scholarly journals Nitrogen Utilization and Metabolism in Ruminococcus albus 8

2014 ◽  
Vol 80 (10) ◽  
pp. 3095-3102 ◽  
Author(s):  
Jong Nam Kim ◽  
Emily DeCrescenzo Henriksen ◽  
Isaac K. O. Cann ◽  
Roderick I. Mackie
Keyword(s):  
Growth Rate ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Enzyme Activities ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Sole Nitrogen Source ◽  
Ruminococcus Albus ◽  
Content Type ◽  
Maximum Cell

ABSTRACTThe model rumenFirmicutesorganismRuminococcus albus8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth ofR. albus8 on ammonia and urea showed the same growth rate (0.08 h−1) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD600] was 1.01; and for urea, the OD600was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h−1) and a lower maximum cell density (OD600= 0.58). To identify differences in gene expression and enzyme activities, the transcript abundances of 10 different genes involved in nitrogen metabolism and specific enzyme activities were analyzed by harvesting mRNA and crude protein from cells at the mid- and late exponential phases of growth on the different N sources. Transcript abundances and enzyme activities varied according to nitrogen source, ammonia concentration, and growth phase. Growth ofR. albus8 on ammonia and urea was similar, with the only observed difference being an increase in urease transcript abundance and enzyme activity in urea-grown cultures. Growth ofR. albus8 on peptides showed a different nitrogen metabolism pattern, with higher gene transcript abundance levels ofgdhA,glnA,gltB,amtB,glnK, andureC, as well as higher activities of glutamate dehydrogenase and urease. These results demonstrate that ammonia, urea, and peptides can all serve as nitrogen sources forR. albusand that nitrogen metabolism genes and enzyme activities ofR. albus8 are regulated by nitrogen source and the level of ammonia in the growth medium.

scholarly journals Nutrient-ColimitedTrichodesmiumas a Nitrogen Source or Sink in a Future Ocean

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Michael D. Lee ◽  
Xiaoni Cai ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Organic Nitrogen ◽  
Open Ocean ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Nitrogen Inputs ◽  
Ocean Conditions ◽  
Nitrogen Scavenging

ABSTRACTNitrogen-fixing (N2) cyanobacteria provide bioavailable nitrogen to vast ocean regions but are in turn limited by iron (Fe) and/or phosphorus (P), which may force them to employ alternative nitrogen acquisition strategies. The adaptive responses of nitrogen fixers to global-change drivers under nutrient-limited conditions could profoundly alter the current ocean nitrogen and carbon cycles. Here, we show that the globally important N2fixerTrichodesmiumfundamentally shifts nitrogen metabolism toward organic-nitrogen scavenging following long-term high-CO2adaptation under iron and/or phosphorus (co)limitation. Global shifts in transcripts and proteins under high-CO2/Fe-limited and/or P-limited conditions include decreases in the N2-fixing nitrogenase enzyme, coupled with major increases in enzymes that oxidize trimethylamine (TMA). TMA is an abundant, biogeochemically important organic nitrogen compound that supports rapidTrichodesmiumgrowth while inhibiting N2fixation. In a future high-CO2ocean, this whole-cell energetic reallocation toward organic nitrogen scavenging and away from N2fixation may reduce new-nitrogen inputs byTrichodesmiumwhile simultaneously depleting the scarce fixed-nitrogen supplies of nitrogen-limited open-ocean ecosystems.IMPORTANCETrichodesmiumis among the most biogeochemically significant microorganisms in the ocean, since it supplies up to 50% of the new nitrogen supporting open-ocean food webs. We usedTrichodesmiumcultures adapted to high-CO2conditions for 7 years, followed by additional exposure to iron and/or phosphorus (co)limitation. We show that “future ocean” conditions of high CO2and concurrent nutrient limitation(s) fundamentally shift nitrogen metabolism away from nitrogen fixation and instead toward upregulation of organic nitrogen-scavenging pathways. We show that the responses ofTrichodesmiumto projected future ocean conditions include decreases in the nitrogen-fixing nitrogenase enzymes coupled with major increases in enzymes that oxidize the abundant organic nitrogen source trimethylamine (TMA). Such a shift toward organic nitrogen uptake and away from nitrogen fixation may substantially reduce new-nitrogen inputs byTrichodesmiumto the rest of the microbial community in the future high-CO2ocean, with potential global implications for ocean carbon and nitrogen cycling.

