The dynamics of the macromolecular composition of biomass

The biomass composition of microorganisms depends on the growth conditions. This study explores whether a two-component model can explain how the elemental and macromolecular composition of the biomass of bacteria varies with the specific growth rate. The model describes the rates at which microorganisms assimilate substrates into reserves and utilize reserves for maintenance and growth. Crucial model assumptions are that biomass consists of reserves and structure and that each of these components has an invariant composition. The composition of biomass can vary when the ratio between reserves and structure varies. Literature data on the macromolecular composition of Escherichia coli, cultivated on various substrates, show that the protein, RNA and DNA content of biomass follow a distinctive trend when plotted as a function of the dry-weight-specific growth rate. This observation leads to the proposition that the macromolecular composition of E. coli depends directly on the growth rate, and only indirectly on the carbon- and energy-source used as substrate. We show that the variation of the macromolecular composition of E. coli over its entire range of growth rates can be described with invariant macromolecular compositions of the reserve and structural components of biomass. The model is also applied to our data on a succinate-limited continuous culture of Paracoccus denitrificans.     

Macromolecular composition of a Cellulomonas sp. cultivated in continuous culture under glucose and zinc limitation.

The mutant strain of Cellulomonas sp. (ATCC 21399) was cultivated under glucose and zinc limitation at a variety of growth rates in continuous culture. The growth characteristics and macromolecular composition of the population varied with the limitation imposed and the growth rate. Glucose- and zinc-limited cultures maintained a constant relative protein content. The relative ribonucleic acid content increased, whereas the carbohydrate and deoxyribonucleic acid contents decreased with an increase in the population growth rate in glucose-limited cultures. Free unbound lipid remained constant. The maximum population growth rate in zinc-limited cultures was directly proportional to the zinc concentration and demonstrated a traditional steady-state function. The nucleic acid content increased with increased growth rate; however, the relative nucleic acid content was significantly depressed when compared to glucose limited cells. This manner of cultivation may prove to be a useful tool for the production of single cell protein with lowered nucleic acid content and the elucidation of micronutrient involvement in growth-related processes.     

Macromolecular composition of a Cellulomonas sp. cultivated in continuous culture under glucose and zinc limitation.

The mutant strain of Cellulomonas sp. (ATCC 21399) was cultivated under glucose and zinc limitation at a variety of growth rates in continuous culture. The growth characteristics and macromolecular composition of the population varied with the limitation imposed and the growth rate. Glucose- and zinc-limited cultures maintained a constant relative protein content. The relative ribonucleic acid content increased, whereas the carbohydrate and deoxyribonucleic acid contents decreased with an increase in the population growth rate in glucose-limited cultures. Free unbound lipid remained constant. The maximum population growth rate in zinc-limited cultures was directly proportional to the zinc concentration and demonstrated a traditional steady-state function. The nucleic acid content increased with increased growth rate; however, the relative nucleic acid content was significantly depressed when compared to glucose limited cells. This manner of cultivation may prove to be a useful tool for the production of single cell protein with lowered nucleic acid content and the elucidation of micronutrient involvement in growth-related processes.     

The relationship between glucose transport and the production of succinoglucan exopolysaccharide by Agrobacterium radiobacter

Agrobacterium radiobacter NCIB 11883 was grown in ammonia-limited continuous culture at low dilution rate with glucose as the carbon source. Under these conditions the organism produced an extracellular succinoglucan polysaccharide and transported glucose using the same periplasmic glucose-binding proteins (GBP1 and GBP2) as during glucose-limited growth. Transition from glucose- to ammonia-limited growth was accompanied by a very rapid decrease in glucose uptake capacity, whereas the glucose-binding proteins were diluted out much more slowly (t1/2 approximately 1 h and 14 h respectively). Although the rate of glucose uptake and the concentrations of GBP1 and GBP2 were much lower during ammonia limitation, the activities of enzymes involved in the early stages of glucose metabolism and in the production of succinoglucan precursors were essentially unchanged. Glucose transport was also investigated in two new strains of A. radiobacter which had been isolated following prolonged growth under glucose limitation. Glucose uptake by strain AR18 was significantly less repressed during ammonia limitation compared with either the original parent strain or strain AR9, and this was reflected both in its relatively high concentration of GBP1 and in its significantly higher rate of succinoglucan synthesis. Flux control analysis using 6-chloro-6-deoxy-D-glucose as an inhibitor of glucose transport showed that the latter was a major kinetic control point for succinoglucan production. It is concluded that glucose uptake by A. radiobacter, particularly via the GBP1-dependent system, is only moderately repressed during ammonia-limited growth and that the organism avoids the potentially deleterious effects of accumulating excess glucose by converting the surplus into succinoglucan.     

