Metabolic flux analysis of the halophilic archaeon Haladaptatus paucihalophilus.

This work reports the (13)C-assisted metabolic flux analysis of Haladaptatus paucihalophilus, a halophilic archaeon possessing an intriguing osmoadaption mechanism. We showed that the carbon flow is through the oxidative tricarboxylic acid (TCA) cycle whereas the reductive TCA cycle is not operative in H. paucihalophilus. In addition, both threonine and the citramalate pathways contribute to isoleucine biosynthesis, whereas lysine is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. Unexpected, the labeling patterns of glycine from the cells grown on [1-(13)C]pyruvate and [2-(13)C]pyruvate suggest that, unlike all the organisms investigated so far, in which glycine is produced exclusively from the serine hydroxymethyltransferase (SHMT) pathway, glycine biosynthesis in H. paucihalophilus involves different pathways including SHMT, threonine aldolase (TA) and the reverse reaction of glycine cleavage system (GCS), demonstrating for the first time that other pathways instead of SHMT can also make a significant contribution to the cellular glycine pool. Transcriptional analysis confirmed that both TA and GCS genes were transcribed in H. paucihalophilus, and the transcriptional level is independent of salt concentrations in the culture media. This study expands our understanding of amino acid biosynthesis and provides valuable insights into the metabolism of halophilic archaea.

Evolution of threonine aldolases, a diverse family involved in the second pathway of glycine biosynthesis.

Threonine aldolases (TAs) catalyze the interconversion of threonine and glycine plus acetaldehyde in a pyridoxal phosphate-dependent manner. This class of enzymes complements the primary glycine biosynthetic pathway catalyzed by serine hydroxymethyltransferase (SHMT), and was shown to be necessary for yeast glycine auxotrophy. Because the reverse reaction of TA involves carbon-carbon bond formation, resulting in a ß-hydroxyl-α-amino acid with two adjacent chiral centers, TAs are of high interests in synthetic chemistry and bioengineering studies. Here, we report systematic phylogenetic analysis of TAs. Our results demonstrated that L-TAs and D-TAs that are specific for L- and D-threonine, respectively, are two phylogenetically unique families, and both enzymes are different from their closely related enzymes SHMTs and bacterial alanine racemases (ARs). Interestingly, L-TAs can be further grouped into two evolutionarily distinct families, which share low sequence similarity with each other but likely possess the same structural fold, suggesting a convergent evolution of these enzymes. The first L-TA family contains enzymes of both prokaryotic and eukaryotic origins, and is related to fungal ARs, whereas the second contains only prokaryotic L-TAs. Furthermore, we show that horizontal gene transfer may occur frequently during the evolution of both L-TA families. Our results indicate the complex, dynamic, and convergent evolution process of TAs and suggest an updated classification scheme for L-TAs.

Genome Sequence of Streptomyces violaceusniger Strain SPC6, a Halotolerant Streptomycete That Exhibits Rapid Growth and Development.

Streptomyces violaceusniger strain SPC6 is a halotolerant streptomycete isolated from the Linze desert in China. The strain has a very high growth rate and a short life cycle for a streptomycete. For surface-grown cultures, the period from spore germination to formation of colonies with mature spore chains is only 2 days at 37°C. Additionally, the strain is remarkably resistant to osmotic, heat, and UV stress compared with other streptomycetes. Analysis of the draft genome sequence indicates that the strain has the smallest reported genome (6.4 Mb) of any streptomycete. The availability of this genome sequence allows us to investigate the genetic basis of adaptation for growth in an extremely arid environment.

Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence.

The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.

Bacterial diversity and distribution in the southeast edge of the Tengger Desert and their correlation with soil enzyme activities.

The nature of microbial communities and their relation to enzyme activities in desert soils is a neglected area of investigation. To address this, the bacterial diversity and distribution and soil physico-chemical factors were investigated in the soil crust, the soil beneath the crust and rhizosphere soil at the southeast edge of the Tengger Desert, using the denaturing gradient gel electrophoresis of 16S rRNA genes amplified by the polymerase chain reaction. Phylogenetic analysis of the sequenced DGGE bands revealed a great diversity of bacteria. The Proteobacteria, consisting of the alpha, beta, and gamma subdivisions, were clearly the dominant group at all depths and in rhizosphere soil. Analysis of the enzyme activities indicated that the rhizosphere soil of Caragana korshinskii exhibited the highest protease and polyphenol oxidase activities, and in the soil crust there were increased activities of catalase, urease, dehydrogenase and sucrase. The bacterial community abundance closely correlated with soil enzyme activities in different soils. The presence of Cyanobacteria correlated with significant increases in protease, catalase and sucrase in the soil crust, and increased urease in the rhizosphere soil of Artemisia ordosica. The occurrence of Acidobacteria was associated with significant increases in urease, dehydrogenase, and sucrase in the rhizosphere soil of C. korshinski. The presence of gamma-Proteobacteria correlated with a significant increase in polyphenol oxidase in the rhizosphere soil of A. ordosica. The study indicated a close relationship between the soil bacterial community and soil enzymes, suggesting the necessity of further investigations into bacterial function in this desert ecosystem.

