MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling

BACKGROUND

Kinetic modeling is a powerful tool for understanding the dynamic behavior of biochemical systems. For kinetic modeling, determination of a number of kinetic parameters, such as the Michaelis constant (K_m), is necessary, and global optimization algorithms have long been used for parameter estimation. However, the conventional global optimization approach has three problems: (i) It is computationally demanding. (ii) It often yields unrealistic parameter values because it simply seeks a better model fitting to experimentally observed behaviors. (iii) It has difficulty in identifying a unique solution because multiple parameter sets can allow a kinetic model to fit experimental data equally well (the non-identifiability problem).

RESULTS

To solve these problems, we propose the Machine Learning-Aided Global Optimization (MLAGO) method for K_m estimation of kinetic modeling. First, we use a machine learning-based K_m predictor based only on three factors: EC number, KEGG Compound ID, and Organism ID, then conduct a constrained global optimization-based parameter estimation by using the machine learning-predicted K_m values as the reference values. The machine learning model achieved relatively good prediction scores: RMSE = 0.795 and R² = 0.536, making the subsequent global optimization easy and practical. The MLAGO approach reduced the error between simulation and experimental data while keeping K_m values close to the machine learning-predicted values. As a result, the MLAGO approach successfully estimated K_m values with less computational cost than the conventional method. Moreover, the MLAGO approach uniquely estimated K_m values, which were close to the measured values.

CONCLUSIONS

MLAGO overcomes the major problems in parameter estimation, accelerates kinetic modeling, and thus ultimately leads to better understanding of complex cellular systems. The web application for our machine learning-based K_m predictor is accessible at https://sites.google.com/view/kazuhiro-maeda/software-tools-web-apps , which helps modelers perform MLAGO on their own parameter estimation tasks.

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

The complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a 'rubber band method' to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia.

Generation of the membrane potential and its impact on the motility, ATP production and growth in Campylobacter jejuni

The generation of a membrane potential (Δψ), the major constituent of the proton motive force (pmf), is crucial for ATP synthesis, transport of nutrients and flagellar rotation. Campylobacter jejuni harbors a branched electron transport chain, enabling respiration with different electron donors and acceptors. Here, we demonstrate that a relatively high Δψ is only generated in the presence of either formate as electron donor or oxygen as electron acceptor, in combination with an acceptor/donor respectively. We show the necessity of the pmf for motility and growth of C. jejuni. ATP generation is not only accomplished by oxidative phosphorylation via the pmf, but also by substrate-level phosphorylation via the enzyme AckA. In response to a low oxygen tension, C. jejuni increases the transcription and activity of the donor complexes formate dehydrogenase (FdhABC) and hydrogenase (HydABCD) as well as the transcription of the alternative respiratory acceptor complexes. Our findings suggest that in the gut of warm-blooded animals, C. jejuni depends on at least formate or hydrogen as donor (in the anaerobic lumen) or oxygen as acceptor (near the epithelial cells) to generate a pmf that sustains efficient motility and growth for colonization and pathogenesis.

Macromolecular networks and intelligence in microorganisms

Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity - particularly activity of the human brain - with a phenomenon we call "intelligence." Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as "human" and "brain" out of the defining features of "intelligence," all forms of life - from microbes to humans - exhibit some or all characteristics consistent with "intelligence." We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.

Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective

We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and products occurring at low concentrations, because these are most informative about the enzyme's catalytic mechanism. We hypothesized that at relatively high in vivo concentrations, important molecular monitors of the state of living cells, such as ATP, affect multiple enzymes of the former and that these interactions have gone unnoticed in enzymology. We test this hypothesis in terms of the effect that ATP, ADP, and AMP might have on the major free-energy delivering pathway of the yeast Saccharomyces cerevisiae. Assaying cell-free extracts, we collected a comprehensive set of quantitative kinetic data concerning the enzymes of the glycolytic and the ethanol fermentation pathways. We determined systematically the extent to which the enzyme activities depend on the concentrations of the adenine nucleotides. We found that the effects of the adenine nucleotides on enzymes catalysing reactions in which they are not directly involved as substrate or product, are substantial. This includes effects on the Michaelis-Menten constants, adding new perspective on these, 100 years after their introduction.

Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions

Does the understanding of the dynamics of biochemical networks in vivo, in terms of the properties of their components determined in vitro, require the latter to be determined all under the same conditions? An in vivo-like assay medium for enzyme activity determination was designed based on the concentrations of the major ionic constituents of the Escherichia coli cytosol: K(+), Na(+), Mg(2+), phosphate, glutamate, sulfate and Cl(-). The maximum capacities (V(max)) of the extracted enzymes of two pathways were determined using both this in vivo-like assay medium and the assay medium specific for each enzyme. The enzyme activities differed between the two assay conditions. Most of the differences could be attributed to unsuspected, pleiotropic effects of K(+) and phosphate. K(+) activated some enzymes (aldolase, enolase and glutamate dehydrogenase) and inhibited others (phosphoglucose isomerase, phosphofructokinase, triosephosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase), whereas phosphate inhibited all glycolytic enzymes and glutamine synthetase but only activated glutamine 2-oxoglutarate amidotransferase. Neither a high glutamate concentration, nor macromolecular crowding affected the glycolytic or nitrogen assimilation enzymes, other than through the product inhibition of glutamate dehydrogenase by glutamate. This strategy of assessing all pathway enzymes kinetically under the same conditions may be necessary to avoid inadvertent differences between in vivo and in vitro biochemistry. It may also serve to reveal otherwise unnoticed pleiotropic regulation, such as that demonstrated in the present study by K(+) and phosphate.

Manganese oxidation by spores and spore coats of a marine bacillus species

Bacillus sp. strain SG-1 is a marine bacterial species isolated from a near-shore manganese sediment sample. Its mature dormant spores promote the oxidation of Mn to MnO(2). By quantifying the amounts of immobilized and oxidized manganese, it was established that bound manganese was almost instantaneously oxidized. When the final oxidation of manganese by the spores was partly inhibited by NaN(3) or anaerobiosis, an equivalent decrease in manganese immobilization was observed. After formation of a certain amount of MnO(2) by the spores, the oxidation rate decreased. A maximal encrustment was observed after which no further oxidation occurred. The oxidizing activity could be recovered by reduction of the MnO(2) with hydroxylamine. Once the spores were encrusted, they could bind significant amounts of manganese, even when no oxidation occurred. Purified spore coat preparations oxidized manganese at the same rate as intact spores. During the oxidation of manganese in spore coat preparations, molecular oxygen was consumed and protons were liberated. The data indicate that a spore coat component promoted the oxidation of Mn in a biologically catalyzed process, after adsorption of the ion to incipiently formed MnO(2). Eventually, when large amounts of MnO(2) were allowed to accumulate, the active sites were masked and further oxidation was prevented.

Floating filters, a novel technique for isolation and enumeration of fastidious, acidophilic, iron-oxidizing, autotrophic bacteria

Nuclepore polycarbonate filters floating on a liquid, FeSO(4)-containing medium (pH 1.6) were used to isolate a moderately thermophilic bacterium from a pyrite-oxidizing enrichment culture. The isolate failed to grow on any of the conventional solid media tried. To test the general applicability of the method, the enumeration of a fastidious acidophilic organism, Thiobacillus ferrooxidans, was carried out and the results compared with those obtained with other filters, solid media, and the most probable number technique. T. ferrooxidans showed better viability on the floating polycarbonate filters and grew in a much shorter time (4 to 5 days) than with the other techniques.

Oxygen and carbon dioxide mass transfer and the aerobic, autotrophic cultivation of moderate and extreme thermophiles: a case study related to the microbial desulfurization of coal

