Inactivation of aspartic transcarbamylase in sporulating Bacillus subtilis: demonstration of a requirement for metabolic energy

Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait

Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.

Energy and calcium ion dependence of proteolysis during sporulation of Bacillus subtilis cells

Bacterial cells degrade intracellular proteins at elevated rates during starvation and can selectively degrade proteins by energy-dependent processes. Sporulating bacteria can degrade protein with apparent first-order rate constants of over 0.20 h-1. We have shown, with an optimized [14C]leucine-labeling and chasing procedure, in a chemically defined sporulation medium, that intracellular protein degradation in sporulating cells of Bacillus subtilis 168 (trpC2) is apparently energy dependent. Sodium arsenate, sodium azide, carbonyl cyanide m-chlorophenylhydrozone, and N,N'-dicyclohexylcarbodiimide, at levels which did not induce appreciable lysis (less than or equal to 10%) over 10-h periods of sporulation, inhibited intracellular proteolysis by 13 to 93%. Exponentially growing cells acquired arsenate resistance. In contrast to earlier reports, we found that chloramphenicol (100 micrograms/ml) strongly inhibited proteolysis (68%) even when added 6 h into the sporulation process. Restricting the calcium ion concentration (less than 2 microM) in the medium had no effect on rates or extent of vegetative growth, strongly inhibited sporulation (98%), and inhibited rates of proteolysis by 60% or more. Inhibitors of energy metabolism, at the same levels which inhibited proteolysis, did not affect the rate or degree of uptake of Ca2+ by cells, which suggested that the Ca2+ and metabolic energy requirements of proteolysis were independent. Restricting the Ca2+ concentration in the medium reduced by threefold the specific activity in cells of the major intracellular serine proteinase after 12 h of sporulation. Finally, cells of a mutant of B. subtilis bearing an insertionally inactivated gene for the Ca2(+)-dependent intracellular proteinase-1 degraded protein in chemically defined sporulation medium at a rate indistinguishable from that of the wild-type cells for periods of 8 h.

Stability and synthesis of the penicillin-binding proteins during sporulation

The penicillin-binding proteins (PBPs) of Bacillus subtilis were examined after incubation of vegetative and sporulating cultures with chloramphenicol, an inhibitor of protein synthesis. The results indicate that the sporulation-specific increases in vegetative PBPs 2B and 3 and the appearance of two new PBPs, 4* and 5*, depend on concurrent protein synthesis, which is most likely to be de novo synthesis of the PBPs rather than synthesis of an activator or processing enzyme. It was also learned that in vivo the PBPs differ in their individual stabilities, which helps to explain some of the quantitative changes that occur in the PBP profile during sporulation. All the membrane-bound PBPs, except possibly PBP 1, were found to be stable in the presence of crude extracts of sporulating cells that contained proteolytic activity.

Degradation of ornithine transcarbamylase in sporulating Bacillus subtilis cells

When Bacillus subtilis cells grew and sporulated on glucose-nutrient broth, ornithine transcarbamylase (OTCase) was synthesized in the early stationary phase and then inactivated. The loss of OTCase activity was much slower in a mutant that was deficient in a major intracellular serine protease (ISP). Immunochemical analysis showed that synthesis of OTCase decreased to a low, but detectable, level during its inactivation and that loss of activity was paralleled by loss of cross-reactive protein. Because the antibodies were capable of detecting denatured and fragmented forms of OTCase, we conclude that inactivation involved or was rapidly followed by degradation in vivo. Native OTCase was not degraded in crude extracts or when purified ISP and OTCase were incubated together under a variety of conditions. Synthesis of OTCase was not shut off normally in the ISP-deficient mutant. When the effects of continued synthesis were minimized, OTCase was degraded only slightly slower in the mutant than in its parent. Thus, the mutant had unanticipated pleiotropic characteristics, and it was unlikely that ISP played a major role in the degradation of OTCase in vivo.

