Nitrogen Metabolism Genes Research Articles

Role of GlnR in Controlling Expression of Nitrogen Metabolism Genes in Listeria monocytogenes.

Listeria monocytogenes is a fastidious bacterial pathogen that can utilize only a limited number of nitrogen sources for growth. Both glutamine and ammonium are common nitrogen sources used in listerial defined growth media, but little is known about the regulation of their uptake or utilization. The functional role of L. monocytogenes GlnR, the transcriptional regulator of nitrogen metabolism genes in low-G+C Gram-positive bacteria, was determined using transcriptome sequencing and real-time reverse transcription-PCR experiments. The GlnR regulon included transcriptional units involved in ammonium transport (amtB glnK) and biosynthesis of glutamine (glnRA) and glutamate (gdhA) from ammonium. As in other bacteria, GlnR proved to be an autoregulatory repressor of the glnRA operon. Unexpectedly, GlnR was most active during growth with ammonium as the nitrogen source and less active in the glutamine medium, apparently because listerial cells perceive growth with glutamine as a nitrogen-limiting condition. Therefore, paradoxically, expression of the glnA gene, encoding glutamine synthetase, was highest in the glutamine medium. For the amtB glnK operon, GlnR served as both a negative regulator in the presence of ammonium and a positive regulator in the glutamine medium. The gdhA gene was subject to a third mode of regulation that apparently required an elevated level of GlnR for repression. Finally, activity of glutamate dehydrogenase encoded by the gdhA gene appeared to correlate inversely with expression of gltAB, the operon that encodes the other major glutamate-synthesizing enzyme, glutamate synthase. Both gdhA and amtB were also regulated, in a negative manner, by the global transcriptional regulator CodY.IMPORTANCEL. monocytogenes is a widespread foodborne pathogen. Nitrogen-containing compounds, such as the glutamate-containing tripeptide, glutathione, and glutamine, have been shown to be important for expression of L. monocytogenes virulence genes. In this work, we showed that a transcriptional regulator, GlnR, controls expression of critical listerial genes of nitrogen metabolism that are involved in ammonium uptake and biosynthesis of glutamine and glutamate. A different mode of GlnR-mediated regulation was found for each of these three pathways.

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico.

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.

Spatial Distribution of Nitrogen Metabolism Functional Genes of Eubacteria and Archaebacteria in Dianchi Lake

Nitrogen metabolism plays an important role in the nitrogen cycle and transformation in Dianchi Lake. Not only do eukaryotes participate in nitrogen transformation but prokaryotes, as the main drivers of the nitrogen cycle, also play an extremely important role in the nitrogen cycle. Based on 16S rDNA high-throughput sequencing technology, 13 sites in Caohai and Waihai of Dianchi Lake were monitored, and PICRUSt function analysis method was adopted to analyze the microbial community diversity and key genes of nitrogen metabolism in Dianchi Lake. Bacteria belonging to 35 phyla and 427 genera were found in Dianchi Lake water and mainly included Proteobacteria and Bacteroidetes. Archaea had 14 phyla and 61 genera and mainly belonged to Euryarchaeota. The overall bacterial richness index of Dianchi Lake was higher than that of archaea, and the bacterial diversity index of Caohai was higher than that of Waihai. Functional prediction showed functional richness of bacteria and archaea. There were 35 KO pathways involved in nitrogen metabolism in bacteria, including key genes such as nitrogenous nitrate-reducing gene nirB, nitric oxide reductase gene norB in denitrification, and nitroreductase gene nasK. There were 23 KO pathways involved in nitrogen metabolism in archaea, involving nifH, nifK, and nifD nitrogenase genes in nitrogen fixation. The copy number of nitrogenase genes was significantly higher than that of other nitrogenase genes. The copy number of nitrogen-fixing genes of archaea was higher than that of bacteria, the nitrogen metabolism capacity of archaea in Caohai was higher than that in Waihai, and the potential of nitrogen-fixation of archaea in Dianchi Lake water was higher than that of bacteria. From the perspective of community structure and function prediction of bacteria and archaea, this study discussed the differences of nitrogen cycle in bacteria and archaea in different areas of Dianchi Lake and provided a decision basis for water environment management in Dianchi Lake.

