scholarly journals Deciphering the Principles of Bacterial Nitrogen Dietary Preferences: a Strategy for Nutrient Containment

mBio ◽  
2016 ◽  
Vol 7 (4) ◽  
Author(s):  
Jilong Wang ◽  
Dalai Yan ◽  
Ray Dixon ◽  
Yi-Ping Wang
Keyword(s):  
Amino Acids ◽  
Growth Rate ◽  
Growth Rates ◽  
Regulatory Networks ◽  
Metabolic Flux ◽  
Nitrogen Sources ◽  
Fast Growth ◽  
Ammonia Assimilation ◽  
Wild Type ◽  
Dietary Preferences

ABSTRACT A fundamental question in microbial physiology concerns why organisms prefer certain nutrients to others. For example, among different nitrogen sources, ammonium is the preferred nitrogen source, supporting fast growth, whereas alternative nitrogen sources, such as certain amino acids, are considered to be poor nitrogen sources, supporting much slower exponential growth. However, the physiological/regulatory logic behind such nitrogen dietary choices remains elusive. In this study, by engineering Escherichia coli , we switched the dietary preferences toward amino acids, with growth rates equivalent to that of the wild-type strain grown on ammonia. However, when the engineered strain was cultured together with wild-type E. coli , this growth advantage was diminished as a consequence of ammonium leakage from the transport-and-catabolism (TC)-enhanced (TCE) cells, which are preferentially utilized by wild-type bacteria. Our results reveal that the nitrogen regulatory (Ntr) system fine tunes the expression of amino acid transport and catabolism components to match the flux through the ammonia assimilation pathway such that essential nutrients are retained, but, as a consequence, the fast growth rate on amino acids is sacrificed. IMPORTANCE Bacteria exhibit different growth rates under various nutrient conditions. These environmentally related behaviors reflect the coordination between metabolism and the underlying regulatory networks. In the present study, we investigated the intertwined nitrogen metabolic and nitrogen regulatory systems to understand the growth differences between rich and poor nitrogen sources. Although maximal growth rate is considered to be evolutionarily advantageous for bacteria (as remarked by François Jacob, who said that the “dream” of every cell is to become two cells), we showed that negative-feedback loops in the regulatory system inhibit growth rates on amino acids. We demonstrated that in the absence of regulatory feedback, amino acids are capable of supporting fast growth rates, but this results in ammonia leaking out from cells as “waste,” benefiting the growth of competitors. These findings provide important insights into the regulatory logic that controls metabolic flux and ensures nutrient containment but consequently sacrifices growth rate.

Regulation of the start of DNA replication in Schizosaccharomyces pombe

1999 ◽  
Vol 112 (6) ◽  
pp. 939-946 ◽  
Author(s):  
C.R. Carlson ◽  
B. Grallert ◽  
T. Stokke ◽  
E. Boye
Keyword(s):  
Cell Cycle ◽  
Flow Cytometry ◽  
Growth Rate ◽  
Schizosaccharomyces Pombe ◽  
Growth Rates ◽  
Cell Separation ◽  
Cell Mass ◽  
Nitrogen Sources ◽  
S Phase ◽  
G1 Phase

Cells of Schizosaccharomyces pombe were grown in minimal medium with different nitrogen sources under steady-state conditions, with doubling times ranging from 2.5 to 14 hours. Flow cytometry and fluorescence microscopy confirmed earlier findings that at rapid growth rates, the G1 phase was short and cell separation occurred at the end of S phase. For some nitrogen sources, the growth rate was greatly decreased, the G1 phase occupied 30–50% of the cell cycle, and cell separation occurred in early G1. In contrast, other nitrogen sources supported low growth rates without any significant increase in G1 duration. The method described allows manipulation of the length of G1 and the relative cell cycle position of S phase in wild-type cells. Cell mass was measured by flow cytometry as scattered light and as protein-associated fluorescence. The extensions of G1 were not related to cell mass at entry into S phase. Our data do not support the hypothesis that the cells must reach a certain fixed, critical mass before entry into S. We suggest that cell mass at the G1/S transition point is variable and determined by a set of molecular parameters. In the present experiments, these parameters were influenced by the different nitrogen sources in a way that was independent of the actual growth rate.

