited By ~ 12

Author(s):

Methode Bacanamwo ◽

James E. Harper

Keyword(s):

Bradyrhizobium Japonicum ◽

Nitrogenase Activity ◽

C:N Ratio ◽

N Status

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Molecular analysis of the Penicillium marneffei glyceraldehyde-3-phosphate dehydrogenase-encoding gene (gpdA) and differential expression of gpdA and the isocitrate lyase-encoding gene (acuD) upon internalization by murine macrophages

Journal of Medical Microbiology ◽

10.1099/jmm.0.2008/002832-0 ◽

2008 ◽

Vol 57 (11) ◽

pp. 1322-1328 ◽

Cited By ~ 15

Author(s):

Sophit Thirach ◽

Chester R. Cooper ◽

Nongnuch Vanittanakom

Keyword(s):

Differential Expression ◽

Isocitrate Lyase ◽

Glyoxylate Cycle ◽

Evolutionary Relationship ◽

Amino Acid Sequences ◽

Penicillium Marneffei ◽

Macrophage Infection ◽

Dimorphic Fungus ◽

Isolation And Characterization ◽

Encoding Gene

Penicillium marneffei is an intracellular dimorphic fungus that can cause a fatal disseminated disease in human immunodeficiency virus-infected patients. The factors that affect the pathogenicity of this fungus remain unclear. Here, we report the isolation and characterization of the gpdA cDNA and genomic clones encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in P. marneffei. Phylogenetic analysis of GAPDH amino acid sequences demonstrated the evolutionary relationship of P. marneffei to other fungi, including the intracellular pathogen Ajellomyces capsulatus. To assess the central importance of phagocytic cells in defence against P. marneffei infection, we used Northern blotting to investigate the response of the isocitrate lyase-encoding gene (acuD) and gpdA to nutrient deprivation inside macrophages. The results revealed that after macrophage internalization, the gene involved in the glyoxylate cycle, acuD, showed higher expression levels as early as 2 h from the start of co-incubation, and the differential expression could be observed again at 8 h after infection. In contrast, the expression of gpdA was downregulated in the yeast phase, as well as during macrophage infection after 2, 4 and 8 h of infection. The induction of P. marneffei acuD was shown to be coordinated with the downregulation of the glycolytic gpdA gene, implying that the cytoplasmic environment of macrophages is deficient in glucose and the glyoxylate pathway could be used by this pathogen to allow subsistence on two-carbon compounds within the host cell following its intracellular persistence.

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Acetate metabolism in Escherichia coli

Canadian Journal of Microbiology ◽

10.1139/m78-027 ◽

1978 ◽

Vol 24 (2) ◽

pp. 149-153 ◽

Cited By ~ 5

Author(s):

T. M. Lakshmi ◽

Robert B. Helling

Keyword(s):

Isocitrate Dehydrogenase ◽

Citrate Synthase ◽

Isocitrate Lyase ◽

Glyoxylate Cycle ◽

Acetate Metabolism ◽

Wild Type ◽

Intermediary Metabolites ◽

Lyase Activity ◽

Acetate Medium ◽

The Glyoxylate Cycle

Levels of several intermediary metabolites were measured in cells grown in acetate medium in order to test the hypothesis that the glyoxylate cycle is repressed by phosphoenolpyruvate (PEP). Wild-type cells had less PEP than either isocitrate dehydrogenase – deficient cells (which had greater isocitrate lyase activity than the wild type) or isocitrate dehydrogenase – deficient, citrate synthase – deficient cells (which are poorly inducible). Thus induction of the glyoxylate cycle is more complicated than a simple function of PEP concentration. No correlation between enzyme activity and the level of oxaloacetate, pyruvate, or citrate was found either. Citrate was synthesized in citrate synthase – deficient mutants, possibly via citrate lyase.

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A simple dynamic model of photosynthesis in oak leaves: coupling leaf conductance and photosynthetic carbon fixation by a variable intracellular CO2 pool

Functional Plant Biology ◽

10.1071/fp03251 ◽

2004 ◽

Vol 31 (12) ◽

pp. 1195 ◽

Cited By ~ 23

Author(s):

Steffen M. Noe ◽

Christoph Giersch

Keyword(s):

Carbon Fixation ◽

Calvin Cycle ◽

Target Function ◽

Vapour Pressure Deficit ◽

Co2 Assimilation ◽

Leaf Conductance ◽

Co2 Partial Pressure ◽

Sink Term ◽

Essential Components ◽

Oak Leaves

Modelling the diurnal course of photosynthesis in oak leaves (Quercus robur L.) requires appropriate description of the dynamics of leaf photosynthesis of which diurnal variations in leaf conductance and in CO2 assimilation are essential components. We propose and analyse a simple photosynthesis model with three variables: leaf conductance (gs), the CO2 partial pressure inside the leaf (pi), and a pool of Calvin cycle intermediates (aps). The environmental factors light (I) and vapour pressure deficit (VPD) are used to formulate a target function G(I, VPD) from which the actual leaf conductance is calculated. Using this gs value and a CO2 consumption term representing CO2 fixation, a differential equation for pi is derived. Carboxylation corresponds to the sink term of the pi pool and is assumed to be feedback-inhibited by aps. This simple model is shown to produce reasonable to excellent fits to data on the diurnal time courses of photosythesis, pi and gs sampled for oak leaves.

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Impact of elevated CO2 on carbohydrate and ureide concentrations in soybean inoculated with different strains of Bradyrhizobium japonicum

Botany ◽

10.1139/b11-034 ◽

2011 ◽

Vol 89 (7) ◽

pp. 481-490 ◽

Cited By ~ 10

Author(s):

Annick Bertrand ◽

Danielle Prévost ◽

Christine Juge ◽

François-P. Chalifour

Keyword(s):

Bradyrhizobium Japonicum ◽

Feedback Inhibition ◽

Nitrogenase Activity ◽

Soluble Sugars ◽

Dry Mass ◽

Energy Reserves ◽

Commercial Strain ◽

Growth Chambers ◽

Different Strains ◽

Selection Of

Elevated CO2 increases soybean growth and photosynthesis, and the resulting additional supply of photosynthates stimulates nodule activity. To characterize its biochemical response to both CO2 and bradyrhizobial strains, soybean inoculated with three strains of Bradyrhizobium japonicum was grown in growth chambers under ambient (400 µmol·mol–1) or elevated (800 µmol·mol–1) CO2. Soluble sugars were generally more abundant in leaves and nodules under elevated CO2, while starch and pinitol were depleted, indicating that additional photosynthates were rapidly used, in particular for nodule growth (dry mass increased by 65%). Ureides (allantoin and allantoic acid) increased under elevated CO2 in leaves, while this increase was not significant in nodules. The indigenous strain 12NS14 induced the highest ureides concentration in nodules under elevated CO2 along with the highest nitrogenase activity and increase in shoot dry mass, indicating a positive-feedback stimulation: soybean mobilized energy reserves to support more nodules, and in return nodules synthesized more ureides to support plant growth. In contrast, the commercial strain 532c resulted in the highest ureide concentrations in leaves, coupled with the lowest nitrogenase activity and nodules yield, suggesting a feedback inhibition of nodule activity. Our results show that selection of B. japonicum strains better adapted to elevated CO2 could improve soybean performance.

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