Control of respiration and metabolism in growing Klebsiella aerogenes. The role of adenine nucleotides

1. A rapid-sampling technique was used to obtain perchloric acid extracts of cells growing in a chemostat culture, so that meaningful values for ATP content could be obtained in spite of the fact that the turnover time for the total ATP content was about 1sec. 2. For steady-state growth, it was found that, in a glucose-limited chemostat culture, the ATP/ADP concentration ratio was approximately constant with changes in dissolved-oxygen tensions above the critical value, but fell when the culture was grown under oxygen-limited conditions and was at a minimum in anaerobically grown cultures. The steady-state ATP content was lower in cells growing under nitrogen-limited conditions with glucose in excess than in glucose-limited cells. The steady-state ATP content was independent of growth rate at growth rates over 0.1hr.(-1). 3. When the respiration rate of the cells was stimulated by lowering the oxygen tension the ATP content did not increase, indicating either an increased turnover rate of ATP or a fall in the P/O ratio. The sudden addition of extra glucose or succinate to a glucose-limited culture increased the respiration rate of the cells, but the ATP content quickly returned to the steady-state value after initial perturbations. This control over ATP content is explained in terms of regulation by adenine nucleotides of the catabolism and anabolism of glucose. An exception to this control over ATP content was found when the respiration rate was stimulated by addition of an antifoam.     

ppGpp is the major source of growth rate control in E. coli

It is widely accepted that the DNA, RNA and protein content of Enterobacteriaceae is regulated as a function of exponential growth rates; macromolecular content increases with faster growth regardless of specific composition of the growth medium. This phenomenon, called growth rate control, primarily involves regulation of ribosomal RNA and ribosomal protein synthesis. However, it was uncertain whether the global regulator ppGpp is the major determinant for growth rate control. Therefore, here we re-evaluate the effect of ppGpp on macromolecular content for different balanced growth rates in defined media. We find that when ppGpp is absent, RNA/protein and RNA/DNA ratios are equivalent in fast and slow growing cells. Moreover, slow growing ppGpp-deficient cells with increased RNA content, display a normal ribosomal subunit composition although polysome content is reduced when compared with fast growing wild-type cells. From this we conclude that growth rate control does not occur in the absence of ppGpp. Also, artificial elevation of ppGpp or introduction of stringent RNA polymerase mutants in ppGpp-deficient cells restores this control. We believe these findings strongly argue in favour of ppGpp and against redundant regulation of growth rate control by other factors in Escherichia coli and other enteric bacteria.     

Dependence of macromolecular composition and morphology of Streptomyces hygroscopicus on specific growth rate.

The dependence of macromolecular composition and morphology of Streptomyces hygroscopicus on specific growth rate micron was investigated. The percentage of DNA on dry weight (%DNA) is constant, % protein is also nearly independent of micron whereas %RNA rises considerably with increasing micron, regarding mycelia grown in glucose-limited and ammonium-limited continuous cultures as well as in discontinuous cultures with various carbon sources. It is probable that the overall synthesis of DNA, RNA and protein is regulated in the mycelium-forming bacterium S. hygroscopicus by the same mechanisms found in unicellular bacteria like Escherichia coli because of the qualitatively similar dependence of %DNA, %RNA and %protein on micron. But differences exist in quantitative regard whereby %DNA, %RNA and %protein of S. hygroscopicus are much smaller at low micron and, with increasing micron, approach those of unicellular bacteria. The hypothesis about the increase of the hyphal regions showing high synthesis activity in S. hygroscopicus mycelia grown in glucose-limited continuous cultures with increasing micron -- derived from comparison of macromolecular composition of S. hygroscopicus and unicellular bacteria -- was confirmed autoradiographically with respect to protein synthesis. The increase of the part of mycelial regions showing high cytoplasmic activity results in an increase of mean hyphal diameter, of mean relative apical growth rate alpha and/or mean relative branching rate beta. Beta depends sigmoidally and alpha inverses sigmoidally on micron. Therefore, the morphology of the mycelium determined by alpha and beta also depends on micron. The hyphal growth unit L/N, the distance from apex to first branch Lp and the mean distance between neighbouring branches Ln decline with increasing micron and reach a minimum at micron = 0.32 (1/h). A further rise of micron is accompanied with an increase of L/N, Lp and Ln. This means that mycelia growing slowly or very quickly have a loose form whereas quickly growing mycelia are characterized by a more compact form. The complicated dependence of alpha, beta, L/N, Lp and Ln on micron indicates that the morphology is regulated by different mechanisms depending on the specific growth rate.     

