scholarly journals SAR11 Cells Rely on Enzyme Multifunctionality to Transport and Metabolize a Range of Polyamine Compounds

2021 ◽  
Author(s):  
Stephen E Noell ◽  
Gregory E Barrell ◽  
Christopher Suffridge ◽  
Jeff T Morré ◽  
Kevin P Gable ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Organic Cations ◽  
Spermidine Synthase ◽  
Carbon And Nitrogen ◽  
Surface Ocean ◽  
Polyamine Transport ◽  
Metabolic Footprinting ◽  
Living Organisms ◽  
Ocean Environment ◽  
Ocean Surface Layer

In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells transport and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, Ca. Pelagibacter st. HTCC7211 and C. P. ubique st. HTCC1062. Both strains transported all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but we did not find evidence of use as carbon sources. We propose potABCD transports cadaverine, agmatine, and norspermidine, in addition to its usual substrates of spermidine and putrescine, and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they oxidize.

The monogenean Paradiplozoon ichthyoxanthon behaves like a micropredator on two of its hosts, as indicated by stable isotopes

2018 ◽  
Vol 93 (1) ◽  
pp. 71-75 ◽  
Author(s):  
B. Sures ◽  
M. Nachev ◽  
B.M. Gilbert ◽  
Q.M. Dos Santos ◽  
M.A. Jochmann ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Trophic Level ◽  
Trophic Interactions ◽  
Carbon Sources ◽  
Food Sources ◽  
Carbon And Nitrogen ◽  
Blood Sucking ◽  
Vaal Dam ◽  
Living Organisms ◽  
Host Fishes

AbstractThe analysis of stable isotopes of carbon and nitrogen has been used as a fingerprint for understanding the trophic interactions of organisms. Most of these studies have been applied to free-living organisms, while parasites have largely been neglected. Studies dealing with parasites so far have assessed the carbon and nitrogen signatures in endoparasites or ectoparasites of different hosts, without showing general trends concerning the nutritional relationships within host–parasite associations. Moreover, in most cases such systems involved a single host and parasite species. The present study is therefore the first to detail the trophic interactions of a freshwater monogenean–host model using δ13C and δ15N, where a single monogenean species infects two distinctly different hosts. Host fishes, Labeobarbus aeneus and Labeobarbus kimberleyensis from the Vaal Dam, South Africa, were assessed for the monogenean parasite Paradiplozoon ichthyoxanthon, individuals of which were removed from the gills of the hosts. The parasites and host muscle samples were analysed for signatures of δ13C and δ15N using an elemental analyser connected to an isotope ratio mass spectrometer. Host fish appear to use partly different food sources, with L. aeneus having slightly elevated δ13C signatures compared to L. kimberleyensis, and showed only small differences with regard to their nitrogen signatures, suggesting that both species range on the same trophic level. Carbon and nitrogen signatures in P. ichthyoxanthon showed that the parasites mirrored the small differences in dietary carbon sources of the host but, according to δ15N signatures, the parasite ranged on a higher trophic level than the hosts. This relationship resembles predator–prey relationships and therefore suggests that P. ichthyoxanthon might act as a micropredator, similar to blood-sucking arthropods such as mites and fleas.

Environmental significance of atrazine in aqueous systems and its removal by biological processes: an overview

2013 ◽  
Vol 8 (2) ◽  
pp. 159-178 ◽  
Keyword(s):  
Drinking Water ◽  
Ground Water ◽  
Water Environment ◽  
Biological Processes ◽  
Biological Degradation ◽  
Environmental Significance ◽  
Carbon And Nitrogen ◽  
Carbon Nitrogen Ratio ◽  
Nitrogen Ratio ◽  
Living Organisms

Atrazine, a chlorinated s-triazine group of herbicide is one of the most widely used pesticides in the World. Due to its extensive use, long half-life and various toxic properties, it has very high environmental significance. Up to 22 mg l-1 of atrazine was found in ground water whereas permissible limit of atrazine is in ppb level in drinking water. As per Indian standard there should not be any pesticide present in drinking water. Among many other treatment processes available, Incineration, adsorption, chemical treatment, phytoremediation and biodegradation are the most commonly used ones. Biological degradation of atrazine depends upon various factors like the operating environment, external carbon and nitrogen sources, carbon/ nitrogen ratio (C/N), water content and the bacterial strain. Although, general atrazine degradation pathways are available, the specific pathways in specific conditions are not yet clearly defined. In this paper extensive review has been made on the occurrence of atrazine in surface and ground water bodies, probable sources and causes of its occurrence in water environment, the toxicity of atrazine on various living organisms and its removal by biological processes.

scholarly journals Production of Feruloyl Esterase from Aspergillus niger by Solid-State Fermentation on Different Carbon Sources