HMW-GS at Glu-B1 Locus Affects Gluten Quality Possibly Regulated by the Expression of Nitrogen Metabolism Enzymes and Glutenin-Related Genes in Wheat.

In this study, we investigated the effect of high-molecular-weight glutenin subunits (HMW-GSs) on gluten quality and glutenin synthesis based on the cytological, physicochemical, and transcriptional levels using Xinong1718 and its three near-isogenic lines (NILs). Cytological observations showed that the endosperm of Glu-1Bh with Bx14+By15 accumulated more abundant and larger protein bodies at 10 and 16 days after anthesis than the other NILs. Glu-1Bh exhibited higher nitrogen metabolism enzyme gene expression and activity levels. The transcriptional levels of genes encoding HMW-GSs, protein folding, and transcription factors differed significantly among the NILs, and they were highest in Glu-1Bh. Our results demonstrate that variations in the expression patterns of nitrogen metabolism and glutenin synthesis-related genes may account for the differences in the accumulation of glutenin, glutenin macropolymers, and protein bodies, thereby affecting the structural and thermal stability of gluten. These findings provide novel insights into how different HMW-GSs might improve the quality of wheat.

Effects of Elevated Root-Zone CO2 on Root Morphology and Nitrogen Metabolism Revealed by Physiological and Transcriptome Analysis in Oriental Melon Seedling Roots.

Rhizosphere CO2 is vital for crop growth, development, and productivity. However, the mechanisms of plants’ responses to root-zone CO2 are unclear. Oriental melons are sensitive to root-zone gas, often encountering high root-zone CO2 during cultivation. We investigated root growth and nitrogen metabolism in oriental melons under T1 (0.5%) and T2 (1.0%) root-zone CO2 concentrations using physiology and comparative transcriptome analysis. T1 and T2 increased root vigor and the nitrogen content in the short term. With increased treatment time and CO2 concentration, root inhibition increased, characterized by decreased root absorption, incomplete root cell structure, accelerated starch accumulation and hydrolysis, and cell aging. We identified 1280 and 1042 differentially expressed genes from T1 and T2, respectively, compared with 0.037% CO2-grown plants. Among them, 683 co-expressed genes are involved in stress resistance and nitrogen metabolism (enhanced phenylpropanoid biosynthesis, hormone signal transduction, glutathione metabolism, and starch and sucrose metabolism). Nitrogen metabolism gene expression, enzyme activity, and nitrogen content analyses showed that short-term elevated root-zone CO2 mainly regulated plant nitrogen metabolism post-transcriptionally, and directly inhibited it transcriptionally in the long term. These findings provided a basis for further investigation of nitrogen regulation by candidate genes in oriental melons under elevated root-zone CO2.

The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in Streptomyces and Related Actinobacteria.

Soil dwelling Streptomyces species are faced with large variations in carbon or nitrogen sources, phosphate, oxygen, iron, sulfur, and other nutrients. These drastic changes in key nutrients result in an unbalanced metabolism that have undesirable consequences for growth, cell differentiation, reproduction, and secondary metabolites biosynthesis. In the last decades evidence has accumulated indicating that mechanisms to correct metabolic unbalances in Streptomyces species take place at the transcriptional level, mediated by different transcriptional factors. For example, the master regulator PhoP and the large SARP-type regulator AfsR bind to overlapping sequences in the afsS promoter and, therefore, compete in the integration of signals of phosphate starvation and S-adenosylmethionine (SAM) concentrations. The cross-talk between phosphate control of metabolism, mediated by the PhoR–PhoP system, and the pleiotropic orphan nitrogen regulator GlnR, is very interesting; PhoP represses GlnR and other nitrogen metabolism genes. The mechanisms of control by GlnR of several promoters of ATP binding cassettes (ABC) sugar transporters and carbon metabolism are highly elaborated. Another important cross-talk that governs nitrogen metabolism involves the competition between GlnR and the transcriptional factor MtrA. GlnR and MtrA exert opposite effects on expression of nitrogen metabolism genes. MtrA, under nitrogen rich conditions, represses expression of nitrogen assimilation and regulatory genes, including GlnR, and competes with GlnR for the GlnR binding sites. Strikingly, these sites also bind to PhoP. Novel examples of interacting transcriptional factors, discovered recently, are discussed to provide a broad view of this interactions. Altogether, these findings indicate that cross-talks between the major transcriptional factors protect the cell metabolic balance. A detailed analysis of the transcriptional factors binding sequences suggests that the transcriptional factors interact with specific regions, either by overlapping the recognition sequence of other factors or by binding to adjacent sites in those regions. Additional interactions on the regulatory backbone are provided by sigma factors, highly phosphorylated nucleotides, cyclic dinucleotides, and small ligands that interact with cognate receptor proteins and with TetR-type transcriptional regulators. We propose to define the signal integration DNA regions (so called integrator sites) that assemble responses to different stress, nutritional or environmental signals. These integrator sites constitute nodes recognized by two, three, or more transcriptional factors to compensate the unbalances produced by metabolic stresses. This interplay mechanism acts as a safety net to prevent major damage to the metabolism under extreme nutritional and environmental conditions.

