Direct uptake of nitrogen by Pfiesteria piscicida and Pfiesteria shumwayae, and nitrogen nutritional preferences

The rates of uptake of a range of forms of nitrogenous nutrients were measured in cultures of Pfiesteria piscicida and Pfiesteria shumwayae maintained at varying physiological states. The measured rates of dissolved N uptake under some conditions approached the rates of N uptake that are achieved through phagotrophy. Rates of dissolved N uptake by P. piscicida contributed <10% of the cellular N of flagellated cells feeding on algae, but were equal to or greater than phagotrophic N acquisition in cells recently removed from fish cultures. Specific N uptake rates (V, h⁻¹) were higher for cells that were maintained on algal prey for long periods (months) than those that were grown with live fish. However, rates of N uptake on a cellular basis for cells grown on or recently removed from fish were comparable to those maintained on algal prey, likely reflecting differences in the sizes of cells of different physiological condition. Preferences for form of N generally followed a decreasing trend of amino acids > urea > NH₄⁺ > NO₃⁻. Nitrate consistently was not a preferred form of N. Although Pfiesteria spp. are often found in eutrophic environments, the relationship between Pfiesteria spp. and nutrient availability is likely to be primarily indirect, mediated through the production of various prey on which Pfiesteria spp. feed. These findings also confirm, however, that when dissolved N concentrations are elevated, they can contribute to the supplemental nutrition of these cells, and thus may provide a significant source of N to Pfiesteria spp. in nature.     

Kinetics of ammonium, nitrate and phosphorus uptake by Canna indica and Schoenoplectus validus

Canna indica L. is an upright perennial rhizomatous herb, and Schoenoplectus validus (Vahl) A. Löve and D. Löve is a tall, perennial, herbaceous sedge. The nutrient uptake kinetics of C. indica and S. validus were investigated using the modified depletion method after plants were grown for 4 weeks in simulated secondary-treated wastewater. The maximum uptake rate (I_max) and Michaelis–Menten constant (K_m) were estimated by iterative curve fitting. The I_max for NH₄N (623 μmol g⁻¹ dry root weight h⁻¹) was significantly higher than that for NO₃N (338 μmol g⁻¹ dry root weight h⁻¹) in S. validus. In contrast, no difference was observed in C. indica. The I_max values for NO₃N and NH₄N were higher in S. validus than in C. indica. A significantly lower K_m was detected for NO₃N uptake in C. indica (385 μmol L⁻¹) compared to that in S. validus (1908 μmol L⁻¹). The I_max for PO₄P did not differ between the plant species. The K_m for PO₄P was significantly higher in C. indica (157 μmol L⁻¹) than in S. validus (60 μmol L⁻¹). In conclusion, we found that S. validus preferred NH₄N over NO₃N, had greater capacity for N uptake and higher affinity for PO₄P, but C. indica had greater affinity for NO₃N. Nutrient uptake capacity is likely related to habitat preference, and is influenced by the structure of roots and rhizomes.     

Bioinformatic identification of novel regulatory DNA sequence motifs in <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis>

Background  

Streptomyces coelicolor is a bacterium with a vast repertoire of metabolic functions and complex systems of cellular development. Its genome sequence is rich in genes that encode regulatory proteins to control these processes in response to its changing environment. We wished to apply a recently published bioinformatic method for identifying novel regulatory sequence signals to gain new insights into regulation in S. coelicolor.     

Biodegradation of Methyl red by Galactomyces geotrichum MTCC 1360

Galactomyces geotrichum MTCC 1360 can decolorize triphenylmethane, azo and reactive high exhaust textile dyes. At shaking condition this strain showed 100% decolorization of a toxic azo dye Methyl red (100 m gl⁻¹) within 1 h in deionized water at 30 °C. The degradation of Methyl red was possible through a broad pH (3–12) and temperature (5–50 °C) range. Glucose and mycelium concentration had increased the decolorization rate, but the addition of 1 gl⁻¹ molasses in deionized water made decolorization possible in only 10 min. Induction in the NADH–dichloro phenol indophenol (NADH–DCIP) reductase, Malachite green reductase, laccase and lignin peroxidase (Lip) activities were observed in the cells obtained after complete decolorization, showing that there is direct involvement in the degradation of Methyl red. The absence of N-N′-dimethyl-p-phenylenediamine (DMPD) in 5 °C, 2-aminobenzoic acid (ABA) in 50 °C and both the compounds in 30 °C sample have shown the differences in the metabolic fate of Methyl red at different temperatures. The untreated dye at 300 mg l⁻¹ concentration showed 88% germination inhibition in Sorghum bicolor, whereas it was 72% in Triticum aestivum. There was no germination inhibition for both the plants by Methyl red metabolites at 300 mg l⁻¹ concentration.