Nutritional regulation of degradation of aspartate transcarbamylase and of bulk protein in exponentially growing Bacillus subtilis cells

The rate of degradation of aspartate transcarbamylase in exponentially growing Bacillus subtilis cells was determined by measurement of enzyme activity after the addition of uridine to repress further enzyme synthesis and by specific immunoprecipitation of the enzyme from cells grown in the presence of [3H]leucine. Aspartate transcarbamylase was degraded with a half-life of about 1.5 h in cells growing on a glucose-salts medium with NH4+ ions as the sole source of nitrogen. Replacement of NH4+ in this medium with a combination of the amino acids aspartate, glutamate, isoleucine, proline, and threonine reduced the degradation rate to an undetectable level. Various other amino acids and amino acid mixtures had smaller effects on the rate of degradation. The carbon source also influenced the degradation rate, but to a smaller extent than the nitrogen source. The effects of these nutritional variables on the rate of bulk protein turnover in growing cells were generally similar to their effects on degradation of aspartate transcarbamylase. Since the degradation of aspartate transcarbamylase has been shown to be 10 to 20 times faster than bulk protein turnover, the results suggest that a substantial portion of protein turnover in growing cells represents regulable, rapid degradation of a number of normal proteins, of which aspartate transcarbamylase is an example.

Coordinate synthesis of the enzymes of pyrimidine biosynthesis in Bacillus subtilis

Strains of Bacillus subtilis that were resistant to repression of pyrimidine nucleotide biosynthetic enzymes were selected by isolating spontaneous uracil-tolerant derivatives of a uracil-sensitive strain, which lacks arginine-repressible carbamyl phosphate synthetase. The relative content of all six enzymes of uridylic acid biosynthesis de novo in these strains was in a constant ratio over a 10-fold range of derepression, which indicates that synthesis of these enzymes is coordinately regulated.

Enzyme changes during Bacillus subtilis sporulation caused by deprivation of guanine nucleotides

When sporulation is initiated by nutrient limitation, e.g., at the end of growth, certain biochemical processes occur in sequence. To determine which of these processes occur, even when the cells sporulate in the presence of a rapidly metabolizable carbon source, we induced sporulation of Bacillus subtilis by deprivation of guanine nucleotides, in a synthetic medium containing excess glucose, ammonium ions, and phosphate. The deprivation was produced either by decoyinine addition to a standard strain or by guanosin limitation of a guanine auxotroph. At 1 h after the onset of this deprivation, an extensive turnover of proteins began whose appearance was chloramphenicol sensitive. At least one enzyme (aspartate transcarbamylase) lost 70% of its activity within 15 min, indicating its rapid destruction. Whereas the magnitude of the above two changes was similar to that observed during sporulation at the end of growth in nutrient sporulation medium, protease (intracellular and extracellular) increased to less than one-tenth of the specific activity in nutrient sporulation medium, and alkaline phosphatase increased to less than one-half. However, glucose dehydrogenase, an enzyme made only in forespores, increased to the same specific activity under both conditions, presumably because the forespore compartment is protected from media (e.g., glucose) influences by the double membrane (two bilayers with opposite polarity).

Regulation of lysine- and lysine-plus-threonine-inhibitable aspartokinases in Bacillus brevis

Further studies on the expression of the two aspartokinase activities in Bacillus bovis are presented. Aspartokinase I (previously shown to be inhibited and repressed by lysine) was found to be repressed by diaminopimelate in the wild-type strain. However, in a mutant unable to convert diaminopimelate to lysine, starvation for lysine resulted in an increase in aspartokinase I activity. Thus, lysine itself or an immediate metabolite was the true effector of repression. Aspartokinase II (previously shown to be inhibited by lysine plus threonine) was repressed by threonine. Studies with the parent strain and auxotrophs inidicated that only threonine or an immediate metabolite of threonine was involved in this repression. Methionine and isoleucine were not effectors of any of the detected aspartokinase activities. Apart from inhibition and repression controls, a third as yet undefined regulatory mechanism operated to decrease the levels of both aspartokinases as growth declined, even in mutants in which repression control was absent. In thiosine-resistant, lysine-excreting mutants with elevated levels of aspartokinase, the increase in activity could always be attributed to one enzyme or the other, never both. The existence of separate structural genes for each aspartokinase is therefore suggested.