2011 ◽  
Vol 2011 ◽  
pp. 1-4 ◽  
Author(s):  
Shiyi Ou ◽  
Jing Zhang ◽  
Yong Wang ◽  
Ning Zhang
Keyword(s):  
Carbon Source ◽  
Nitrogen Source ◽  
Wheat Bran ◽  
Cell Walls ◽  
Carbon Sources ◽  
Feruloyl Esterase ◽  
Plant Cell Walls ◽  
Optimal Conditions ◽  
Carbon And Nitrogen ◽  
Maize Bran

A mixture of wheat bran with maize bran as a carbon source and addition of (NH4)SO4 as nitrogen source was found to significantly increase production of feruloyl esterase (FAE) enzyme compared with wheat bran as a sole carbon and nitrogen source. The optimal conditions in conical flasks were carbon source (30 g) to water 1 : 1, maize bran to wheat bran 1 : 2, (NH4)SO4 1.2 g and MgSO4 70 mg. Under these conditions, FAE activity was 7.68 mU/g. The FAE activity on the mixed carbon sources showed, high activity against the plant cell walls contained in the cultures.

scholarly journals Crystal structures of γ-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine

2020 ◽  
pp. jbc.RA120.015952
Author(s):  
Ning Wang ◽  
Xiu-Lan Chen ◽  
Chao Gao ◽  
Ming Peng ◽  
Peng Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Trace Gas ◽  
Microbial Genomes ◽  
Carbon And Nitrogen ◽  
Tetrahedral Intermediate ◽  
Surface Ocean ◽  
Biochemical Analyses ◽  
Global Carbon

Monomethylamine (MMA) is an important climate-active oceanic trace gas and ubiquitous in the oceans. The γ-glutamylmethylamide synthetase (GmaS) catalyzes the conversion of MMA to γ-glutamylmethylamide (GMA), the first step in MMA metabolism in many marine bacteria. The gmaS gene occurs in ~23% of microbial genomes in the surface ocean and is a validated biomarker to detect MMA-utilizing bacteria. However, the catalytic mechanism of GmaS has not been studied due to the lack of structural information. Here, the GmaS from Rhodovulum sp. 12E13 (RhGmaS) was characterized, and the crystal structures of apo-RhGmaS and RhGmaS with different ligands in five states were solved. Based on structural and biochemical analyses, the catalytic mechanism of RhGmaS was explained. ATP is first bound in RhGmaS, leading to a conformational change of a flexible loop (Lys287-Ile305), which is essential for the subsequent binding of glutamate. During the catalysis of RhGmaS, the residue Arg312 participates in polarizing the γ-phosphate of ATP and in stabilizing the γ-glutamyl phosphate intermediate; Asp177 is responsible for the deprotonation of MMA, assisting the attack of MMA on γ-glutamyl phosphate to produce a tetrahedral intermediate; and Glu186 acts as a catalytic base to abstract a proton from the tetrahedral intermediate to finally generate GMA. Sequence analysis suggested that the catalytic mechanism of RhGmaS proposed in this study has universal significance in bacteria containing GmaS. Our results provide novel insights into MMA metabolism, contributing to a better understanding of MMA catabolism in global carbon and nitrogen cycles.

The Use of Carbon and Nitrogen Stable Isotope Analysis to Characterize Food Web Changes in Aquatic Systems for Reclamation of Oil Sands Process-Affected Materials

2009 ◽  
Vol 44 (4) ◽  
pp. 313-322 ◽  
Author(s):  
Monalisa Elshayeb ◽  
Michael D. MacKinnon ◽  
D. George Dixon ◽  
Michael Power
Keyword(s):  
Food Web ◽  
Oil Sands ◽  
Isotope Analysis ◽  
Naphthenic Acid ◽  
Carbon Sources ◽  
Nitrogen Isotope ◽  
Isotopic Signatures ◽  
Carbon And Nitrogen ◽  
Aquatic Food ◽  
Northern Alberta

Abstract One strategy for reclamation of oil sands leases in northern Alberta is the construction of lakes and wetlands by capping oil sands process-affected material (OSPM) with water. To assess this approach, experimental sites containing a range of OSPM have been constructed to monitor the evolution of the resulting aquatic habitats. Stable isotopes of carbon and nitrogen were used to assess the effects of OSPM on aquatic food webs. Carbon and nitrogen isotopic signatures of sediment, dissolved inorganic and organic carbon, particulate organic matter, periphyton, plants, plankton, aquatic invertebrates, and fish were used to assess differences related to the naphthenic acid (NA) concentration in OSPM and reference sites. NAs are a principal contaminant of concern in OSPM. Sites were grouped into low (0 to 4 mg/L), medium (4 to 15 mg/L), and high (>15 mg/L) NA concentrations. There were no significant differences in food web area or length among the three NA groupings. In most cases, carbon isotope analyses of samples from low, medium, and high NA concentration sites were not significantly different, suggesting that OSPM is not a significant contributor to food web carbon sources. Significant differences were found in nitrogen isotope signatures between low, medium, and high NA sites. Ammonia from OSPM is suggested as the main contributor to δ15N enrichment.