Ammonia Assimilation by Thiocapsa roseopersicina Grown on Various Nitrogen and Carbon/Electron Sources

1980 ◽  
Vol 35 (5-6) ◽  
pp. 439-444 ◽  
Author(s):  
Eckhard Bast
Keyword(s):  
Amino Acids ◽  
Glutamate Synthase ◽  
Nitrogen Sources ◽  
Ammonia Assimilation ◽  
Synthetic Activity ◽  
Transferase Activity ◽  
Organic Substrates ◽  
Batch Cultures ◽  
Electron Sources ◽  
Thiocapsa Roseopersicina

Abstract Batch cultures of the phototrophic bacterium, Thiocapsa roseopersicina, were grown anaero­ bically in the light either on sulfide with various ammonia concentrations, N 2 or amino acids as nitrogen sources, or on several simple organic substrates in the absence of reduced sulfur com­ pounds using 6 mM NH4Cl as source of nitrogen. At high ammonia concentrations high activities of (NADPH-linked) glutamate dehydrogenase (GDH), but rather low transferase and no bio­ synthetic activity of glutamine synthetase (GS) were obtained, while under conditions of ammonia deficiency (growth with N 2 or glutamate) GDH activity was very low and both GS activities were strongly increased. Glutamate synthase (GOGAT) activity (NADH-dependent) showed little variation. These data indicate that at high NH+ concentrations ammonia is assimilated via GDH, under NHJ limitation, however, via the GS/GOGAT system. Glutamine as nitrogen source may be utilized via GOGAT as well as via an active glutaminase plus GDH. Ammonia, but not glutamine, seems to cause repression and inactivation of GS. Alanine and asparagine inactivate the enzyme inhibiting the biosynthetic, but not the transferase activity. These amino acids in part also influence the activities of GDH, GOGAT, malate dehydrogenase (MDH) and isocitrate dehydrogenase (ICDH). Cultures grown on acetate or pyruvate instead of sulfide showed increased GDH activities and high GS transferase activities possibly reflecting an increase of intracellular a-ketoglutarate concentration. On malate or fructose also increased GS transferase activities, but rather low GDH activities were observed. High biosynthetic GS activities and elevated GOGAT activities were found only in fructose-grown cells. On the organic substrates the ICDH activities always were somewhat higher than after lithoautotrophic growth. With the exception of acetate, the MDH activities were considerably elevated, especially on pyruvate. The different pathways of ar-keto-glutarate formation and their influence on the enzymes of ammonia assimilation are discussed.

ℵ0-categorical structures with arbitrarily fast growth of algebraic closure

2002 ◽  
Vol 67 (3) ◽  
pp. 897-909
Author(s):  
David M. Evans ◽  
M. E. Pantano
Keyword(s):  
Growth Rate ◽  
Automorphism Group ◽  
Finite Subset ◽  
Growth Rates ◽  
Algebraic Closure ◽  
Fast Growth ◽  
Permutation Groups ◽  
Natural Numbers ◽  
Categorical Structure ◽  
Image Position

Various results have been proved about growth rates of certain sequences of integers associated with infinite permutation groups. Most of these concern the number of orbits of the automorphism group of an ℵ0-categorical structure on the set of unordered n-subsets or on the set of n-tuples of elements of . (Recall that by the Ryll-Nardzewski Theorem, if is countable and ℵ0-categorical, the number of the orbits of its automorphism group Aut() on the set of n-tuples from is finite and equals the number of complete n-types consistent with the theory of .) The book [Ca90] is a convenient reference for these results. One of the oldest (in the realms of ‘folklore’) is that for any sequence (Kn)n∈ℕ of natural numbers there is a countable ℵ0-categorical structure such that the number of orbits of Aut() on the set of n-tuples from is greater than kn for all n.These investigations suggested the study of the growth rate of another sequence. Let be an ℵ0-categorical structure and X be a finite subset of . Let acl(X) be the algebraic closure of X, that is, the union of the finite X-definable subsets of . Equivalently, this is the union of the finite orbits on of Aut()(X), the pointwise stabiliser of X in Aut(). Define

Nitrogen nutrition and regulation of cephalosporin production in Streptomyces clavuligerus

1979 ◽  
Vol 25 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Yair Aharonowitz ◽  
Arnold L. Demain
Keyword(s):  
Amino Acids ◽  
Growth Rate ◽  
Nitrogen Nutrition ◽  
Antibiotic Production ◽  
Inorganic Nitrogen ◽  
Amino Nitrogen ◽  
Nitrogen Sources ◽  
Streptomyces Clavuligerus ◽  
Defined Medium ◽  
Repressive Effect