In vivo inactivation of glycerol dehydrogenase in Klebsiella aerogenes: properties of active and inactivated proteins

Glycerol:oxidized nicotinamide adenine dinucleotide (NAD+) 2-oxidoreductase (EC 1.1.1.6), an inducible enzyme for anaerobic glycerol catabolism in Klebsiella aerogenes, was purified and found to have a molecular weight of 79,000 by gel electrophoresis. The protein seemed to be enzymatically active either as a dimer of a 40,000-dalton peptide at pH 8.6 or as a tetramer of 160,000 molecular weight at pH 7.0. The enzyme activity was present at high levels in cells growing anaerobically on glycerol, but disappeared with a half-life of about 45 min if molecular oxygen was introduced to the culture. In contrast, no such phenomenon occurred with dihydroxyacetone kinase activity, the second enzyme in the pathway. Immunochemical analysis showed that the inactivation of the oxidoreductase did not involve degradation of the protein. Furthermore, subunits of the active and inactive forms of the enzyme were indistinguishable in size on polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and had similar isoelectric points (pH 4.7). Inactivation did, however, alter the gel filtration properties of the enzyme protein and, more importantly, reduced its affinity for the dye Cibacron F3GA and the coenzyme NAD+.

Synthesis and inactivation of carbamyl phosphate synthetase isozymes of Bacillus subtilis during growth and sporulation

Pyrimidine-repressible carbamyl phosphate synthetase P was synthesized in parallel with aspartate transcarbamylase during growth of Bacillus subtilis on glucose-nutrient broth. Both enzymes were inactivated at the end of exponential growth, but at different rates and by different mechanisms. Unlike the inactivation of aspartate transcarbamylase, the inactivation of carbamyl phosphate synthetase P was not interrupted by deprivation for oxygen or in a tricarboxylic acid cycle mutant. The arginine-repressible isozyme carbamyl phosphate synthetase A was synthesized in parallel with ornithine transcarbamylase during the stationary phase under these growth conditions. Again, both enzymes were subsequently inactivated, but at different rates and by apparently different mechanisms. The inactivation of carbamyl phosphate synthetase A was not affected in a protease-deficient mutatn the inactivation of ornithine transcarbamylase was greatly slowed.

Aspartate transcarbamylase synthesis ceases prior to inactivation of the enzyme in Bacillus subtilis

Aspartate transcarbamylase is synthesized during exponential growth of Bacillus subtilis and is inactivated when the cells enter the stationary phase. This work is a study of the regulation of aspartate transcarbamylase synthesis during growth and the stationary phase. Using specific immunoprecipitation of aspartate transcarbamylase from extracts of cells pulse-labeled with tritiated leucine, we showed that the synthesis of the enzyme decreased very rapidly at the end of exponential growth and was barely detectable during inactivation of the enzyme. Synthesis of most cell proteins continued during this time. When the cells ceased growing because of pyrimidine starvation of a uracil auxotroph, however, synthesis and inactivation occurred simultaneously. Measurement of pools of pyrimidine nucleotides and guanosine tetra- and pentaphosphate demonstrated that failure to synthesize aspartate transcarbamylase in the stationary phase was not explained by simple repression by these compounds. The cessation of aspartate transcarbamylase synthesis may reflect the shutting off of a "vegetative gene" as part of the program of differential gene expression during sporulation. However, aspartate transcarbamylase synthesis decreased normally at the end of exponential growth at the nonpermissive temperature in a mutant strain that is temperature-sensitive in sporulation and RNA polymerase function. Cessation of aspartate transcarbamylase synthesis appeared to be normal in three other temperature-sensitive RNA polymerase mutants and in several classes of spo0 mutants.