Gene expression during maize kernel development

1994 ◽  
Vol 4 (3) ◽  
pp. 299-305 ◽  
Author(s):  
Douglas C. Doehlert ◽  
Leslie J. Smith ◽  
Edwin R. Duke
Keyword(s):  
Gene Expression ◽  
Enzyme Activities ◽  
Dry Weight ◽  
Transcript Abundance ◽  
Starch Accumulation ◽  
Lag Phase ◽  
Gene Transcript ◽  
Kernel Development ◽  
Storage Product ◽  
Product Accumulation

AbstractRelationships have been investigated between gene transcript abundance, enzyme activities and storage product accumulation in developing maize (Zea maysL.) kernels from 10 to 55 days postpollination (DPP). At the early stages of kernel development, there was very little increase in dry weight but kernels accumulated high concentrations of sugars and amino acids. At the end of this ‘lag’ phase (at 15 DPP), many transcripts appeared with little evidence of their translation. The initiation of the kernel-fill period at 20 DPP was characterized by a sudden rise in total RNA, increases in enzyme activities, and the initiation of storage product accumulation. Zein accumulation during this phase was highly correlated with α-zein transcript abundance. Starch accumulation was correlated with both the activity of ADP-GIc pyrophosphorylase and the abundance of gene transcripts encoding this enzyme (Shrunken-2andBrittle-2). DNA content of kernels increased linearly up to 30 DPP as a result of endoreplication, but had no apparent relationship to gene expression. DNA may accumulate as a storage product. Kernel-fill terminated when the moisture content fell below 36% and was marked by a decline of transcripts and a reduction of enzyme activities.

scholarly journals Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage

2013 ◽  
Vol 79 (12) ◽  
pp. 3716-3723 ◽  
Author(s):  
Christopher A. Gulvik ◽  
Alison Buchan
Keyword(s):  
Salt Marshes ◽  
Aromatic Compounds ◽  
Soil Bacteria ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Content Type ◽  
Coastal Salt Marshes ◽  
Metabolic Versatility ◽  
Organic Carbon Pool ◽  
Ruegeria Pomeroyi

ABSTRACTPlant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, includingSagittula stellataE-37, utilize aromatic compounds as primary growth substrates. The genome sequence ofS. stellatacontains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists inS. stellatawhen the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them,p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated thatS. stellatasimultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed whenS. stellatawas provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,Ruegeria pomeroyiDSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.

scholarly journals Outer Cell Surface Components Essential for Fe(III) Oxide Reduction by Geobacter metallireducens

2012 ◽  
Vol 79 (3) ◽  
pp. 901-907 ◽  
Author(s):  
Jessica A. Smith ◽  
Derek R. Lovley ◽  
Pier-Luc Tremblay
Keyword(s):  
Outer Surface ◽  
Surface Protein ◽  
Transcript Abundance ◽  
Geobacter Sulfurreducens ◽  
Extracellular Electron Transfer ◽  
Outer Cell ◽  
Gene Transcript ◽  
Oxide Reduction ◽  
Geobacter Metallireducens ◽  
Content Type

ABSTRACTGeobacterspecies are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail inGeobacter sulfurreducens, but a number of the most thoroughly studied outer surface components ofG. sulfurreducens, particularlyc-type cytochromes, are not well conserved amongGeobacterspecies. In order to identify cellular components potentially important for Fe(III) oxide reduction inGeobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes forc-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified sixc-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of thec-type cytochromes which were essential for Fe(III) oxide reduction inG. metallireducenshave homologs inG. sulfurreducensthat are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer betweenG. metallireducensandG. sulfurreducensbut the outer-surfacec-type cytochromes involved in Fe(III) oxide reduction are different.