Indirect effect of different dietary protein to energy ratio of bait fish mori diets on growth performance, body composition, nitrogen metabolism and relative AMPK & mTOR pathway gene expression of Chinese perch

Chinese perch (Siniperca chuatsi) is an important economic freshwater carnivorous fish. Commonly feeds on other live fish or bait fish, and accept an artificial diet only after standard training. The feeding habit of Chinese perch caused high aquaculture costs and consumer prices. However, only a few studies are conducted on Chinese perch live feed (bait fish) or live feed (mori) feeds. Therefore, the present study was conducted to investigate the effect of live feed (mori) and live feed (mori) feeds protein to energy ratio on Chinese perch. Three Iso-energetic diets (16 kJ/g) with graded levels of P/E ratios (19.79, 22.19 and 24.46 mg protein/kJ) each with a protein level of 28.18 %, 31.36 %, and 33.91 % (named A, B, and C) were formulated. Two separate experimental tanks systems were used. In one tanks system, a total of 90 kg live bait fish C. mrigala were distributed into three groups (triplicate tanks (1000 L) for each group) and fed with respective P/E ratio diets. In another tanks system, a total of 270 Chinese perch (30 fish/tank) were divided into three groups (triplicate tanks for each group), distributed into 9 (1000-L) fiberglass tanks and fed with assigned live bait fish at 4 % fish wet body weight, twice a day for 8 weeks. The results showed that P/E ratio in bait fish diets significantly affected bait fish and Chinese perch growth performance, feed utilization, body composition, nitrogen metabolism, protein synthesis, and energy homeostasis. Bait fish in Group A showed significantly lower weight gain (WG), specific growth rate (SGR), and higher Viscerosomatic index (VSI) and Hepatosomatic index (HSI) as compared to other groups. Correspondingly, bait fish in Group A showed significantly low whole-body crude protein and high lipid contents as compared to other groups. Similarly, Chinese perch in Group A, showed significantly lower WG, SGR, protein efficiency ratio (PER) and highest feed intake (FI), feed conversion ratio (FCR), VSI, HSI, and Intraperitoneal fat (IPF), as compared to other groups. Furthermore, Chinese perch in Group A, showed significantly lower whole body and muscle crude protein, and higher lipid contents as compared to other groups. Similarly, the nitrogen metabolism enzyme activities (ALT, AST, GDH, AMPD) and gene expression of GDH and AMPD in Group A of Chinese perch, were significantly lower than other groups. Moreover, the AMPK and mTOR pathways gene expression showed a low energy status and protein catabolism in Group A of Chinese perch as compared to other groups. From our results, we conclude that the P/E ratio in bait fish diet significantly affected bait fish and Chinese perch growth performance and nutrients metabolism.