Evidence for the degradation of nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase of Candida utilis during rapid enzyme inactivation

The nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase (NADP-GDH) from the food yeast Candida utilis was found to be rapidly inactivated when cultures were starved of a carbon source. The addition of glutamate or alanine to the starvation medium stimulated the rate of inactivation. Loss of enzyme activity was irreversible since the reappearance of enzyme activity, following the addition of glucose to carbon-starved cultures, was blocked by cycloheximide. A specific rabbit antibody was prepared against the NADP-GDH from C. utilis and used to quantitate the enzyme during inactivation promoted by carbon starvation. The amount of precipitable antigenic material paralleled the rapid decrease of enzyme activity observed after transition of cells from NH(4) (+)-glucose to glutamate medium. No additional small-molecular-weight protein was precipitated by the antibody as a result of the inactivation, suggesting that the enzyme is considerably altered during the primary steps of the inactivation process. Analysis by immunoprecipitation of the reappearance of enzyme activity after enzyme inactivation showed that increase of NADP-GDH activity was almost totally due to de novo synthesis, ruling out the possibility that enzyme activity modulation is achieved by reversible covalent modification. Enzyme degradation was also measured during steady-state growth and other changes in nitrogen and carbon status of the culture media. In all instances so far estimated, the enzyme was found to be very stable and not normally subject to high rates of degradation. Therefore, the possibility that inactivation was caused by a change in the ratio of synthesis to degradation can be excluded.

Energy-dependent inactivation of citrate lyase in Enterobacter aerogenes

Enterobacter aerogenes was grown in continous culture with ammonia as the growth-limiting substrate, and changes in citrate lyase and citrate synthase activities were monitored after growth shifts from anaerobic growth on citrate to aerobic growth on citrate, aerobic growth on glucose, anaerobic growth on glucose, and anaerobic growth on glucose plus nitrate. Citrate lyase was inactivated during aerobic growth on glucose and during anaerobic growth with glucose plus nitrate. Inactivation did not occur during anaerobic growth on glucose, and as a result of the simultaneous presence of citrate lyase and citrate synthase, growth difficulties were observed. Citrate lyase inactivation consisted of deacetylation of the enzyme. The corresponding deacetylase could not be demonstrated in cell extracts, and it is concluded that, as in a number of other inactivations, electron transport to oxygen or nitrate was required for inactivation.

The regulation of glutamate metabolism in Candida utilis. Evidence for two interconvertible forms of NAD-dependent glutamate dehydrogenase

An earlier observation from this laboratory (J. Gen. Microbiol. 64, 423--427) that NAD-dependent glutamate dehydrogenase activity is modulated by rapid inactivation has been extended to show that this mechanism is completely reversible. Changes in properties of the enzyme accompany inactivation and two different forms active (a) and inactive (b) of the enzyme with distinctive properties have been isolated. Incubation of the inactive enzyme with magnesium in vitro produced a rapid increase of activity; this was accompanied by a change in the properties of the enzyme to those of the a form. This control mechanism of enzyme interconversion appears widespread among yeasts. Its probable role in modulating glutamate synthesis and degration is discussed.

Pyrimidine biosynthetic pathway of Baccillus subtilis

Biochemical and genetic data were obtained from a series of 51 Pyr- strains of Bacillus subtilis. The observed enzymatic deficiencies allowed the mutants to be placed into 12 clases, some of which represent defects in more than one of the six known pyrimidine biosynthetic enzymes. Mapping analysis by transformation has shown that all the Pyr- mutations are located in a single small area of the B. subtilis genome. A correlation of the biochemical defects and the genetic data has been made. Those mutations conferring similar enzymatic deficiencies were found to be contiguous on the B. subtilis map. Regulatory aspects of the pyrimidine pathway have also been investigated and are compared to previously reported results from other organisms. Evidence is presented which bears upon the possible physical association of the first three enzymes and the association of at least some of the enzymes of this pathway with particulate elements of the cell. A model for the organization of the enzymes is presented with dihydroorotate dehydrogenase as the central enzyme in a proposed aggregate.