The conversion of leucine to α-ketoisocaproic acid and its metabolic consequences for Escherichia coli K12

1976 ◽  
Vol 22 (7) ◽  
pp. 922-928 ◽  
Author(s):  
E. B. Newman ◽  
T. Adley ◽  
J. Fraser ◽  
R. Potter ◽  
V. Kapoor
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Amino Acid ◽  
Nitrogen Source ◽  
Sole Nitrogen Source ◽  
Escherichia Coli K12 ◽  
Nitrogen Donor

The amino acid L-leucine serves as a good auxiliary nitrogen source for Escherichia coli K12, and in so doing is converted to alpha-ketoisocaproic acid which is excreted into the medium.L-Leucine does not serve as sole nitrogen source. Cells incubated with L-leucine as sole nitrogen source do not grow, although they do metabolize leucine, and accumulate ketoisocaproic acid in the medium.Where glycine is the only other nitrogen source, the presence of L-leucine greatly increases the growth rate even at concentrations so low that its contribution as nitrogen donor is unlikely to be important.

Interrelationship of Oxygen and Nitrogen Metabolism in the Filamentous Cyanobacterium Oscillatoria chalybea

1989 ◽  
Vol 44 (11-12) ◽  
pp. 946-954 ◽  
Author(s):  
J. Bednarz ◽  
S. Höper ◽  
M. Bockstette ◽  
K. P. Bader ◽  
G. H. Schmid
Keyword(s):  
Electron Transport ◽  
Photosystem Ii ◽  
Nitrate Reductase ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Light Illumination ◽  
Filamentous Cyanobacterium ◽  
Sole Nitrogen Source ◽  
Light Intensities ◽  
Oscillatoria Chalybea

Abstract Filamentous Cyanobacteria. Hydrogen Peroxide, Photosystem II. Nitrogen Metabolism By means of mass spectrometric analysis we have been able to demonstrate H 20 2-production and its decomposition by photosystem II in thylakoids of the filamentous cyanobacterium Oscil­ latoria chalybea. This H2O2-production and its quasi simultaneous decomposition by the S-state system can be readily demonstrated in flash light illumination (K. P. Bader and G. H. Schmid, Biochim. Biophys. Acta 936, 179-186 (1988)) or as shown in the present paper in continuous light at low light intensities. These light conditions correspond essentially to the culturing condition of the organism on nitrate as the sole nitrogen source. Under these conditions, however, electron transport between the two photosystems seems to be mostly disconnected and respiratory activity practically non existent. Under these conditions, on the other hand, nitrate reductase is induced and nitrate reduced. The present paper addresses the question how this organism might solve the metabolic problems of nitrate reduction with such an electron transport system. Tested under high light intensities under which the organism would not grow at all, electron transport between the two photosystems is optimally linked and the system funnels part of its photosynthetically pro­duced electrons into a conventional cyanide-sensitive respiratory electron transport chain and even into an alternative Sham-sensitive (cyanide-insensitive) respiratory chain. This is made possible by the overweight of photosystem II capacity in comparison to photosystem I activity as reported in this paper. Under the conditions described, the cyanobacterium grows also on ar­ginine as the sole nitrogen source. Most interestingly under these conditions nitrate reductase induction is not shut off as is the case with other aminoacids like ornithine or alanine in the medium. Nitrite reductase is not induced in these bacteria, if grown on arginine as the sole nitrogen source. This observation is discussed in context with the fact that arginine is a major storage product (cyanophycin) in this organism and that the observed photosystem II mediated H2O2-production might be correlated with arginine metabolism.

scholarly journals Molecular Analysis of the Metabolic Rates of Discrete Subsurface Populations of Sulfate Reducers