The phenotype and pathogenicity of Ralstonia solanacearum transformed under prolonged stress of excessive exogenous nitrogen

AbstractBacterial wilt, caused by soil‐borne pathogen Ralstonia solanacearum, is a serious disease in many plants such as Solanaceae. To investigate the effects of accumulated nitrogen in soil on the phenotype and pathogenicity of the R. solanacearum, a serial passage experiment (SPE) was designed. Specifically speaking, minimal medium supplied with a slight excess of ammonium sulphate (AS) or ammonium nitrate (AN) was used to simulate the nutrition of soil containing excess nitrogen. During the period of 30 SPE, the phenotype, pathogenicity and relative expression of nitrogen metabolism genes in R. solanacearum were monitored. Phenotypic analysis results illustrated that the colony morphology of R. solanacearum changed after long‐term culture, from high virulence colonies with strong fluidity to small, round non‐mucoid colonies; The strain after prolonged stress of excessive exogenous nitrogen was a no‐virulence phenotype conversion type (PC‐type). The time for a change in colony morphology to occur after exposure to exogenous AS or AN was significantly less than the untreated samples, which treated without exogenous nitrogen. The results of pathogenicity also demonstrated that the cultures treated with exogenous AN or AS reduced virulence more quickly than the control. The disease index of 10 SPE with AN treatment or AS treatment was 89% or 68% lower than that of the control, respectively. In addition, as the incubation time increased, the swimming motility and the number of biofilms formation of the cultures were significantly changed under both treatments in comparison to the untreated samples. Furthermore, the relative expression of the nitric oxide reductase norB gene in the cultures treated with AN was 1.51‐fold higher compared with the control after 30 SPE. These results indicated that excessive nitrogen supply in the environment could accelerate the transformation of R. solanacearum from high virulence wild‐type into a PC‐type, probably for the purpose of adapting to the adverse environment.

CRISPR/Cas9 knockout of leghemoglobin genes in Lotus japonicus uncovers their synergistic roles in symbiotic nitrogen fixation.

Legume nodules contain high concentrations of leghemoglobins (Lbs) encoded by several genes. The reason for this multiplicity is unknown. CRISPR/Cas9 technology was used to generate stable mutants of the three Lbs of Lotus japonicus. The phenotypes were characterized at the physiological, biochemical and molecular levels. Nodules of the triple mutants were examined by electron microscopy and subjected to RNA-sequencing (RNA-seq) analysis. Complementation studies revealed that Lbs function synergistically to maintain optimal N2 fixation. The nodules of the triple mutants overproduced superoxide radicals and hydrogen peroxide, which was probably linked to activation of NADPH oxidases and changes in superoxide dismutase isoforms expression. The mutant nodules showed major ultrastructural alterations, including vacuolization, accumulation of poly-β-hydroxybutyrate and disruption of mitochondria. RNA-seq of c.20000 genes revealed significant changes in expression of carbon and nitrogen metabolism genes, transcription factors, and proteinases. Lb-deficient nodules had c.30-50-fold less heme but similar transcript levels of heme biosynthetic genes, suggesting a post-translational regulatory mechanism of heme synthesis. We conclude that Lbs act additively in nodules and that the lack of Lbs results in early nodule senescence. Our observations also provide insight into the reprogramming of the gene expression network associated with Lb deficiency, probably as a result of uncontrolled intracellular free O2 concentration.

Bacterial community structure and function in soils from tidal freshwater wetlands in a Chinese delta: Potential impacts of salinity and nutrient