The scientific relevance of the paper

The azo dye Methyl red (100 mg l⁻¹) was decolorized by G. geotrichum MTCC 1360 within 1 h at shaking condition in deionized water. This organism could decolorize Methyl red at wide pH and temperature ranges. Decolorization time was reduced to 10 min by the addition of molasses to deionized water. There was induction in laccase and Lip, NADH–DCIP reductase and Malachite green reductase activities. The metabolic fate of Methyl red changes with temperature which can be evidenced by the formation of 2-ABA at 5 °C, N-N′-DMPD at 50 °C and both the compounds were absent at 30 °C. Phytotoxicity showed that metabolites of dye had induced shoot and root length of both the tested plants.     

Cytokinesis is blocked in mammalian cells transfected with Chlamydia trachomatis gene CT223

Background  

The chlamydiae alter many aspects of host cell biology, including the division process, but the molecular biology of these alterations remains poorly characterized. Chlamydial inclusion membrane proteins (Incs) are likely candidates for direct interactions with host cell cytosolic proteins, as they are secreted to the inclusion membrane and exposed to the cytosol. The inc gene CT223 is one of a sequential set of orfs that encode or are predicted to encode Inc proteins. CT223p is localized to the inclusion membrane in all tested C. trachomatis serovars.     

Free amino acid mediated volume regulation of isolatedNoetia ponderosa red blood cells: Control by Ca2+ and ATP

Summary The ionic and metabolic requirements of cellular volume regulation and the free amino acid (FAA) efflux from hypoosmotically stressedNoetia ponderosa (Mollusca: Arcidae) red blood cells was studied. Deletion of Ca²⁺ from 50% ASW prevented cell volume regulation and decreased the FAA efflux. Addition of Co²⁺, Mn²⁺, or La³⁺ to 50% ASW increased volume regulation and the FAA efflux, while verapamil, a Ca²⁺ antagonist, inhibited volume regulation and the FAA efflux. Volume regulation by the blood cells has a metabolic component also since DNP or incubation of the cells at 4°C both inhibited volume regulation and the FAA efflux. Thus, the FAA permeability ofN. ponderosa blood cell membranes can be manipulated by altering seawater [Ca²⁺] or by indirectly modifying intracellular levels of ATP.Abbreviations FAA free amino acid - ASW artificial seawater - DMSO dimethylsulfoxide - DNP dinitrophenol     

Genomic island excisions in Bordetella petrii

Background  

Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs). These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds.     

Diet and physiological responses of Spondyliosoma cantharus (Linnaeus, 1758) to the Caulerpa racemosa var. cylindracea invasion

Marine invasions are a worldwide problem that involves changes in communities and the acclimation of organisms to them. The invasive Chlorophyte Caulerpa racemosa var. cylindracea is widespread in the Mediterranean and colonises large areas from 0 to 70 m in depth. The omnivorous fish Spondyliosoma cantharus presents a high frequency of occurrence of C. racemosa in the stomach contents at invaded areas (76.3%) while no presence of C. racemosa was detected in control areas. The isotopic composition of muscle differed significantly between invaded and non-invaded sites for δ¹³C (− 16.67‰ ± 0.09 and − 17.67‰ ± 0.08, respectively), δ¹⁵N (10.22‰ ± 0.22 and 9.32‰ ± 0.18, respectively) and the C:N ratio (2.01 ± 0.0002 and 1.96 ± 0.009, respectively). Despite the high frequency of occurrence of C. racemosa in the stomach contents of S. cantharus and its important contribution to the δ¹³C source (20.7% ± 16.2), the contribution of C. racemosa to the δ¹⁵N in S. cantharus food sources was very low (6.6% ± 5.8). Other invertebrate prey such as decapods and polychaetes were more important contributors to the δ¹⁵N source at both invaded and non-invaded sites. Activation of enzymatic pathways (catalase, superoxide dismutase, glutathione-s-tranferase, 7-ethoxy resorufin O-de-ethylase) but not a significant increase in lipid peroxidation MDA (0.49 ± 0.01 nmol/mg prot at non-invaded and 0.53 ± 0.01 nmol/mg prot at invaded sites) was observed in S. cantharus individuals living in C. racemosa-invaded sites compared with control specimens. The low δ¹⁵N contribution values of C. racemosa by S. cantharus together with the toxicity demonstrated by the activation of the antioxidant defences and the important contribution of invertebrate prey to the δ¹⁵N could mean that the ingestion of C. racemosa by S. cantharus might be unintentional during the predation of invertebrate preys living underneath the entanglement of the C. racemosa fronds and stolons mats.     