Mass transfers of O(2), CO(2), and water vapor are among the key processes in the aerobic, autotrophic cultivation of moderate and extreme thermophiles. The dynamics and kinetics of these processes are, in addition to the obvious microbial kinetics, of crucial importance for the industrial desulfurization of high-pyritic coal by such thermophiles. To evaluate the role of the temperature on the gas mass transfer, k(L)a measurements have been used to supplement the existing published data. Oxygen mass transfer from gas (air) to liquid (5 mM H(2)SO(4) in water) phase as a function of the temperature has been studied in a laboratory-scale fermentor. At 15, 30, 45, and 70 degrees C, (k(L)a)(o) values (for oxygen) were determined under three different energy input conditions by the dynamic gassing in/out method. The (k(L)a)(o) was shown to increase under these conditions with increasing temperature, and straight lines were obtained when the logarithm of (k(L)a)(o) was plotted against the temperature. By multiplying the equilibrium concentration of O(2) in water with (k(L)a)(o) maximal, O(2) transfer capacities were calculated. It appeared that in finite of a decreased solubility of O(2) at elevated temperature in mechanically mixed fermentors the calculated transfer capacities showed only minor changes for the range between 15 and 70 degrees C. However, in an air-mixed fermentor the transfer capacity of O(2) decreased slowly but steadily.Carbon dioxide mass transfer was predicted by calculations on the basis of the data for oxygen transfer. The maximal CO(2) transfer capacity, calculated as the product of the equilibrium CO(2) concentration times (k(L)a)(c), decreased slowly as the temperature increased over the range 15-70 degrees C under all three energy input conditions. Subsequent process design calculations showed that for aerobic, autotrophic cultures, CO(2) limitation is more likely to occur than O(2) limitation.

Introduction to systems biology

The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experimental data. Many different types of modeling approaches are useful depending on the amount and quality of the molecular data available and the purpose of the model. Analysis of such models and the structure of molecular networks have led to the discovery of principles of cell functioning overarching single species. Two main approaches of systems biology can be distinguished. Top-down systems biology is a method to characterize cells using system-wide data originating from the Omics in combination with modeling. Those models are often phenomenological but serve to discover new insights into the molecular network under study. Bottom-up systems biology does not start with data but with a detailed model of a molecular network on the basis of its molecular properties. In this approach, molecular networks can be quantitatively studied leading to predictive models that can be applied in drug design and optimization of product formation in bioengineering. In this chapter we introduce analysis of molecular network by use of models, the two approaches to systems biology, and we shall discuss a number of examples of recent successes in systems biology.

The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica

Ammonium assimilation in Escherichia coli is regulated through multiple mechanisms (metabolic, signal transduction leading to covalent modification, transcription, and translation), which (in-)directly affect the activities of its two ammonium-assimilating enzymes, i.e. glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Much is known about the kinetic properties of the components of the regulatory network that these enzymes are part of, but the ways in which, and the extents to which the network leads to subtle and quasi-intelligent regulation are unappreciated. To determine whether our present knowledge of the interactions between and the kinetic properties of the components of this network is complete - to the extent that when integrated in a kinetic model it suffices to calculate observed physiological behaviour - we now construct a kinetic model of this network, based on all of the kinetic data on the components that is available in the literature. We use this model to analyse regulation of ammonium assimilation at various carbon statuses for cells that have adapted to low and high ammonium concentrations. We show how a sudden increase in ammonium availability brings about a rapid redirection of the ammonium assimilation flux from GS/glutamate synthase (GOGAT) to GDH. The extent of redistribution depends on the nitrogen and carbon status of the cell. We develop a method to quantify the relative importance of the various regulators in the network. We find the importance is shared among regulators. We confirm that the adenylylation state of GS is the major regulator but that a total of 40% of the regulation is mediated by ADP (22%), glutamate (10%), glutamine (7%) and ATP (1%). The total steady-state ammonium assimilation flux is remarkably robust against changes in the ammonium concentration, but the fluxes through GS and GDH are completely nonrobust. Gene expression of GOGAT above a threshold value makes expression of GS under ammonium-limited conditions, and of GDH under glucose-limited conditions, sufficient for ammonium assimilation.

Macromolecular intelligence in microorganisms

Biochemistry and molecular biology have been focusing on the structural, catalytic, and regulatory properties of individual macromolecules from the perspective of clarifying the mechanisms of metabolism and gene expression. Complete genomes of 'primitive' living organisms seem to be substantially larger than necessary for metabolism and gene expression alone. This is in line with the findings of silent phenotypes for supposedly important genes, apparent redundancy of functions, and variegated networks of signal transduction and transcription factors. Here we propose that evolutionary optimization has been much more intensive than to lead to the bare minima necessary for autonomous life. Much more complex organisms prevail. Much of this complexity arises in the nonlinear interactions between cellular macromolecules and in subtle differences between paralogs (isoenzymes). The complexity can only be understood when analyzed quantitatively, for which quantitative experimentation is needed in living systems that are as simple and manipulatable as possible, yet complex in the above sense. We illustrate this for the glutamine synthetase cascade in Escherichia coli. By reviewing recent molecular findings, we show that this cascade is much more complex than necessary for simple regulation of ammonia assimilation. Simulations suggest that the function of this complexity may lie in quasi-intelligent behavior, including conditioning and learning.