Microorganisms in tidal freshwater wetlands affect biogeochemical cycling of nutrients, but the structures and functions of the wetland communities change due to natural and anthropogenic stresses. Soil samples were collected along a 350-m sampling belt in typical tidal freshwater wetlands of Yellow River Delta to investigate nutrient distributions, bacterial community structures and potential metabolic functions under tide and runoff stress by high-throughput sequencing and PICRUSt analysis. The total nitrogen (TN) contents varied greatly while total phosphorous (TP) contents were relatively stable. The bacterial community structures and predicted functions varied along a 350-m sampling belt. Some sulfate-reducing bacteria, nitrifying bacteria, Marmoricola, unclassified_f_Salinisphaeraceae and Oceanococcus exhibited a decreased trend with increasing distances far away from the river bank (B-0m). However, Salinisphaera was more dominant far away from the river bank (B-350m), indicating the stronger tolerance degree under salt stress. Marinobacterium and Marinobacter could be widely detected from B-0m to B-350m, demonstrating that those bacteria could tolerate a broad range of salinity and have its exceptional adaptation capacities. Redundancy analysis (RDA) indicated that nutrient and salinity played an important role in shaping bacterial community composition. NH4+-N and AP were the key factors in explaining the variance of the genus level. Predicted by PICRUSt analysis, nitrogen fixation (NF), nitrogen mineralization (NM), denitrification and dissimilatory nitrate reduction to ammonium (DNRA) might be the dominant processes of nitrogen metabolism and related genes abundance were abundant in tidal freshwater wetland soils. These findings could provide new insights into the prevention and control of potential nutrient pollution in tidal freshwater wetlands under the dual stress of tide and runoff.

Metabolic Functional Analysis of Dominant Microbial Communities in the Rapid Sand Filters for Drinking Water

Rapid sand filter (RSF) is widely used in drinking water treatment plants. Rapid filtration is always considered a physicochemical process, but the effect of the microorganisms that attach to the filter media remain inadequately investigated. In order to understand the composition and functional characteristics of microbial communities in RSFs, influent water, effluent water, and filter materials from eleven RSFs in eight Chinese cities were sampled and analyzed. After filtration, dissolved organic carbon (DOC) showed a slight but significant removal due to the growth of heterotrophic microbes. The activity of ammonia-oxidizing microbes and nitrite-oxidizing microbes promoted a significant decrease in ammonia nitrogen (NH4+-N) and a significant increase in nitrate nitrogen (NO3--N) in water. No significant changes in total nitrogen (TN) were observed, indicating that denitrification and anammox were weak in the RSFs. The composition and function of the microbial communities of RSFs were assessed using metagenomic methods. Genera in the top 10% with respect to relative abundance (14 genera in total) were identified as the dominant genera, including the two ammonia-oxidizing bacteria Nitrospira and Nitrosomonas. Functional gene information for the dominant genera was also extracted for analysis. The dominant genera exhibited higher relative abundances of carbohydrate, nitrogen, sulfur, and xenobiotic metabolic pathways. Aeromonas had the highest relative abundance of carbohydrate metabolic genes, and Bradyrhizobium had the highest relative abundance of nitrogen, sulfur, and xenobiotics metabolic genes, indicating that these two genera play an important role in the transformation of substances in drinking water. Finally, the metabolic potential of the dominant genera on xenobiotics was evaluated, and the results showed that Bradyrhizobium, Sphingomonas, Methyloglobulus, Sphingopyxis, and Klebsiella were the key bacterial genera for the removal of micropollutants in RSFs.

Dominant soil bacteria and their ecological attributes across the deserts in northern China

AbstractSoils harbour highly diverse bacterial communities that are essential for nutrient cycling and carbon storage. However, this diversity impedes the efforts to characterize individual taxa and their ecological attributes. In particular, comprehensive assessments of soil bacterial communities in drylands in China are limited. In this study, soil samples were collected across 12 deserts, covering four climatic regions (dry sub‐humid, semi‐arid, arid and hyper‐arid) in northern China to examine the dominant phylotypes, and their environmental preferences and functional traits. Only 3.2% of the bacterial phylotypes (913 phylotypes) were dominant. These dominant phylotypes can be grouped into six major ecological clusters based on high pH, high elevation, low aridity index, high aridity index, low mean annual temperature and low soil water content, each with multiple phyla. Based on the association between diversity indexes for dominant and subdominant phylotypes, these dominant bacteria might be the drivers or indicators of key soil processes across desert soils in northern China. Genes involved in carbon fixation and decomposition and nitrogen metabolism varied across desert soils, suggesting functional differences. These findings provide deeper insights into soil bacterial communities, which are critical for forecasting the ecological consequences of ongoing global environmental change and for a better mechanistic understanding of the biogeochemical cycle.Highlights 3.2% of the bacterial phylotypes were dominant across 12 deserts in northern China. The dominant phylotypes were grouped into six major ecological clusters. Carbon fixation, decomposition and nitrogen metabolism genes varied across desert soils. Some northern China desert soils might undergo nitrogen and carbon loss in the near future.