2011 ◽  
Vol 77 (18) ◽  
pp. 6502-6509 ◽  
Author(s):  
M. Miletto ◽  
K. H. Williams ◽  
A. L. N'Guessan ◽  
D. R. Lovley
Keyword(s):  
Transcript Abundance ◽  
Sulfite Reductase ◽  
Gene Transcript ◽  
Content Type ◽  
Sulfate Reducers ◽  
Sulfate Reducing ◽  
Sedimentary Environments ◽  
Predominant Component ◽  
Reducing Activity ◽  
The Individual

ABSTRACTElucidating thein situmetabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis ofdsrABsequences prior to the addition of acetate indicated thatDesulfobacteraceae,Desulfobulbaceae, andSyntrophaceae-related sulfate reducers were the most abundant. QuantifyingdsrBtranscripts of the individual populations suggested thatDesulfobacteraceaeinitially had higherdsrBtranscripts per cell thanDesulfobulbaceaeorSyntrophaceaepopulations and that the activity ofDesulfobacteraceaeincreased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast,dsrBtranscript abundance inDesulfobulbaceaeandSyntrophaceaeremained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in theDesulfobacteraceaewas consistent with the finding thatDesulfobacteraceaebecame the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline indsrBtranscript abundance in theDesulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.

scholarly journals Alternative Pathway for 3-Cyanoalanine Assimilation in Pseudomonas pseudoalcaligenes CECT5344 under Noncyanotrophic Conditions

2021 ◽  
Author(s):  
María D. Pérez ◽  
Alfonso Olaya-Abril ◽  
Purificación Cabello ◽  
Lara P. Sáez ◽  
M. Dolores Roldán ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Stress Tolerance ◽  
Sulfur Metabolism ◽  
Alternative Pathway ◽  
Industrial Applications ◽  
Sole Nitrogen Source ◽  
Pseudomonas Pseudoalcaligenes ◽  
Content Type ◽  
Degrading Bacterium ◽  
As Stress

Nitriles are organic cyanides with important industrial applications, but they are also found in nature. 3-Cyanoalanine is synthesized by plants and some bacteria to detoxify cyanide from endogenous or exogenous sources, but this nitrile may be also involved in other processes such as stress tolerance, nitrogen and sulfur metabolism, and signaling. The cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344 grows with 3-cyanoalanine as the sole nitrogen source, but it does not use this nitrile as an intermediate in the cyanide assimilation pathway.

scholarly journals Transcriptomic and Genetic Analysis of Direct Interspecies Electron Transfer

2013 ◽  
Vol 79 (7) ◽  
pp. 2397-2404 ◽  
Author(s):  
Pravin Malla Shrestha ◽  
Amelia-Elena Rotaru ◽  
Zarath M. Summers ◽  
Minita Shrestha ◽  
Fanghua Liu ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Expression Patterns ◽  
Transcript Abundance ◽  
Geobacter Sulfurreducens ◽  
Acetate Metabolism ◽  
Gene Transcript ◽  
Content Type ◽  
Direct Interspecies Electron Transfer ◽  
Interspecies Electron Transfer ◽  
Pilin Gene

ABSTRACTThe possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in whichGeobacter sulfurreducenswas the electron-accepting partner for eitherGeobacter metallireducens, which performs DIET, orPelobacter carbinolicus, which relies on HIT. Transcript abundance forG. sulfurreducensuptake hydrogenase genes was 7-fold lower in cocultures withG. metallireducensthan in cocultures withP. carbinolicus, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures withG. metallireducensthan in cocultures withP. carbinolicus. The pilin genepilAwas moderately expressed despite a mutation that might be expected to represspilAexpression. Lower transcript abundance forG. sulfurreducensgenes associated with acetate metabolism in the cocultures withP. carbinolicuswas consistent with the repression of these genes by H2during HIT. Genes for the biogenesis of pili and flagella and severalc-type cytochrome genes were among the most highly expressed inG. metallireducens. Mutant strains that lacked the ability to produce pili, flagella, or the outer surfacec-type cytochrome encoded by Gmet_2896 were not able to form cocultures withG. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.

Sign in / Sign up

Export Citation Format

Share Document