钝齿棒杆菌GlnK在氮代谢调控及L-精氨酸合成中的功能

【目的】钝齿棒杆菌是重要的氨基酸生产菌株,本研究针对氮代谢PⅡ信号转导蛋白GlnK展开相关功能研究,分析其在钝齿棒杆菌氮代谢调控及L-精氨酸合成中的作用。【方法】以GlnK蛋白为研究对象,通过基因敲除等遗传方法获得过表达、敲除及敲弱glnK的重组钝齿棒杆菌,研究GlnK对NH_4~+吸收的影响,通过RT-qPCR和酶活测定,从转录水平和蛋白水平上揭示GlnK对氮代谢和L-精氨酸合成相关基因表达水平及酶活的影响,通过5-L发酵罐发酵产L-精氨酸研究GlnK对L-精氨酸合成的影响。【结果】过表达glnK能明显促进NH_4~+的吸收,而敲除glnK后则会抑制NH_4~+的摄取;RT-qPCR和酶活测定发现,相比于野生型菌株Cc5-5,glnK过表达菌株Cc-glnK中与铵吸收相关的基因,表达量平均上调约4.58倍,L-精氨酸合成基因簇中基因的表达水平平均上调1.50倍。Cc-glnK中氮代谢相关蛋白的酶活平均提高46.97%;L-精氨酸合成途径上7个关键酶的酶活平均提高30.00%;5-L发酵罐发酵各重组菌株结果表明,Cc-glnK菌株的产量可达49.53 g/L,产率为0.516 g/(L·h),相比于出发菌株Cc5-5,其L-精氨酸产量提高了28.65%。【结论】过表达GlnK能促进NH_4~+的吸收及利用,并通过影响L-精氨酸合成途径上关键基因的表达水平,提高关键酶的酶活,最终提高L-精氨酸的产量。本研究为后续探索钝齿棒杆菌氮代谢调控机制及代谢工程改造钝齿棒杆菌生产L-精氨酸提供了一种新的策略。     

Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of vertical migration and cell division

To better understand the mechanism underlying the bloom outbreaks of dinoflagellates, Ceratium furca, and Ceratium fusus in the temperate coastal area of Sagami Bay, we investigated the diel changes of vertical migration, swimming speed, cell volume, and cell division. Our results from both the field and laboratory indicate that C. furca and C. fusus can migrate vertically between surface and sub-surface layers to avoid strong sunlight (>1000 μmol m⁻² s⁻¹). Diel vertical migration (DVM) of C. furca was observed in the laboratory, while that of C. fusus was not observed. C. furca demonstrated a constant DVM rhythm, i.e., their cells began to descend from the surface before the light was extinguished, and ascended into the surface before the light was turned on. The downward and upward migrations of the cells occurred at every 3 h before turning on and off the light, suggesting that the DVM pattern was independent of nutrient concentration. The swimming speeds of C. furca (avg. 250 μm s⁻¹) were always faster than those of C. fusus (avg. 75 μm s⁻¹). In addition, the speeds of C. furca during light periods were faster than those during dark periods, whereas the speeds of C. fusus remained relatively constant. A higher proportion of dividing cells was recorded near dawn (05:00–07:00 h). Cell volumes of C. furca and C. fusus did not markedly change between 12:00 and 21:00 h, but gradually increased until 03:00 h and then sharply decreased. Furthermore, the cell volume of the two Ceratium species was significantly shifted to the temporal pattern of cell division. Combined with the DVM manner of two Ceratium and cell division timing, only C. furca divided at the bottom, and then moved toward the surface shortly before the dark to light transition. Based on our observations, C. furca has an ecological advantage due to their DVM activity, since nutrients can be obtained well in the near bottom layers, while during the daytime, light present in nutrient-depleted surface water can be obtained using their high swimming speed. On the other hand, C. fusus stimulated by low salinity conditions, might be dependent on external environmental conditions such as additional nutrients following freshwater discharge by heavy rainfall because they may not perform active DVM due to a slow swimming ability. Our findings support that specific characteristics, including the DVM behavior in C. furca, yield a competitive advantage over C. fusus in Sagami Bay.     