A MYST family histone acetyltransferase, MoSAS3, is required for development and pathogenicity in the rice blast fungus.

SummaryHistone acetylation has been established as a principal epigenetic regulatory mechanism in eukaryotes. Sas3, a histone acetyltransferase belonging to the largest family of acetyltransferase, MYST, is the catalytic subunit of a conserved histone acetyltransferase complex. To date, the functions of Sas3 and its orthologues have been extensively studied in yeast, humans and flies in relation to global acetylation and transcriptional regulation. However, its precise impact on development and pathogenicity in fungal plant pathogens has yet to be elucidated. Considering the importance of Sas3 in H3K14 acetylation, here we investigate the roles of its orthologue in the rice blast fungus, Magnaporthe oryzae (Pyricularia oryzae). Unlike a previously reported Sas3 deletion in yeast, which led to no remarkable phenotypic changes, we found that MoSAS3 deletion alone had a profound effect on fungal growth and development, including asexual reproduction, germination and appressorium formation in M. oryzae. Such defects in pre‐penetration development resulted in complete loss of pathogenicity in the deletion mutant. Furthermore, genetic analysis of MoSAS3 and MoGCN5 encoding a Gcn5‐related N‐acetyltransferase family histone acetyltransferase suggested that two conserved components of histone acetylation are integrated differently into epigenetic regulatory mechanisms in the yeast and a filamentous fungus. RNA‐seq analysis of ΔMosas3 showed two general trends: many DNA repair and DNA damage response genes are up‐regulated, while carbon and nitrogen metabolism genes are down‐regulated in ΔMosas3. Our work demonstrates the importance of MYST family histone acetyltransferase as a developmental regulator and illuminates a degree of functional variation in conserved catalytic subunits among different fungal species.

The developmental regulator MtrA binds GlnR boxes and represses nitrogen metabolism genes in Streptomyces coelicolor.

In Streptomyces, GlnR is an activator protein that activates nitrogen-assimilation genes under nitrogen-limiting conditions. However, less is known regarding the regulation of these genes under nitrogen-rich conditions. We determined that the developmental regulator MtrA represses nitrogen-assimilation genes in nitrogen-rich media and that it competes with GlnR for binding to GlnR boxes. The GlnR boxes upstream of multiple nitrogen genes, such as amtB, were confirmed as MtrA binding sites in vitro by electrophoretic mobility shift assays and in vivo by ChIP-qPCR analysis. Transcriptional analysis indicated that, on nutrient-rich medium, MtrA profoundly repressed expression of nitrogen-associated genes, indicating opposing roles for MtrA and GlnR in the control of nitrogen metabolism. Using in vitro and in vivo analysis, we also showed that glnR is itself a direct target of MtrA and that MtrA represses glnR transcription. We further demonstrated functional conservation of MtrA homologues in the recognition of GlnR boxes upstream of nitrogen genes from different actinobacterial species. As mtrA and glnR are widespread among actinomycetes, this mechanism of potential competitive control over nitrogen metabolism genes may be common in this group, adding a major new layer of complexity to the known regulatory network for nitrogen metabolism in Streptomyces and related species.

Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor

Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3− could be used as electron acceptor and Hg0 as electron donor in denitrification.

Nitric oxide alters nitrogen metabolism and PIN gene expressions by playing protective role in arsenic challenged Brassica juncea L.