Identification of Enzymes and Quantification of Metabolic Fluxes in the Wild Type and in a Recombinant Aspergillus oryzae Strain

Two α-amylase-producing strains of Aspergillus oryzae, a wild-type strain and a recombinant containing additional copies of the α-amylase gene, were characterized with respect to enzyme activities, localization of enzymes to the mitochondria or cytosol, macromolecular composition, and metabolic fluxes through the central metabolism during glucose-limited chemostat cultivations. Citrate synthase and isocitrate dehydrogenase (NAD) activities were found only in the mitochondria, glucose-6-phosphate dehydrogenase and glutamate dehydrogenase (NADP) activities were found only in the cytosol, and isocitrate dehydrogenase (NADP), glutamate oxaloacetate transaminase, malate dehydrogenase, and glutamate dehydrogenase (NAD) activities were found in both the mitochondria and the cytosol. The measured biomass components and ash could account for 95% (wt/wt) of the biomass. The protein and RNA contents increased linearly with increasing specific growth rate, but the carbohydrate and chitin contents decreased. A metabolic model consisting of 69 fluxes and 59 intracellular metabolites was used to calculate the metabolic fluxes through the central metabolism at several specific growth rates, with ammonia or nitrate as the nitrogen source. The flux through the pentose phosphate pathway increased with increasing specific growth rate. The fluxes through the pentose phosphate pathway were 15 to 26% higher for the recombinant strain than for the wild-type strain.     

The regulatory effects of growth rate and cyclic AMP levels on carbon catabolism and respiration in Escherichia coli K-12.

Cyclic AMP levels in glucose and succinate-limited and ammonia-limited glucose-containing continuous cultures of Escherichia coli were measured at different bacterial growth rates. Intracellular cyclic AMP concentrations were fairly constant (about 5 micrometer) at all dilution rates used when glucose was limiting. In ammonia-limited glucose cultures the cyclic AMP content was much lower (about 0.3 micrometer). In succinate-limited cultures cyclic AMP levels fell from 2.7 to 0.8 micrometer as dilution rate increased from 0.05 to 0.4 h-1. The effects of cyclic AMP on respiratory and carbon catabolic enzyme levels were studied. There was no indication of a direct cyclic AMP involvement in the regulation of these cellular functions. It seems more likely that the variations in enzyme levels observed resulted from variation of the specific growth rate of cultures.     

The regulatory effects of growth rate of cyclic AMP levels on carbon catabolism and respiration in Escherichia coli K-12

Cyclic AMP levels in glucose and succinate-fluid and ammonia-limited glucose-containing continuous cultures of Escherichia coli were measured at different bacterial growth rates. Intracellular cyclic AMP concentrations were fairly constant (about 5 μM) at all dilution rates used when glucose was limiting. In ammonia-limited glucose cultures the cyclic AMP content was much lower (about 0.3 μM). In succinate-limited cultures cyclic AMP levels fell from 2.7 to 0.8 μM as dilution rate increased from 0.05 to 0.4 h^?1.The effects of cyclic AMP on respiratory and carbon catabolic enzyme levels were studied. There was no indication of a direct cyclic AMP involvement in the regulation of these cellular functions. It seems more likely that the variations in enzyme levles observed resulted from variation of the specific growth rate of cultures.     

Regulation of urease and ammonia assimilatory enzymes in Selenomonas ruminantium.