atp Mutants of Escherichia coli fail to grow on succinate due to a transport deficiency

Escherichia coli atp mutants, which lack a functional H+-ATPase complex, are capable of growth on glucose but not on succinate or other C4-dicarboxylates (Suc- phenotype). Suc+ revertants of an atp deletion strain were isolated which were capable of growth on succinate even though they lack the entire H+-ATPase complex. Complementation in trans with the yhiF gene suppressed the growth of the Suc+ mutants on succinate, which implicates the yhiF gene product in the regulation of C4-dicarboxylate metabolism. Indeed, when the E. coli C4-dicarboxylate transporter (encoded by the dctA gene) was expressed in trans, the Suc- phenotype of the atp deletion strain reverted to Suc+, which shows that the reason why the E. coli atp mutant is unable to grow aerobically on C4-dicarboxylates is insufficient transport capacity for these substrates.

Coproporphyrin excretion by Azorhizobium caulinodans under micro-aerobic conditions

Azorhizobium caulinodans ORS571 was found to excrete moderate amounts of a fluorescent pigment into the culture medium in response to dissolved oxygen tensions below 1.0 kPa. The pigment was identified as coproporphyrin, on the basis of its optical and fluorescence spectra. FixLJ and fixK mutant derivatives of ORS571 were found to excrete 25-fold higher amounts of coproporphyrin under micro-aerobic conditions than the wild type strain. These observations suggest that A. caulinodans switches from an aerobic to an anaerobic coproporphyrinogen oxidase when the dissolved oxygen tension falls below 1.0 kPa and that the fixLJ and fixK genes are involved in the regulation of expression of the anaerobic coproporphyrinogen oxidase.

Oxygen protection of nitrogen fixation in free-living Azorhizobium caulinodans: the role of cytochrome aa3

The growth properties of Azorhizobium caulinodans wild-type and a cytochrome aa3 mutant strain, both growing with N2 as N source at fixed dissolved partial oxygen pressures in the range 0.5--4.0 kPa, were studied by making use of continuous cultures (chemostats and pH-auxostats) and transient cultures. In succinate-limited chemostats, the wild-type exhibited a higher growth yield than the aa3 mutant at every dissolved oxygen tension tested, indicating activity of cytochrome aa3 in this entire oxygen regime. The growth yield of both the wild-type and the aa3 mutant declined when the dissolved oxygen tension was raised. In contrast, for growth on ammonia at the same dilution rate, the wild-type showed an increase in growth yield with increasing dissolved oxygen tension, whereas the growth yield of the aa3 mutant remained constant. The transient changes in growth properties observed in chemostat cultures after pulsing with succinate pointed to a negative effect of oxygen on the maximum specific growth rate. This was studied further in steady-state pH-auxostat cultures. The specific growth rate of both strains decreased with increasing dissolved oxygen tension. The less steep decline in growth rate of the wild-type compared to the aa3 mutant confirmed that cytochrome aa3 is active in the wild-type. Again, the growth yield of both strains decreased with the dissolved oxygen tension, but in contrast to the results obtained with chemostats, no difference in growth yield was observed between wild-type and mutant at any oxygen tension. In either type of continuous culture a decrease in the overall P/O ratio with increasing dissolved oxygen tension is improbable for the wild-type, and even more so for the aa3 mutant. Therefore, the adverse effects of oxygen on the growth of A. caulinodans are not readily explained by respiratory protection; alternatively, it is proposed that the catalytic oxidation of nitrogen-fixation-specific redox enzymes by oxygen (auto-protection) enables the bacterium to deal with intracellular oxygen at the expense of reducing equivalents and free energy. To compensate for the loss of free energy, respiration increases and an active cytochrome aa3 contributes to this by keeping the P/O ratio high.