Correlations of carbon isotope discrimination with element and ash contents in two Sabina evergreen trees in northwest China: patterns and implications.

Foliar carbon isotope discrimination (Δ) is widely used as an integrator of physiological plant responses to environmental change. However, the relationship between foliar Δ and mineral nutrient accumulation is still not well-known. The foliar Δ, K, Ca, Mg, Si and ash contents of S. przewalskii Kom. (SP) and S. chinensis (Lin.) Ant. (SC), two over-winter trees distributed on high altitude plateaux and lower altitude plains, respectively, were measured at monthly intervals over two years under the same growing conditions to examine the genetic and seasonal variation in foliar nutrient concentrations in relation to foliar Δ. The foliar Δ, Mg, K and ash contents were markedly lower in SP than in SC, and the foliar Si content was significantly higher in SP than SC, while the differences in Ca contents between the two Sabina trees were not significant. There was higher foliar Δ in winter than in summer for both Sabina trees. Close negative correlations of foliar Δ with K and Mg content, and significant positive correlations between foliar Δ and Si contents, were observed in SP but not in SC. Thus, higher water-use efficiency of SP than of SC is related to higher Si and lower Mg and K contents that have positive effects on the reduction of transpiration rates or stomatal conductances. The results obtained by the present study will advance the understanding of the adaptive strategies of mineral nutrition and water use in harsh environments.

Regulation of the plasma membrane during exposure to low temperatures in suspension-cultured cells from a cryophyte (Chorispora bungeana).

As the outermost boundary of the cell, the plasma membrane plays an important role in determining the stress resistance of organisms. To test this concept in a cryophyte, we analyzed alterations of several components in plasma membranes isolated from suspension-cultured cells of Chorispora bungeana Fisch. & C.A. Mey in response to treatment at 0 and -4 degrees C for 192 h. When compared with the controls growing at 25 degrees C, both the membrane permeability and fluidity showed recovery after the initial impairment. Linolenic acid and membrane lipid unsaturation increased by about 0.8-fold following cold treatments, although the kinetics of the increase varied with the temperatures examined. During the treatments, the plasma membrane H(+)-ATPase (EC 3.6.1.3) activity increased by 78.06% at 0 degrees C and 100.47% at -4 degrees C. However, the plasma membrane NADH oxidase (EC 1.6.99.3) activity only decreased when exposed to a lower temperature (-4 degrees C), and remained at 63.93% after being treated for 192 h. After the treatments, the physical properties of the plasma membranes of suspension-cultured cells, especially the -4 degrees C treated cells, were similar to those in the wild plants. These findings indicate that the specific mechanism of cold resistance of C. bungeana is tightly linked with the rapid and flexible regulation of membrane lipids and membrane-associated enzymes, which ensure the structural and functional integrity of the plasma membrane that is essential for withstanding low temperature.

[Seasonal changes in foliar micro-and ultra structure of two Sabina species and their relationships with cold tolerance].

In this paper, the foliar micro-and ultra structure of Sabina przewalskii and S. chinensis during growth and dormancy seasons was observed under microscope and transmission electron microscope, and the foliar soluble sugar content was measured, aimed to probe into their relationships with cold tolerance. The results showed that the foliar surface cells of these two Sabina species were covered with thick cuticular membrane, and the well-developed arenchyma appeared in the mesophyll. In growth season, starch grains accumulated in chloroplasts, but in dormancy season, the accumulated starch grains disappeared or diminished, while soluble sugar content had a larger increase. In wintertime, the chloroplasts of S. chinensis were injured, with some abnormal chloroplasts, increased plastoglobuli and some lipid drops, while those of S. przewalskii were not obviously injured. It was suggested that the cold tolerance of the two Sabina species was related to their well-developed arenchyma, accumulation of starch grains in growth season, and increase of soluble sugar content in dormancy season. S. przewalskii had more marked increase of soluble sugar content, and its chloroplasts were more stable than S. chinensis.

Role of poly-galacturonase inhibiting protein in plant defense.

Polygalacturonase-inhibiting proteins (PGIPs) are plant proteins believed to play an important role in the defense against plant pathogen fungals. PGIPs are glycoproteins located in plant cell wall which reduce the hydrolytic activity of polygalacturonases (PGs), limit the growth of plant pathogens, and also elicit defense responses in plant. Furthermore, PGIPs belong to the super family of leucine reach repeat (LRR) proteins which also include the products of several plant resistance genes. Many of the studies show the PGIP properties, molecular characteristics, and PGIP gene expression induced by some elicitors. Some of the studies review individual PGIP gene expression in different signal transduction pathways. This article summarizes the properties, different signal transduction mechanisms, detecting methods, transgenic plants, and function of PGIP. It also presents PGIP gene expression in different stages of maturity, tissues, and varieties. The review especially reports the particular PGIP gene expression induced by different biotic and abiotic stresses, offers some questions, and prospects the future study, which are needed in order to develop efficient strategies for disease-resistant plants. They may be useful for genetic engineering to obtain transgenic plants with increased tolerance to fungal infection, which decrease the use of insecticide.