Urease and glutamine synthetase activities in Selenomonas ruminantium strain D were highest in cells grown in ammonia-limited, linear-growth cultures or when certain compounds other than ammonia served as the nitrogen source and limited the growth rate in batch cultures. Glutamate dehydrogenase activity was highest during glucose (energy)-limited growth or when ammonia was not growth limiting. A positive correlation (R = 0.96) between glutamine synthetase and urease activities was observed for a variety of growth conditions, and both enzyme activities were simultaneously repressed when excess ammonia was added to ammonia-limited, linear-growth cultures. The glutamate analog methionine sulfoximine (MSX), inhibited glutamine synthetase activity in vitro, but glutamate dehydrogenase, glutamate synthase, and urease activities were not affected. The addition of MSX (0.1 to 100 mM) to cultures growing with 20 mM ammonia resulted in growth rate inhibition that was dependent upon the concentration of MSX and was overcome by glutamine addition. Urease activity in MSX-inhibited cultures was increased significantly, suggesting that ammonia was not the direct repressor of urease activity. In ammonia-limited, linear-growth cultures, MSX addition resulted in growth inhibition, a decrease in GS activity, and an increase in urease activity. These results are discussed with respect to the importance of glutamine synthetase and glutamate dehydrogenase for ammonia assimilation under different growth conditions and the relationship of these enzymes to urease.     

Phenotypic changes in the chemistry of Aspergillus nidulans: Influence of culture conditions on mycelial composition

A quantitative study was made of macromolecular (nucleic acids, protein), carbohydrate and mineral (magnesium, potassium and phosphorus) components of Aspergillus nidulans in glucose limited chemostat cultures, under varying conditions of dilution rate, temperature, pH and NaCl concentration.The overall mineral content showed greatest variation in response to changes in culture salinity, which also affected the mycelial carbohydrate content. Concomitant and opposite changes in the conent of cations and carbohydrates under conditions of increasing salinity may be interpreted in terms of mycelial osmoregulation. Slight variations in DNA content but gross fluctuations in the level of RNA were noted under the different cultural conditions examined. Co-ordinate changes in RNA and Mg²⁺ contents were evident only under certain conditions: dilution rate from 0.05–0.07 h^-1 or temperature from 22–30° C. The constant molar stoichiometry between RNA and Mg²⁺ characteristic of unicellular microorganisms was not a feature of fungal growth. The protein content was most affected by shifts of temperature and reached minimal values at 25 and 50° C.The growth environment had a marked influence on the protein synthesising activity of RNA, which increased eightfold as the dilution rate was increased from 0.02–0.175 h^-1, doubled within the temperature range 20–30° C and fell by 50% between 40 and 50° C. These observations are discussed in the context of the constant ribosomal efficiency in protein synthesis hypothesis.     

Macromolecular composition of bacteria

Equations are presented that describe the macromolecular composition in exponential bacterial cultures as functions of five parameters: doubling time of the culture (τ), protein per origin of replication (P₀), chromosome replication time (C-period), peptide chain elongation rate (c_p), and the time between termination of replication and cell division (D-period). Implicit in the value for some of these parameters is a specific macromolecular control system: the control of the growth rate (τ), the timing of initiation of rounds of chromosome replication (P₀), and the regulation of cell division (D). The utility of these relations is illustrated by using updated measurements of the macromolecular composition of E. coli B/r to calculate values for the fundamental parameters and to predict the composition of a mutant which has a defect in the control of DNA replication. Furthermore, the meaning of several often-cited physiological parameters (RNA/protein, RNA/cell and RNA/genome) is examined. The relations presented here show that these parameters and their variation with growth rate are not directly relevant to arguments about control of ribosome synthesis or culture growth.     

Frequency-Dependent Selection for Plasmid-Containing Cells of ESCHERICHIA COLI

Colicin-producing plasmid-containing cells of E. coli exhibit frequency-dependent selection when grown in glucose-limited continuous culture with the corresponding plasmid-free strain. The bases of this frequency-dependent effect are shown to be (1) the lower growth rate of the plasmid-containing strain under these conditions, and (2) the production of colicin, which attenuates the growth rate of the plasmid-free strain. These results are discussed in relationship to the maintenance of genetic variation in prokaryotes.     