scholarly journals β-Fructofuranosidase andβ–D-Fructosyltransferase from NewAspergillus carbonariusPC-4 Strain Isolated from Canned Peach Syrup: Effect of Carbon and Nitrogen Sources on Enzyme Production

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Gustavo Carvalho do Nascimento ◽  
Ryhára Dias Batista ◽  
Claudia Cristina Auler do Amaral Santos ◽  
Ezequiel Marcelino da Silva ◽  
Fabrício Coutinho de Paula ◽  
...  
Keyword(s):  
Yeast Extract ◽  
Soybean Protein ◽  
Low Cost ◽  
Carbon Sources ◽  
Nitrogen Sources ◽  
Culture Conditions ◽  
Carbon And Nitrogen ◽  
Production Values ◽  
Pure Carbon ◽  
Fermentation Parameters

β-fructofuranosidase (invertase) andβ-D-fructosyltransferase (FTase) are enzymes used in industrial processes to hydrolyze sucrose aiming to produce inverted sugar syrup or fructooligosaccharides. In this work, a blackAspergillussp. PC-4 was selected among six filamentous fungi isolated from canned peach syrup which were initially screened for invertase production. Cultivations with pure carbon sources showed that invertase and FTase were produced from glucose and sucrose, but high levels were also obtained from raffinose and inulin. Pineapple crown was the best complex carbon source for invertase (6.71 U/mL after 3 days of cultivation) and FTase production (14.60 U/mL after 5 days of cultivation). Yeast extract and ammonium chloride nitrogen sources provided higher production of invertase (6.80 U/mL and 6.30 U/mL, respectively), whereas ammonium nitrate and soybean protein were the best nitrogen sources for FTase production (24.00 U/mL and 24.90 U/mL, respectively). Fermentation parameters for invertase using yeast extract wereYP/S= 536.85 U/g andPP= 1.49 U/g/h. FTase production showed values ofYP/S= 2,627.93 U/g andPP= 4.4 U/h using soybean protein. The screening for best culture conditions showed an increase of invertase production values by 5.10-fold after 96 h cultivation compared to initial experiments (fungi bioprospection), while FTase production increased by 14.60-fold (44.40 U/mL) after 168 h cultivation.A. carbonariusPC-4 is a new promising strain for invertase and FTase production from low cost carbon sources, whose synthesized enzymes are suitable for the production of inverted sugar, fructose syrups, and fructooligosaccharides.

scholarly journals Galactose Metabolism Plays a Crucial Role in Biofilm Formation by Bacillus subtilis

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Yunrong Chai ◽  
Pascale B. Beauregard ◽  
Hera Vlamakis ◽  
Richard Losick ◽  
Roberto Kolter
Keyword(s):  
Bacillus Subtilis ◽  
Biofilm Formation ◽  
Carbon Sources ◽  
Galactose Metabolism ◽  
Content Type ◽  
Leloir Pathway ◽  
The Matrix ◽  
Living Organisms ◽  
Galactose Metabolites ◽  
Biofilm Matrix

ABSTRACTGalactose is a common monosaccharide that can be utilized by all living organisms via the activities of three main enzymes that make up the Leloir pathway: GalK, GalT, and GalE. InBacillus subtilis, the absence of GalE causes sensitivity to exogenous galactose, leading to rapid cell lysis. This effect can be attributed to the accumulation of toxic galactose metabolites, since thegalEmutant is blocked in the final step of galactose catabolism. In a screen for suppressor mutants restoring viability to agalEnull mutant in the presence of galactose, we identified mutations insinR, which is the major biofilm repressor gene. These mutations caused an increase in the production of the exopolysaccharide (EPS) component of the biofilm matrix. We propose that UDP-galactose is the toxic galactose metabolite and that it is used in the synthesis of EPS. Thus, EPS production can function as a shunt mechanism for this toxic molecule. Additionally, we demonstrated that galactose metabolism genes play an essential role inB. subtilisbiofilm formation and that the expressions of both thegalandepsgenes are interrelated. Finally, we propose thatB. subtilisand other members of theBacillusgenus may have evolved to utilize naturally occurring polymers of galactose, such as galactan, as carbon sources.IMPORTANCEBacteria switch from unicellular to multicellular states by producing extracellular matrices that contain exopolysaccharides. In such aggregates, known as biofilms, bacteria are more resistant to antibiotics. This makes biofilms a serious problem in clinical settings. The resilience of biofilms makes them very useful in industrial settings. Thus, understanding the production of biofilm matrices is an important problem in microbiology. In studying the synthesis of the biofilm matrix ofBacillus subtilis, we provide further understanding of a long-standing microbiological observation that certain mutants defective in the utilization of galactose became sensitive to it. In this work, we show that the toxicity observed before was because cells were grown under conditions that were not propitious to produce the exopolysaccharide component of the matrix. When cells are grown under conditions that favor matrix production, the toxicity of galactose is relieved. This allowed us to demonstrate that galactose metabolism is essential for the synthesis of the extracellular matrix.