Relation of several antioxidant enzymes to rapid freezing resistance in suspension cultured cells from alpine Chorispora bungeana.

Chorispora bungeana Fisch. & C.A. Mey (Crucifer) is a rare alpine subnival plant surviving sudden snowstorms. In this paper, we have attempted to explore possible roles of autoxidation rate (AR) and the antioxidant enzymes associated with cryoprotective mechanisms in the plant cells. The results showed that when the suspension cultures growing at 25 degrees C were suddenly exposed to -8 degrees C for 15 days, 2,3,5-triphenyltetrazolium chloride reduction was not affected within 9 days and AR remained at a low level in comparison with controls. This indicated that the cells maintained considerable amounts of soluble protein and the integrity of the cell membranes was intact during the whole freezing test. Furthermore, on average, the activity of antioxidant enzymes such as superoxide dismutase, dehydroascorbate reductase, ascorbate peroxidase and glutathione reductase were prominently enhanced in the freezing-stressed cells. Peroxidase activity significantly increased soon after freezing, possibly to make up for the early decrease of catalase activity in the cells. Statistical analysis showed negative correlations between resistance to rapid freezing and antioxidant enzyme activity in the cultured cells after exposure from 25 to -8 degrees C, indicating that the reduction of cell viability with freezing activates a combination of antioxidant enzymes that results in intact cells. All of these findings suggest a synergy between these antioxidant enzymes, leading to a low autoxidation rate that contributes to the protection of the cell membranes and plays an important role in the resistance of suspension cultured cells of C. bungeana to sudden freezing.

Effects of nitric oxide on growth of maize seedling leaves in the presence or absence of ultraviolet-B radiation.

The leaves of maize seedlings were used to measure leaf biomass including leaf length, width and weight, and to examine the relationship between nitric oxide (NO) synthase activity in microsomes and cytosol to the exo- and endo-beta-glucanase activity during growth. It was found that ultraviolet-B radiation (UV-B radiation) strongly induced nitric oxide synthase (NOS) activity but caused both a decrease of leaf biomass and exo- or endo-beta-glucanase activity. In contrast, the NOS inhibitor and NO donor largely decreased the activity of NOS in non-irradiated seedlings. The inhibitor also reduced exo- and endo-beta-glucanase activity and leaf biomass while the donor increased the enzyme activity and leaf biomass under normal conditions. Alternatively, under ultraviolet-B, the additional inhibitor of NOS and NO donor appeared to compromise the effects of ultraviolet-B on glucanase activity and leaf biomass, making the relationship between NOS activity and glucanase activity negatively correlated. This suggests that the changes of NOS activity showed a positive correlation to glucanase activity and leaf biomass in the absence of ultraviolet-B, but a negative correlation to ultraviolet-B irradiation and NO donor treatment alone. It is assumed that exo- and endogenous NO is responsible for the up-regulation of regular growth and development without ultraviolet-B. Under UV-B radiation, however, it might function as a signaling molecule of ultraviolet-B inhibiting leaf growth of maize seedlings to carry out stress-signaling transduction.

The cascade mechanisms of nitric oxide as a second messenger of ultraviolet B in inhibiting mesocotyl elongations.

In this report, a number of physiological aspects was examined during developmental growth of maize seedling's mesocotyl. It was found that ultraviolet B (UVB) radiation was able to significantly induce nitric oxide synthase (NOS) activities and speedup the release of apparent nitric oxide (NO) of mesocotyl and that exogenous NO donor's rhizospheric treatments may mimic the responses of the mesocotyl to UVB radiation, such as the inhibition of mesocotyl elongation, the decrease in exo- and endoglucanase activities and the increase in protein content of cell wall of mesocotyl. When the seedlings were treated with N-nitro-L-arginine, an inhibitor of NOS, the mesocotyl elongation was promoted, the exo- and endoglucanase activities were raised and the protein content was reduced. However, under UVB radiation, the effects of exogenous NO on several physiological aspects of mesocotyl were similar to those of exogenous reactive oxygen species (ROS) eliminator, N-acetyl-cysteine. All the physiological changes were associated with either the exogenous NO supply or the activities of NOS in plant. Accordingly, it is assumed that reduction in mesocotyl length caused by UVB radiation was possibly achieved through modification of the chemical properties of the cell wall polysaccharides, which was induced by NO and ROS synergically mediated changes in exo- and endo-beta-D-glucanases activities in cell walls, and NO was one of the main signaling molecule of UVB radiation in inhibiting mesocotyl elongations. So NO might function as both a second messenger and an antioxidant of UVB radiation during developmental growth of the mesocotyl.