When used as sole nitrogen source, certain amino acids (e.g., proline, asparagine) supported both growth and sporulation by Streptomyces clavuligerus streaked onto solid defined medium. Ammonium supported growth but suppressed sporulation. Amino nitrogen was best for cephalosporin production in liquid defined medium, although urea was almost as useful. A comparison of amino acids showed asparagine and glutamine to be the best nitrogen sources and arginine to be almost as good. Ammonium salts supported a somewhat lower growth rate than asparagine, but antibiotic production was very poor on these inorganic nitrogen sources. Addition of ammonium to asparagine did not affect growth rate but increased mycelial mass; cephalosporin production was reduced by about 75%. Antibiotic production was more closely associated with growth in the absence of ammonium than in its presence, indicating a strong inhibitory and (or) repressive effect of NH4+ on antibiotic production. Ammonium exerted its negative effect when added at 24 h or earlier, i.e. before antibiotic formation began.

Control of growth, secondary metabolism and sporulation in Streptomyces venezuelae ISP5230 by jadW 1, a member of the afsA family of γ-butyrolactone regulatory genes

Microbiology ◽  
2003 ◽  
Vol 149 (8) ◽  
pp. 1991-2004 ◽  
Author(s):  
Liru Wang ◽  
Leo C. Vining
Keyword(s):  
Growth Rate ◽  
Secondary Metabolism ◽  
Morphological Differentiation ◽  
Nitrogen Sources ◽  
Repeat Sequence ◽  
Antibiotic Biosynthesis ◽  
Wild Type ◽  
Streptomyces Venezuelae ◽  
New Genes ◽  
Insertional Inactivation

Three new genes (jadW 1, jadW 2 and jadW 3) were isolated from a region of the Streptomyces venezuelae ISP5230 chromosome at the left-hand end of the jad cluster for jadomycin B (JdB) biosynthesis. The deduced amino acid sequence of jadW 1 showed strong similarity to gene products associated in several streptomycetes with γ-butyrolactone autoregulators controlling morphological differentiation and secondary metabolism. Examination of JadW1 for conserved domains detected a repeat sequence characteristic of proteins in the AfsA regulatory family. Insertional inactivation of jadW 1 reduced the growth rate of S. venezuelae cultures in aerated liquid media containing complex nitrogen sources and altered growth morphology in minimal medium. It also affected sporulation on agar media. Cultures of jadW 1-disrupted mutants grown under conditions supporting biosynthesis of JdB or chloramphenicol by the wild-type strain failed to produce either of the antibiotics. Complementing the disrupted strain by transformation with pJV435, containing a cloned copy of the gene, improved sporulation and restored antibiotic biosynthesis in transformants to titres close to those of the wild-type similarly transformed with pJV435 as a control. The results are consistent with a role for jadW 1 in regulating morphological and metabolic differentiation. Further sequence analysis of jadR 2, which functions with jadR 1 in stress-induced activation of JdB biosynthesis, indicated that this gene encodes a γ-butyrolactone receptor homologue. The growth-rate-sensitive phenotype of the jadW 1-disrupted mutant, and the proximity of jadW 1 to jadR 2 indicate that this region of the jad gene cluster contains a regulatory mechanism incorporating γ-butyrolactone signalling and sensitivity to environmental stress.

scholarly journals Mutant strains of Escherichia coli lacking global regulators, arcA and fis, demonstrate better growth fitness by pathway reprogramming under acetate metabolism

2021 ◽  
Author(s):  
Shikha Jindal ◽  
Mahesh S. Iyer ◽  
Poonam Jyoti ◽  
Shyam Kumar Masakapalli ◽  
K V Venkatesh
Keyword(s):  
Growth Rate ◽  
Metabolic Flux ◽  
Microbial Metabolism ◽  
Metabolic Reprogramming ◽  
Acetate Metabolism ◽  
Flux Analysis ◽  
Wild Type ◽  
Global Regulators ◽  
Acetate Uptake ◽  
Mutant Strains

Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A systems-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the substrates available in a range of nutrient niches such as the mammalian gut and high-fat diet. Therefore, investigating the study on acetate metabolism is highly significant. It is well known that the global regulators arcA and fis regulate acetate uptake genes in E. coli under glucose condition. In this study, we deciphered the growth and flux distribution of E.coli transcription regulatory knockout mutants ΔarcA, Δfis and double deletion mutant, ΔarcAfis under acetate using 13C-Metabolic Flux Analysis which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~1.2-1.6 fold) with a proportionate increase in acetate uptake rates compared to the wild-type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes, which conferred an advantage of faster growth with better carbon usage in all the mutants. Under acetate metabolism, the mutants exhibited higher fluxes in the TCA cycle (~18-90%) and lower gluconeogenesis flux (~15-35%) with the proportional increase in growth rate. This study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate to acetyl-CoA and therefore are potential candidates that can serve as a precursor for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.

