Genetic tools for the investigation of Roseobacter clade bacteria

Background  

The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools.     

Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade

Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade (MRC). Using the model bacterium Ruegeria pomeroyi, we confirm that the betA, betB and betC genes, encoding choline dehydrogenase, betaine aldehyde dehydrogenase and choline sulfatase, respectively, are involved in choline metabolism. The betT gene, encoding an organic solute transporter, was essential for the rapid uptake of choline but not glycine betaine (GBT). Growth of choline and GBT as a sole carbon source resulted in the re‐mineralization of these nitrogen‐rich compounds into ammonium. Oxidation of the methyl groups from choline requires formyltetrahydrofolate synthetase encoded by fhs in R. pomeroyi, deletion of which resulted in incomplete degradation of GBT. We demonstrate that this was due to an imbalance in the supply of reducing equivalents required for choline catabolism, which can be alleviated by the addition of formate. Together, our results demonstrate that choline metabolism is ubiquitous in the MRC and reveal the role of Fhs in methyl group oxidation in R. pomeroyi.     

Unidirectional water and sodium fluxes and respiratory metabolism in the African lung-fish,Protopterus annectens

Summary Simultaneous measurements have been made of the efflux rates of tritiated water and radiosodium from the lung-fishProtopterus annectens under conditions in which the fish can either use its gills, its lungs or both for respiration. Tritiated water efflux rate was similar (43–44% h^–1) when the fish was in oxygenated water with or without access to air but decreased slightly in deoxygenated water. An efflux rate constant of 44% h^–1 obtained in oxygenated water is similar to those of other inactive fish in fresh water. The efflux rate constant for sodium was 0.84% h^–1 and total sodium flux was comparable to that of fresh-water fish. The decrease in both tritiated water and sodium efflux rates in deoxygenated water are explained in terms of diversion of blood flow away from the functional gills to the lungs. Oxygen consumption was highest (38.7 ml kg^–1 h^–1) in deoxygenated water and lowest when the fish was out of water. Despite the reduced functional significance of the gill for respiration, it is still as permeable to water and electrolytes as that of fresh-water teleosts.This work was supported by a travel grant from the Commonwealth Universities Interchange Scheme of the British Council and laboratory facilities of the Department of Biological Sciences, University of Lancaster     

Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria

A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.     

Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism

Shewanella spp. are a group of facultative anaerobic bacteria widely distributed in marine and freshwater environments. In this study, we profiled the central metabolic fluxes of eight recently sequenced Shewanella species grown under the same condition in minimal medium with [3‐¹³C] lactate. Although the tested Shewanella species had slightly different growth rates (0.23–0.29 h^?1) and produced different amounts of acetate and pyruvate during early exponential growth (pseudo‐steady state), the relative intracellular metabolic flux distributions were remarkably similar. This result indicates that Shewanella species share similar regulation in regard to central carbon metabolic fluxes under steady growth conditions: the maintenance of metabolic robustness is not only evident in a single species under genetic perturbations (Fischer and Sauer, 2005; Nat Genet 37(6):636–640), but also observed through evolutionary related microbial species. This remarkable conservation of relative flux profiles through phylogenetic differences prompts us to introduce the concept of metabotype as an alternative scheme to classify microbial fluxomics. On the other hand, Shewanella spp. display flexibility in the relative flux profiles when switching their metabolism from consuming lactate to consuming pyruvate and acetate. Biotechnol. Bioeng. 2009;102: 1161–1169. © 2008 Wiley Periodicals, Inc.     

Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS.

We describe here a novel methodology for rapid diagnosis of metabolic changes, which is based on probabilistic equations that relate GC-MS-derived mass distributions in proteinogenic amino acids to in vivo enzyme activities. This metabolic flux ratio analysis by GC-MS provides a comprehensive perspective on central metabolism by quantifying 14 ratios of fluxes through converging pathways and reactions from [1-13C] and [U-13C]glucose experiments. Reliability and accuracy of this method were experimentally verified by successfully capturing expected flux responses of Escherichia coli to environmental modifications and seven knockout mutations in all major pathways of central metabolism. Furthermore, several mutants exhibited additional, unexpected flux responses that provide new insights into the behavior of the metabolic network in its entirety. Most prominently, the low in vivo activity of the Entner-Doudoroff pathway in wild-type E. coli increased up to a contribution of 30% to glucose catabolism in mutants of glycolysis and TCA cycle. Moreover, glucose 6-phosphate dehydrogenase mutants catabolized glucose not exclusively via glycolysis, suggesting a yet unidentified bypass of this reaction. Although strongly affected by environmental conditions, a stable balance between anaplerotic and TCA cycle flux was maintained by all mutants in the upper part of metabolism. Overall, our results provide quantitative insight into flux changes that bring about the resilience of metabolic networks to disruption.     