Influence of environmental factors on endo-beta-1,4-glucanase production by Bacillus HR68, isolated from a Zimbabwean hot spring

The production of endo-beta-1,4-glucanase by a Bacillus strain isolated from a hot spring in Zimbabwe was studied in batch culture, chemostat culture, and carbon dioxide-regulated auxostat (CO2-auxostat). The bacteria produced the enzyme in the presence of excess glucose or sucrose, but not under carbon-limited conditions in a chemostat using mineral medium. There was a specific growth rate dependent linear increase in enzyme production in glucose excess, nitrogen-limited chemostat cultures. A high specific growth rate of 2.2 h-1 and a high rate of enzyme production of 362 nkat (mg dry mass.h)-1 were attained under nutrient rich conditions in the CO2-auxostat. The bacteria had the highest specific growth rate and endo-beta-1,4-glucanase enzyme production at 50 degrees C. The maximum specific growth rate and the rate of enzyme production increased when yeast extract and tryptone were added in increasing amounts to the mineral medium used for cultivation in separate experiments. Increasing the glucose concentration in the CO2-auxostat cultures increased the rate of enzyme production but did not affect the specific growth rate.

Genetic and phenetic analyses of Bradyrhizobium strains nodulating peanut (Arachis hypogaea L.) roots

Seventeen Bradyrhizobium sp. strains and one Azorhizobium strain were compared on the basis of five genetic and phenetic features: (i) partial sequence analyses of the 16S rRNA gene (rDNA), (ii) randomly amplified DNA polymorphisms (RAPD) using three oligonucleotide primers, (iii) total cellular protein profiles, (iv) utilization of 21 aliphatic and 22 aromatic substrates, and (v) intrinsic resistances to seven antibiotics. Partial 16S rDNA analysis revealed the presence of only two rDNA homology (i.e., identity) groups among the 17 Bradyrhizobium strains. The partial 16S rDNA sequences of Bradyrhizobium sp. strains form a tight similarity (> 95%) cluster with Rhodopseudomonas palustris, Nitrobacter species, Afipia species, and Blastobacter denitrificans but were less similar to other members of the alpha-Proteobacteria, including other members of the Rhizobiaceae family. Clustering the Bradyrhizobium sp. strains for their RAPD profiles, protein profiles, and substrate utilization data revealed more diversity than rDNA analysis. Intrinsic antibiotic resistance yielded strain-specific patterns that could not be clustered. High rDNA similarity appeared to be a prerequisite, but it did not necessarily lead to high similarity values between RAPD profiles, protein profiles, and substrate utilization. The various relationship structures, coming forth from each of the studied features, had low compatibilities, casting doubt on the usefulness of a polyphasic approach in rhizobial taxonomy.

Nicotinate catabolism is dispensable and nicotinate anabolism is crucial in Azorhizobium caulinodans growing in batch culture and chemostat culture on N2 as The N source

When Azorhizobium caulinodans was grown in chemostat cultures with N2 as the N source at a constant dilution rate of 0.1 h-1 in media with a constant concentration (50 mM) of succinate and variable concentrations (1.5 to 585 microM) of nicotinate, neither the growth yield on succinate, the specific rate of O2 consumption, nor the specific rate of CO2 production showed linear regression with the concentration of nicotinate. Moreover, for transient continuous cultures in which the nicotinate concentration was gradually lowered, growth parameters remained unchanged until an apparently critical level of 0.7 microM nicotinate was reached. Below this nicotinate level, an immediate washout of the chemostat population began. A. caulinodans nicotinate hydroxylase-negative mutant 61007, unable to catabolize nicotinate, and the wild type behaved similarly. Thus, for continuous cultures supplied with N2 as the N source, submicromolar concentrations of nicotinate both sustained pyridine nucleotide biosynthesis at sufficient levels and precluded the use of nicotinate as a catabolic substrate. Furthermore, when more nicotinate was provided, dual succinate-nicotinate limitation in continuous cultures did not occur. Finally, when nicotinate is present in suboptimal concentrations, the specific growth rate is directly proportional to the amount of nicotinate present per unit of biomass. By contrast, in batch cultures with different nicotinate concentrations and with either succinate or lactate as the carbon and energy source, anomalous growth curves were obtained. With a low concentration (1.5 microM) of nicotinate, growth on N2 occurred, albeit at low rates. With a high concentration (195 microM) of nicotinate, growth on N2 was temporarily stimulated, but nicotinate was quickly exhausted and growth was thereafter nicotinate limited. Continuous supplementation of batch cultures with nicotinate allowed only transient exponential growth followed by linear growth. Thus, also for batch cultures, nicotinate catabolism is dispensable, although a high concentration of nicotinate temporarily stimulates growth on N2. Ut us concluded that A. caulinodans is a true diazotroph.