Isolation and expression analysis of low temperature-induced genes in white poplar (Populus alba)

Poplar is an important crop and a model system to understand molecular processes of growth, development and responses to environmental stimuli in trees. In this study, we analyzed gene expression in white poplar (Populus alba) plants subjected to chilling. Two forward suppression-subtractive-hybridization libraries were constructed from P. alba plants exposed to low non-freezing temperature for 6 or 48 h. Hundred and sixty-two cDNAs, 54 from the 6-h library and 108 from the 48-h library, were obtained. Isolated genes belonged to six categories of genes, specifically those that: (i) encode stress and defense proteins; (ii) are involved in signal transduction; (iii) are related to regulation of gene expression; (iv) encode proteins involved in cell cycle and DNA processing; (v) encode proteins involved in metabolism and energetic processes; and (vi) are involved in protein fate.Different expression patterns at 3, 6, 12, 24, 48 h at 4 °C and after a recovery of 24 h at 20 °C were observed for isolated genes, as expected according to the class in which the gene putatively belongs. Forty-four of 162 genes contained DRE/LTRE cis-elements in the 5′ proximal promoter of their orthologs in Populus trichocarpa, suggesting that they putatively belong to the CBF regulon. The results contribute new data to the list of possible candidate genes involved in cold response in poplar.     

Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis

Background  

Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H₂ and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations.     

Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade

Background  

In the present work the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis was studied at the level of metabolic fluxes. These two strains belong to the marine Roseobacter clade, a dominant bacterial group in various marine habitats, and represent surface-associated, biofilm-forming growth (P. gallaeciensis) and symbiotic growth with eukaryotic algae (D. shibae). Based on information from recently sequenced genomes, a rich repertoire of pathways has been identified in the carbon core metabolism of these organisms, but little is known about the actual contribution of the various reactions in vivo.     

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana

Background  

Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We investigated the metabolic network between wild-type and 2 mutant (methionine-over accumulation 1 [mto1] and transparent testa4 [tt4]) plants regarding the alteration of metabolite accumulation in Arabidopsis thaliana.     

Processing of predicted substrates of fungal Kex2 proteinases from Candida albicans, C. glabrata, Saccharomyces cerevisiae and Pichia pastoris

Background  

Kexin-like proteinases are a subfamily of the subtilisin-like serine proteinases with multiple regulatory functions in eukaryotes. In the yeast Saccharomyces cerevisiae the Kex2 protein is biochemically well investigated, however, with the exception of a few well known proteins such as the α-pheromone precursors, killer toxin precursors and aspartic proteinase propeptides, very few substrates are known. Fungal kex2 deletion mutants display pleiotropic phenotypes that are thought to result from the failure to proteolytically activate such substrates.     

The outcome of Cryptococcus neoformans intracellular pathogenesis in human monocytes

Background  

Cryptococcus neoformans is an encapsulated yeast that is a facultative intracellular pathogen. The interaction between macrophages and C. neoformans is critical for extrapulmonary dissemination of this pathogenic yeast. C. neoformans can either lyse macrophages or escape from within them through a process known as phagosomal extrusion. However, most studies of intracellular pathogenesis have been made with mouse cells and their relevance to human infection is uncertain. In this study we extended studies of C. neoformans-macrophage cellular interaction/s to human peripheral blood monocytes.     

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

Background  

In silico genome-scale metabolic models enable the analysis of the characteristics of metabolic systems of organisms. In this study, we reconstructed a genome-scale metabolic model of Corynebacterium glutamicum on the basis of genome sequence annotation and physiological data. The metabolic characteristics were analyzed using flux balance analysis (FBA), and the results of FBA were validated using data from culture experiments performed at different oxygen uptake rates.