Metabolic and ventilatory responses to hypoxia in two altitudinal populations of the toad, Bufo bankorensis

Effects of hypoxia on resting oxygen consumption ( ), lung ventilation, and heart rate at different ambient P_O2 were compared between lowland and high altitude populations of the toad, Bufo bankorensis. Resting decreased significantly in mild hypoxia (P_O2=120 mm Hg) at 10°C and in moderate hypoxia (P_O2=80 mm Hg) at 25°C in both altitudinal populations; however, resting did not differ significantly between the two populations. Numbers of lung ventilation periods (VP) and total inspired volume (V_L) did not change with P_O2 at 10°C, but did increase at moderate and severe hypoxia (40 mm Hg), respectively, at 25°C. Resting heart rates did not change during hypoxia and did not differ between altitude populations. The results suggest (1) the effect of P_O2 change on should be considered in future studies involving transfer of anurans to a different altitude; and (2) the metabolic and ventilatory physiology in B. bankorensis does not compensate for the low temperature and P_O2 at high altitude.     

Relations between carbon dioxide fluxes and environmental factors of Kobresia humilis meadows and Potentilla fruticosa meadows

Carbon dioxide fluxes of Kobresia humilis and Potentilla fruticosa shrub meadows, two typical ecosystems in the Qinghai-Tibet Plateau, were measured by eddy covariance technology and the data collected in August 2003 were employed to analyze the relations between carbon dioxide fluxes and environmental factors of the ecosystems. August is the time when the two ecosystems reach their peak leaf area indexes and stay stable, and also the period when the net carbon absorptions of Kobresia humilis and Potentilla fruticosa shrub meadows reach 56.2 g C·m⁻² and 32.6 g C·m⁻², with their highest daily carbon dioxide absorptions standing at 12.7 μmol·m⁻²·s⁻¹ and 9.3 μmol·m⁻²·s⁻¹, and their highest carbon discharges at 5.1 μmol·m⁻²·s⁻¹ and 5.7 μmol·m⁻²·s⁻¹, respectively. At the same photosynthetic photo flux densities (PPFD), the carbon dioxide-uptake rate of the Kobresia humilis meadow is higher than that of the Potentilla fruticosa shrub meadow; where the PPFD are higher than 1,200 μmol·m⁻²·s⁻¹. The carbon dioxide uptake rates of the two ecosystems declined as air temperature increased, but the carbon dioxide uptake rate of the Kobresia humilis meadow decreased more quickly (−0.086) than that of the Potentilla fruticosa shrub meadow (−0.016). Soil moistures exert influence on the soil respirations and this varies with the vegetation type. The daily carbon dioxide absorptions of the ecosystems increase with increased diurnal temperature differences and higher diurnal temperature differences result in higher carbon dioxide exchanges. There exists a negative correlation between the vegetation albedos and the carbon dioxide fluxes. Translated from Acta Bot Boreal—Occident Sin, 2006, 26(1): 133–142 [译自: 西北植物学报]     

Ocean acidification and hypoxia alter organic carbon fluxes in marine soft sediments

Anthropogenic stressors can alter the structure and functioning of infaunal communities, which are key drivers of the carbon cycle in marine soft sediments. Nonetheless, the compounded effects of anthropogenic stressors on carbon fluxes in soft benthic systems remain largely unknown. Here, we investigated the cumulative effects of ocean acidification (OA) and hypoxia on the organic carbon fate in marine sediments, through a mesocosm experiment. Isotopically labelled macroalgal detritus (¹³C) was used as a tracer to assess carbon incorporation in faunal tissue and in sediments under different experimental conditions. In addition, labelled macroalgae (¹³C), previously exposed to elevated CO₂, were also used to assess the organic carbon uptake by fauna and sediments, when both sources and consumers were exposed to elevated CO₂. At elevated CO₂, infauna increased the uptake of carbon, likely as compensatory response to the higher energetic costs faced under adverse environmental conditions. By contrast, there was no increase in carbon uptake by fauna exposed to both stressors in combination, indicating that even a short‐term hypoxic event may weaken the ability of marine invertebrates to withstand elevated CO₂ conditions. In addition, both hypoxia and elevated CO₂ increased organic carbon burial in the sediment, potentially affecting sediment biogeochemical processes. Since hypoxia and OA are predicted to increase in the face of climate change, our results suggest that local reduction of hypoxic events may mitigate the impacts of global climate change on marine soft‐sediment systems.     

Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members

The tautomerase superfamily consists of structurally homologous proteins that are characterized by a β-α-β fold and a catalytic amino-terminal proline. 4-Oxalocrotonate tautomerase (4-OT) family members have been identified and categorized into five subfamilies on the basis of multiple sequence alignments and the conservation of key catalytic and structural residues. Representative members from two subfamilies have been cloned, expressed, purified, and subjected to kinetic and structural characterization. The crystal structure of DmpI from Helicobacter pylori (HpDmpI), a 4-OT homolog in subfamily 3, has been determined to high resolution (1.8 Å and 2.1 Å) in two different space groups. HpDmpI is a homohexamer with an active site cavity that includes Pro-1, but lacks the equivalent of Arg-11 and Arg-39 found in 4-OT. Instead, the side chain of Lys-36 replaces that of Arg-11 in a manner similar to that observed in the trimeric macrophage migration inhibitory factor (MIF), which is the title protein of another family in the superfamily. The electrostatic surface of the active site is also quite different and suggests that HpDmpI might prefer small, monoacid substrates. A kinetic analysis of the enzyme is consistent with the structural analysis, but a biological role for the enzyme remains elusive. The crystal structure of DmpI from Archaeoglobus fulgidus (AfDmpI), a 4-OT homolog in subfamily-4, has been determined to 2.4 Å resolution. AfDmpI is also a homohexamer, with a proposed active site cavity that includes Pro-1, but lacks any other residues that are readily identified as catalytic ones related to 4-OT activity. Indeed, the electrostatic potential of the active site differs significantly in that it is mostly neutral, in contrast to the usual electropositive features found in other 4-OT family members, suggesting that AfDmpI might accommodate hydrophobic substrates. A kinetic analysis has been carried out, but does not provide any clues about the type of reaction the enzyme might catalyze.     

Photosynthetic carbon metabolism of a marine grass

The δ¹³C value of a tropical marine grass Thalassia testudinum is −9.04‰. This value is similar to the δ¹³C value of terrestrial tropical grasses. The δ¹³C values of the organic acid fraction, the amino acid fraction, the sugar fraction, malic acid, and glucose are: −11.2‰, −13.1‰, −10.1‰, −11.1‰, and −11.5‰, respectively. The δ¹³C values of malic acid and glucose of Thalassia are similar to the δ¹³C values of these intermediates in sorghum leaves and attest to the presence of the photosynthetic C₄-dicarboxylic acid pathway in this marine grass. The inorganic HCO₃⁻ for the growth of the grass fluctuates between −6.7 to −2.7‰ during the day. If CO₂ fixation in Thalassia is catalyzed by phosphoenolpyruvate carboxylase (which would result in a −3‰ fractionation between HCO₃⁻ and malic acid), the predicted δ¹³C value for Thalassia would be −9.7 to −5.7‰. This range is close to the observed range of −12.6 to −7.8‰ for Thalassia and agree with the operation of the C₄-dicarboxylic acid pathway in this plant. The early products of the fixation of HCO₃⁻ in the leaf sections are malic acid and aspartic acid which are similar to the early products of CO₂ fixation in C₄ terrestrial plants.     

Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic fluxes by C-labeling experiments

The effect of sucA or sucC gene knockout on the metabolism in Escherichia coli was investigated for the aerobic cell growth in batch and continuous cultivations based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic flux analysis. In the batch cultivation, the cell growth rate and the glucose uptake rate were lower for sucA mutant as compared with the parent strain, while it was not the case for sucC mutant. A significantly higher amount of acetate was produced, and it was not utilized in sucC mutant, while a little less acetate was produced in sucA mutant as compared with the parent strain. Unlike the parent strain and sucC mutant, sucA mutant excreted a little amount of l-glutamate. Enzyme activity results show that some of the glycolytic enzymes such as Tpi and Pgk were up-regulated, while Pfk, Fba and Pyk activities were down-regulated for sucA mutant as compared with the parent strain. For sucC mutant, the activities of Pfk, Fba, Tpi, GAPDH, Pgk and Pyk activities were down-regulated. As for the TCA cycle enzymes, the activities of CS and ICDH were down-regulated, while those of Icl, MS, Fum and MDH were up-regulated for sucA mutant. The activities of the oxidative pentose phosphate (PP) pathway enzymes such as G6PDH and 6PGDH and the gluconeogenic pathway enzyme such as Mez were up-regulated in sucA mutant. The Ack activity was down-regulated for sucA mutant, but not for sucC mutant. In continuous cultivation, the gene expression results indicate that the global regulatory genes such as fadR and iclR were slightly down-regulated in sucA mutant, which enhanced the expression of aceA gene and caused the up-regulation of the isocitrate lyase activity in sucA mutant, while fadR and iclR of sucC mutant changed little and no isocitrate lyase activation was observed for sucC mutant. Some other global regulatory genes such as arcA and fnr genes were down-regulated in both mutants, which caused some of the TCA cycle genes to be up-regulated. The effect of the sucA gene knockout on the metabolic flux distributions was investigated based on ¹H–¹³C NMR spectra and GC–MS signals obtained from ¹³C-labeling experiments. Flux analysis results indicate that the knockout of sucA gene caused the activation of PP pathway and the glyoxylate shunt. The fluxes through glycolysis and the TCA cycle were down-regulated in the sucA mutant. On the other hand, the fluxes through PP pathway and the anaplerotic reactions of Ppc-Pck and Mez increased.     

Metabolic and cardiovascular adaptations in the western chipmunks, genusEutamias

Summary The metabolic and cardiac responses to temperature were studied in two species (four subspecies) of western chipmunks (genusEutamias), inhabiting boreal and alpine environments. A specially designed (Fig. 1) implantable biopential radiotransmitter was used to measure heart rate in unrestrained animals. The estimated basal metabolic rates (EBMR) were 1.78 (E. minimus borealis), 1.64 (E. m. oreocetes), 1.50 (E. m. operarius), and 1.69 ml O₂ g^–1 h^–1 (E. amoenus luteiventris), or 839, 752, 698, and 628 ml O₂ kg^–0.75 h^–1, respectively, for the four subspecies (Table 1). The two alpine species (E.m.or. andE.m.op.) had significantly lower EBMR than both of their boreal counterparts. The EBMR from all animals are 120–135% of the predicted values based on body weights of the animals. The thermal neutral zone for the four subspecies ranged from 23.5 to 32°C and the minimum thermal conductances were 0.113, 0.111, 0.112 and 0.112 ml O₂ g^–1 h^–1 °C^–1, respectively, or 54.4, 54.0, 50.4 and 52.1 ml O₂ kg^–0.75 h^–1 °C^–1, respectively (Fig. 2). No interspecific diffence in conductance was observed. These values are 72 to 85% of their weight specific values. The body temperature ranged between 35.0 and 39.5°C and was usually maintained between 36 and 38°C in all subspecies between ambient temperatures of 3 and 32°C. The estimated basal heart rates were 273, 296, 273 and 264 beats/min, respectively, for the four subspecies, 49–55% of their predicted weight specific values. The resultant oxygen pulses (metabolic rate/heart rate) were 5.49, 4.50, 4.48 and 5.56×10^–3 ml O₂/beat, respectively, which are 2 to 2.4 times their weight specific values (Table 2).The observed reduction of basal heart rate without the corresponding decreases of basal metabolic rate and body temperature indicate sufficient compensatory increases in stroke volume and/or A-V oxygen difference at rest. Such cardiovascular modifications provide extra reserves when demand for aerobic metabolism rises during bursts of activity typically observed in the western chipmunk.Abbreviations A-V arterio-venous - EBMR estimated basal metabolic rate (ml O₂ g^–1 h^–1) - HR heart rate (beats/min) - MR metabolic rate (ml O₂ g^–1 h^–1) - OP oxygen pulse (ml O₂/heart beat) - T_a, T_b ambient and body temperature (°C)