Influence of peptides and amino acids on ammonia assimilation by cellulolytic ruminal bacteria

2001 ◽  
Vol 2001 ◽  
pp. 131-131
Author(s):  
R. J. Wallace ◽  
C. Atasoglu ◽  
C. J. Newbold
Keyword(s):  
Amino Acids ◽  
Nitrogen Sources ◽  
Ammonia Assimilation ◽  
Ruminal Fermentation ◽  
Ruminal Bacteria ◽  
Protein Requirements ◽  
Main Species ◽  
Fermenting Bacteria ◽  
Structural Carbohydrate ◽  
N Incorporation

An understanding of the nitrogen compounds required for growth of ruminal bacteria is of importance to optimising ruminal fermentation and in formulating optimal protein requirements of ruminants. Bryant (1973) concluded that cellulolytic ruminal bacteria used only NH3 as N source for growth. The main species were unable to grow on other nitrogen sources in the absence of NH3, and the incorporation of radioactive pre-formed amino acids appeared to be minimal. Disappearance of NH3-N from the growth medium was equal to N incorporation into bacterial protein. As a consequence, the assumption was made in drawing up the Cornell Net Carbohydrate and Protein System (CNCPS) that structural carbohydrate-fermenting bacteria use ammonia as their only source of nitrogen (Russell et al., 1992). More recent studies with mixed cultures suggest, however, that fibrolytic bacteria incorporate significant quantities of amino acids (Griswold et al., 1996; Carro and Miller, 1999). The present experiments were undertaken to clarify the N sources for growth of the three main species of cellulolytic ruminal bacteria in pure culture.

scholarly journals Importance of pfkA for Rapid Growth ofEnterobacter cloacae during Colonization of Crop Seeds

2000 ◽  
Vol 66 (1) ◽  
pp. 87-91 ◽  
Author(s):  
D. P. Roberts ◽  
P. D. Dery ◽  
I. Yucel ◽  
J. S. Buyer
Keyword(s):  
Amino Acids ◽  
Growth Rate ◽  
Growth Rates ◽  
Rapid Growth ◽  
Sweet Corn ◽  
Natural Soil ◽  
Transposon Insertion ◽  
Carbon Compounds ◽  
The Impact

ABSTRACT Enterobacter cloacae A-11 is a prototrophic, glycolytic mutant of strain 501R3 with a single transposon insertion inpfkA. The populations of strain A-11 on cucumber and radish seeds were smaller than the populations of strain 501R3 in natural soil, but the populations of these two strains on pea, soybean, sunflower, and sweet corn seeds were similar (D. P. Roberts, P. D. Dery, I. Yucel, J. Buyer, M. A. Holtman, and D. Y. Kobayashi, Appl. Environ. Microbiol. 65:2513–2519, 1999). The net effect of the mutation in pfkA in vitro was a shift from rapid growth on certain carbohydrates detected in seed exudates to much slower growth on other carbohydrates, amino acids, and organic acids. The impact of the mutation in pfkA was greatest on the growth rate of E. cloacae on the seeds that released the smallest quantities of fructose, other carbohydrates, and amino acids. Corn, pea, soybean, and sunflower seeds released total amounts of carbohydrates and amino acids at rates that were approximately 10- to 100-fold greater than the rates observed with cucumber and radish seeds for the first 24 h after inhibition began. The growth rate of strain A-11 was significantly less (50% less) than the growth rate of strain 501R3 on radish seeds, and the growth rate of strain A-11 was too low to estimate on cucumber seeds in sterile sand for the first 24 h after inhibition began. The growth rate of strain A-11 was also significantly lower on soybean seeds, but it was only 17% lower than the growth rate of strain 501R3. The growth rates of strains 501R3 and A-11 were similar on pea, sunflower, and corn seeds in sterile sand for the first 30 h after imbibition began. Large reductions in the growth rates of strain A-11 on seeds were correlated with subsequent decreased levels of colonization of seeds compared to the levels of colonization of strain 501R3. The strain A-11 populations were significantly smaller than the strain 501R3 populations only on radish and cucumber seeds. The mutation in pfkA appears to decrease the level of colonization by E. cloacae for seeds that release small quantities of reduced carbon compounds by decreasing the size of the pool of compounds that support rapid growth by this bacterium.