Two-sided turbulent boundary layer parameterizations for assessing ocean – atmosphere fluxes

2020 ◽  
Author(s):  
Florian Lemarie ◽  
Charles Pelletier ◽  
Pierre-Etienne Brilouet ◽  
Eric Blayo ◽  
Jean-Luc Redelsperger ◽  
...  
Keyword(s):  
Boundary Layer ◽  
Surface Layer ◽  
Ocean Surface ◽  
Near Surface ◽  
Surface Ocean ◽  
Turbulent Closure ◽  
Surface Fields ◽  
Ocean Surface Layer ◽  
Vertical Level ◽  
Layer Solution

<p><span>Standard </span><span>methods for determining air – sea fluxes typically rely on bulk algorithms derived from the Monin-Obukhov stability theory (MOST), </span><span>using ocean surface fields and atmosphere near-surface fields. In the context of coupled ocean – atmosphere simulations, </span><span>the </span><span>shallowest ocean vertical level is usually assimilated to </span><span>the surface, and the turbulent closure is one-sided: it aims at extrapolating atmosphere near-surface solution profiles (for wind speed, temperature and humidity) to the prescribed ocean surface values. </span><span>Assimilating near-surface ocean fields as surface ones is equivalent to considering that in the ocean surface layer, solution profiles are constant instead of also being determined by a turbulent closure. Here we introduce a method for extending existing turbulent parameterization</span><span>s</span><span> to a two-sided </span><span>context, by including the ocean surface layer and the viscous sublayers, which are also generally neglected in </span><span>standard air – sea fluxes computation. </span><span>The formalism we use for this method is derived from that of classical turbulent closure, so that our novelties can easily be implemented within existing formulations.</span> <span>Special care is taken to </span><span>ensure the smoothness of </span><span>resulting solution profiles. </span><span>We</span> <span>investigate the </span><span>impact of such two-sided bulk formulations on air - sea fluxes and </span><span>discuss further implications such as resulting bulk formulation retuning. We also present leads on incorporating </span><span>other mechanisms impacting air – sea fluxes within our framework, such as waves and radiation penetration.<br></span></p>

scholarly journals Growth responses of aquatic hyphomycetes to different sources of carbon and nitrogen

2013 ◽  
Vol 5 (2) ◽  
pp. 313-317 ◽  
Author(s):  
Saraswati Bisht
Keyword(s):  
Carbon Sources ◽  
Nitrogen Sources ◽  
Dry Weight ◽  
Maximum Growth ◽  
Fungal Species ◽  
Aquatic Hyphomycetes ◽  
Growth Responses ◽  
Carbon And Nitrogen ◽  
Fungal Isolates ◽  
Different Sources

Assessment of different sources of carbon and nitrogen in terms of dry weight biomass of four selected aquatic hyphomycetes viz; Flagellospora penicilloides Ingold, Pestalotiopsis submersus Sati and Tiwari, Tetrachaetum elegans Ingold and Tetracladium marchalianum De Wildeman was made for their nutritional requirements. Eight carbon sources and ten nitrogen sources were singly added to the basal media in order to provide 4g of carbon and 1g of nitrogen per litre of distilled water. Among carbon compounds glucose and sucrose were found to be most suitable sources of carbon for all the four fungal isolates, where as fructose proved good for T. marchalianum, P. submersus and F.penicilloides fairly. Cellulose was found a poor source of carbon for the growth of all these isolates. The inorganic sources of nitrogen were found as good nitrogen sources with preference for ammonium ions. Suitability of amino acids was found variable from species to species for nitrogen. T.elegans and T.marchalianum had their maximum growth in asparagines, whereas, P. submersus had their highest growth in proline. Cysteine was observed as a good source of nitrogen for almost all the fungal isolates used. Anova calculated for these observed data showed significant variations in the dry weight production of different fungal species grown in different sources of carbon and nitrogen(P<0.01).

Sign in / Sign up

Export Citation Format

Share Document