Inactivation of glucose 6-phosphate dehydrogenase during germination and outgrowth of Bacillus cereus T endospores

The specific activity and total activity of glucose 6-phosphate dehydrogenase (EC 1.1.1.49) under conditions of complete cell breakage fall 10-20-fold during a 3h period of spore germination and outgrowth. The spores must germinate (lose refractility), but do not have to undergo outgrowth, for the loss of activity to occur. Glucose 6-phosphate dehydrogenase activity from cells as any stage of development is completely stable in extracts at 4 degrees C or 30 degrees C. All of the enzyme activity is found in a soluble (50000g supernatant) fraction and remains completely soluble throughout development. Soluble protein and total cellular protein remain constant for about 2h. Proteinases could not be detected or protein turnover demonstrated during the morphogenetic process. Phenylmethanesuophony fluoride and o-phenanthroline, inhibitors of proteolytic enzymes, do not prevent glucose 6-phosphate dehydrogenase inactivation when added to whole cells. Mixing experiments show no inhibitor of glucose 6-phosphate dehydrogenase to be present in late-stage cells. The enzyme is not excreted into the culture medium. Chloramphenicol and rifampicine immediately stop protein synthesis and development but not the inactivation of glucose 6-phosphate dehydrogenase. NaN3, 2,4-dinitrophenol or anaerobiosis immediately stop development and prevent the loss of enzyme activity. A requirement for metabolic energy is therefore probable. Extracts of spores pre-labelled with L[14C]leucine were made at various stages of morphogenesis and subjected to polyacrylamide-gel electrophoresis. Glucose 6-phosphate dehydrogenase, which was identified by a specific stain, did not lose 14C label, and therefore may not be degraded during the inactivation process.

Oxygen-dependent inactivation of glutamine phosphoribosylpyrophosphate amidotransferase in stationary-phase cultures of Bacillus subtilis

Glutamine phosphoribosylpyrophosphate amidotransferase (ATase) activity is rapidly inactivated in stationary-phase cells of Bacillus subtilis. The inactivation of APase requires both the cessation of rapid cell growth and the presence of oxygen. ATase is inactivated in two protease-deficient mutant strains at a rate similar to that seen in the wild type, and is stable in anaerobic cell-free extracts of the parent strain. These results suggest that the inactivation of ATase is not the result of general proteolysis. The inactivation of ATase in stationary-phase cultures can be inhibited by oxygen starvation. This oxygen requirement does not reflect a dependence on the generation of metabolic energy, but appears to be a direct requirement for molecular oxygen. ATase synthesis is repressed by the addition of adenosine, and is inactivated only after the cessation of exponential growth. Addition of chloramphenicol or rifampin to exponential- and stationary-phase cells does not inhibit ATase inactivation, suggesting that protein or ribonucleic acid synthesis is not required for inactivation. ATase is inactivated at the end of exponential growth in cells that have exhausted a required amino acid.

Inactivation of isocitrate lyase during myxospore development in Myxococcus xanthus

The inactivation of isocitrate lyase which occurs during late stages of myxospore formation in Myxococcus xanthus was studied. Several findings are reported. (i) Protein synthesis is required over a specific time interval in order for isocitrate lyase inactivation to occur at a later time. (ii) Metabolic energy is required at all times during myxospore development if the inactivation is to occur. (iii) It was possible to inhibit protein turnover to a considerable extent without affecting the net loss in isocitrate lyase activity.