scholarly journals Do Growing Rabbits with a High Growth Rate Require Diets with High Levels of Essential Amino Acids? A Choice-Feeding Trial

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 824
Author(s):  
Pablo Jesús Marín-García ◽  
Mari Carmen López-Luján ◽  
Luís Ródenas ◽  
Eugenio Martínez-Paredes ◽  
María Cambra-López ◽  
...  
Keyword(s):  
Amino Acids ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Nutrient Retention ◽  
High Growth ◽  
Feeding Trial ◽  
Nutritional Recommendations ◽  
Sulphur Amino Acids ◽  
Choice Feeding

As a consequence of the genetic selection process in growing rabbits, there are currently fast-growing animals exhibiting an average daily gain that may exceed 45 g/d. The protein requirements of these animals, namely amino acid requirements, may differ from animals with low growth rates. The objective of this work was to evaluate growth performance, the coefficient of total tract apparent digestibility (CTTAD), the apparent ileal digestibility (AID) of amino acids and nutrient retention of fast-growing rabbits when they had access to a diet with high levels of amino acids and/or a diet formulated with current nutritional recommendations in a choice-feeding trial. To this end, two diets were formulated: the M diet following current nutritional recommendations for growing rabbits (including 8.1, 5.8 and 6.9 g/kg dry matter (DM) of total lysine, sulphur amino acids and threonine, respectively) and the H diet with higher levels of total lysine, sulphur amino acids and threonine (9.4, 6.6 and 7.8 g/kg DM, respectively). A total of 220 weaned rabbits, from a paternal line selected for the growth rate, had free access to the M diet, the H diet or both (MH) diets from 28 to 63 days of age. The CTTAD of DM, crude protein and gross energy from 49 to 53 days of age as well as the AID of amino acids of the diets at 63 days of age were determined. Protein, amino acids and energy retained in the empty body from 28 to 63 days of age were also registered. No significant differences in growth performance, CTTAD, AID and nutrient retention between dietary treatments were observed. However, animals fed the H diet showed a higher AID of cysteine (p < 0.05) and higher threonine retention (p < 0.05) compared to the M diet. As regards the choice-feeding trial, MH animals showed a higher feed intake of the M diet compared to the H diet (+8.61%; p < 0.001), and furthermore, more than 50% of the animals preferred the M diet throughout the experimental period (p < 0.05). Our results suggest that animals with high growth rates do not show significantly higher productive traits when fed the H diet compared to the M diet. As regards choice feeding, MH animals were capable of choosing their preferred diet, showing high intra-individual repeatability in preference for the M diet. It would be interesting to continue studying this behaviour of choice based on amino acid levels.

scholarly journals XMAP215 promotes microtubule catastrophe by disrupting the growing microtubule end

2020 ◽  
Author(s):  
Veronica Farmer ◽  
Göker Arpağ ◽  
Sarah Hall ◽  
Marija Zanic
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Fast Growth ◽  
Fast Growing ◽  
Microtubule Stability ◽  
Large Fluctuations ◽  
Microtubule Growth ◽  
Enhanced Stability

ABSTRACTThe GTP-tubulin cap is widely accepted to protect microtubules against catastrophe. The GTP-cap size is thought to increase with the microtubule growth rate, presumably endowing fast-growing microtubules with enhanced stability. It is unknown what GTP-cap properties permit frequent microtubule catastrophe despite fast growth. Here, we investigate microtubules grown in vitro in the presence and absence of the microtubule polymerase XMAP215. Using EB1 as a GTP-cap marker, we find that GTP-cap size increases regardless of whether growth acceleration is achieved by increasing tubulin concentration or by XMAP215. In spite of the increased mean GTP-cap size, microtubules grown with XMAP215 display increased catastrophe frequency, in contrast to microtubules grown with more tubulin, for which catastrophe is abolished. However, microtubules polymerized with XMAP215 have large fluctuations in growth rate and EB1 intensity; display tapered and curled ends; and undergo catastrophe at faster growth rates and with higher EB1 end-localization. Our results underscore the role of growth irregularities in overall microtubule stability.

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