Nitrogen Fixation and Hydrogen Metabolism in Relation to the Dissolved Oxygen Tension in Chemostat Cultures of the Wild Type and a Hydrogenase-Negative Mutant of Azorhizobium caulinodans

Both the wild type and an isogenic hydrogenase-negative mutant of Azorhizobium caulinodans growing ex planta on N 2 as the N source were studied in succinate-limited steady-state chemostat cultures under 0.2 to 3.0% dissolved O 2 tension. Production or consumption of O 2 , H 2 , and CO 2 was measured with an on-line-connected mass spectrometer. In the range of 0.2 to 3.0%, growth of both the wild type and the mutant was equally dependent on the dissolved O 2 tension: the growth yield decreased, and the specific O 2 consumption and CO 2 production increased. A similar dependency on the dissolved O 2 tension was found for the mutant with 2.5% H 2 in the influent gas. The H 2 /N 2 ratio (moles of H 2 evolved per mole of N 2 consumed via nitrogenase) of the mutant, growing with or without 2.5% H 2 , increased with increasing dissolved O 2 tensions. This increase in the H 2 /N 2 ratio was small but significant. The dependencies of the ATP/N 2 ratio (moles of ATP consumed per mole of N 2 fixed) and the ATP/2e - ratio [moles of ATP consumed per mole of electron pairs transferred from NAD(P)H to nitrogenase] on the dissolved O 2 tension were estimated. These dependencies were interpreted in terms of the physiological concepts of respiratory protection and autoprotection.

In situ determination of the reduction levels of cytochromes b and c in growing bacteria: a case study with N2-fixing Azorhizobium caulinodans

The determination of the in situ reduction levels of cytochromes b and c in growing bacteria is achieved by coupling a chemostat with a dual wavelength spectrophotometer. Visible light absorption spectra of cytochromes present in bacterial cells actively growing in a chemostat at a specific growth rate of 0.1 h-1 are recorded. This is accomplished by transporting the emitted light from the spectrophotometer via glass fibers to one side of the chemostat vessel and detecting the transmitted light via a photomultiplier at the other side. The vessel itself is enclosed in a dark box, which contains mirrors on the inside surfaces. The reduction levels of cytochromes b and c during steady state in chemostat cultures are expressed as percentage absorbance of fully reduced cytochromes in the alpha-region of the spectrum. Steady state spectra are recorded in N2-fixing, succinate-limited continuous cultures of Azorhizobium caulinodans at dissolved oxygen tensions in the range between 0.1 and 3.5% O2. Spectra of fully reduced cytochromes are obtained on the basis of spectra recorded after having reached anoxic conditions by sparging pure nitrogen gas through the culture. These spectra of cytochromes b and c reduced by endogenous substrates are corrected as to give the spectrum of fully reduced cytochromes. The respective contributions of cytochromes b and c to spectra in the alpha-region are estimated by deconvolution using best-fit analysis. Using this in situ technique it is observed that at each dissolved oxygen tension the reduction level of the cytochromes b is higher than that of the cytochromes c.(ABSTRACT TRUNCATED AT 250 WORDS)

Manganese oxidation by Leptothrix discophora

Cells of Leptothrix discophora SS1 released Mn2+-oxidizing factors into the medium during growth in batch culture. Manganese was optimally oxidized when the medium was buffered with HEPES (N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid) at pH 7.5. Manganese-oxidizing activity in the culture medium in which this strain had been grown previously was sensitive to heat, phosphate, Tris, NaN3, HgCl2 NaCl, sodium dodecyl sulfate, and pronase; 0.5 mol of O2 was consumed per mol of MnO2 formed. During Mn2+ oxidation, protons were liberated. With sodium dodecyl sulfate-polyacrylamide gel electrophoresis, two protein-containing bands were detected in the spent culture medium. One band had an apparent molecular weight of 110,000 and was predominant in Mn2+-oxidizing activity. The second product (Mr 85,000) was only detected in some cases and probably represents a proteolytic breakdown moiety of the 110,000-Mr protein. The Mn2+-oxidizing factors were associated with the MnO2 aggregates that had been formed in spent culture medium. After solubilization of this MnO2 with ascorbate, Mn2+-oxidizing activity could be recovered.