Plants have ability to adapt themselves through altering their growth process. In the present study, we examined exogenous application of nitric oxide (NO) on nitrogen metabolism and auxin (PIN) gene expression, and its possible role in alleviation of arsenic (As) toxicity in Brassica juncea seedlings. Seven days old hydroponically grown B. juncea seedlings were exposed to AsIII (150 μM), Sodium nitroprusside (NO donor, 100 μM), AsIII + SNP and control (without metal)for 48 h. Experimental results revealed that AsIII stress: enhanced the level of nitrite, NiR activity, NO3− and NH4+content as well as NADH-GOGAT activity; but GDH level decreased; enhanced content of amino acids; upregulated gene expression level of N metabolism and downregulated polar auxin transporter genes (PIN); inhibited plant growth and morphological parameters; increased MDA, H2O2, cysteine, proline content, enzymatic antioxidants (SOD, CAT, APX; GSH, TT, NPT); and decreased nutrient content. AsIII + SNP combination reduced the accumulation of As; improved growth; chlorophyll, protein and mineral nutrient content by scavenging ROS generation; maintained amino acids content; downregulated expression of N metabolism genes and upregulated expression of auxin transporter (PIN) genes . Additional biochemical data depicts reduction in the level of nitrogen related enzymatic activities, and other stress related parameters. Overall, this study provides an integrated view that exogenous SNP (NO donor) supplementation alleviated the inhibitory role of AsIII in B. juncea seedlings by altering nutrients, amino acids and auxin redistribution via expression of nitrogen and PIN gene profiling.

Functionally Related Genes Cluster into Genomic Regions That Coordinate Transcription at a Distance in Saccharomyces cerevisiae.

Balancing gene expression is a fundamental challenge of all cell types. To properly regulate transcription on a genome-wide level, there are myriad mechanisms employed by the cell. One layer to this regulation is through spatial positioning, with particular chromosomal loci exerting an influence on transcription throughout a region. Many coregulated gene families utilize spatial positioning to coordinate transcription, with functionally related genes clustering together which can allow coordinated expression via adjacent gene coregulation. The mechanisms underlying this process have not been elucidated, though there are many coregulated gene families that exhibit this genomic distribution. In the present study, we tested for a role for the enhancer-promoter (EP) hypothesis, which demonstrates that regulatory elements can exert transcriptional effects over a broad distance, in coordinating transcriptional coregulation using budding yeast, Saccharomyces cerevisiae We empirically validated the EP model, finding that the genomic distance a promoter can affect varies by locus, which can profoundly affect levels of transcription, phenotype, and the extent of transcriptional disruption throughout a genomic region. Using the nitrogen metabolism, ribosomal protein, toxin response, and heat shock gene families as our test case, we report functionally clustered genes localize to genomic loci that are more conducive to transcriptional regulation at a distance compared to the unpaired members of the same families. Furthermore, we report that the coregulation of functional clusters is dependent, in part, on chromatin maintenance and remodeling, providing one mechanism underlying adjacent gene coregulation.IMPORTANCE The two-dimensional, physical positioning of genes along a chromosome can impact proper transcriptional regulation throughout a genomic region. The transcription of neighboring genes is correlated in a genome-wide manner, which is a characteristic of eukaryotes. Many coregulated gene families can be found clustered with another member of the same set-which can result in adjacent gene coregulation of the pair. Due to the myriad gene families that exhibit a nonrandom genomic distribution, there are likely multiple mechanisms working in concert to properly regulate transcriptional coordination of functionally clustered genes. In this study, we utilized budding yeast in an attempt to elucidate mechanisms that underlie this coregulation: testing and empirically validating the enhancer-promoter hypothesis in this species and reporting that functionally related genes cluster to genomic regions that are more conducive to transcriptional regulation at a distance. These clusters rely, in part, on chromatin maintenance and remodelers to maintain proper transcriptional coordination. Our work provides insight into the mechanisms underlying adjacent gene coregulation.

Metabolic Engineering Strategies Based on Secondary Messengers (p)ppGpp and C-di-GMP To Increase Erythromycin Yield in Saccharopolyspora erythraea.