Levels of protein, RNA, DNA, glycogen and lipid during growth and development of Daphnia magna Straus (Crustacea: Cladocera)

1. Protein, RNA, DNA, glycogen and lipid content were determined in Daphnia magna on days 0, 2, 4, 6, 8 and 21 of growth and development. The composition of D. magna as percentage of reconstituted dry weight was similar to other zooplankton with the exception of DNA content, which was lower than values previously reported.
2. The relative content of protein, RNA, DNA and reconstituted dry weight changed during the 21-day growth period, and these changes were related to growth rate and total growth of D. magna . RNA:protein, RNA: reconstituted dry weight, and protein:RNA : DNA ratios were highly correlated to relative growth rate and total growth as measured by protein content or reconstituted dry weight.
3. Addition of progeny biomass to adult biomass increased correlations between biochemical ratios and absolute growth rate, but had little effect on relationships involving relative growth rate or total growth.
4. The relationship between biomolecule ratios and growth established for D. magna grown under optimal conditions was not successful in predicting growth of D. magna reared under crowded conditions.
5. These data indicate that variation in biochemical ratios among life, stages of D. magna may be used to predict growth of organisms grown under similar conditions, but may not be extended to other situations. It is suggested, however, that variation in biochemical ratios in a particular life stage of a zooplankton species may be related to the productivity for that species.     

The establishment of reproducible, complex communities of oral bacteria in the chemostat using defined inocula

Nine commonly isolated oral bacterial populations were inoculated into a glucose-limited and a glucose-excess (amino acid-limited) chemostat maintained at a constant pH 7.0 and a mean community generation time of 13.9 h. The bacterial populations were Streptococcus mutans ATCC 2-27351, Strep. sanguis NCTC 7865, Strep. mitior EF 186, Actinomyces viscosus WVU 627, Lactobacillus casei AC 413, Neisseria sp. A1078, Veillonella alkalescens ATCC 17745, Bacteroides intermedius T 588 and Fusobacterium nucleatum NCTC 10593. All nine populations became established in the glucose-limited chemostat although Strep. sanguis and Neisseria sp. were present only after a second and third inoculation, respectively. In contrast, even following repeated inoculations, Strep. mutans, B. intermedius and Neisseria sp. could not be maintained under glucose-excess conditions. A more extensive pattern of fermentation products and amino acid catabolism occurred under glucose-limited growth; this simultaneous utilization of mixed substrates also contributed to the higher yields (Y molar glucose) and greater species diversity of these communities. Microscopic and biochemical evidence suggested that cell-to-cell interactions and food chains were occurring among community members. To compare the reproductibility of this system, communities were established on three occasions under glucose-limitation and twice under glucose-excess conditions. The bacterial composition of the steady-state communities and their metabolic behaviour were similar when grown under identical conditions but varied in a consistent manner according to the nutrient responsible for limiting growth. Although a direct simulation of the oral cavity was not attempted, the results show that the chemostat could be used as an environmentally-related model to grow complex but reproducible communities of oral bacteria for long periods from a defined inoculum.     

Long-term nutrient starvation of continuously cultured (glucose-limited) Selenomonas ruminantium.

Selenomonas ruminantium, a strictly anaerobic ruminal bacterium, was grown at various dilution rates (D = 0.05, 0.25, and 0.35 h-1) under glucose-limited continuous culture conditions. Suspensions of washed cells prepared anaerobically in mineral buffer were subjected to nutrient starvation (24 to 36 h; 39 degrees C; N2 atmosphere). Regardless of growth rate, viability declined logarithmically, and within about 2.5 h, about 50% of the populations were nonviable. After 24 h of starvation, the numbers of viable cells appeared to be inversely related to growth rate, the highest levels occurring with the slowest grown population. Cell dry weight, carbohydrate, protein, ribonucleic acid (RNA), and deoxyribonucleic acid declined logarithmically during starvation, and the decline rates of each were generally greater with cells grown at higher D values. Both cellular carbohydrate and RNA declined substantially during the first 12 h of starvation. Most of the cellular RNA that disappeared was found in the suspending buffer as low-molecular-weight, orcinol-positive materials. During growth, S. ruminantium made a variety of fermentation acids from glucose, but during starvation, acetate was the only acid made from catabolism of cellular material. Addition of glucose or vitamins to starving cell suspensions did not decrease loss of viability, whereas a starvation in the spent culture medium resulted in a slight decrease in the rate of viability loss. Overall, the data indicate that S. ruminantium strain D has very little survival capacity under the conditions tested compared with other bacterial species that have been studied.