Manganese reduction by a marine Bacillus species

Mature dormant spores of marine Bacillus sp. strain SG1 catalyze the oxidation of Mn(II) to MnO2. We report that vegetative cells of the same strain reduced MnO2 under low-oxygen conditions. The rate of reduction was a function of cell concentration. The process had a pH optimum of 7.5 to 8.0 and was inhibited by HgCl2, by preheating of the cells at 80 degrees C for 5 min, by antimycin A, and by N-heptyl-hydroxy-quinoline-N-oxide. At a nonlimiting O2 concentration, little MnO2 reduction was observed. Under these conditions, the process could be induced by the addition of NaN3. Spectrophotometric analysis of the Bacillus cells indicated the presence of type b and c cytochromes. Both types can be oxidized in situ by addition of MnO2 to the cells.

The bioenergetics of denitrification

In anaerobically grown Paracoccus denitrificans the dissimilatory nitrate reductase is linked to the respiratory chain at the level of cytochromes b. Electron transport to nitrite and nitrous oxide involves c-type cytochromes. During electron transport from NADH to nitrate one phosphorylation site is passed, whereas two sites are passed during electron transport from NADH to oxygen, nitrite and nitrous oxide. The presentation of a respiratory chain as a linear array of electron carriers gives a misleading picture of the efficiency of energy conservation since the location of the reductases is not taken into account. For the reduction of nitrite and nitrous oxide, protons are utilized from the periplasmic space, whereas for the reduction of oxygen and nitrate, protons are utilized from the cytoplasmic side of the inner membrane. Evidence for two transport systems for nitrate was obtained. One is driven by the proton motive force; this system is used to initiate nitrate reduction. The second system is a nitrate-nitrite antiport system. A scheme for proton translocation and electron transport to nitrate, nitrite, nitrous oxide and oxygen is presented. The number of charges translocated across the membrane during flow of two electrons from NADH is the same for all nitrogenous oxides and is 67-71% of that during electron transfer to oxygen via cytochrome o. These findings are in accordance with growth yield studies. YMAX electron values determined in chemostat cultures for growth with various substrates and hydrogen acceptors are proportional to the number of charges translocated to these hydrogen acceptors during electron transport.

Respiration-driven proton translocation with nitrite and nitrous oxide in Paracoccus denitrificans

(1)H+ leads to/electron acceptor ratios have been determined with the oxidant pulse method for cells of denitrifying Paracoccus denitrificans oxidizing endogenous substrates during reduction of O2, NO2- or N2O. Under optimal H+-translocation conditions, the ratios leads to H+/O, H+ leads to/N2O, H+ leads to/NO2- for reduction to N2 and H+ leads to/NO2- for reduction to N2O were 6.0-6.3, 4.02, 5.79 and 3.37, respectively. (2) With ascorbate/N,N,N,'N'-tetramethyl-p-phenylene-diamine as exogenous substrate, addition of NO2- or N2O to an anaerobic cell suspension resulted in rapid alkalinization of the outer bulk medium. H+/N2O, H+/NO2- for reduction to N2 and H+/NO2- for reduction to N2O were -0.84, -2.33 and -1.90, respectively. (3) The H+/oxidant ratios, mentioned in item 2, were not altered in the presence of valinomycin/K+ and the triphenylmethylphosphonium cation. (4) A simplified scheme of electron transport to O2, NO2- and N2O is presented which shows a periplasmic orientation of the nitrite reductase as well as the nitrous oxide reductase. Electrons destined for NO2-, N2O or O2 pass two H+-trans-locating sites. The H+ leads to/electron acceptor ratios predicted by this scheme are in good agreement with the experimental values.