Secondary messengers (such as (p)ppGpp and c-di-GMP) were proved to play important roles in antibiotic biosynthesis in actinobacteria. In this study, we found that transcription levels of erythromycin-biosynthetic ( ery) genes were upregulated in nutrient limitation, which depended on (p)ppGpp in Saccharopolyspora erythraea. Further study demonstrated that the expression of ery genes and intracellular concentrations of (p)ppGpp showed synchronization during culture process. The erythromycin yield was significantly improved (about 200%) by increasing intracellular concentration of (p)ppGpp through introduction of C-terminally truncated (p)ppGpp synthetase RelA (1.43 kb of the N-terminal segment) from Streptomyces coelicolor into S.erythraea strain NRRL2338 (named as WT/pIB-P BAD- relA1-489). As the intracellular concentration of (p)ppGpp in an industrial erythromycin-high-producing strain E3 was greatly higher (about 10- to 100-fold) than WT strain, the applications of the above-described strategy did not work in E3 strain. Further research revealed that low concentration of 2-oxoglutarate in E3 strain exerted a "nitrogen-rich" pseudosignal, leading to the downregulation of nitrogen metabolism genes, which limited the use of nitrogen sources and thus the high intracellular (p)ppGpp concentration. Furthermore, the secondary messenger, c-di-GMP, was proved to be able to activate ery genes transcription by enhancing binding of BldD to promoters of ery genes. Overexpressing the diguanylate cyclase CdgB from S.coelicolor in S.erythraea increased the intracellular c-di-GMP concentration, and improved erythromycin production. These findings demonstrated that increasing the concentration of intracellular secondary messengers can activate ery genes transcription, and provided new strategies for designing metabolic engineering based on secondary messengers to improve antibiotics yield in actinobacteria.

Influence of N, P, Fe Nutrients Availability on Nitrogen Metabolism- Relevant Genes Expression in Skeletonema marinoi

Nitrogen (N), Phosphorus (P), and Iron (Fe) are essential elements for cellular structure and metabolism. In addition to dissolved inorganic nitrogen (DIN), phytoplankton is able to utilize dissolved organic nitrogen (DON). There is general consensus that both bacteria and higher plants nitrogen metabolism is affected by phosphate availability; this was also found to be true in coccolithophorid. Iron affects the structure and function of ecosystems through its effects on nitrogen metabolism. However, it is unclear how these nutrients affect Skeletonema marinoi’s nitrogen metabolism. Here, using RT-qPCR, we investigate effects of N, P, and Fe on S. marinoi’s nitrogen metabolism and nitrate reductase activity. These results illuminate that in S. marinoi, various nutrients have direct regulation on these genes expression at the molecular level. The varying degree of responses for these genes expression with differing N sources may act to increase the efficiency of nutrient capture when nitrate is limited. Suitable gene expression occurs at a N/P ratio of 16, which represents the atomic N/P ratio of phytoplankton cells and N/P concentrations in ocean; thus, nitrogen metabolism gene expression should be regulated by the existing N/P ratios in the phytoplankton’s internal and external environment. Fe concentration has a direct and significant effect on nitrogen metabolism by regulating gene expression and nitrate reductase activity. Gene expression profiles identified in S. marinoi provide a foundation for understanding molecular mechanisms behind diatom nitrogen metabolism with changing N, P, and Fe nutrients allowing a basic understanding of how diatom growth is affected by nutrient utilization.

Identification of traits associated with barley yield performance using contrasting nitrogen fertilizations and genotypes

Much attention has been paid to understanding the traits associated with crop performance and the associated underlying physiological mechanisms, with less effort done towards combining different plant scales, levels of observation, or including hybrids of autogamous species. We aim to identify mechanisms at canopy, leaf and transcript levels contributing to crop performance under contrasting nitrogen supplies in three barley genotypes, two hybrids and one commercial line. High nitrogen fertilization did not affect photosynthetic capacity on a leaf area basis and lowered nitrogen partial factor productivity past a certain point, but increased leaf area and biomass accumulation, parameters that were closely tracked using various different high throughput remote sensing based phenotyping techniques. These aspects, together with a larger catabolism of leaf nitrogen compounds amenable to sink translocation, contributed to higher crop production. Better crop yield and growth in hybrids compared to the line was linked to a nitrogen-saving strategy in source leaves to the detriment of larger sink size, as indicated by the lower leaf nitrogen content and downregulation of nitrogen metabolism and aquaporin genes. While these changes did not reduce photosynthesis capacity on an area basis, they were related with better nitrogen use in the hybrids compared with the line.